format-version: 1.2
date: 04:09:2015 13:56
saved-by: kareneilbeck
auto-generated-by: OBO-Edit 2.3.1
subsetdef: biosapiens "biosapiens protein feature ontology"
subsetdef: DBVAR "database of genomic structural variation"
subsetdef: SOFA "SO feature annotation"
synonymtypedef: aa1 "amino acid 1 letter code"
synonymtypedef: aa3 "amino acid 3 letter code"
synonymtypedef: AAMOD "amino acid modification"
synonymtypedef: BS "biosapiens"
synonymtypedef: dbsnp "dbsnp variant terms"
synonymtypedef: dbvar "DBVAR"
synonymtypedef: ebi_variants "ensembl variant terms"
synonymtypedef: RNAMOD "RNA modification" EXACT
synonymtypedef: VAR "variant annotation term"
default-namespace: sequence
remark: autogenerated-by:   DAG-Edit version 1.417\nsaved-by:       eilbeck\ndate:         Tue May 11 15:18:44 PDT 2004\nversion: $Revision: 1.45 $
ontology: so-xp.obo

[Term]
id: SO:0000000
name: Sequence_Ontology
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000001
name: region
def: "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]
subset: SOFA
synonym: "sequence" EXACT []
is_a: SO:0000110 ! sequence_feature
disjoint_from: SO:0000699 ! junction

[Term]
id: SO:0000002
name: sequence_secondary_structure
def: "A folded sequence." [SO:ke]
synonym: "sequence secondary structure" EXACT []
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000003
name: G_quartet
def: "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract]
synonym: "G quartet" EXACT []
synonym: "G tetrad" EXACT []
synonym: "G-quadruplex" EXACT []
synonym: "G-quartet" EXACT []
synonym: "G-tetrad" EXACT []
synonym: "G_quadruplex" EXACT []
synonym: "guanine tetrad" EXACT []
xref: http://en.wikipedia.org/wiki/G-quadruplex "wiki"
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000004
name: interior_coding_exon
subset: SOFA
synonym: "interior coding exon" EXACT []
is_a: SO:0000195 ! coding_exon

[Term]
id: SO:0000005
name: satellite_DNA
def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "satellite DNA" EXACT []
xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki"
is_a: SO:0000705 ! tandem_repeat

[Term]
id: SO:0000006
name: PCR_product
def: "A region amplified by a PCR reaction." [SO:ke]
comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
subset: SOFA
synonym: "amplicon" RELATED []
synonym: "PCR product" EXACT []
xref: http://en.wikipedia.org/wiki/RAPD "wiki"
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000007
name: read_pair
def: "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]
subset: SOFA
synonym: "mate pair" EXACT []
synonym: "read-pair" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000149 ! contig
relationship: part_of SO:0001790 ! paired_end_fragment

[Term]
id: SO:0000008
name: gene_sensu_your_favorite_organism
is_obsolete: true

[Term]
id: SO:0000009
name: gene_class
is_obsolete: true

[Term]
id: SO:0000010
name: protein_coding
synonym: "protein-coding" EXACT []
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000011
name: non_protein_coding
synonym: "non protein-coding" EXACT []
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000012
name: scRNA_primary_transcript
def: "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]
synonym: "scRNA primary transcript" EXACT []
synonym: "scRNA transcript" EXACT []
synonym: "small cytoplasmic RNA" RELATED []
synonym: "small cytoplasmic RNA transcript" EXACT []
synonym: "small_cytoplasmic_RNA" RELATED []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000013
name: scRNA
def: "A small non coding RNA sequence, present in the cytoplasm." [SO:ke]
subset: SOFA
synonym: "small cytoplasmic RNA" EXACT []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000012 ! scRNA_primary_transcript

[Term]
id: SO:0000014
name: INR_motif
def: "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]
comment: Binds TAF1, TAF2.
synonym: "DMp2" RELATED []
synonym: "initiator" EXACT []
synonym: "initiator motif" EXACT []
synonym: "INR motif" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter

[Term]
id: SO:0000015
name: DPE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739\:12537576, PMID:16858867]
comment: Binds TAF6, TAF9.
synonym: "CRWMGCGWKCGCTTS" NARROW []
synonym: "downstream core promoter element" EXACT []
synonym: "DPE motif" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter

[Term]
id: SO:0000016
name: BREu_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]
comment: Binds TFIIB.
synonym: "B-recognition element" EXACT []
synonym: "BRE motif" EXACT []
synonym: "BREu" RELATED []
synonym: "BREu motif" EXACT []
synonym: "TFIIB recognition element" RELATED []
synonym: "transcription factor B-recognition element" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter

[Term]
id: SO:0000017
name: PSE_motif
def: "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]
synonym: "proximal sequence element" EXACT []
synonym: "PSE motif" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000167 ! promoter

[Term]
id: SO:0000018
name: linkage_group
def: "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046]
synonym: "linkage group" EXACT []
xref: http://en.wikipedia.org/wiki/Linkage_group "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000020
name: RNA_internal_loop
def: "A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]
synonym: "RNA internal loop" EXACT []
is_a: SO:0000715 ! RNA_motif

[Term]
id: SO:0000021
name: asymmetric_RNA_internal_loop
def: "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]
synonym: "asymmetric RNA internal loop" EXACT []
is_a: SO:0000020 ! RNA_internal_loop

[Term]
id: SO:0000022
name: A_minor_RNA_motif
def: "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]
synonym: "A minor RNA motif" EXACT []
is_a: SO:0000715 ! RNA_motif

[Term]
id: SO:0000023
name: K_turn_RNA_motif
def: "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]
synonym: "K turn RNA motif" EXACT []
synonym: "K-turn" EXACT []
synonym: "kink turn" EXACT []
synonym: "kink-turn motif" EXACT []
xref: http://en.wikipedia.org/wiki/K-turn "wiki"
is_a: SO:0000021 ! asymmetric_RNA_internal_loop

[Term]
id: SO:0000024
name: sarcin_like_RNA_motif
def: "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]
synonym: "sarcin like RNA motif" EXACT []
synonym: "sarcin/ricin domain" EXACT []
synonym: "sarcin/ricin loop" EXACT []
synonym: "sarcin/ricin RNA domain" EXACT []
is_a: SO:0000021 ! asymmetric_RNA_internal_loop

[Term]
id: SO:0000025
name: symmetric_RNA_internal_loop
def: "An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]
synonym: "A-minor RNA motif" EXACT []
is_a: SO:0000020 ! RNA_internal_loop

[Term]
id: SO:0000026
name: RNA_junction_loop
synonym: "RNA junction loop" EXACT []
is_a: SO:0000715 ! RNA_motif

[Term]
id: SO:0000027
name: RNA_hook_turn
synonym: "hook turn" RELATED []
synonym: "hook-turn motif" EXACT []
synonym: "RNA hook turn" EXACT []
is_a: SO:0000026 ! RNA_junction_loop

[Term]
id: SO:0000028
name: base_pair
synonym: "base pair" EXACT []
xref: http://en.wikipedia.org/wiki/Base_pair "wiki"
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000029
name: WC_base_pair
def: "The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]
synonym: "canonical base pair" EXACT []
synonym: "Watson Crick base pair" EXACT []
synonym: "Watson-Crick base pair" RELATED []
synonym: "Watson-Crick pair" EXACT []
synonym: "WC base pair" EXACT []
is_a: SO:0000028 ! base_pair

[Term]
id: SO:0000030
name: sugar_edge_base_pair
def: "A type of non-canonical base-pairing." [PMID:12177293]
synonym: "sugar edge base pair" EXACT []
is_a: SO:0000028 ! base_pair

[Term]
id: SO:0000031
name: aptamer
def: "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]
xref: http://en.wikipedia.org/wiki/Aptamer "wiki"
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000032
name: DNA_aptamer
def: "DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]
synonym: "DNA aptamer" EXACT []
is_a: SO:0000031 ! aptamer

[Term]
id: SO:0000033
name: RNA_aptamer
def: "RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]
synonym: "RNA aptamer" EXACT []
is_a: SO:0000031 ! aptamer

[Term]
id: SO:0000034
name: morpholino_oligo
def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]
synonym: "morphant" BROAD []
synonym: "morpholino" EXACT []
synonym: "morpholino oligo" EXACT []
is_a: SO:0001247 ! synthetic_oligo
intersection_of: SO:0001247 ! synthetic_oligo
intersection_of: has_quality SO:0001183 ! morpholino_backbone
relationship: has_quality SO:0001183 ! morpholino_backbone

[Term]
id: SO:0000035
name: riboswitch
def: "A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]
synonym: "riboswitch RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Riboswitch "wiki"
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000036
name: matrix_attachment_site
def: "A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]
synonym: "MAR" EXACT []
synonym: "matrix association region" EXACT []
synonym: "matrix attachment region" EXACT []
synonym: "matrix attachment site" EXACT []
synonym: "nuclear matrix association region" EXACT []
synonym: "nuclear matrix attachment site" EXACT []
synonym: "S/MAR" EXACT []
synonym: "S/MAR element" RELATED []
synonym: "scaffold attachment site" EXACT []
synonym: "scaffold matrix attachment region" EXACT []
synonym: "SMAR" EXACT []
xref: http://en.wikipedia.org/wiki/Matrix_attachment_site "wiki"
is_a: SO:0000626 ! chromosomal_regulatory_element

[Term]
id: SO:0000037
name: locus_control_region
def: "A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]
synonym: "LCR" EXACT []
synonym: "locus control element" RELATED []
synonym: "locus control region" EXACT []
xref: http://en.wikipedia.org/wiki/Locus_control_region "wiki"
is_a: SO:0000727 ! CRM

[Term]
id: SO:0000038
name: match_set
def: "A collection of match parts." [SO:ke]
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000039
name: match_part
def: "A part of a match, for example an hsp from blast is a match_part." [SO:ke]
subset: SOFA
synonym: "match part" EXACT []
is_a: SO:0001410 ! experimental_feature
relationship: part_of SO:0000343 ! match

[Term]
id: SO:0000040
name: genomic_clone
def: "A clone of a DNA region of a genome." [SO:ma]
synonym: "genomic clone" EXACT []
is_a: SO:0000151 ! clone
intersection_of: SO:0000151 ! clone
intersection_of: has_quality SO:0000991 ! genomic_DNA
relationship: has_quality SO:0000991 ! genomic_DNA

[Term]
id: SO:0000041
name: sequence_operation
def: "An operation that can be applied to a sequence, that results in a change." [SO:ke]
synonym: "sequence operation" EXACT []
is_obsolete: true

[Term]
id: SO:0000042
name: pseudogene_attribute
def: "An attribute of a pseudogene (SO:0000336)." [SO:ma]
synonym: "pseudogene attribute" EXACT []
is_obsolete: true

[Term]
id: SO:0000043
name: processed_pseudogene
def: "A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp]
comment: Please not the synonym R psi M uses the spelled out form of the greek letter.
synonym: "processed pseudogene" EXACT []
synonym: "pseudogene by reverse transcription" RELATED []
synonym: "R psi G" RELATED []
synonym: "retropseudogene" EXACT []
is_a: SO:0000336 ! pseudogene

[Term]
id: SO:0000044
name: pseudogene_by_unequal_crossing_over
def: "A pseudogene caused by unequal crossing over at recombination." [SO:ke]
synonym: "pseudogene by unequal crossing over" EXACT []
is_a: SO:0001760 ! non_processed_pseudogene

[Term]
id: SO:0000045
name: delete
def: "To remove a subsection of sequence." [SO:ke]
is_obsolete: true

[Term]
id: SO:0000046
name: insert
def: "To insert a subsection of sequence." [SO:ke]
is_obsolete: true

[Term]
id: SO:0000047
name: invert
def: "To invert a subsection of sequence." [SO:ke]
is_obsolete: true

[Term]
id: SO:0000048
name: substitute
def: "To substitute a subsection of sequence for another." [SO:ke]
is_obsolete: true

[Term]
id: SO:0000049
name: translocate
def: "To translocate a subsection of sequence." [SO:ke]
is_obsolete: true

[Term]
id: SO:0000050
name: gene_part
def: "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene." [SO:ke]
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000051
name: probe
def: "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]
xref: http://en.wikipedia.org/wiki/Hybridization_probe "wiki"
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000052
name: assortment_derived_deficiency
synonym: "assortment-derived_deficiency" RELATED []
is_obsolete: true

[Term]
id: SO:0000053
name: sequence_variant_affecting_regulatory_region
def: "A sequence_variant_effect which changes the regulatory region of a gene." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting regulatory region" RELATED []
synonym: "sequence variant affecting regulatory region" EXACT []
is_obsolete: true
replaced_by: SO:0001556

[Term]
id: SO:0000054
name: aneuploid
def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
xref: http://en.wikipedia.org/wiki/Aneuploid "wiki"
is_a: SO:1000182 ! chromosome_number_variation

[Term]
id: SO:0000055
name: hyperploid
def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]
xref: http://en.wikipedia.org/wiki/Hyperploid "wiki"
is_a: SO:0000054 ! aneuploid

[Term]
id: SO:0000056
name: hypoploid
def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]
xref: http://en.wikipedia.org/wiki/Hypoploid "wiki"
is_a: SO:0000054 ! aneuploid

[Term]
id: SO:0000057
name: operator
def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]
subset: SOFA
synonym: "operator segment" EXACT []
xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki"
is_a: SO:0000752 ! gene_group_regulatory_region

[Term]
id: SO:0000058
name: assortment_derived_aneuploid
synonym: "assortment-derived_aneuploid" RELATED []
is_obsolete: true

[Term]
id: SO:0000059
name: nuclease_binding_site
def: "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]
subset: SOFA
synonym: "nuclease binding site" EXACT []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site

[Term]
id: SO:0000060
name: compound_chromosome_arm
comment: FLAG - this term is should probably be a part of rather than an is_a.
synonym: "compound chromosome arm" EXACT []
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:0000061
name: restriction_enzyme_binding_site
def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]
comment: A region of a molecule that binds to a restriction enzyme.
synonym: "restriction endonuclease binding site" EXACT []
synonym: "restriction enzyme binding site" EXACT []
is_a: SO:0000059 ! nuclease_binding_site

[Term]
id: SO:0000062
name: deficient_intrachromosomal_transposition
def: "An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]
synonym: "deficient intrachromosomal transposition" EXACT []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000041 ! intrachromosomal_transposition
relationship: has_part SO:0000159 ! deletion

[Term]
id: SO:0000063
name: deficient_interchromosomal_transposition
def: "An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]
synonym: "deficient interchromosomal transposition" EXACT []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:0000064
name: gene_by_transcript_attribute
comment: This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.
is_obsolete: true

[Term]
id: SO:0000065
name: free_chromosome_arm
def: "A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]
synonym: "free chromosome arm" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:0000066
name: gene_by_polyadenylation_attribute
is_obsolete: true

[Term]
id: SO:0000067
name: gene_to_gene_feature
synonym: "gene to gene feature" EXACT []
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000068
name: overlapping
def: "An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]
is_a: SO:0000067 ! gene_to_gene_feature

[Term]
id: SO:0000069
name: inside_intron
def: "An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]
synonym: "inside intron" EXACT []
is_a: SO:0000068 ! overlapping

[Term]
id: SO:0000070
name: inside_intron_antiparallel
def: "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]
synonym: "inside intron antiparallel" EXACT []
is_a: SO:0000069 ! inside_intron

[Term]
id: SO:0000071
name: inside_intron_parallel
def: "An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]
synonym: "inside intron parallel" EXACT []
is_a: SO:0000069 ! inside_intron

[Term]
id: SO:0000072
name: end_overlapping_gene
is_obsolete: true

[Term]
id: SO:0000073
name: five_prime_three_prime_overlap
def: "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]
synonym: "five prime-three prime overlap" EXACT []
is_a: SO:0000068 ! overlapping

[Term]
id: SO:0000074
name: five_prime_five_prime_overlap
def: "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]
synonym: "five prime-five prime overlap" EXACT []
is_a: SO:0000068 ! overlapping

[Term]
id: SO:0000075
name: three_prime_three_prime_overlap
def: "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]
synonym: "three prime-three prime overlap" EXACT []
is_a: SO:0000068 ! overlapping

[Term]
id: SO:0000076
name: three_prime_five_prime_overlap
def: "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]
synonym: "5' 3' overlap" EXACT []
synonym: "three prime five prime overlap" EXACT []
is_a: SO:0000068 ! overlapping

[Term]
id: SO:0000077
name: antisense
def: "A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]
xref: http://en.wikipedia.org/wiki/Antisense "wiki"
is_a: SO:0000068 ! overlapping

[Term]
id: SO:0000078
name: polycistronic_transcript
def: "A transcript that is polycistronic." [SO:xp]
synonym: "polycistronic transcript" EXACT []
is_a: SO:0000673 ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000880 ! polycistronic
relationship: has_quality SO:0000880 ! polycistronic

[Term]
id: SO:0000079
name: dicistronic_transcript
def: "A transcript that is dicistronic." [SO:ke]
synonym: "dicistronic transcript" EXACT []
is_a: SO:0000078 ! polycistronic_transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000879 ! dicistronic
relationship: has_quality SO:0000879 ! dicistronic

[Term]
id: SO:0000080
name: operon_member
synonym: "operon member" EXACT []
is_a: SO:0000081 ! gene_array_member

[Term]
id: SO:0000081
name: gene_array_member
synonym: "gene array member" EXACT []
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000082
name: processed_transcript_attribute
is_obsolete: true

[Term]
id: SO:0000083
name: macronuclear_sequence
synonym: "macronuclear sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence

[Term]
id: SO:0000084
name: micronuclear_sequence
synonym: "micronuclear sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence

[Term]
id: SO:0000085
name: gene_by_genome_location
is_obsolete: true

[Term]
id: SO:0000086
name: gene_by_organelle_of_genome
is_obsolete: true

[Term]
id: SO:0000087
name: nuclear_gene
def: "A gene from nuclear sequence." [SO:xp]
synonym: "nuclear gene" EXACT []
xref: http://en.wikipedia.org/wiki/Nuclear_gene "wiki"
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_origin SO:0000738 ! nuclear_sequence
relationship: has_origin SO:0000738 ! nuclear_sequence

[Term]
id: SO:0000088
name: mt_gene
def: "A gene located in mitochondrial sequence." [SO:xp]
synonym: "mitochondrial gene" EXACT []
synonym: "mt gene" EXACT []
xref: http://en.wikipedia.org/wiki/Mitochondrial_gene "wiki"
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_origin SO:0000737 ! mitochondrial_sequence
relationship: has_origin SO:0000737 ! mitochondrial_sequence

[Term]
id: SO:0000089
name: kinetoplast_gene
def: "A gene located in kinetoplast sequence." [SO:xp]
synonym: "kinetoplast gene" EXACT []
is_a: SO:0000088 ! mt_gene
intersection_of: SO:0000088 ! mt_gene
intersection_of: has_origin SO:0000741 ! kinetoplast
relationship: has_origin SO:0000741 ! kinetoplast

[Term]
id: SO:0000090
name: plastid_gene
def: "A gene from plastid sequence." [SO:xp]
synonym: "plastid gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_origin SO:0000740 ! plastid_sequence
relationship: has_origin SO:0000740 ! plastid_sequence

[Term]
id: SO:0000091
name: apicoplast_gene
def: "A gene from apicoplast sequence." [SO:xp]
synonym: "apicoplast gene" EXACT []
is_a: SO:0000090 ! plastid_gene
intersection_of: SO:0000090 ! plastid_gene
intersection_of: has_origin SO:0000743 ! apicoplast_sequence
relationship: has_origin SO:0000743 ! apicoplast_sequence

[Term]
id: SO:0000092
name: ct_gene
def: "A gene from chloroplast sequence." [SO:xp]
synonym: "chloroplast gene" EXACT []
synonym: "ct gene" EXACT []
is_a: SO:0000090 ! plastid_gene
intersection_of: SO:0000090 ! plastid_gene
intersection_of: has_origin SO:0000745 ! chloroplast_sequence
relationship: has_origin SO:0000745 ! chloroplast_sequence

[Term]
id: SO:0000093
name: chromoplast_gene
def: "A gene from chromoplast_sequence." [SO:xp]
synonym: "chromoplast gene" EXACT []
is_a: SO:0000090 ! plastid_gene
intersection_of: SO:0000090 ! plastid_gene
intersection_of: has_origin SO:0000744 ! chromoplast_sequence
relationship: has_origin SO:0000744 ! chromoplast_sequence

[Term]
id: SO:0000094
name: cyanelle_gene
def: "A gene from cyanelle sequence." [SO:xp]
synonym: "cyanelle gene" EXACT []
is_a: SO:0000090 ! plastid_gene
intersection_of: SO:0000090 ! plastid_gene
intersection_of: has_origin SO:0000746 ! cyanelle_sequence
relationship: has_origin SO:0000746 ! cyanelle_sequence

[Term]
id: SO:0000095
name: leucoplast_gene
def: "A plastid gene from leucoplast sequence." [SO:xp]
synonym: "leucoplast gene" EXACT []
is_a: SO:0000090 ! plastid_gene
intersection_of: SO:0000090 ! plastid_gene
intersection_of: has_origin SO:0000747 ! leucoplast_sequence
relationship: has_origin SO:0000747 ! leucoplast_sequence

[Term]
id: SO:0000096
name: proplastid_gene
def: "A gene from proplastid sequence." [SO:ke]
synonym: "proplastid gene" EXACT []
is_a: SO:0000090 ! plastid_gene
intersection_of: SO:0000090 ! plastid_gene
intersection_of: has_origin SO:0000748 ! proplastid_sequence
relationship: has_origin SO:0000748 ! proplastid_sequence

[Term]
id: SO:0000097
name: nucleomorph_gene
def: "A gene from nucleomorph sequence." [SO:xp]
synonym: "nucleomorph gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_origin SO:0000739 ! nucleomorphic_sequence
relationship: has_origin SO:0000739 ! nucleomorphic_sequence

[Term]
id: SO:0000098
name: plasmid_gene
def: "A gene from plasmid sequence." [SO:xp]
synonym: "plasmid gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_origin SO:0000749 ! plasmid_location
relationship: has_origin SO:0000749 ! plasmid_location

[Term]
id: SO:0000099
name: proviral_gene
def: "A gene from proviral sequence." [SO:xp]
synonym: "proviral gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_origin SO:0000751 ! proviral_location
relationship: has_origin SO:0000751 ! proviral_location

[Term]
id: SO:0000100
name: endogenous_retroviral_gene
def: "A proviral gene with origin endogenous retrovirus." [SO:xp]
synonym: "endogenous retroviral gene" EXACT []
is_a: SO:0000099 ! proviral_gene
intersection_of: SO:0000099 ! proviral_gene
intersection_of: has_origin SO:0000903 ! endogenous_retroviral_sequence
relationship: has_origin SO:0000903 ! endogenous_retroviral_sequence

[Term]
id: SO:0000101
name: transposable_element
def: "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]
subset: SOFA
synonym: "transposable element" EXACT []
synonym: "transposon" EXACT []
xref: http://en.wikipedia.org/wiki/Transposable_element "wiki"
is_a: SO:0001039 ! integrated_mobile_genetic_element

[Term]
id: SO:0000102
name: expressed_sequence_match
def: "A match to an EST or cDNA sequence." [SO:ke]
subset: SOFA
synonym: "expressed sequence match" EXACT []
is_a: SO:0000347 ! nucleotide_match

[Term]
id: SO:0000103
name: clone_insert_end
def: "The end of the clone insert." [SO:ke]
subset: SOFA
synonym: "clone insert end" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000753 ! clone_insert

[Term]
id: SO:0000104
name: polypeptide
alt_id: SO:0000358
def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.
subset: SOFA
synonym: "protein" EXACT []
xref: http://en.wikipedia.org/wiki/Polypeptide "wiki"
is_a: SO:0001411 ! biological_region
relationship: derives_from SO:0000316 ! CDS

[Term]
id: SO:0000105
name: chromosome_arm
def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]
synonym: "chromosome arm" EXACT []
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0000106
name: non_capped_primary_transcript
is_obsolete: true

[Term]
id: SO:0000107
name: sequencing_primer
synonym: "sequencing primer" EXACT []
is_a: SO:0000112 ! primer

[Term]
id: SO:0000108
name: mRNA_with_frameshift
def: "An mRNA with a frameshift." [SO:xp]
synonym: "frameshifted mRNA" EXACT []
synonym: "mRNA with frameshift" EXACT []
is_a: SO:0000234 ! mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000865 ! frameshift
relationship: has_quality SO:0000865 ! frameshift

[Term]
id: SO:0000109
name: sequence_variant_obs
def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
subset: SOFA
synonym: "mutation" RELATED []
is_obsolete: true

[Term]
id: SO:0000110
name: sequence_feature
def: "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]
subset: SOFA
synonym: "located sequence feature" RELATED []
synonym: "located_sequence_feature" EXACT []
synonym: "sequence feature" EXACT []
disjoint_from: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000111
name: transposable_element_gene
def: "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]
synonym: "transposable element gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: part_of SO:0000101 ! transposable_element
relationship: part_of SO:0000101 ! transposable_element

[Term]
id: SO:0000112
name: primer
def: "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]
subset: SOFA
synonym: "DNA primer" EXACT []
synonym: "primer oligonucleotide" EXACT []
synonym: "primer polynucleotide" EXACT []
synonym: "primer sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology) "wiki"
is_a: SO:0000441 ! ss_oligo

[Term]
id: SO:0000113
name: proviral_region
def: "A viral sequence which has integrated into a host genome." [SO:ke]
subset: SOFA
synonym: "proviral region" EXACT []
synonym: "proviral sequence" RELATED []
is_a: SO:0001039 ! integrated_mobile_genetic_element

[Term]
id: SO:0000114
name: methylated_cytosine
def: "A methylated deoxy-cytosine." [SO:ke]
subset: SOFA
synonym: "methylated C" EXACT []
synonym: "methylated cytosine" EXACT []
synonym: "methylated cytosine base" EXACT []
synonym: "methylated cytosine residue" EXACT []
synonym: "methylated_C" EXACT []
is_a: SO:0000306 ! methylated_DNA_base_feature
is_a: SO:0001963 ! modified_cytosine

[Term]
id: SO:0000115
name: transcript_feature
is_obsolete: true

[Term]
id: SO:0000116
name: edited
def: "An attribute describing a sequence that is modified by editing." [SO:ke]
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000117
name: transcript_with_readthrough_stop_codon
is_obsolete: true

[Term]
id: SO:0000118
name: transcript_with_translational_frameshift
def: "A transcript with a translational frameshift." [SO:xp]
synonym: "transcript with translational frameshift" EXACT []
is_a: SO:0000673 ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000887 ! translationally_frameshifted
relationship: has_quality SO:0000887 ! translationally_frameshifted

[Term]
id: SO:0000119
name: regulated
def: "An attribute to describe a sequence that is regulated." [SO:ke]
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000120
name: protein_coding_primary_transcript
def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]
comment: May contain introns.
subset: SOFA
synonym: "pre mRNA" RELATED []
synonym: "protein coding primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000121
name: forward_primer
def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "DNA forward primer" EXACT []
synonym: "forward DNA primer" EXACT []
synonym: "forward primer" EXACT []
synonym: "forward primer oligo" EXACT []
synonym: "forward primer oligonucleotide" EXACT []
synonym: "forward primer polynucleotide" EXACT []
synonym: "forward primer sequence" EXACT []
is_a: SO:0000112 ! primer
intersection_of: SO:0000112 ! primer
intersection_of: has_quality SO:0001030 ! forward
relationship: has_quality SO:0001030 ! forward

[Term]
id: SO:0000122
name: RNA_sequence_secondary_structure
def: "A folded RNA sequence." [SO:ke]
synonym: "RNA sequence secondary structure" EXACT []
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000123
name: transcriptionally_regulated
def: "An attribute describing a gene that is regulated at transcription." [SO:ma]
comment: By:<protein_id>.
synonym: "transcriptionally regulated" EXACT []
is_a: SO:0000119 ! regulated

[Term]
id: SO:0000124
name: transcriptionally_constitutive
def: "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]
synonym: "transcriptionally constitutive" EXACT []
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000125
name: transcriptionally_induced
def: "An inducer molecule is required for transcription to occur." [SO:ke]
synonym: "transcriptionally induced" EXACT []
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000126
name: transcriptionally_repressed
def: "A repressor molecule is required for transcription to stop." [SO:ke]
synonym: "transcriptionally repressed" EXACT []
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000127
name: silenced_gene
def: "A gene that is silenced." [SO:xp]
synonym: "silenced gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000893 ! silenced
relationship: has_quality SO:0000893 ! silenced

[Term]
id: SO:0000128
name: gene_silenced_by_DNA_modification
def: "A gene that is silenced by DNA modification." [SO:xp]
synonym: "gene silenced by DNA modification" EXACT []
is_a: SO:0000127 ! silenced_gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000894 ! silenced_by_DNA_modification
relationship: has_quality SO:0000894 ! silenced_by_DNA_modification

[Term]
id: SO:0000129
name: gene_silenced_by_DNA_methylation
def: "A gene that is silenced by DNA methylation." [SO:xp]
synonym: "gene silenced by DNA methylation" EXACT []
synonym: "methylation-silenced gene" EXACT []
is_a: SO:0000128 ! gene_silenced_by_DNA_modification
intersection_of: SO:0000128 ! gene_silenced_by_DNA_modification
intersection_of: has_quality SO:0000895 ! silenced_by_DNA_methylation
relationship: has_quality SO:0000895 ! silenced_by_DNA_methylation

[Term]
id: SO:0000130
name: post_translationally_regulated
def: "An attribute describing a gene that is regulated after it has been translated." [SO:ke]
synonym: "post translationally regulated" EXACT []
synonym: "post-translationally regulated" EXACT []
is_a: SO:0000119 ! regulated

[Term]
id: SO:0000131
name: translationally_regulated
def: "An attribute describing a gene that is regulated as it is translated." [SO:ke]
synonym: "translationally regulated" EXACT []
is_a: SO:0000119 ! regulated

[Term]
id: SO:0000132
name: reverse_primer
def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "DNA reverse primer" EXACT []
synonym: "reverse DNA primer" EXACT []
synonym: "reverse primer" EXACT []
synonym: "reverse primer oligo" EXACT []
synonym: "reverse primer oligonucleotide" EXACT []
synonym: "reverse primer sequence" EXACT []
is_a: SO:0000112 ! primer
intersection_of: SO:0000112 ! primer
intersection_of: has_quality SO:0001031 ! reverse
relationship: has_quality SO:0001031 ! reverse

[Term]
id: SO:0000133
name: epigenetically_modified
def: "This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]
synonym: "epigenetically modified" EXACT []
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000134
name: genomically_imprinted
def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]
synonym: "genomically imprinted" EXACT []
synonym: "imprinted" BROAD []
xref: http:http\://en.wikipedia.org/wiki/Genomic_imprinting "wiki"
is_a: SO:0000119 ! regulated
is_a: SO:0000133 ! epigenetically_modified

[Term]
id: SO:0000135
name: maternally_imprinted
def: "The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]
synonym: "maternally imprinted" EXACT []
is_a: SO:0000134 ! genomically_imprinted

[Term]
id: SO:0000136
name: paternally_imprinted
def: "The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]
synonym: "paternally imprinted" EXACT []
is_a: SO:0000134 ! genomically_imprinted

[Term]
id: SO:0000137
name: allelically_excluded
def: "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke]
comment: Examples are x-inactivation and immunoglobulin formation.
synonym: "allelically excluded" EXACT []
is_a: SO:0000133 ! epigenetically_modified

[Term]
id: SO:0000138
name: gene_rearranged_at_DNA_level
def: "An epigenetically modified gene, rearranged at the DNA level." [SO:xp]
synonym: "gene rearranged at DNA level" EXACT []
is_a: SO:0000898 ! epigenetically_modified_gene
intersection_of: SO:0000898 ! epigenetically_modified_gene
intersection_of: has_quality SO:0000904 ! rearranged_at_DNA_level
relationship: has_quality SO:0000904 ! rearranged_at_DNA_level

[Term]
id: SO:0000139
name: ribosome_entry_site
def: "Region in mRNA where ribosome assembles." [SO:ke]
subset: SOFA
synonym: "ribosome entry site" EXACT []
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000204 ! five_prime_UTR

[Term]
id: SO:0000140
name: attenuator
def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]
subset: SOFA
synonym: "attenuator sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Attenuator "wiki"
is_a: SO:0001680 ! translation_regulatory_region
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000141
name: terminator
def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "terminator sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki"
is_a: SO:0001679 ! transcription_regulatory_region
relationship: part_of SO:0000673 ! transcript

[Term]
id: SO:0000142
name: DNA_sequence_secondary_structure
def: "A folded DNA sequence." [SO:ke]
synonym: "DNA sequence secondary structure" EXACT []
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000143
name: assembly_component
def: "A region of known length which may be used to manufacture a longer region." [SO:ke]
subset: SOFA
synonym: "assembly component" EXACT []
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0000144
name: primary_transcript_attribute
is_obsolete: true

[Term]
id: SO:0000145
name: recoded_codon
def: "A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]
synonym: "recoded codon" EXACT []
is_a: SO:0000360 ! codon

[Term]
id: SO:0000146
name: capped
def: "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke]
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000147
name: exon
def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Exon "wiki"
is_a: SO:0000833 ! transcript_region

[Term]
id: SO:0000148
name: supercontig
def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]
subset: SOFA
synonym: "scaffold" RELATED []
is_a: SO:0001876 ! partial_genomic_sequence_assembly
relationship: part_of SO:0000719 ! ultracontig

[Term]
id: SO:0000149
name: contig
def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Contig "wiki"
is_a: SO:0000143 ! assembly_component
is_a: SO:0000353 ! sequence_assembly
relationship: part_of SO:0000148 ! supercontig

[Term]
id: SO:0000150
name: read
def: "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000149 ! contig

[Term]
id: SO:0000151
name: clone
def: "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]
subset: SOFA
xref: http:http\://en.wikipedia.org/wiki/Clone_(genetics) "wiki"
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000152
name: YAC
def: "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "yeast artificial chromosome" EXACT []
is_a: SO:0000440 ! vector_replicon

[Term]
id: SO:0000153
name: BAC
def: "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "bacterial artificial chromosome" EXACT []
is_a: SO:0000440 ! vector_replicon

[Term]
id: SO:0000154
name: PAC
def: "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome.
synonym: "P1" EXACT []
synonym: "P1 artificial chromosome" EXACT []
xref: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome "wiki"
is_a: SO:0000440 ! vector_replicon

[Term]
id: SO:0000155
name: plasmid
def: "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "plasmid sequence" EXACT []
is_a: SO:0001235 ! replicon

[Term]
id: SO:0000156
name: cosmid
def: "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]
comment: Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "cosmid vector" EXACT []
xref: http://en.wikipedia.org/wiki/Cosmid "wiki"
is_a: SO:0000440 ! vector_replicon

[Term]
id: SO:0000157
name: phagemid
def: "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]
synonym: "phagemid vector" RELATED []
xref: http://en.wikipedia.org/wiki/Phagemid "wiki"
is_a: SO:0000440 ! vector_replicon

[Term]
id: SO:0000158
name: fosmid
def: "A cloning vector that utilizes the E. coli F factor." [SO:ma]
comment: Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.
synonym: "fosmid vector" RELATED []
xref: http://en.wikipedia.org/wiki/Fosmid "wiki"
is_a: SO:0000440 ! vector_replicon

[Term]
id: SO:0000159
name: deletion
alt_id: SO:1000033
def: "The point at which one or more contiguous nucleotides were excised." [SO:ke]
subset: SOFA
synonym: "deleted_sequence" EXACT []
synonym: "nucleotide deletion" EXACT []
synonym: "nucleotide_deletion" EXACT []
xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki"
xref: loinc:LA6692-3 "Deletion"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000160
name: lambda_clone
def: "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]
is_obsolete: true

[Term]
id: SO:0000161
name: methylated_adenine
def: "A modified  base in which adenine has been methylated." [SO:ke]
subset: SOFA
synonym: "methylated A" EXACT []
synonym: "methylated adenine" EXACT []
synonym: "methylated adenine base" EXACT []
synonym: "methylated adenine residue" EXACT []
synonym: "methylated_A" EXACT []
is_a: SO:0000306 ! methylated_DNA_base_feature
is_a: SO:0001962 ! modified_adenine

[Term]
id: SO:0000162
name: splice_site
def: "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]
comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery.
subset: SOFA
synonym: "splice site" EXACT []
xref: http://en.wikipedia.org/wiki/Splice_site "wiki"
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000163
name: five_prime_cis_splice_site
def: "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]
subset: SOFA
synonym: "5' splice site" EXACT []
synonym: "donor" RELATED []
synonym: "donor splice site" EXACT []
synonym: "five prime splice site" EXACT []
synonym: "splice donor site" EXACT []
is_a: SO:0001419 ! cis_splice_site

[Term]
id: SO:0000164
name: three_prime_cis_splice_site
def: "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]
subset: SOFA
synonym: "3' splice site" RELATED []
synonym: "acceptor" RELATED []
synonym: "acceptor splice site" EXACT []
synonym: "splice acceptor site" EXACT []
synonym: "three prime splice site" EXACT []
is_a: SO:0001419 ! cis_splice_site

[Term]
id: SO:0000165
name: enhancer
def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki"
is_a: SO:0000727 ! CRM

[Term]
id: SO:0000166
name: enhancer_bound_by_factor
def: "An enhancer bound by a factor." [SO:xp]
synonym: "enhancer bound by factor" EXACT []
is_a: SO:0000165 ! enhancer
intersection_of: SO:0000165 ! enhancer
intersection_of: has_quality SO:0000277 ! bound_by_factor
relationship: has_quality SO:0000277 ! bound_by_factor

[Term]
id: SO:0000167
name: promoter
def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
subset: SOFA
synonym: "promoter sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Promoter "wiki"
is_a: SO:0001055 ! transcriptional_cis_regulatory_region

[Term]
id: SO:0000168
name: restriction_enzyme_cut_site
def: "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." [SO:ma]
is_obsolete: true

[Term]
id: SO:0000169
name: RNApol_I_promoter
def: "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]
synonym: "pol I promoter" EXACT []
synonym: "polymerase I promoter" EXACT []
synonym: "RNA polymerase A promoter" EXACT []
synonym: "RNApol I promoter" EXACT []
is_a: SO:0001203 ! RNA_polymerase_promoter

[Term]
id: SO:0000170
name: RNApol_II_promoter
def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]
synonym: "pol II promoter" RELATED []
synonym: "polymerase II promoter" EXACT []
synonym: "RNA polymerase B promoter" EXACT []
synonym: "RNApol II promoter" EXACT []
is_a: SO:0001203 ! RNA_polymerase_promoter

[Term]
id: SO:0000171
name: RNApol_III_promoter
def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]
synonym: "pol III promoter" EXACT []
synonym: "polymerase III promoter" EXACT []
synonym: "RNA polymerase C promoter" EXACT []
synonym: "RNApol III promoter" EXACT []
is_a: SO:0001203 ! RNA_polymerase_promoter

[Term]
id: SO:0000172
name: CAAT_signal
def: "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "CAAT box" EXACT []
synonym: "CAAT signal" EXACT []
synonym: "CAAT-box" EXACT []
xref: http://en.wikipedia.org/wiki/CAAT_box "wiki"
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000173
name: GC_rich_promoter_region
def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "GC rich promoter region" EXACT []
synonym: "GC-rich region" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000174
name: TATA_box
def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]
comment: Binds TBP.
synonym: "Goldstein-Hogness box" EXACT []
synonym: "TATA box" EXACT []
xref: http://en.wikipedia.org/wiki/TATA_box "wiki"
is_a: SO:0001660 ! core_promoter_element

[Term]
id: SO:0000175
name: minus_10_signal
def: "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "-10 signal" EXACT []
synonym: "minus 10 signal" EXACT []
synonym: "Pribnow box" EXACT []
synonym: "Pribnow Schaller box" EXACT []
synonym: "Pribnow-Schaller box" EXACT []
xref: http://en.wikipedia.org/wiki/Pribnow_box "wiki"
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70
relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf

[Term]
id: SO:0000176
name: minus_35_signal
def: "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "-35 signal" EXACT []
synonym: "minus 35 signal" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70
relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf

[Term]
id: SO:0000177
name: cross_genome_match
def: "A nucleotide match against a sequence from another organism." [SO:ma]
subset: SOFA
synonym: "cross genome match" EXACT []
is_a: SO:0000347 ! nucleotide_match

[Term]
id: SO:0000178
name: operon
def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Operon "wiki"
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0000179
name: clone_insert_start
def: "The start of the clone insert." [SO:ke]
subset: SOFA
synonym: "clone insert start" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000753 ! clone_insert

[Term]
id: SO:0000180
name: retrotransposon
def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]
synonym: "class I" RELATED []
synonym: "class I transposon" EXACT []
synonym: "retrotransposon element" EXACT []
xref: http://en.wikipedia.org/wiki/Retrotransposon "wiki"
is_a: SO:0000101 ! transposable_element

[Term]
id: SO:0000181
name: translated_nucleotide_match
def: "A match against a translated sequence." [SO:ke]
subset: SOFA
synonym: "translated nucleotide match" EXACT []
is_a: SO:0000347 ! nucleotide_match

[Term]
id: SO:0000182
name: DNA_transposon
def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]
synonym: "class II" RELATED []
synonym: "class II transposon" EXACT []
synonym: "DNA transposon" EXACT []
is_a: SO:0000101 ! transposable_element

[Term]
id: SO:0000183
name: non_transcribed_region
def: "A region of the gene which is not transcribed." [SO:ke]
subset: SOFA
synonym: "non transcribed region" EXACT []
synonym: "non-transcribed sequence" EXACT []
synonym: "nontranscribed region" EXACT []
synonym: "nontranscribed sequence" EXACT []
is_a: SO:0000842 ! gene_component_region

[Term]
id: SO:0000184
name: U2_intron
def: "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]
comment: May have either GT-AG or AT-AG 5' and 3' boundaries.
synonym: "U2 intron" EXACT []
is_a: SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000185
name: primary_transcript
def: "A transcript that in its initial state requires modification to be functional." [SO:ma]
subset: SOFA
synonym: "precursor RNA" EXACT []
synonym: "primary transcript" EXACT []
xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki"
is_a: SO:0000673 ! transcript

[Term]
id: SO:0000186
name: LTR_retrotransposon
def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke]
synonym: "long terminal repeat retrotransposon" EXACT []
synonym: "LTR retrotransposon" EXACT []
is_a: SO:0000180 ! retrotransposon

[Term]
id: SO:0000187
name: repeat_family
def: "A group of characterized repeat sequences." [SO:ke]
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000188
name: intron
def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Intron "wiki"
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000189
name: non_LTR_retrotransposon
def: "A retrotransposon without long terminal repeat sequences." [SO:ke]
synonym: "non LTR retrotransposon" EXACT []
is_a: SO:0000180 ! retrotransposon

[Term]
id: SO:0000190
name: five_prime_intron
synonym: "5' intron" EXACT []
synonym: "5' intron sequence" EXACT []
synonym: "five prime intron" EXACT []
is_a: SO:0000188 ! intron

[Term]
id: SO:0000191
name: interior_intron
synonym: "interior intron" EXACT []
is_a: SO:0000188 ! intron

[Term]
id: SO:0000192
name: three_prime_intron
synonym: "3' intron" EXACT []
synonym: "3' intron sequence" RELATED []
synonym: "three prime intron" EXACT []
is_a: SO:0000188 ! intron

[Term]
id: SO:0000193
name: RFLP_fragment
def: "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]
subset: SOFA
synonym: "restriction fragment length polymorphism" EXACT []
synonym: "RFLP" EXACT []
synonym: "RFLP fragment" EXACT []
xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki"
is_a: SO:0000412 ! restriction_fragment

[Term]
id: SO:0000194
name: LINE_element
def: "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
synonym: "LINE" EXACT []
synonym: "LINE element" EXACT []
synonym: "Long interspersed element" EXACT []
synonym: "Long interspersed nuclear element" EXACT []
is_a: SO:0000189 ! non_LTR_retrotransposon

[Term]
id: SO:0000195
name: coding_exon
def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]
subset: SOFA
synonym: "coding exon" EXACT []
is_a: SO:0000147 ! exon

[Term]
id: SO:0000196
name: five_prime_coding_exon_coding_region
def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]
subset: SOFA
synonym: "five prime exon coding region" EXACT []
is_a: SO:0001215 ! coding_region_of_exon
relationship: part_of SO:0000200 ! five_prime_coding_exon

[Term]
id: SO:0000197
name: three_prime_coding_exon_coding_region
def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]
subset: SOFA
synonym: "three prime exon coding region" EXACT []
is_a: SO:0001215 ! coding_region_of_exon
relationship: part_of SO:0000202 ! three_prime_coding_exon

[Term]
id: SO:0000198
name: noncoding_exon
def: "An exon that does not contain any codons." [SO:ke]
subset: SOFA
synonym: "noncoding exon" EXACT []
is_a: SO:0000147 ! exon

[Term]
id: SO:0000199
name: translocation
def: "A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions." [NCBI:th, SO:ke]
subset: DBVAR
synonym: "transchr" RELATED [http://www.ncbi.nlm.nih.gov/dbvar/]
synonym: "translocated sequence" EXACT []
is_a: SO:0001785 ! structural_alteration

[Term]
id: SO:0000200
name: five_prime_coding_exon
def: "The 5' most coding exon." [SO:ke]
subset: SOFA
synonym: "5' coding exon" EXACT []
synonym: "five prime coding exon" EXACT []
is_a: SO:0000195 ! coding_exon

[Term]
id: SO:0000201
name: interior_exon
def: "An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]
synonym: "interior exon" EXACT []
is_a: SO:0000147 ! exon

[Term]
id: SO:0000202
name: three_prime_coding_exon
def: "The coding exon that is most 3-prime on a given transcript." [SO:ma]
synonym: "3' coding exon" RELATED []
synonym: "three prime coding exon" EXACT []
is_a: SO:0000195 ! coding_exon

[Term]
id: SO:0000203
name: UTR
def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]
subset: SOFA
synonym: "untranslated region" EXACT []
is_a: SO:0000836 ! mRNA_region

[Term]
id: SO:0000204
name: five_prime_UTR
def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "5' UTR" EXACT []
synonym: "five prime UTR" EXACT []
synonym: "five_prime_untranslated_region" EXACT []
xref: http://en.wikipedia.org/wiki/5'_UTR "wiki"
is_a: SO:0000203 ! UTR

[Term]
id: SO:0000205
name: three_prime_UTR
def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "three prime untranslated region" EXACT []
synonym: "three prime UTR" EXACT []
xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki"
is_a: SO:0000203 ! UTR

[Term]
id: SO:0000206
name: SINE_element
def: "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]
synonym: "Short interspersed element" EXACT []
synonym: "Short interspersed nuclear element" EXACT []
synonym: "SINE element" EXACT []
xref: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element "wiki"
is_a: SO:0000189 ! non_LTR_retrotransposon

[Term]
id: SO:0000207
name: simple_sequence_length_variation
synonym: "simple sequence length polymorphism" RELATED []
synonym: "simple sequence length variation" EXACT []
synonym: "SSLP" RELATED []
is_a: SO:0000248 ! sequence_length_variation

[Term]
id: SO:0000208
name: terminal_inverted_repeat_element
def: "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]
synonym: "terminal inverted repeat element" EXACT []
synonym: "TIR element" EXACT []
is_a: SO:0000182 ! DNA_transposon

[Term]
id: SO:0000209
name: rRNA_primary_transcript
def: "A primary transcript encoding a ribosomal RNA." [SO:ke]
subset: SOFA
synonym: "ribosomal RNA primary transcript" EXACT []
synonym: "rRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000210
name: tRNA_primary_transcript
def: "A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]
synonym: "tRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000211
name: alanine_tRNA_primary_transcript
def: "A primary transcript encoding alanyl tRNA." [SO:ke]
synonym: "alanine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000212
name: arginine_tRNA_primary_transcript
def: "A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]
synonym: "arginine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000213
name: asparagine_tRNA_primary_transcript
def: "A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]
synonym: "asparagine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000214
name: aspartic_acid_tRNA_primary_transcript
def: "A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]
synonym: "aspartic acid tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000215
name: cysteine_tRNA_primary_transcript
def: "A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]
synonym: "cysteine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000216
name: glutamic_acid_tRNA_primary_transcript
def: "A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]
synonym: "glutamic acid tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000217
name: glutamine_tRNA_primary_transcript
def: "A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]
synonym: "glutamine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000218
name: glycine_tRNA_primary_transcript
def: "A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]
synonym: "glycine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000219
name: histidine_tRNA_primary_transcript
def: "A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]
synonym: "histidine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000220
name: isoleucine_tRNA_primary_transcript
def: "A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]
synonym: "isoleucine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000221
name: leucine_tRNA_primary_transcript
def: "A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]
synonym: "leucine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000222
name: lysine_tRNA_primary_transcript
def: "A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]
synonym: "lysine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000223
name: methionine_tRNA_primary_transcript
def: "A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]
synonym: "methionine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000224
name: phenylalanine_tRNA_primary_transcript
def: "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]
synonym: "phenylalanine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000225
name: proline_tRNA_primary_transcript
def: "A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]
synonym: "proline tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000226
name: serine_tRNA_primary_transcript
def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
synonym: "serine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000227
name: threonine_tRNA_primary_transcript
def: "A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]
synonym: "threonine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000228
name: tryptophan_tRNA_primary_transcript
def: "A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]
synonym: "tryptophan tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000229
name: tyrosine_tRNA_primary_transcript
def: "A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]
synonym: "tyrosine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000230
name: valine_tRNA_primary_transcript
def: "A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]
synonym: "valine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000231
name: snRNA_primary_transcript
def: "A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]
synonym: "snRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000232
name: snoRNA_primary_transcript
def: "A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]
synonym: "snoRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000233
name: mature_transcript
def: "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]
comment: A processed transcript cannot contain introns.
subset: SOFA
synonym: "mature transcript" EXACT []
xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki"
is_a: SO:0000673 ! transcript
relationship: derives_from SO:0000185 ! primary_transcript

[Term]
id: SO:0000234
name: mRNA
def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]
comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "messenger RNA" EXACT []
xref: http://en.wikipedia.org/wiki/MRNA "wiki"
is_a: SO:0000233 ! mature_transcript

[Term]
id: SO:0000235
name: TF_binding_site
def: "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]
subset: SOFA
synonym: "TF binding site" EXACT []
synonym: "transcription factor binding site" EXACT []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site
is_a: SO:0001679 ! transcription_regulatory_region

[Term]
id: SO:0000236
name: ORF
def: "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]
comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "open reading frame" EXACT []
is_a: SO:0000717 ! reading_frame

[Term]
id: SO:0000237
name: transcript_attribute
synonym: "transcript attribute" EXACT []
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000238
name: foldback_element
def: "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]
synonym: "foldback element" EXACT []
synonym: "long inverted repeat element" RELATED []
synonym: "LVR element" RELATED []
is_a: SO:0000182 ! DNA_transposon

[Term]
id: SO:0000239
name: flanking_region
def: "The sequences extending on either side of a specific region." [SO:ke]
subset: SOFA
synonym: "flanking region" EXACT []
is_a: SO:0001412 ! topologically_defined_region

[Term]
id: SO:0000240
name: chromosome_variation
synonym: "chromosome variation" EXACT []
is_a: SO:0001507 ! variant_collection
disjoint_from: SO:0000400 ! sequence_attribute
relationship: part_of SO:0001524 ! chromosomally_aberrant_genome

[Term]
id: SO:0000241
name: internal_UTR
def: "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]
synonym: "internal UTR" EXACT []
is_a: SO:0000203 ! UTR

[Term]
id: SO:0000242
name: untranslated_region_polycistronic_mRNA
def: "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]
synonym: "untranslated region polycistronic mRNA" EXACT []
is_a: SO:0000203 ! UTR

[Term]
id: SO:0000243
name: internal_ribosome_entry_site
def: "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]
synonym: "internal ribosomal entry sequence" EXACT []
synonym: "internal ribosomal entry site" EXACT []
synonym: "internal ribosome entry sequence" RELATED []
synonym: "internal ribosome entry site" EXACT []
synonym: "IRES" EXACT []
xref: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site "wiki"
is_a: SO:0000139 ! ribosome_entry_site

[Term]
id: SO:0000244
name: four_cutter_restriction_site
synonym: "4-cutter_restriction_site" RELATED []
synonym: "four-cutter_restriction_sit" RELATED []
is_obsolete: true

[Term]
id: SO:0000245
name: mRNA_by_polyadenylation_status
is_obsolete: true

[Term]
id: SO:0000246
name: polyadenylated
def: "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute

[Term]
id: SO:0000247
name: mRNA_not_polyadenylated
is_obsolete: true

[Term]
id: SO:0000248
name: sequence_length_variation
synonym: "sequence length variation" EXACT []
is_a: SO:1000002 ! substitution

[Term]
id: SO:0000249
name: six_cutter_restriction_site
synonym: "6-cutter_restriction_site" RELATED []
synonym: "six-cutter_restriction_site" RELATED []
is_obsolete: true

[Term]
id: SO:0000250
name: modified_RNA_base_feature
def: "A post_transcriptionally modified base." [SO:ke]
synonym: "modified RNA base feature" EXACT []
is_a: SO:0001236 ! base

[Term]
id: SO:0000251
name: eight_cutter_restriction_site
synonym: "8-cutter_restriction_site" RELATED []
synonym: "eight-cutter_restriction_site" RELATED []
is_obsolete: true

[Term]
id: SO:0000252
name: rRNA
def: "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]
subset: SOFA
synonym: "ribosomal ribonucleic acid" EXACT []
synonym: "ribosomal RNA" EXACT []
xref: http://en.wikipedia.org/wiki/RRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000209 ! rRNA_primary_transcript

[Term]
id: SO:0000253
name: tRNA
def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "transfer ribonucleic acid" RELATED []
synonym: "transfer RNA" RELATED []
xref: http://en.wikipedia.org/wiki/TRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0000254
name: alanyl_tRNA
def: "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]
synonym: "alanyl tRNA" EXACT []
synonym: "alanyl-transfer ribonucleic acid" EXACT []
synonym: "alanyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000211 ! alanine_tRNA_primary_transcript

[Term]
id: SO:0000255
name: rRNA_small_subunit_primary_transcript
def: "A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]
synonym: "rRNA small subunit primary transcript" EXACT []
is_a: SO:0000209 ! rRNA_primary_transcript

[Term]
id: SO:0000256
name: asparaginyl_tRNA
def: "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]
synonym: "asparaginyl tRNA" EXACT []
synonym: "asparaginyl-transfer ribonucleic acid" EXACT []
synonym: "asparaginyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000213 ! asparagine_tRNA_primary_transcript

[Term]
id: SO:0000257
name: aspartyl_tRNA
def: "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]
synonym: "aspartyl tRNA" EXACT []
synonym: "aspartyl-transfer ribonucleic acid" EXACT []
synonym: "aspartyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000214 ! aspartic_acid_tRNA_primary_transcript

[Term]
id: SO:0000258
name: cysteinyl_tRNA
def: "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]
synonym: "cysteinyl tRNA" EXACT []
synonym: "cysteinyl-transfer ribonucleic acid" EXACT []
synonym: "cysteinyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000215 ! cysteine_tRNA_primary_transcript

[Term]
id: SO:0000259
name: glutaminyl_tRNA
def: "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]
synonym: "glutaminyl tRNA" EXACT []
synonym: "glutaminyl-transfer ribonucleic acid" EXACT []
synonym: "glutaminyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000216 ! glutamic_acid_tRNA_primary_transcript

[Term]
id: SO:0000260
name: glutamyl_tRNA
def: "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]
synonym: "glutamyl tRNA" EXACT []
synonym: "glutamyl-transfer ribonucleic acid" EXACT []
synonym: "glutamyl-transfer RNA" RELATED []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000217 ! glutamine_tRNA_primary_transcript

[Term]
id: SO:0000261
name: glycyl_tRNA
def: "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]
synonym: "glycyl tRNA" EXACT []
synonym: "glycyl-transfer ribonucleic acid" RELATED []
synonym: "glycyl-transfer RNA" RELATED []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000218 ! glycine_tRNA_primary_transcript

[Term]
id: SO:0000262
name: histidyl_tRNA
def: "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]
synonym: "histidyl tRNA" EXACT []
synonym: "histidyl-transfer ribonucleic acid" EXACT []
synonym: "histidyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000219 ! histidine_tRNA_primary_transcript

[Term]
id: SO:0000263
name: isoleucyl_tRNA
def: "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]
synonym: "isoleucyl tRNA" EXACT []
synonym: "isoleucyl-transfer ribonucleic acid" EXACT []
synonym: "isoleucyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000220 ! isoleucine_tRNA_primary_transcript

[Term]
id: SO:0000264
name: leucyl_tRNA
def: "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]
synonym: "leucyl tRNA" EXACT []
synonym: "leucyl-transfer ribonucleic acid" EXACT []
synonym: "leucyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000221 ! leucine_tRNA_primary_transcript

[Term]
id: SO:0000265
name: lysyl_tRNA
def: "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]
synonym: "lysyl tRNA" EXACT []
synonym: "lysyl-transfer ribonucleic acid" EXACT []
synonym: "lysyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000222 ! lysine_tRNA_primary_transcript

[Term]
id: SO:0000266
name: methionyl_tRNA
def: "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]
synonym: "methionyl tRNA" EXACT []
synonym: "methionyl-transfer ribonucleic acid" EXACT []
synonym: "methionyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000223 ! methionine_tRNA_primary_transcript

[Term]
id: SO:0000267
name: phenylalanyl_tRNA
def: "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]
synonym: "phenylalanyl tRNA" EXACT []
synonym: "phenylalanyl-transfer ribonucleic acid" EXACT []
synonym: "phenylalanyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000224 ! phenylalanine_tRNA_primary_transcript

[Term]
id: SO:0000268
name: prolyl_tRNA
def: "A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]
synonym: "prolyl tRNA" EXACT []
synonym: "prolyl-transfer ribonucleic acid" EXACT []
synonym: "prolyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000225 ! proline_tRNA_primary_transcript

[Term]
id: SO:0000269
name: seryl_tRNA
def: "A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]
synonym: "seryl tRNA" EXACT []
synonym: "seryl-transfer ribonucleic acid" RELATED []
synonym: "seryl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000226 ! serine_tRNA_primary_transcript

[Term]
id: SO:0000270
name: threonyl_tRNA
def: "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]
synonym: "threonyl tRNA" EXACT []
synonym: "threonyl-transfer ribonucleic acid" EXACT []
synonym: "threonyl-transfer RNA" RELATED []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000227 ! threonine_tRNA_primary_transcript

[Term]
id: SO:0000271
name: tryptophanyl_tRNA
def: "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]
synonym: "tryptophanyl tRNA" EXACT []
synonym: "tryptophanyl-transfer ribonucleic acid" EXACT []
synonym: "tryptophanyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000228 ! tryptophan_tRNA_primary_transcript

[Term]
id: SO:0000272
name: tyrosyl_tRNA
def: "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]
synonym: "tyrosyl tRNA" EXACT []
synonym: "tyrosyl-transfer ribonucleic acid" EXACT []
synonym: "tyrosyl-transfer RNA" RELATED []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000229 ! tyrosine_tRNA_primary_transcript

[Term]
id: SO:0000273
name: valyl_tRNA
def: "A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]
synonym: "valyl tRNA" EXACT []
synonym: "valyl-transfer ribonucleic acid" EXACT []
synonym: "valyl-transfer RNA" RELATED []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000230 ! valine_tRNA_primary_transcript

[Term]
id: SO:0000274
name: snRNA
def: "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "small nuclear RNA" EXACT []
xref: http://en.wikipedia.org/wiki/SnRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000231 ! snRNA_primary_transcript

[Term]
id: SO:0000275
name: snoRNA
def: "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]
subset: SOFA
synonym: "small nucleolar RNA" EXACT []
xref: http://en.wikipedia.org/wiki/SnoRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0000276
name: miRNA
alt_id: SO:0000649
def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:11081512, PMID:12592000]
subset: SOFA
synonym: "micro RNA" EXACT []
synonym: "microRNA" EXACT []
synonym: "small temporal RNA" EXACT []
synonym: "stRNA" EXACT []
xref: http://en.wikipedia.org/wiki/MiRNA "wiki"
xref: http://en.wikipedia.org/wiki/StRNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA
is_a: SO:0000655 ! ncRNA
relationship: part_of SO:0001244 ! pre_miRNA

[Term]
id: SO:0000277
name: bound_by_factor
def: "An attribute describing a sequence that is bound by another molecule." [SO:ke]
comment: Formerly called transcript_by_bound_factor.
synonym: "bound by factor" EXACT []
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000278
name: transcript_bound_by_nucleic_acid
def: "A transcript that is bound by a nucleic acid." [SO:xp]
comment: Formerly called transcript_by_bound_nucleic_acid.
synonym: "transcript bound by nucleic acid" EXACT []
is_a: SO:0000673 ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000876 ! bound_by_nucleic_acid
relationship: has_quality SO:0000876 ! bound_by_nucleic_acid

[Term]
id: SO:0000279
name: transcript_bound_by_protein
def: "A transcript that is bound by a protein." [SO:xp]
comment: Formerly called transcript_by_bound_protein.
synonym: "transcript bound by protein" EXACT []
is_a: SO:0000673 ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000875 ! bound_by_protein
relationship: has_quality SO:0000875 ! bound_by_protein

[Term]
id: SO:0000280
name: engineered_gene
def: "A gene that is engineered." [SO:xp]
synonym: "engineered gene" EXACT []
is_a: SO:0000704 ! gene
is_a: SO:0000804 ! engineered_region
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000281
name: engineered_foreign_gene
def: "A gene that is engineered and foreign." [SO:xp]
synonym: "engineered foreign gene" EXACT []
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000285 ! foreign_gene
is_a: SO:0000805 ! engineered_foreign_region
intersection_of: SO:0000280 ! engineered_gene
intersection_of: has_quality SO:0000783 ! engineered
intersection_of: has_quality SO:0000784 ! foreign
relationship: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000784 ! foreign

[Term]
id: SO:0000282
name: mRNA_with_minus_1_frameshift
def: "An mRNA with a minus 1 frameshift." [SO:xp]
synonym: "mRNA with minus 1 frameshift" EXACT []
is_a: SO:0000108 ! mRNA_with_frameshift
intersection_of: SO:0000108 ! mRNA_with_frameshift
intersection_of: has_quality SO:0000866 ! minus_1_frameshift
relationship: has_quality SO:0000866 ! minus_1_frameshift

[Term]
id: SO:0000283
name: engineered_foreign_transposable_element_gene
def: "A transposable_element that is engineered and foreign." [SO:xp]
synonym: "engineered foreign transposable element gene" EXACT []
is_a: SO:0000111 ! transposable_element_gene
is_a: SO:0000281 ! engineered_foreign_gene
intersection_of: SO:0000111 ! transposable_element_gene
intersection_of: has_quality SO:0000783 ! engineered
intersection_of: has_quality SO:0000784 ! foreign
relationship: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000784 ! foreign

[Term]
id: SO:0000284
name: type_I_enzyme_restriction_site
def: "The recognition site is bipartite and interrupted." [http://www.promega.com]
is_obsolete: true

[Term]
id: SO:0000285
name: foreign_gene
def: "A gene that is foreign." [SO:xp]
synonym: "foreign gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000784 ! foreign
relationship: has_quality SO:0000784 ! foreign

[Term]
id: SO:0000286
name: long_terminal_repeat
def: "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "direct terminal repeat" RELATED []
synonym: "long terminal repeat" EXACT []
synonym: "LTR" EXACT []
xref: http://en.wikipedia.org/wiki/Long_terminal_repeat "wiki"
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000186 ! LTR_retrotransposon

[Term]
id: SO:0000287
name: fusion_gene
def: "A gene that is a fusion." [SO:xp]
synonym: "fusion gene" EXACT []
xref: http://en.wikipedia.org/wiki/Fusion_gene "wiki"
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000806 ! fusion
relationship: has_quality SO:0000806 ! fusion

[Term]
id: SO:0000288
name: engineered_fusion_gene
def: "A fusion gene that is engineered." [SO:xp]
synonym: "engineered fusion gene" EXACT []
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000287 ! fusion_gene
intersection_of: SO:0000287 ! fusion_gene
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000289
name: microsatellite
def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]
subset: SOFA
synonym: "microsatellite locus" EXACT []
synonym: "microsatellite marker" EXACT []
synonym: "VNTR" EXACT []
xref: http://en.wikipedia.org/wiki/Microsatellite "wiki"
is_a: SO:0000005 ! satellite_DNA

[Term]
id: SO:0000290
name: dinucleotide_repeat_microsatellite_feature
synonym: "dinucleotide repeat microsatellite" EXACT []
synonym: "dinucleotide repeat microsatellite feature" EXACT []
synonym: "dinucleotide repeat microsatellite locus" EXACT []
synonym: "dinucleotide repeat microsatellite marker" EXACT []
is_a: SO:0000289 ! microsatellite

[Term]
id: SO:0000291
name: trinucleotide_repeat_microsatellite_feature
synonym: "dinucleotide repeat microsatellite marker" RELATED []
synonym: "rinucleotide repeat microsatellite" EXACT []
synonym: "trinucleotide repeat microsatellite feature" EXACT []
synonym: "trinucleotide repeat microsatellite locus" EXACT []
is_a: SO:0000289 ! microsatellite

[Term]
id: SO:0000292
name: repetitive_element
is_obsolete: true

[Term]
id: SO:0000293
name: engineered_foreign_repetitive_element
def: "A repetitive element that is engineered and foreign." [SO:xp]
synonym: "engineered foreign repetitive element" EXACT []
is_a: SO:0000657 ! repeat_region
is_a: SO:0000805 ! engineered_foreign_region
intersection_of: SO:0000657 ! repeat_region
intersection_of: has_quality SO:0000783 ! engineered
intersection_of: has_quality SO:0000784 ! foreign
relationship: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000784 ! foreign

[Term]
id: SO:0000294
name: inverted_repeat
def: "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]
subset: SOFA
synonym: "inverted repeat" EXACT []
synonym: "inverted repeat sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki"
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000295
name: U12_intron
def: "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]
comment: May have either GT-AC or AT-AC 5' and 3' boundaries.
synonym: "U12 intron" EXACT []
synonym: "U12-dependent intron" EXACT []
is_a: SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000296
name: origin_of_replication
def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "ori" EXACT []
synonym: "origin of replication" EXACT []
xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki"
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0001235 ! replicon

[Term]
id: SO:0000297
name: D_loop
def: "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "D-loop" EXACT []
synonym: "displacement loop" RELATED []
xref: http://en.wikipedia.org/wiki/D_loop "wiki"
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000298
name: recombination_feature
synonym: "recombination feature" EXACT []
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000299
name: specific_recombination_site
synonym: "specific recombination site" EXACT []
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000300
name: recombination_feature_of_rearranged_gene
synonym: "recombination feature of rearranged gene" EXACT []
is_a: SO:0000299 ! specific_recombination_site

[Term]
id: SO:0000301
name: vertebrate_immune_system_gene_recombination_feature
synonym: "vertebrate immune system gene recombination feature" EXACT []
is_a: SO:0000300 ! recombination_feature_of_rearranged_gene

[Term]
id: SO:0000302
name: J_gene_recombination_feature
def: "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J gene recombination feature" EXACT []
synonym: "J-RS" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature

[Term]
id: SO:0000303
name: clip
def: "Part of the primary transcript that is clipped off during processing." [SO:ke]
subset: SOFA
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000304
name: type_II_enzyme_restriction_site
def: "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site." [http://www.promega.com]
is_obsolete: true

[Term]
id: SO:0000305
name: modified_DNA_base
def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Modified base:<modified_base>.
subset: SOFA
synonym: "modified base site" EXACT []
is_a: SO:0001236 ! base
is_a: SO:0001720 ! epigenetically_modified_region

[Term]
id: SO:0000306
name: methylated_DNA_base_feature
def: "A nucleotide modified by methylation." [SO:ke]
subset: SOFA
synonym: "methylated base feature" EXACT []
is_a: SO:0000305 ! modified_DNA_base

[Term]
id: SO:0000307
name: CpG_island
def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]
subset: SOFA
synonym: "CG island" EXACT []
synonym: "CpG island" EXACT []
xref: http://en.wikipedia.org/wiki/CpG_island "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000308
name: sequence_feature_locating_method
is_obsolete: true

[Term]
id: SO:0000309
name: computed_feature
is_obsolete: true

[Term]
id: SO:0000310
name: predicted_ab_initio_computation
is_obsolete: true

[Term]
id: SO:0000311
name: computed_feature_by_similarity
def: "." [SO:ma]
comment: similar to:<sequence_id>
is_obsolete: true

[Term]
id: SO:0000312
name: experimentally_determined
def: "Attribute to describe a feature that has been experimentally verified." [SO:ke]
synonym: "experimentally determined" EXACT []
is_a: SO:0000789 ! validated

[Term]
id: SO:0000313
name: stem_loop
alt_id: SO:0000019
def: "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "RNA_hairpin_loop" EXACT []
synonym: "stem loop" EXACT []
synonym: "stem-loop" EXACT []
xref: http://en.wikipedia.org/wiki/Stem_loop "wiki"
is_a: SO:0000122 ! RNA_sequence_secondary_structure

[Term]
id: SO:0000314
name: direct_repeat
def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA." [SO:ke]
subset: SOFA
synonym: "direct repeat" EXACT []
xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki"
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000315
name: TSS
def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]
subset: SOFA
synonym: "transcription start site" EXACT []
synonym: "transcription_start_site" EXACT []
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000316
name: CDS
def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]
subset: SOFA
synonym: "coding sequence" EXACT []
synonym: "coding_sequence" EXACT []
is_a: SO:0000836 ! mRNA_region

[Term]
id: SO:0000317
name: cDNA_clone
def: "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "cDNA clone" EXACT []
is_a: SO:0000151 ! clone
intersection_of: SO:0000151 ! clone
intersection_of: has_quality SO:0000756 ! cDNA
relationship: has_quality SO:0000756 ! cDNA

[Term]
id: SO:0000318
name: start_codon
def: "First codon to be translated by a ribosome." [SO:ke]
subset: SOFA
synonym: "initiation codon" EXACT []
synonym: "start codon" EXACT []
xref: http://en.wikipedia.org/wiki/Start_codon "wiki"
is_a: SO:0000360 ! codon

[Term]
id: SO:0000319
name: stop_codon
def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]
subset: SOFA
synonym: "stop codon" EXACT []
xref: http://en.wikipedia.org/wiki/Stop_codon "wiki"
is_a: SO:0000360 ! codon

[Term]
id: SO:0000320
name: intronic_splice_enhancer
def: "Sequences within the intron that modulate splice site selection for some introns." [SO:ke]
synonym: "intronic splice enhancer" EXACT []
is_a: SO:0000344 ! splice_enhancer
relationship: part_of SO:0000841 ! spliceosomal_intron_region

[Term]
id: SO:0000321
name: mRNA_with_plus_1_frameshift
def: "An mRNA with a plus 1 frameshift." [SO:ke]
synonym: "mRNA with plus 1 frameshift" EXACT []
is_a: SO:0000108 ! mRNA_with_frameshift
intersection_of: SO:0000108 ! mRNA_with_frameshift
intersection_of: has_quality SO:0000868 ! plus_1_frameshift
relationship: has_quality SO:0000868 ! plus_1_frameshift

[Term]
id: SO:0000322
name: nuclease_hypersensitive_site
synonym: "nuclease hypersensitive site" EXACT []
is_a: SO:0000684 ! nuclease_sensitive_site

[Term]
id: SO:0000323
name: coding_start
def: "The first base to be translated into protein." [SO:ke]
synonym: "coding start" EXACT []
synonym: "translation initiation site" EXACT []
synonym: "translation start" RELATED []
is_a: SO:0000851 ! CDS_region

[Term]
id: SO:0000324
name: tag
def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]
subset: SOFA
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000325
name: rRNA_large_subunit_primary_transcript
def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]
subset: SOFA
synonym: "35S rRNA primary transcript" EXACT []
synonym: "rRNA large subunit primary transcript" EXACT []
is_a: SO:0000209 ! rRNA_primary_transcript

[Term]
id: SO:0000326
name: SAGE_tag
def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]
subset: SOFA
synonym: "SAGE tag" EXACT []
is_a: SO:0000324 ! tag

[Term]
id: SO:0000327
name: coding_end
def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke]
synonym: "coding end" EXACT []
synonym: "translation termination site" EXACT []
synonym: "translation_end" EXACT []
is_a: SO:0000851 ! CDS_region

[Term]
id: SO:0000328
name: microarray_oligo
synonym: "microarray oligo" EXACT []
synonym: "microarray oligonucleotide" EXACT []
is_a: SO:0000051 ! probe

[Term]
id: SO:0000329
name: mRNA_with_plus_2_frameshift
def: "An mRNA with a plus 2 frameshift." [SO:xp]
synonym: "mRNA with plus 2 frameshift" EXACT []
is_a: SO:0000108 ! mRNA_with_frameshift
intersection_of: SO:0000108 ! mRNA_with_frameshift
intersection_of: has_quality SO:0000869 ! plus_2_framshift
relationship: has_quality SO:0000869 ! plus_2_framshift

[Term]
id: SO:0000330
name: conserved_region
def: "Region of sequence similarity by descent from a common ancestor." [SO:ke]
subset: SOFA
synonym: "conserved region" EXACT []
xref: http://en.wikipedia.org/wiki/Conserved_region "wiki"
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0000331
name: STS
def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]
subset: SOFA
synonym: "sequence tag site" EXACT []
is_a: SO:0000324 ! tag

[Term]
id: SO:0000332
name: coding_conserved_region
def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke]
subset: SOFA
synonym: "coding conserved region" EXACT []
is_a: SO:0000330 ! conserved_region

[Term]
id: SO:0000333
name: exon_junction
def: "The boundary between two exons in a processed transcript." [SO:ke]
subset: SOFA
synonym: "exon junction" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000233 ! mature_transcript

[Term]
id: SO:0000334
name: nc_conserved_region
def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]
subset: SOFA
synonym: "nc conserved region" EXACT []
synonym: "noncoding conserved region" EXACT []
is_a: SO:0000330 ! conserved_region

[Term]
id: SO:0000335
name: mRNA_with_minus_2_frameshift
def: "A mRNA with a minus 2 frameshift." [SO:ke]
synonym: "mRNA with minus 2 frameshift" EXACT []
is_a: SO:0000108 ! mRNA_with_frameshift
intersection_of: SO:0000108 ! mRNA_with_frameshift
intersection_of: has_quality SO:0000867 ! minus_2_frameshift
relationship: has_quality SO:0000867 ! minus_2_frameshift

[Term]
id: SO:0000336
name: pseudogene
def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Pseudogene "wiki"
is_a: SO:0001411 ! biological_region
relationship: non_functional_homolog_of SO:0000704 ! gene

[Term]
id: SO:0000337
name: RNAi_reagent
def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]
subset: SOFA
synonym: "RNAi reagent" EXACT []
is_a: SO:0000442 ! ds_oligo

[Term]
id: SO:0000338
name: MITE
def: "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]
synonym: "miniature inverted repeat transposable element" EXACT []
is_a: SO:0000208 ! terminal_inverted_repeat_element

[Term]
id: SO:0000339
name: recombination_hotspot
def: "A region in a genome which promotes recombination." [SO:rd]
synonym: "recombination hotspot" EXACT []
xref: http://en.wikipedia.org/wiki/Recombination_hotspot "wiki"
is_a: SO:0000298 ! recombination_feature

[Term]
id: SO:0000340
name: chromosome
def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Chromosome "wiki"
is_a: SO:0001235 ! replicon

[Term]
id: SO:0000341
name: chromosome_band
def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]
subset: SOFA
synonym: "chromosome band" EXACT []
synonym: "cytoband" EXACT []
synonym: "cytological band" EXACT []
xref: http://en.wikipedia.org/wiki/Cytological_band "wiki"
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0000342
name: site_specific_recombination_target_region
synonym: "site specific recombination target region" EXACT []
is_a: SO:0000299 ! specific_recombination_site

[Term]
id: SO:0000343
name: match
def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]
subset: SOFA
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0000344
name: splice_enhancer
def: "Region of a transcript that regulates splicing." [SO:ke]
subset: SOFA
synonym: "splice enhancer" EXACT []
is_a: SO:0000165 ! enhancer
is_a: SO:0001056 ! splicing_regulatory_region

[Term]
id: SO:0000345
name: EST
def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "expressed sequence tag" EXACT []
is_a: SO:0000324 ! tag
relationship: derives_from SO:0000234 ! mRNA

[Term]
id: SO:0000346
name: loxP_site
synonym: "Cre-recombination target region" RELATED []
synonym: "loxP site" EXACT []
is_a: SO:0000947 ! resolution_site

[Term]
id: SO:0000347
name: nucleotide_match
def: "A match against a nucleotide sequence." [SO:ke]
subset: SOFA
synonym: "nucleotide match" EXACT []
is_a: SO:0000343 ! match

[Term]
id: SO:0000348
name: nucleic_acid
def: "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]
synonym: "nucleic acid" EXACT []
xref: http://en.wikipedia.org/wiki/Nucleic_acid "wiki"
is_a: SO:0000443 ! polymer_attribute

[Term]
id: SO:0000349
name: protein_match
def: "A match against a protein sequence." [SO:ke]
subset: SOFA
synonym: "protein match" EXACT []
is_a: SO:0000343 ! match

[Term]
id: SO:0000350
name: FRT_site
def: "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]
synonym: "FLP recombination target region" EXACT []
synonym: "FRT site" EXACT []
is_a: SO:0000948 ! inversion_site

[Term]
id: SO:0000351
name: synthetic_sequence
def: "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma]
synonym: "synthetic sequence" EXACT []
is_a: SO:0000443 ! polymer_attribute

[Term]
id: SO:0000352
name: DNA
def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0000353
name: sequence_assembly
def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]
subset: SOFA
synonym: "sequence assembly" EXACT []
xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki"
is_a: SO:0001248 ! assembly

[Term]
id: SO:0000354
name: group_1_intron_homing_endonuclease_target_region
def: "A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]
synonym: "group 1 intron homing endonuclease target region" EXACT []
is_a: SO:0000684 ! nuclease_sensitive_site

[Term]
id: SO:0000355
name: haplotype_block
def: "A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma]
synonym: "haplotype block" EXACT []
is_a: SO:0000298 ! recombination_feature

[Term]
id: SO:0000356
name: RNA
def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0000357
name: flanked
def: "An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000359
name: floxed
def: "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke]
xref: http://en.wikipedia.org/wiki/Floxed "wiki"
is_a: SO:0000357 ! flanked

[Term]
id: SO:0000360
name: codon
def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Codon "wiki"
is_a: SO:0000851 ! CDS_region

[Term]
id: SO:0000361
name: FRT_flanked
def: "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke]
synonym: "FRT flanked" EXACT []
is_a: SO:0000357 ! flanked

[Term]
id: SO:0000362
name: invalidated_by_chimeric_cDNA
def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]
synonym: "invalidated by chimeric cDNA" EXACT []
is_a: SO:0000790 ! invalidated

[Term]
id: SO:0000363
name: floxed_gene
def: "A transgene that is floxed." [SO:xp]
synonym: "floxed gene" EXACT []
is_a: SO:0000902 ! transgene
intersection_of: SO:0000902 ! transgene
intersection_of: has_quality SO:0000359 ! floxed
relationship: has_quality SO:0000359 ! floxed

[Term]
id: SO:0000364
name: transposable_element_flanking_region
def: "The region of sequence surrounding a transposable element." [SO:ke]
synonym: "transposable element flanking region" EXACT []
is_a: SO:0000239 ! flanking_region

[Term]
id: SO:0000365
name: integron
def: "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]
xref: http://en.wikipedia.org/wiki/Integron "wiki"
is_a: SO:0001039 ! integrated_mobile_genetic_element

[Term]
id: SO:0000366
name: insertion_site
def: "The junction where an insertion occurred." [SO:ke]
subset: SOFA
synonym: "insertion site" EXACT []
is_a: SO:0000699 ! junction

[Term]
id: SO:0000367
name: attI_site
def: "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]
synonym: "attI site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0000365 ! integron

[Term]
id: SO:0000368
name: transposable_element_insertion_site
def: "The junction in a genome where a transposable_element has inserted." [SO:ke]
subset: SOFA
synonym: "transposable element insertion site" EXACT []
is_a: SO:0000366 ! insertion_site

[Term]
id: SO:0000369
name: integrase_coding_region
is_obsolete: true

[Term]
id: SO:0000370
name: small_regulatory_ncRNA
def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]
subset: SOFA
synonym: "small regulatory ncRNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000371
name: conjugative_transposon
def: "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]
synonym: "conjugative transposon" EXACT []
is_a: SO:0000182 ! DNA_transposon

[Term]
id: SO:0000372
name: enzymatic_RNA
def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]
comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts.
subset: SOFA
synonym: "enzymatic RNA" EXACT []
is_a: SO:0000673 ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0001185 ! enzymatic
relationship: has_quality SO:0001185 ! enzymatic

[Term]
id: SO:0000373
name: recombinationally_inverted_gene
def: "A recombinationally rearranged gene by inversion." [SO:xp]
synonym: "recombinationally inverted gene" EXACT []
is_a: SO:0000456 ! recombinationally_rearranged_gene
intersection_of: SO:0000456 ! recombinationally_rearranged_gene
intersection_of: has_quality SO:1000036 ! inversion
relationship: has_quality SO:1000036 ! inversion

[Term]
id: SO:0000374
name: ribozyme
def: "An RNA with catalytic activity." [SO:ma]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Ribozyme "wiki"
is_a: SO:0000372 ! enzymatic_RNA
intersection_of: SO:0000372 ! enzymatic_RNA
intersection_of: has_quality SO:0001186 ! ribozymic
relationship: has_quality SO:0001186 ! ribozymic

[Term]
id: SO:0000375
name: rRNA_5_8S
def: "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]
subset: SOFA
synonym: "5.8S LSU rRNA" EXACT []
synonym: "5.8S ribosomal RNA" EXACT []
synonym: "5.8S rRNA" EXACT []
synonym: "rRNA 5 8S" EXACT []
xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki"
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0000376
name: RNA_6S
def: "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]
synonym: "6S RNA" EXACT []
synonym: "RNA 6S" EXACT []
xref: http://en.wikipedia.org/wiki/6S_RNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000377
name: CsrB_RsmB_RNA
def: "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]
synonym: "CsrB RsmB RNA" EXACT []
synonym: "CsrB-RsmB RNA" EXACT []
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000378
name: DsrA_RNA
def: "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]
synonym: "DsrA RNA" EXACT []
xref: http://en.wikipedia.org/wiki/DsrA_RNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000379
name: GcvB_RNA
def: "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]
synonym: "GcvB RNA" EXACT []
xref: http://en.wikipedia.org/wiki/GcvB_RNA "wiki"
is_a: SO:0000378 ! DsrA_RNA

[Term]
id: SO:0000380
name: hammerhead_ribozyme
def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]
subset: SOFA
synonym: "hammerhead ribozyme" EXACT []
xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki"
is_a: SO:0000715 ! RNA_motif
intersection_of: SO:0000715 ! RNA_motif
intersection_of: has_quality SO:0001186 ! ribozymic
relationship: has_quality SO:0001186 ! ribozymic

[Term]
id: SO:0000381
name: group_IIA_intron
synonym: "group IIA intron" EXACT []
is_a: SO:0000603 ! group_II_intron

[Term]
id: SO:0000382
name: group_IIB_intron
synonym: "group IIB intron" EXACT []
is_a: SO:0000603 ! group_II_intron

[Term]
id: SO:0000383
name: MicF_RNA
def: "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]
synonym: "MicF RNA" EXACT []
xref: http://en.wikipedia.org/wiki/MicF_RNA "wiki"
is_a: SO:0000644 ! antisense_RNA

[Term]
id: SO:0000384
name: OxyS_RNA
def: "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]
synonym: "OxyS RNA" EXACT []
xref: http://en.wikipedia.org/wiki/OxyS_RNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000385
name: RNase_MRP_RNA
def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]
subset: SOFA
synonym: "RNase MRP RNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000386
name: RNase_P_RNA
def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]
subset: SOFA
synonym: "RNase P RNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000387
name: RprA_RNA
def: "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]
synonym: "RprA RNA" EXACT []
xref: http://en.wikipedia.org/wiki/RprA_RNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000388
name: RRE_RNA
def: "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]
synonym: "RRE RNA" EXACT []
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000389
name: spot_42_RNA
def: "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]
synonym: "spot-42 RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Spot_42_RNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000390
name: telomerase_RNA
def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]
subset: SOFA
synonym: "telomerase RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000391
name: U1_snRNA
def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]
subset: SOFA
synonym: "small nuclear RNA U1" EXACT [RSC:cb]
synonym: "snRNA U1" EXACT [RSC:cb]
synonym: "U1 small nuclear RNA" EXACT [RSC:cb]
synonym: "U1 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000392
name: U2_snRNA
def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]
subset: SOFA
synonym: "small nuclear RNA U2" EXACT [RSC:CB]
synonym: "snRNA U2" EXACT [RSC:CB]
synonym: "U2 small nuclear RNA" EXACT [RSC:CB]
synonym: "U2 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000393
name: U4_snRNA
def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
subset: SOFA
synonym: "small nuclear RNA U4" EXACT [RSC:cb]
synonym: "snRNA U4" EXACT [RSC:cb]
synonym: "U4 small nuclear RNA" EXACT [RSC:cb]
synonym: "U4 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000394
name: U4atac_snRNA
def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]
subset: SOFA
synonym: "small nuclear RNA U4atac" EXACT [RSC:cb]
synonym: "snRNA U4atac" EXACT [RSC:cb]
synonym: "U4atac small nuclear RNA" EXACT [RSC:cb]
synonym: "U4atac snRNA" EXACT []
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000395
name: U5_snRNA
def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]
subset: SOFA
synonym: "small nuclear RNA U5" EXACT [RSC:cb]
synonym: "snRNA U5" EXACT [RSC:cb]
synonym: "U5 small nuclear RNA" EXACT [RSC:cb]
synonym: "U5 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000396
name: U6_snRNA
def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
subset: SOFA
synonym: "small nuclear RNA U6" EXACT [RSC:cb]
synonym: "snRNA U6" EXACT [RSC:cb]
synonym: "U6 small nuclear RNA" EXACT [RSC:cb]
synonym: "U6 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000397
name: U6atac_snRNA
def: "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]
subset: SOFA
synonym: "snRNA U6atac" EXACT [RSC:cb]
synonym: "U6atac small nuclear RNA" EXACT [RSC:cb]
synonym: "U6atac snRNA" EXACT [RSC:cb]
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000398
name: U11_snRNA
def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]
subset: SOFA
synonym: "small nuclear RNA U11" EXACT [RSC:cb]
synonym: "snRNA U11" EXACT [RSC:cb]
synonym: "U11 small nuclear RNA" EXACT [RSC:cb]
synonym: "U11 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000399
name: U12_snRNA
def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]
subset: SOFA
synonym: "small nuclear RNA U12" EXACT [RSC:cb]
synonym: "snRNA U12" EXACT [RSC:cb]
synonym: "U12 small nuclear RNA" EXACT [RSC:cb]
synonym: "U12 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki"
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0000400
name: sequence_attribute
def: "An attribute describes a quality of sequence." [SO:ke]
synonym: "sequence attribute" EXACT []

[Term]
id: SO:0000401
name: gene_attribute
synonym: "gene attribute" EXACT []
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000402
name: enhancer_attribute
is_obsolete: true

[Term]
id: SO:0000403
name: U14_snoRNA
alt_id: SO:0005839
def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]
comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
subset: SOFA
synonym: "small nucleolar RNA U14" EXACT []
synonym: "snoRNA U14" EXACT []
synonym: "U14 small nucleolar RNA" EXACT []
synonym: "U14 snoRNA" EXACT []
is_a: SO:0000593 ! C_D_box_snoRNA
relationship: derives_from SO:0005837 ! U14_snoRNA_primary_transcript

[Term]
id: SO:0000404
name: vault_RNA
def: "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]
subset: SOFA
synonym: "vault RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000405
name: Y_RNA
def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]
subset: SOFA
synonym: "Y RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Y_RNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000406
name: twintron
def: "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]
xref: http://en.wikipedia.org/wiki/Twintron "wiki"
is_a: SO:0000188 ! intron

[Term]
id: SO:0000407
name: rRNA_18S
def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "18S ribosomal RNA" EXACT []
synonym: "18S rRNA" EXACT []
synonym: "rRNA 18S" EXACT []
xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki"
is_a: SO:0000650 ! small_subunit_rRNA

[Term]
id: SO:0000408
name: site
def: "The interbase position where something (eg an aberration) occurred." [SO:ke]
is_obsolete: true

[Term]
id: SO:0000409
name: binding_site
alt_id: BS:00033
def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]
comment: See GO:0005488 : binding.
subset: biosapiens
subset: SOFA
synonym: "binding_or_interaction_site" EXACT []
synonym: "site" RELATED []
xref: http://en.wikipedia.org/wiki/Binding_site "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000410
name: protein_binding_site
def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]
comment: See GO:0042277 : peptide binding.
subset: SOFA
synonym: "protein binding site" EXACT []
is_a: SO:0000409 ! binding_site

[Term]
id: SO:0000411
name: rescue_region
def: "A region that rescues." [SO:xp]
synonym: "rescue fragment" EXACT []
synonym: "rescue region" EXACT []
synonym: "rescue segment" RELATED []
is_a: SO:0000695 ! reagent
intersection_of: SO:0000695 ! reagent
intersection_of: has_quality SO:0000814 ! rescue
relationship: has_quality SO:0000814 ! rescue

[Term]
id: SO:0000412
name: restriction_fragment
def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]
subset: SOFA
synonym: "restriction fragment" EXACT []
xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki"
is_a: SO:0000143 ! assembly_component

[Term]
id: SO:0000413
name: sequence_difference
def: "A region where the sequence differs from that of a specified sequence." [SO:ke]
subset: SOFA
synonym: "sequence difference" EXACT []
is_a: SO:0000700 ! remark

[Term]
id: SO:0000414
name: invalidated_by_genomic_contamination
def: "An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke]
synonym: "invalidated by genomic contamination" EXACT []
is_a: SO:0000790 ! invalidated

[Term]
id: SO:0000415
name: invalidated_by_genomic_polyA_primed_cDNA
def: "An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke]
synonym: "invalidated by genomic polyA primed cDNA" EXACT []
is_a: SO:0000790 ! invalidated

[Term]
id: SO:0000416
name: invalidated_by_partial_processing
def: "An attribute to describe a feature that is invalidated due to partial processing." [SO:ke]
synonym: "invalidated by partial processing" EXACT []
is_a: SO:0000790 ! invalidated

[Term]
id: SO:0000417
name: polypeptide_domain
alt_id: BS:00012
alt_id: BS:00134
alt_id: SO:0001069
def: "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]
comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
subset: biosapiens
synonym: "domain" BROAD BS [uniprot:feature_type]
synonym: "polypeptide domain" EXACT []
synonym: "polypeptide_structural_domain" EXACT BS []
synonym: "structural domain" BROAD BS []
is_a: SO:0001070 ! polypeptide_structural_region
is_a: SO:0100021 ! polypeptide_conserved_region

[Term]
id: SO:0000418
name: signal_peptide
alt_id: BS:00159
def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
subset: biosapiens
subset: SOFA
synonym: "signal" RELATED [uniprot:feature_type]
synonym: "signal peptide" EXACT []
synonym: "signal peptide coding sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki"
is_a: SO:0001527 ! peptide_localization_signal
relationship: part_of SO:0001062 ! propeptide

[Term]
id: SO:0000419
name: mature_protein_region
alt_id: BS:00149
def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]
comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
subset: biosapiens
subset: SOFA
synonym: "chain" RELATED [uniprot:feature_type]
synonym: "mature peptide" RELATED []
synonym: "mature protein region" EXACT []
is_a: SO:0000839 ! polypeptide_region
relationship: part_of SO:0001063 ! immature_peptide_region

[Term]
id: SO:0000420
name: five_prime_terminal_inverted_repeat
synonym: "5' TIR" EXACT []
synonym: "five prime terminal inverted repeat" EXACT []
is_a: SO:0000481 ! terminal_inverted_repeat

[Term]
id: SO:0000421
name: three_prime_terminal_inverted_repeat
synonym: "3' TIR" EXACT []
synonym: "three prime terminal inverted repeat" EXACT []
is_a: SO:0000481 ! terminal_inverted_repeat

[Term]
id: SO:0000422
name: U5_LTR_region
synonym: "U5 long terminal repeat region" EXACT []
synonym: "U5 LTR region" EXACT []
is_a: SO:0000848 ! LTR_component

[Term]
id: SO:0000423
name: R_LTR_region
synonym: "R long terminal repeat region" EXACT []
synonym: "R LTR region" EXACT []
is_a: SO:0000848 ! LTR_component

[Term]
id: SO:0000424
name: U3_LTR_region
synonym: "U3 long terminal repeat region" EXACT []
synonym: "U3 LTR region" EXACT []
is_a: SO:0000848 ! LTR_component

[Term]
id: SO:0000425
name: five_prime_LTR
synonym: "5' long terminal repeat" EXACT []
synonym: "5' LTR" EXACT []
synonym: "five prime LTR" EXACT []
is_a: SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000426
name: three_prime_LTR
synonym: "3' long terminal repeat" EXACT []
synonym: "3' LTR" EXACT []
synonym: "three prime LTR" EXACT []
is_a: SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000427
name: R_five_prime_LTR_region
synonym: "R 5' long term repeat region" EXACT []
synonym: "R five prime LTR region" EXACT []
is_a: SO:0000423 ! R_LTR_region
is_a: SO:0000850 ! five_prime_LTR_component

[Term]
id: SO:0000428
name: U5_five_prime_LTR_region
synonym: "U5 5' long terminal repeat region" EXACT []
synonym: "U5 five prime LTR region" EXACT []
is_a: SO:0000422 ! U5_LTR_region
is_a: SO:0000850 ! five_prime_LTR_component

[Term]
id: SO:0000429
name: U3_five_prime_LTR_region
synonym: "U3 5' long term repeat region" EXACT []
synonym: "U3 five prime LTR region" EXACT []
is_a: SO:0000424 ! U3_LTR_region
is_a: SO:0000850 ! five_prime_LTR_component

[Term]
id: SO:0000430
name: R_three_prime_LTR_region
synonym: "R 3' long terminal repeat region" EXACT []
synonym: "R three prime LTR region" EXACT []
is_a: SO:0000849 ! three_prime_LTR_component

[Term]
id: SO:0000431
name: U3_three_prime_LTR_region
synonym: "U3 3' long terminal repeat region" EXACT []
synonym: "U3 three prime LTR region" EXACT []
is_a: SO:0000849 ! three_prime_LTR_component

[Term]
id: SO:0000432
name: U5_three_prime_LTR_region
synonym: "U5 3' long terminal repeat region" EXACT []
synonym: "U5 three prime LTR region" EXACT []
is_a: SO:0000849 ! three_prime_LTR_component

[Term]
id: SO:0000433
name: non_LTR_retrotransposon_polymeric_tract
def: "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]
synonym: "non LTR retrotransposon polymeric tract" EXACT []
is_a: SO:0000657 ! repeat_region
is_a: SO:0000840 ! repeat_component
relationship: part_of SO:0000189 ! non_LTR_retrotransposon

[Term]
id: SO:0000434
name: target_site_duplication
def: "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]
synonym: "target site duplication" EXACT []
is_a: SO:0000314 ! direct_repeat
intersection_of: SO:0000314 ! direct_repeat
intersection_of: derives_from SO:0000101 ! transposable_element
relationship: derives_from SO:0000101 ! transposable_element

[Term]
id: SO:0000435
name: RR_tract
def: "A polypurine tract within an LTR_retrotransposon." [SO:ke]
synonym: "LTR retrotransposon poly purine tract" RELATED []
synonym: "RR tract" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0000186 ! LTR_retrotransposon

[Term]
id: SO:0000436
name: ARS
def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]
subset: SOFA
synonym: "autonomously replicating sequence" EXACT []
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000437
name: assortment_derived_duplication
is_obsolete: true

[Term]
id: SO:0000438
name: gene_not_polyadenylated
is_obsolete: true

[Term]
id: SO:0000439
name: inverted_ring_chromosome
synonym: "inverted ring chromosome" EXACT []
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000045 ! ring_chromosome

[Term]
id: SO:0000440
name: vector_replicon
def: "A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "vector" EXACT []
synonym: "vector replicon" EXACT []
xref: http://en.wikipedia.org/wiki/Vector_(molecular_biology) "wiki"
is_a: SO:0001235 ! replicon
relationship: part_of SO:0000151 ! clone

[Term]
id: SO:0000441
name: ss_oligo
def: "A single stranded oligonucleotide." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "single strand oligo" EXACT []
synonym: "single strand oligonucleotide" EXACT []
synonym: "single stranded oligonucleotide" EXACT []
synonym: "ss oligo" EXACT []
synonym: "ss oligonucleotide" EXACT []
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000442
name: ds_oligo
def: "A double stranded oligonucleotide." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "double stranded oligonucleotide" EXACT []
synonym: "ds oligo" EXACT []
synonym: "ds-oligonucleotide" EXACT []
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000443
name: polymer_attribute
def: "An attribute to describe the kind of biological sequence." [SO:ke]
synonym: "polymer attribute" EXACT []
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000444
name: three_prime_noncoding_exon
def: "Non-coding exon in the 3' UTR." [SO:ke]
synonym: "three prime noncoding exon" EXACT []
is_a: SO:0000198 ! noncoding_exon

[Term]
id: SO:0000445
name: five_prime_noncoding_exon
def: "Non-coding exon in the 5' UTR." [SO:ke]
synonym: "5' nc exon" EXACT []
synonym: "5' non coding exon" EXACT []
synonym: "five prime noncoding exon" EXACT []
is_a: SO:0000198 ! noncoding_exon

[Term]
id: SO:0000446
name: UTR_intron
def: "Intron located in the untranslated region." [SO:ke]
synonym: "UTR intron" EXACT []
is_a: SO:0000188 ! intron

[Term]
id: SO:0000447
name: five_prime_UTR_intron
def: "An intron located in the 5' UTR." [SO:ke]
synonym: "five prime UTR intron" EXACT []
is_a: SO:0000446 ! UTR_intron

[Term]
id: SO:0000448
name: three_prime_UTR_intron
def: "An intron located in the 3' UTR." [SO:ke]
synonym: "three prime UTR intron" EXACT []
is_a: SO:0000446 ! UTR_intron

[Term]
id: SO:0000449
name: random_sequence
def: "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components." [SO:ma]
synonym: "random sequence" EXACT []
is_a: SO:0000351 ! synthetic_sequence

[Term]
id: SO:0000450
name: interband
def: "A light region between two darkly staining bands in a polytene chromosome." [SO:ma]
synonym: "chromosome interband" RELATED []
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0000451
name: gene_with_polyadenylated_mRNA
def: "A gene that encodes a polyadenylated mRNA." [SO:xp]
synonym: "gene with polyadenylated mRNA" EXACT []
is_a: SO:0001217 ! protein_coding_gene
intersection_of: SO:0001217 ! protein_coding_gene
intersection_of: transcribed_to SO:0000871 ! polyadenylated_mRNA
relationship: transcribed_to SO:0000871 ! polyadenylated_mRNA

[Term]
id: SO:0000452
name: transgene_attribute
is_obsolete: true

[Term]
id: SO:0000453
name: chromosomal_transposition
def: "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]
synonym: "chromosomal transposition" EXACT []
synonym: "transposition" NARROW []
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:0000454
name: rasiRNA
def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]
subset: SOFA
synonym: "repeat associated small interfering RNA" EXACT []
xref: http://en.wikipedia.org/wiki/RasiRNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000455
name: gene_with_mRNA_with_frameshift
def: "A gene that encodes an mRNA with a frameshift." [SO:xp]
synonym: "gene with mRNA with frameshift" EXACT []
is_a: SO:0001217 ! protein_coding_gene
intersection_of: SO:0001217 ! protein_coding_gene
intersection_of: has_quality SO:0000865 ! frameshift
relationship: has_quality SO:0000865 ! frameshift

[Term]
id: SO:0000456
name: recombinationally_rearranged_gene
def: "A gene that is recombinationally rearranged." [SO:ke]
synonym: "recombinationally rearranged gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000940 ! recombinationally_rearranged
relationship: has_quality SO:0000940 ! recombinationally_rearranged

[Term]
id: SO:0000457
name: interchromosomal_duplication
def: "A chromosome duplication involving an insertion from another chromosome." [SO:ke]
synonym: "interchromosomal duplication" EXACT []
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:0000458
name: D_gene_segment
def: "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D gene" EXACT []
synonym: "D-GENE" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment

[Term]
id: SO:0000459
name: gene_with_trans_spliced_transcript
def: "A gene with a transcript that is trans-spliced." [SO:xp]
synonym: "gene with trans spliced transcript" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: transcribed_to SO:0000479 ! trans_spliced_transcript
relationship: transcribed_to SO:0000479 ! trans_spliced_transcript

[Term]
id: SO:0000460
name: vertebrate_immunoglobulin_T_cell_receptor_segment
comment: I am using the term segment instead of gene here to avoid confusion with the region 'gene'.
synonym: "vertebrate immunoglobulin T cell receptor segment" EXACT []
synonym: "vertebrate_immunoglobulin/T-cell receptor gene" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000461
name: inversion_derived_bipartite_deficiency
def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]
synonym: "inversion derived bipartite deficiency" EXACT []
is_a: SO:1000029 ! chromosomal_deletion

[Term]
id: SO:0000462
name: pseudogenic_region
def: "A non-functional descendant of a functional entity." [SO:cjm]
subset: SOFA
synonym: "pseudogenic region" EXACT []
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000463
name: encodes_alternately_spliced_transcripts
def: "A gene that encodes more than one transcript." [SO:ke]
synonym: "encodes alternately spliced transcripts" EXACT []
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000464
name: decayed_exon
def: "A non-functional descendant of an exon." [SO:ke]
subset: SOFA
synonym: "decayed exon" EXACT []
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000147 ! exon

[Term]
id: SO:0000465
name: inversion_derived_deficiency_plus_duplication
def: "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]
synonym: "inversion derived deficiency plus duplication" EXACT []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:0000466
name: V_gene_segment
def: "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V gene" EXACT []
synonym: "V-GENE" EXACT []
synonym: "variable_gene" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment

[Term]
id: SO:0000467
name: post_translationally_regulated_by_protein_stability
def: "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]
synonym: "post translationally regulated by protein stability" EXACT []
synonym: "post-translationally regulated by protein stability" EXACT []
is_a: SO:0000130 ! post_translationally_regulated

[Term]
id: SO:0000468
name: golden_path_fragment
def: "One of the pieces of sequence that make up a golden path." [SO:rd]
subset: SOFA
synonym: "golden path fragment" EXACT []
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000688 ! golden_path

[Term]
id: SO:0000469
name: post_translationally_regulated_by_protein_modification
def: "An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]
synonym: "post translationally regulated by protein modification" EXACT []
synonym: "post-translationally regulated by protein modification" EXACT []
is_a: SO:0000130 ! post_translationally_regulated

[Term]
id: SO:0000470
name: J_gene_segment
def: "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J gene" EXACT []
synonym: "J-GENE" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment

[Term]
id: SO:0000471
name: autoregulated
def: "The gene product is involved in its own transcriptional regulation." [SO:ke]
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000472
name: tiling_path
def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]
subset: SOFA
synonym: "tiling path" EXACT []
is_a: SO:0000353 ! sequence_assembly

[Term]
id: SO:0000473
name: negatively_autoregulated
def: "The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]
synonym: "negatively autoregulated" EXACT []
is_a: SO:0000126 ! transcriptionally_repressed
is_a: SO:0000471 ! autoregulated

[Term]
id: SO:0000474
name: tiling_path_fragment
def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]
subset: SOFA
synonym: "tiling path fragment" EXACT []
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000472 ! tiling_path

[Term]
id: SO:0000475
name: positively_autoregulated
def: "The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]
synonym: "positively autoregulated" EXACT []
is_a: SO:0000125 ! transcriptionally_induced
is_a: SO:0000471 ! autoregulated

[Term]
id: SO:0000476
name: contig_read
def: "A DNA sequencer read which is part of a contig." [SO:ke]
synonym: "contig read" EXACT []
is_a: SO:0000150 ! read

[Term]
id: SO:0000477
name: polycistronic_gene
def: "A gene that is polycistronic." [SO:ke]
is_obsolete: true

[Term]
id: SO:0000478
name: C_gene_segment
def: "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "C gene" EXACT []
synonym: "C_GENE" EXACT []
synonym: "constant gene" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment

[Term]
id: SO:0000479
name: trans_spliced_transcript
def: "A transcript that is trans-spliced." [SO:xp]
synonym: "trans spliced transcript" EXACT []
synonym: "trans-spliced transcript" EXACT []
is_a: SO:0000673 ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000870 ! trans_spliced
relationship: has_quality SO:0000870 ! trans_spliced

[Term]
id: SO:0000480
name: tiling_path_clone
def: "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]
synonym: "tiling path clone" EXACT []
is_a: SO:0000151 ! clone
is_a: SO:0000474 ! tiling_path_fragment

[Term]
id: SO:0000481
name: terminal_inverted_repeat
def: "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]
synonym: "terminal inverted repeat" EXACT []
synonym: "TIR" EXACT []
is_a: SO:0000294 ! inverted_repeat
relationship: part_of SO:0000208 ! terminal_inverted_repeat_element

[Term]
id: SO:0000482
name: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
synonym: "vertebrate immunoglobulin T cell receptor gene cluster" EXACT []
synonym: "vertebrate_immunoglobulin/T-cell receptor gene cluster" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000483
name: nc_primary_transcript
def: "A primary transcript that is never translated into a protein." [SO:ke]
subset: SOFA
synonym: "nc primary transcript" EXACT []
synonym: "noncoding primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000484
name: three_prime_coding_exon_noncoding_region
def: "The sequence of the 3' exon that is not coding." [SO:ke]
subset: SOFA
synonym: "three prime coding exon noncoding region" EXACT []
synonym: "three_prime_exon_noncoding_region" EXACT []
is_a: SO:0001214 ! noncoding_region_of_exon
relationship: part_of SO:0000202 ! three_prime_coding_exon

[Term]
id: SO:0000485
name: DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(DJ)-J-CLUSTER" EXACT []
synonym: "DJ J cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000486
name: five_prime_coding_exon_noncoding_region
def: "The sequence of the 5' exon preceding the start codon." [SO:ke]
subset: SOFA
synonym: "five prime coding exon noncoding region" EXACT []
synonym: "five_prime_exon_noncoding_region" EXACT []
is_a: SO:0001214 ! noncoding_region_of_exon
relationship: part_of SO:0000200 ! five_prime_coding_exon

[Term]
id: SO:0000487
name: VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VDJ)-J-C-CLUSTER" EXACT []
synonym: "VDJ J C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment

[Term]
id: SO:0000488
name: VDJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VDJ)-J-CLUSTER" EXACT []
synonym: "VDJ J cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment

[Term]
id: SO:0000489
name: VJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VJ)-C-CLUSTER" RELATED []
synonym: "VJ C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment

[Term]
id: SO:0000490
name: VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VJ)-J-C-CLUSTER" EXACT []
synonym: "VJ J C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment

[Term]
id: SO:0000491
name: VJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VJ)-J-CLUSTER" EXACT []
synonym: "VJ J cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment

[Term]
id: SO:0000492
name: D_gene_recombination_feature
synonym: "D gene recombination feature" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature

[Term]
id: SO:0000493
name: three_prime_D_heptamer
def: "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "3'D-HEPTAMER" EXACT []
synonym: "three prime D heptamer" EXACT []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence

[Term]
id: SO:0000494
name: three_prime_D_nonamer
def: "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "3'D-NOMAMER" EXACT []
synonym: "three prime D nonamer" EXACT []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence

[Term]
id: SO:0000495
name: three_prime_D_spacer
def: "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "3'D-SPACER" EXACT []
synonym: "three prime D spacer" EXACT []
is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence

[Term]
id: SO:0000496
name: five_prime_D_heptamer
def: "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "5'D-HEPTAMER" EXACT []
synonym: "five prime D heptamer" EXACT []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence

[Term]
id: SO:0000497
name: five_prime_D_nonamer
def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "5'D-NONAMER" EXACT []
synonym: "five prime D nonamer" EXACT []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence

[Term]
id: SO:0000498
name: five_prime_D_spacer
def: "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "5'-SPACER" EXACT []
synonym: "five prime D spacer" EXACT []
synonym: "five prime D-spacer" EXACT []
is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence

[Term]
id: SO:0000499
name: virtual_sequence
def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]
subset: SOFA
synonym: "virtual sequence" EXACT []
is_a: SO:0000353 ! sequence_assembly

[Term]
id: SO:0000500
name: Hoogsteen_base_pair
def: "A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]
synonym: "Hoogsteen base pair" EXACT []
xref: http://en.wikipedia.org/wiki/Hoogsteen_base_pair "wiki"
is_a: SO:0000028 ! base_pair

[Term]
id: SO:0000501
name: reverse_Hoogsteen_base_pair
def: "A type of non-canonical base-pairing." [SO:ke]
synonym: "reverse Hoogsteen base pair" EXACT []
is_a: SO:0000028 ! base_pair

[Term]
id: SO:0000502
name: transcribed_region
def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke]
comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
subset: SOFA
is_obsolete: true

[Term]
id: SO:0000503
name: alternately_spliced_gene_encodeing_one_transcript
is_obsolete: true

[Term]
id: SO:0000504
name: D_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D DJ C cluster" EXACT []
synonym: "D-(DJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000505
name: D_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D DJ cluster" EXACT []
synonym: "D-(DJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000506
name: D_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D DJ J C cluster" EXACT []
synonym: "D-(DJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000507
name: pseudogenic_exon
def: "A non functional descendant of an exon, part of a pseudogene." [SO:ke]
comment: This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
synonym: "pseudogenic exon" EXACT []
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000147 ! exon
relationship: part_of SO:0000516 ! pseudogenic_transcript

[Term]
id: SO:0000508
name: D_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D DJ J cluster" EXACT []
synonym: "D-(DJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000509
name: D_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D J C cluster" EXACT []
synonym: "D-J-C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment

[Term]
id: SO:0000510
name: VD_gene_segment
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V_D_GENE" EXACT []
synonym: "VD gene" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment

[Term]
id: SO:0000511
name: J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J C cluster" EXACT []
synonym: "J-C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment

[Term]
id: SO:0000512
name: inversion_derived_deficiency_plus_aneuploid
def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]
synonym: "inversion derived deficiency plus aneuploid" EXACT []
is_a: SO:1000029 ! chromosomal_deletion

[Term]
id: SO:0000513
name: J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J cluster" EXACT []
synonym: "J-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment

[Term]
id: SO:0000514
name: J_nonamer
def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J nonamer" EXACT []
synonym: "J-NONAMER" EXACT []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000302 ! J_gene_recombination_feature

[Term]
id: SO:0000515
name: J_heptamer
def: "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J heptamer" EXACT []
synonym: "J-HEPTAMER" EXACT []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000302 ! J_gene_recombination_feature

[Term]
id: SO:0000516
name: pseudogenic_transcript
def: "A non functional descendant of a transcript, part of a pseudogene." [SO:ke]
comment: This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
synonym: "pseudogenic transcript" EXACT []
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000673 ! transcript
relationship: part_of SO:0000336 ! pseudogene

[Term]
id: SO:0000517
name: J_spacer
def: "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J spacer" EXACT []
synonym: "J-SPACER" EXACT []
is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
relationship: part_of SO:0000302 ! J_gene_recombination_feature

[Term]
id: SO:0000518
name: V_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V DJ cluster" EXACT []
synonym: "V-(DJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000519
name: V_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V DJ J cluster" EXACT []
synonym: "V-(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000520
name: V_VDJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VDJ C cluster" EXACT []
synonym: "V-(VDJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment

[Term]
id: SO:0000521
name: V_VDJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VDJ cluster" EXACT []
synonym: "V-(VDJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment

[Term]
id: SO:0000522
name: V_VDJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VDJ J cluster" EXACT []
synonym: "V-(VDJ)-J-CLUSTER" RELATED []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment

[Term]
id: SO:0000523
name: V_VJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VJ C cluster" EXACT []
synonym: "V-(VJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment

[Term]
id: SO:0000524
name: V_VJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VJ cluster" EXACT []
synonym: "V-(VJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment

[Term]
id: SO:0000525
name: V_VJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VJ J cluster" EXACT []
synonym: "V-(VJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment

[Term]
id: SO:0000526
name: V_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V cluster" EXACT []
synonym: "V-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment

[Term]
id: SO:0000527
name: V_D_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D DJ C cluster" EXACT []
synonym: "V-D-(DJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000528
name: V_D_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D DJ cluster" EXACT []
synonym: "V-D-(DJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000529
name: V_D_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D DJ J C cluster" EXACT []
synonym: "V-D-(DJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000530
name: V_D_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D DJ J cluster" EXACT []
synonym: "V-D-(DJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000531
name: V_D_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D J C cluster" EXACT []
synonym: "V-D-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment

[Term]
id: SO:0000532
name: V_D_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D J cluster" EXACT []
synonym: "V-D-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment

[Term]
id: SO:0000533
name: V_heptamer
def: "7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V heptamer" EXACT []
synonym: "V-HEPTAMER" EXACT []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000538 ! V_gene_recombination_feature

[Term]
id: SO:0000534
name: V_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V J cluster" EXACT []
synonym: "V-J-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment

[Term]
id: SO:0000535
name: V_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V J C cluster" EXACT []
synonym: "V-J-C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment

[Term]
id: SO:0000536
name: V_nonamer
def: "9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V nonamer" EXACT []
synonym: "V-NONAMER" EXACT []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000538 ! V_gene_recombination_feature

[Term]
id: SO:0000537
name: V_spacer
def: "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V spacer" EXACT []
synonym: "V-SPACER" EXACT []
is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
relationship: part_of SO:0000538 ! V_gene_recombination_feature

[Term]
id: SO:0000538
name: V_gene_recombination_feature
def: "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V gene recombination feature" EXACT []
synonym: "V-RS" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature

[Term]
id: SO:0000539
name: DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(DJ)-C-CLUSTER" EXACT []
synonym: "DJ C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000540
name: DJ_J_C_cluster
def: "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(DJ)-J-C-CLUSTER" EXACT []
synonym: "DJ J C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000541
name: VDJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VDJ)-C-CLUSTER" EXACT []
synonym: "VDJ C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment

[Term]
id: SO:0000542
name: V_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V DJ C cluster" EXACT []
synonym: "V-(DJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000543
name: alternately_spliced_gene_encoding_greater_than_one_transcript
is_obsolete: true

[Term]
id: SO:0000544
name: helitron
def: "A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]
synonym: "ISCR" RELATED []
xref: http://en.wikipedia.org/wiki/Helitron "wiki"
is_a: SO:0000182 ! DNA_transposon

[Term]
id: SO:0000545
name: recoding_pseudoknot
def: "The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]
synonym: "recoding pseudoknot" EXACT []
is_a: SO:0000591 ! pseudoknot
relationship: part_of SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:0000546
name: designed_sequence
synonym: "designed sequence" EXACT []
is_a: SO:0000351 ! synthetic_sequence

[Term]
id: SO:0000547
name: inversion_derived_bipartite_duplication
def: "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]
synonym: "inversion derived bipartite duplication" EXACT []
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:0000548
name: gene_with_edited_transcript
def: "A gene that encodes a transcript that is edited." [SO:xp]
synonym: "gene with edited transcript" EXACT []
is_a: SO:0001217 ! protein_coding_gene
intersection_of: SO:0001217 ! protein_coding_gene
intersection_of: transcribed_to SO:0000873 ! edited_transcript
relationship: transcribed_to SO:0000873 ! edited_transcript

[Term]
id: SO:0000549
name: inversion_derived_duplication_plus_aneuploid
def: "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]
synonym: "inversion derived duplication plus aneuploid" EXACT []
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:0000550
name: aneuploid_chromosome
def: "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]
comment: Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila.
synonym: "aneuploid chromosome" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:0000551
name: polyA_signal_sequence
def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "poly(A) signal" EXACT []
synonym: "polyA signal sequence" EXACT []
synonym: "polyadenylation termination signal" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region

[Term]
id: SO:0000552
name: Shine_Dalgarno_sequence
def: "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]
comment: Not found in Eukaryotic sequence.
synonym: "five prime ribosome binding site" EXACT []
synonym: "RBS" RELATED []
synonym: "Shine Dalgarno sequence" EXACT []
synonym: "Shine-Dalgarno sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence "wiki"
is_a: SO:0000139 ! ribosome_entry_site

[Term]
id: SO:0000553
name: polyA_site
alt_id: SO:0001430
def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "polyA cleavage site" EXACT []
synonym: "polyA junction" EXACT []
synonym: "polyA site" EXACT []
synonym: "polyA_junction" EXACT []
synonym: "polyadenylation site" RELATED []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000205 ! three_prime_UTR
relationship: part_of SO:0000233 ! mature_transcript

[Term]
id: SO:0000554
name: assortment_derived_deficiency_plus_duplication
is_obsolete: true

[Term]
id: SO:0000555
name: five_prime_clip
def: "5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "5' clip" RELATED []
synonym: "five prime clip" EXACT []
is_a: SO:0000303 ! clip

[Term]
id: SO:0000556
name: five_prime_D_recombination_signal_sequence
def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "5'RS" EXACT []
synonym: "five prime D recombination signal sequence" EXACT []
synonym: "five prime D-recombination signal sequence" EXACT []
is_a: SO:0000492 ! D_gene_recombination_feature

[Term]
id: SO:0000557
name: three_prime_clip
def: "3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "3'-clip" EXACT []
synonym: "three prime clip" EXACT []
is_a: SO:0000303 ! clip

[Term]
id: SO:0000558
name: C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "C cluster" EXACT []
synonym: "C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000478 ! C_gene_segment

[Term]
id: SO:0000559
name: D_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D cluster" EXACT []
synonym: "D-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment

[Term]
id: SO:0000560
name: D_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D J cluster" EXACT []
synonym: "D-J-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment

[Term]
id: SO:0000561
name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
def: "Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "HEPTAMER" RELATED []
synonym: "heptamer of recombination feature of vertebrate immune system gene" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature

[Term]
id: SO:0000562
name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
synonym: "nonamer of recombination feature of vertebrate immune system gene" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature

[Term]
id: SO:0000563
name: vertebrate_immune_system_gene_recombination_spacer
synonym: "vertebrate immune system gene recombination spacer" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000564
name: V_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V DJ J C cluster" EXACT []
synonym: "V-(DJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment

[Term]
id: SO:0000565
name: V_VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VDJ J C cluster" EXACT []
synonym: "V-(VDJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment

[Term]
id: SO:0000566
name: V_VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VJ J C cluster" EXACT []
synonym: "V-(VJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment

[Term]
id: SO:0000567
name: inversion_derived_aneuploid_chromosome
def: "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]
synonym: "inversion derived aneuploid chromosome" EXACT []
is_a: SO:0000550 ! aneuploid_chromosome

[Term]
id: SO:0000568
name: bidirectional_promoter
def: "An unregulated promoter that allows continuous expression." [SO:ke]
synonym: "bidirectional promoter" EXACT []
is_a: SO:0000167 ! promoter

[Term]
id: SO:0000569
name: retrotransposed
alt_id: SO:0100042
def: "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke]
comment: GO:0003964 RNA-directed DNA polymerase activity.
xref: http://en.wikipedia.org/wiki/Retrotransposed "wiki"
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000570
name: three_prime_D_recombination_signal_sequence
def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "3'D-RS" EXACT []
synonym: "three prime D recombination signal sequence" EXACT []
synonym: "three_prime_D-recombination_signal_sequence" EXACT []
is_a: SO:0000492 ! D_gene_recombination_feature

[Term]
id: SO:0000571
name: miRNA_encoding
synonym: "miRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000572
name: DJ_gene_segment
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D-J-GENE" EXACT []
synonym: "DJ gene" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment

[Term]
id: SO:0000573
name: rRNA_encoding
synonym: "rRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000574
name: VDJ_gene_segment
def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V-D-J-GENE" EXACT []
synonym: "VDJ gene" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment

[Term]
id: SO:0000575
name: scRNA_encoding
synonym: "scRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000576
name: VJ_gene_segment
def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V-J-GENE" EXACT []
synonym: "VJ gene" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment

[Term]
id: SO:0000577
name: centromere
def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Centromere "wiki"
is_a: SO:0000628 ! chromosomal_structural_element

[Term]
id: SO:0000578
name: snoRNA_encoding
synonym: "snoRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000579
name: edited_transcript_feature
def: "A locatable feature on a transcript that is edited." [SO:ma]
synonym: "edited transcript feature" EXACT []
is_a: SO:0000833 ! transcript_region

[Term]
id: SO:0000580
name: methylation_guide_snoRNA_primary_transcript
def: "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]
synonym: "methylation guide snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0000581
name: cap
def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
subset: SOFA
xref: http://en.wikipedia.org/wiki/5%27_cap "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000582
name: rRNA_cleavage_snoRNA_primary_transcript
def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]
synonym: "rRNA cleavage snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0000583
name: pre_edited_region
def: "The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]
synonym: "pre edited region" EXACT []
synonym: "pre-edited region" EXACT []
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000584
name: tmRNA
def: "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]
synonym: "10Sa RNA" RELATED []
synonym: "ssrA" RELATED []
xref: http://en.wikipedia.org/wiki/TmRNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA

[Term]
id: SO:0000585
name: C_D_box_snoRNA_encoding
synonym: "C/D box snoRNA encoding" EXACT []
is_a: SO:0000578 ! snoRNA_encoding

[Term]
id: SO:0000586
name: tmRNA_primary_transcript
def: "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]
synonym: "10Sa RNA primary transcript" RELATED []
synonym: "ssrA RNA primary transcript" RELATED []
synonym: "tmRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000587
name: group_I_intron
def: "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]
comment: GO:0000372.
subset: SOFA
synonym: "group I intron" EXACT []
xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki"
is_a: SO:0000588 ! autocatalytically_spliced_intron

[Term]
id: SO:0000588
name: autocatalytically_spliced_intron
def: "A self spliced intron." [SO:ke]
subset: SOFA
synonym: "autocatalytically spliced intron" EXACT []
is_a: SO:0000188 ! intron
intersection_of: SO:0000188 ! intron
intersection_of: has_quality SO:0001186 ! ribozymic
relationship: has_quality SO:0001186 ! ribozymic

[Term]
id: SO:0000589
name: SRP_RNA_primary_transcript
def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke]
synonym: "SRP RNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000590
name: SRP_RNA
def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]
subset: SOFA
synonym: "7S RNA" RELATED []
synonym: "signal recognition particle RNA" RELATED []
synonym: "SRP RNA" EXACT []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000589 ! SRP_RNA_primary_transcript

[Term]
id: SO:0000591
name: pseudoknot
def: "A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]
xref: http://en.wikipedia.org/wiki/Pseudoknot "wiki"
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000592
name: H_pseudoknot
def: "A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]
synonym: "classical pseudoknot" EXACT []
synonym: "H pseudoknot" EXACT []
synonym: "H-pseudoknot" EXACT []
synonym: "H-type pseudoknot" EXACT []
synonym: "hairpin-type pseudoknot" EXACT []
is_a: SO:0000591 ! pseudoknot

[Term]
id: SO:0000593
name: C_D_box_snoRNA
def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
subset: SOFA
synonym: "box C/D snoRNA" EXACT []
synonym: "C D box snoRNA" EXACT []
synonym: "C/D box snoRNA" EXACT []
is_a: SO:0000275 ! snoRNA
relationship: derives_from SO:0000595 ! C_D_box_snoRNA_primary_transcript

[Term]
id: SO:0000594
name: H_ACA_box_snoRNA
def: "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
synonym: "box H/ACA snoRNA" EXACT []
synonym: "H ACA box snoRNA" EXACT []
synonym: "H/ACA box snoRNA" EXACT []
is_a: SO:0000275 ! snoRNA
relationship: derives_from SO:0000596 ! H_ACA_box_snoRNA_primary_transcript

[Term]
id: SO:0000595
name: C_D_box_snoRNA_primary_transcript
def: "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]
synonym: "C/D box snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0000596
name: H_ACA_box_snoRNA_primary_transcript
def: "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]
synonym: "H ACA box snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0000597
name: transcript_edited_by_U_insertion/deletion
def: "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." [http://www.rna.ucla.edu/index.html]
is_obsolete: true

[Term]
id: SO:0000598
name: edited_by_C_insertion_and_dinucleotide_insertion
synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED []
is_obsolete: true

[Term]
id: SO:0000599
name: edited_by_C_to_U_substitution
is_obsolete: true

[Term]
id: SO:0000600
name: edited_by_A_to_I_substitution
is_obsolete: true

[Term]
id: SO:0000601
name: edited_by_G_addition
is_obsolete: true

[Term]
id: SO:0000602
name: guide_RNA
def: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]
subset: SOFA
synonym: "gRNA" EXACT []
synonym: "guide RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000603
name: group_II_intron
def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]
comment: GO:0000373.
subset: SOFA
synonym: "group II intron" EXACT []
xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki"
is_a: SO:0000588 ! autocatalytically_spliced_intron

[Term]
id: SO:0000604
name: editing_block
def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]
synonym: "editing block" EXACT []
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000605
name: intergenic_region
def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "intergenic region" EXACT []
xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000606
name: editing_domain
def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]
synonym: "editing domain" EXACT []
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000607
name: unedited_region
def: "The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]
synonym: "unedited region" EXACT []
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000608
name: H_ACA_box_snoRNA_encoding
synonym: "H ACA box snoRNA encoding" EXACT []
is_a: SO:0000578 ! snoRNA_encoding

[Term]
id: SO:0000609
name: oligo_U_tail
def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]
synonym: "oligo U tail" EXACT []
is_a: SO:0001411 ! biological_region
relationship: adjacent_to SO:0000602 ! guide_RNA

[Term]
id: SO:0000610
name: polyA_sequence
def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]
subset: SOFA
synonym: "polyA sequence" EXACT []
is_a: SO:0001411 ! biological_region
relationship: adjacent_to SO:0000234 ! mRNA

[Term]
id: SO:0000611
name: branch_site
def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]
subset: SOFA
synonym: "branch point" EXACT []
synonym: "branch site" EXACT []
synonym: "branch_point" EXACT []
is_a: SO:0000841 ! spliceosomal_intron_region

[Term]
id: SO:0000612
name: polypyrimidine_tract
def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]
subset: SOFA
synonym: "polypyrimidine tract" EXACT []
xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki"
is_a: SO:0000841 ! spliceosomal_intron_region

[Term]
id: SO:0000613
name: bacterial_RNApol_promoter
def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]
synonym: "bacterial RNApol promoter" EXACT []
is_a: SO:0000752 ! gene_group_regulatory_region
is_a: SO:0001203 ! RNA_polymerase_promoter

[Term]
id: SO:0000614
name: bacterial_terminator
def: "A terminator signal for bacterial transcription." [SO:ke]
synonym: "bacterial terminator" EXACT []
is_a: SO:0000141 ! terminator
is_a: SO:0000752 ! gene_group_regulatory_region

[Term]
id: SO:0000615
name: terminator_of_type_2_RNApol_III_promoter
def: "A terminator signal for RNA polymerase III transcription." [SO:ke]
synonym: "terminator of type 2 RNApol III promoter" EXACT []
is_a: SO:0000951 ! eukaryotic_terminator

[Term]
id: SO:0000616
name: transcription_end_site
def: "The base where transcription ends." [SO:ke]
subset: SOFA
synonym: "transcription end site" EXACT []
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000617
name: RNApol_III_promoter_type_1
synonym: "RNApol III promoter type 1" EXACT []
is_a: SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000618
name: RNApol_III_promoter_type_2
synonym: "RNApol III promoter type 2" EXACT []
synonym: "tRNA promoter" RELATED []
is_a: SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000619
name: A_box
def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]
comment: Binds TFIIIC.
synonym: "A-box" EXACT []
xref: http://en.wikipedia.org/wiki/A-box "wiki"
is_a: SO:0001660 ! core_promoter_element

[Term]
id: SO:0000620
name: B_box
def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]
comment: Binds TFIIIC.
synonym: "B-box" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2

[Term]
id: SO:0000621
name: RNApol_III_promoter_type_3
synonym: "RNApol III promoter type 3" EXACT []
is_a: SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000622
name: C_box
def: "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]
synonym: "C-box" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1

[Term]
id: SO:0000623
name: snRNA_encoding
synonym: "snRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000624
name: telomere
def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]
subset: SOFA
synonym: "telomeric DNA" EXACT []
synonym: "telomeric sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Telomere "wiki"
is_a: SO:0000628 ! chromosomal_structural_element

[Term]
id: SO:0000625
name: silencer
def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki"
is_a: SO:0000727 ! CRM

[Term]
id: SO:0000626
name: chromosomal_regulatory_element
synonym: "chromosomal regulatory element" EXACT []
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0000627
name: insulator
def: "A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]
subset: SOFA
synonym: "insulator element" EXACT []
xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki"
is_a: SO:0001055 ! transcriptional_cis_regulatory_region

[Term]
id: SO:0000628
name: chromosomal_structural_element
subset: SOFA
synonym: "chromosomal structural element" EXACT []
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0000629
name: five_prime_open_reading_frame
synonym: "five prime open reading frame" EXACT []
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000204 ! five_prime_UTR

[Term]
id: SO:0000630
name: upstream_AUG_codon
def: "A start codon upstream of the ORF." [SO:ke]
synonym: "upstream AUG codon" EXACT []
is_a: SO:0000837 ! UTR_region
relationship: part_of SO:0000203 ! UTR

[Term]
id: SO:0000631
name: polycistronic_primary_transcript
def: "A primary transcript encoding for more than one gene product." [SO:ke]
synonym: "polycistronic primary transcript" EXACT []
is_a: SO:0000078 ! polycistronic_transcript
is_a: SO:0000185 ! primary_transcript
intersection_of: SO:0000185 ! primary_transcript
intersection_of: has_quality SO:0000880 ! polycistronic
relationship: has_quality SO:0000880 ! polycistronic

[Term]
id: SO:0000632
name: monocistronic_primary_transcript
def: "A primary transcript encoding for one gene product." [SO:ke]
synonym: "monocistronic primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript
is_a: SO:0000665 ! monocistronic_transcript
intersection_of: SO:0000185 ! primary_transcript
intersection_of: has_quality SO:0000878 ! monocistronic
relationship: has_quality SO:0000878 ! monocistronic

[Term]
id: SO:0000633
name: monocistronic_mRNA
def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]
synonym: "monocistronic mRNA" EXACT []
synonym: "monocistronic processed transcript" EXACT []
xref: http://en.wikipedia.org/wiki/Monocistronic_mRNA "wiki"
is_a: SO:0000234 ! mRNA
is_a: SO:0000665 ! monocistronic_transcript
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000878 ! monocistronic
relationship: has_quality SO:0000878 ! monocistronic

[Term]
id: SO:0000634
name: polycistronic_mRNA
def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]
synonym: "polycistronic mRNA" EXACT []
synonym: "polycistronic processed transcript" RELATED []
xref: http://en.wikipedia.org/wiki/Polycistronic_mRNA "wiki"
is_a: SO:0000078 ! polycistronic_transcript
is_a: SO:0000234 ! mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000880 ! polycistronic
relationship: has_quality SO:0000880 ! polycistronic

[Term]
id: SO:0000635
name: mini_exon_donor_RNA
def: "A primary transcript that donates the spliced leader to other mRNA." [SO:ke]
synonym: "mini exon donor RNA" EXACT []
synonym: "mini-exon donor RNA" EXACT []
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000636
name: spliced_leader_RNA
synonym: "mini-exon" RELATED []
synonym: "spliced leader RNA" EXACT []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000635 ! mini_exon_donor_RNA

[Term]
id: SO:0000637
name: engineered_plasmid
def: "A plasmid that is engineered." [SO:xp]
synonym: "engineered plasmid" EXACT []
synonym: "engineered plasmid gene" RELATED []
is_a: SO:0000155 ! plasmid
is_a: SO:0000804 ! engineered_region
intersection_of: SO:0000155 ! plasmid
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000638
name: transcribed_spacer_region
def: "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]
synonym: "transcribed spacer region" EXACT []
is_a: SO:0000838 ! rRNA_primary_transcript_region

[Term]
id: SO:0000639
name: internal_transcribed_spacer_region
def: "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]
synonym: "internal transcribed spacer region" EXACT []
is_a: SO:0000638 ! transcribed_spacer_region

[Term]
id: SO:0000640
name: external_transcribed_spacer_region
def: "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]
synonym: "external transcribed spacer region" EXACT []
is_a: SO:0000638 ! transcribed_spacer_region

[Term]
id: SO:0000641
name: tetranucleotide_repeat_microsatellite_feature
synonym: "tetranucleotide repeat microsatellite feature" EXACT []
is_a: SO:0000289 ! microsatellite

[Term]
id: SO:0000642
name: SRP_RNA_encoding
synonym: "SRP RNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000643
name: minisatellite
def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Minisatellite "wiki"
is_a: SO:0000005 ! satellite_DNA

[Term]
id: SO:0000644
name: antisense_RNA
def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]
subset: SOFA
synonym: "antisense RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000645 ! antisense_primary_transcript

[Term]
id: SO:0000645
name: antisense_primary_transcript
def: "The reverse complement of the primary transcript." [SO:ke]
subset: SOFA
synonym: "antisense primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript

[Term]
id: SO:0000646
name: siRNA
def: "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]
subset: SOFA
synonym: "small interfering RNA" EXACT []
xref: http://en.wikipedia.org/wiki/SiRNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000647
name: miRNA_primary_transcript
alt_id: SO:0000648
def: "A primary transcript encoding a micro RNA." [SO:ke]
synonym: "micro RNA primary transcript" EXACT []
synonym: "miRNA primary transcript" EXACT []
synonym: "small temporal RNA primary transcript" EXACT []
synonym: "stRNA primary transcript" EXACT []
synonym: "stRNA_primary_transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA

[Term]
id: SO:0000650
name: small_subunit_rRNA
def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "small subunit rRNA" EXACT []
synonym: "SSU RNA" EXACT [RSC:cb]
synonym: "SSU rRNA" EXACT [RSC:cb]
is_a: SO:0000252 ! rRNA
relationship: derives_from SO:0000255 ! rRNA_small_subunit_primary_transcript

[Term]
id: SO:0000651
name: large_subunit_rRNA
def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "large subunit rRNA" EXACT []
synonym: "LSU RNA" EXACT [RSC:cb]
synonym: "LSU rRNA" EXACT [RSC:cb]
is_a: SO:0000252 ! rRNA
relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript

[Term]
id: SO:0000652
name: rRNA_5S
def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]
subset: SOFA
synonym: "5S LSU rRNA" EXACT []
synonym: "5S ribosomal RNA" EXACT []
synonym: "5S rRNA" EXACT []
synonym: "rRNA 5S" EXACT []
xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki"
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0000653
name: rRNA_28S
def: "A component of the large ribosomal subunit." [SO:ke]
subset: SOFA
synonym: "28S LSU rRNA" EXACT []
synonym: "28S ribosomal RNA" EXACT []
synonym: "28S rRNA" EXACT []
synonym: "rRNA 28S" EXACT []
xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki"
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0000654
name: maxicircle_gene
def: "A mitochondrial gene located in a maxicircle." [SO:xp]
synonym: "maxi-circle gene" EXACT []
synonym: "maxicircle gene" EXACT []
is_a: SO:0000089 ! kinetoplast_gene
intersection_of: SO:0000089 ! kinetoplast_gene
intersection_of: part_of SO:0000742 ! maxicircle
relationship: part_of SO:0000742 ! maxicircle

[Term]
id: SO:0000655
name: ncRNA
def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]
comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
subset: SOFA
synonym: "noncoding RNA" EXACT []
xref: http://en.wikipedia.org/wiki/NcRNA "wiki"
is_a: SO:0000233 ! mature_transcript

[Term]
id: SO:0000656
name: stRNA_encoding
synonym: "stRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000657
name: repeat_region
def: "A region of sequence containing one or more repeat units." [SO:ke]
subset: SOFA
synonym: "repeat region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: has_part SO:0000726 ! repeat_unit

[Term]
id: SO:0000658
name: dispersed_repeat
def: "A repeat that is located at dispersed sites in the genome." [SO:ke]
subset: SOFA
synonym: "dispersed repeat" EXACT []
synonym: "interspersed repeat" EXACT []
xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki"
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000659
name: tmRNA_encoding
synonym: "tmRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000660
name: DNA_invertase_target_sequence
is_obsolete: true

[Term]
id: SO:0000661
name: intron_attribute
is_obsolete: true

[Term]
id: SO:0000662
name: spliceosomal_intron
def: "An intron which is spliced by the spliceosome." [SO:ke]
comment: GO:0000398.
subset: SOFA
synonym: "spliceosomal intron" EXACT []
is_a: SO:0000188 ! intron

[Term]
id: SO:0000663
name: tRNA_encoding
synonym: "tRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000664
name: introgressed_chromosome_region
synonym: "introgressed chromosome region" EXACT []
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0000665
name: monocistronic_transcript
def: "A transcript that is monocistronic." [SO:xp]
synonym: "monocistronic transcript" EXACT []
is_a: SO:0000673 ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000878 ! monocistronic
relationship: has_quality SO:0000878 ! monocistronic

[Term]
id: SO:0000666
name: mobile_intron
def: "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]
synonym: "mobile intron" EXACT []
is_a: SO:0000188 ! intron
is_a: SO:0001037 ! mobile_genetic_element
intersection_of: SO:0000188 ! intron
intersection_of: has_quality SO:0001234 ! mobile
relationship: has_quality SO:0001234 ! mobile

[Term]
id: SO:0000667
name: insertion
alt_id: SO:1000034
def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]
subset: DBVAR
subset: SOFA
synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
synonym: "nucleotide insertion" EXACT []
synonym: "nucleotide_insertion" EXACT []
xref: loinc:LA6687-3 "Insertion"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000668
name: EST_match
def: "A match against an EST sequence." [SO:ke]
subset: SOFA
synonym: "EST match" EXACT []
is_a: SO:0000102 ! expressed_sequence_match

[Term]
id: SO:0000669
name: sequence_rearrangement_feature
synonym: "sequence rearrangement feature" EXACT []
is_a: SO:0000298 ! recombination_feature

[Term]
id: SO:0000670
name: chromosome_breakage_sequence
def: "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]
synonym: "chromosome breakage sequence" EXACT []
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000671
name: internal_eliminated_sequence
def: "A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]
synonym: "internal eliminated sequence" EXACT []
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000672
name: macronucleus_destined_segment
def: "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]
synonym: "macronucleus destined segment" EXACT []
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000673
name: transcript
def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]
subset: SOFA
xref: http://en.wikipedia.org/wiki/RNA "wiki"
is_a: SO:0000831 ! gene_member_region

[Term]
id: SO:0000674
name: non_canonical_splice_site
def: "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke]
synonym: "non canonical splice site" EXACT []
synonym: "non-canonical splice site" EXACT []
is_obsolete: true
consider: SO:0000678
consider: SO:0000679

[Term]
id: SO:0000675
name: canonical_splice_site
def: "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke]
synonym: "canonical splice site" EXACT []
is_obsolete: true
consider: SO:0000676
consider: SO:0000677

[Term]
id: SO:0000676
name: canonical_three_prime_splice_site
def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke]
synonym: "canonical 3' splice site" EXACT []
synonym: "canonical three prime splice site" EXACT []
is_a: SO:0000164 ! three_prime_cis_splice_site

[Term]
id: SO:0000677
name: canonical_five_prime_splice_site
def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke]
synonym: "canonical 5' splice site" EXACT []
synonym: "canonical five prime splice site" EXACT []
is_a: SO:0000163 ! five_prime_cis_splice_site

[Term]
id: SO:0000678
name: non_canonical_three_prime_splice_site
def: "A 3' splice site that does not have the sequence \"AG\"." [SO:ke]
synonym: "non canonical 3' splice site" RELATED []
synonym: "non canonical three prime splice site" EXACT []
synonym: "non-canonical three prime splice site" EXACT []
is_a: SO:0000164 ! three_prime_cis_splice_site

[Term]
id: SO:0000679
name: non_canonical_five_prime_splice_site
def: "A 5' splice site which does not have the sequence \"GT\"." [SO:ke]
synonym: "non canonical 5' splice site" EXACT []
synonym: "non canonical five prime splice site" EXACT []
synonym: "non-canonical five prime splice site" EXACT []
is_a: SO:0000163 ! five_prime_cis_splice_site

[Term]
id: SO:0000680
name: non_canonical_start_codon
def: "A start codon that is not the usual AUG sequence." [SO:ke]
synonym: "non ATG start codon" EXACT []
synonym: "non canonical start codon" EXACT []
synonym: "non-canonical start codon" EXACT []
is_a: SO:0000318 ! start_codon

[Term]
id: SO:0000681
name: aberrant_processed_transcript
def: "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." [SO:ke]
synonym: "aberrant processed transcript" EXACT []
is_a: SO:0000673 ! transcript

[Term]
id: SO:0000682
name: splicing_feature
is_obsolete: true

[Term]
id: SO:0000683
name: exonic_splice_enhancer
def: "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]
synonym: "exonic splice enhancer" EXACT []
is_a: SO:0000344 ! splice_enhancer

[Term]
id: SO:0000684
name: nuclease_sensitive_site
def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]
subset: SOFA
synonym: "nuclease sensitive site" EXACT []
is_a: SO:0000059 ! nuclease_binding_site

[Term]
id: SO:0000685
name: DNAseI_hypersensitive_site
synonym: "DHS" EXACT []
synonym: "DNAseI hypersensitive site" EXACT []
is_a: SO:0000322 ! nuclease_hypersensitive_site

[Term]
id: SO:0000686
name: translocation_element
def: "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]
synonym: "translocation element" EXACT []
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:0000687
name: deletion_junction
def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke]
subset: SOFA
synonym: "deletion junction" EXACT []
is_a: SO:0000699 ! junction

[Term]
id: SO:0000688
name: golden_path
def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]
subset: SOFA
synonym: "golden path" EXACT []
is_a: SO:0000353 ! sequence_assembly

[Term]
id: SO:0000689
name: cDNA_match
def: "A match against cDNA sequence." [SO:ke]
subset: SOFA
synonym: "cDNA match" EXACT []
is_a: SO:0000102 ! expressed_sequence_match

[Term]
id: SO:0000690
name: gene_with_polycistronic_transcript
def: "A gene that encodes a polycistronic transcript." [SO:xp]
synonym: "gene with polycistronic transcript" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: transcribed_to SO:0000078 ! polycistronic_transcript
relationship: transcribed_to SO:0000078 ! polycistronic_transcript

[Term]
id: SO:0000691
name: cleaved_initiator_methionine
alt_id: BS:00067
def: "The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]
subset: biosapiens
synonym: "cleaved initiator methionine" EXACT []
synonym: "init_met" RELATED [uniprot:feature_type]
synonym: "initiator methionine" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region

[Term]
id: SO:0000692
name: gene_with_dicistronic_transcript
def: "A gene that encodes a dicistronic transcript." [SO:xp]
synonym: "gene with dicistronic transcript" EXACT []
is_a: SO:0000690 ! gene_with_polycistronic_transcript
intersection_of: SO:0000690 ! gene_with_polycistronic_transcript
intersection_of: transcribed_to SO:0000079 ! dicistronic_transcript
relationship: transcribed_to SO:0000079 ! dicistronic_transcript

[Term]
id: SO:0000693
name: gene_with_recoded_mRNA
def: "A gene that encodes an mRNA that is recoded." [SO:xp]
synonym: "gene with recoded mRNA" EXACT []
is_a: SO:0001217 ! protein_coding_gene
intersection_of: SO:0001217 ! protein_coding_gene
intersection_of: has_quality SO:0000881 ! recoded
relationship: has_quality SO:0000881 ! recoded

[Term]
id: SO:0000694
name: SNP
def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]
subset: SOFA
synonym: "single nucleotide polymorphism" EXACT []
is_a: SO:0001483 ! SNV

[Term]
id: SO:0000695
name: reagent
def: "A sequence used in experiment." [SO:ke]
comment: Requested by Lynn Crosby, jan 2006.
subset: SOFA
is_a: SO:0001409 ! biomaterial_region

[Term]
id: SO:0000696
name: oligo
def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]
subset: SOFA
synonym: "oligonucleotide" EXACT []
xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki"
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000697
name: gene_with_stop_codon_read_through
def: "A gene that encodes a transcript with stop codon readthrough." [SO:xp]
synonym: "gene with stop codon read through" EXACT []
is_a: SO:0000693 ! gene_with_recoded_mRNA
intersection_of: SO:0000693 ! gene_with_recoded_mRNA
intersection_of: has_part SO:0000883 ! stop_codon_read_through
relationship: has_part SO:0000883 ! stop_codon_read_through

[Term]
id: SO:0000698
name: gene_with_stop_codon_redefined_as_pyrrolysine
def: "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]
synonym: "gene with stop codon redefined as pyrrolysine" EXACT []
is_a: SO:0000697 ! gene_with_stop_codon_read_through
intersection_of: SO:0000693 ! gene_with_recoded_mRNA
intersection_of: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine
relationship: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine

[Term]
id: SO:0000699
name: junction
def: "A sequence_feature with an extent of zero." [SO:ke]
comment: A junction is a boundary between regions. A boundary has an extent of zero.
subset: SOFA
synonym: "boundary" EXACT []
synonym: "breakpoint" EXACT []
is_a: SO:0000110 ! sequence_feature

[Term]
id: SO:0000700
name: remark
def: "A comment about the sequence." [SO:ke]
subset: SOFA
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0000701
name: possible_base_call_error
def: "A region of sequence where the validity of the base calling is questionable." [SO:ke]
subset: SOFA
synonym: "possible base call error" EXACT []
is_a: SO:0000413 ! sequence_difference

[Term]
id: SO:0000702
name: possible_assembly_error
def: "A region of sequence where there may have been an error in the assembly." [SO:ke]
subset: SOFA
synonym: "possible assembly error" EXACT []
is_a: SO:0000413 ! sequence_difference

[Term]
id: SO:0000703
name: experimental_result_region
def: "A region of sequence implicated in an experimental result." [SO:ke]
subset: SOFA
synonym: "experimental result region" EXACT []
is_a: SO:0000700 ! remark

[Term]
id: SO:0000704
name: gene
def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Gene "wiki"
is_a: SO:0001411 ! biological_region
relationship: member_of SO:0005855 ! gene_group

[Term]
id: SO:0000705
name: tandem_repeat
def: "Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]
subset: SOFA
synonym: "tandem repeat" EXACT []
xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki"
xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000706
name: trans_splice_acceptor_site
def: "The 3' splice site of the acceptor primary transcript." [SO:ke]
comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
subset: SOFA
synonym: "3' trans splice site" RELATED []
synonym: "trans splice acceptor site" EXACT []
is_a: SO:0001420 ! trans_splice_site

[Term]
id: SO:0000707
name: trans_splice_donor_site
def: "The 5' five prime splice site region of the donor RNA." [SO:ke]
comment: SL RNA contains a donor site.
synonym: "5 prime trans splice site" RELATED []
synonym: "trans splice donor site" EXACT []
synonym: "trans-splice donor site" EXACT []
is_a: SO:0001420 ! trans_splice_site

[Term]
id: SO:0000708
name: SL1_acceptor_site
def: "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]
synonym: "SL1 acceptor site" EXACT []
is_a: SO:0000706 ! trans_splice_acceptor_site

[Term]
id: SO:0000709
name: SL2_acceptor_site
def: "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL2 acceptor site" EXACT []
is_a: SO:0000706 ! trans_splice_acceptor_site

[Term]
id: SO:0000710
name: gene_with_stop_codon_redefined_as_selenocysteine
def: "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]
synonym: "gene with stop codon redefined as selenocysteine" EXACT []
is_a: SO:0000697 ! gene_with_stop_codon_read_through
intersection_of: SO:0000697 ! gene_with_stop_codon_read_through
intersection_of: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine
relationship: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine

[Term]
id: SO:0000711
name: gene_with_mRNA_recoded_by_translational_bypass
def: "A gene with mRNA recoded by translational bypass." [SO:xp]
synonym: "gene with mRNA recoded by translational bypass" EXACT []
is_a: SO:0000693 ! gene_with_recoded_mRNA
intersection_of: SO:0001217 ! protein_coding_gene
intersection_of: has_quality SO:0000886 ! recoded_by_translational_bypass
relationship: has_quality SO:0000886 ! recoded_by_translational_bypass

[Term]
id: SO:0000712
name: gene_with_transcript_with_translational_frameshift
def: "A gene encoding a transcript that has a translational frameshift." [SO:xp]
synonym: "gene with transcript with translational frameshift" EXACT []
is_a: SO:0000693 ! gene_with_recoded_mRNA
intersection_of: SO:0000693 ! gene_with_recoded_mRNA
intersection_of: has_quality SO:0000887 ! translationally_frameshifted
relationship: has_quality SO:0000887 ! translationally_frameshifted

[Term]
id: SO:0000713
name: DNA_motif
def: "A motif that is active in the DNA form of the sequence." [SO:ke]
synonym: "DNA motif" EXACT []
xref: http://en.wikipedia.org/wiki/DNA_motif "wiki"
is_a: SO:0000714 ! nucleotide_motif

[Term]
id: SO:0000714
name: nucleotide_motif
def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke]
subset: SOFA
synonym: "nucleotide motif" EXACT []
is_a: SO:0001683 ! sequence_motif

[Term]
id: SO:0000715
name: RNA_motif
def: "A motif that is active in RNA sequence." [SO:ke]
subset: SOFA
synonym: "RNA motif" EXACT []
is_a: SO:0000714 ! nucleotide_motif

[Term]
id: SO:0000716
name: dicistronic_mRNA
def: "An mRNA that has the quality dicistronic." [SO:ke]
synonym: "dicistronic mRNA" EXACT []
synonym: "dicistronic processed transcript" RELATED []
is_a: SO:0000079 ! dicistronic_transcript
is_a: SO:0000634 ! polycistronic_mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000879 ! dicistronic
relationship: has_quality SO:0000879 ! dicistronic

[Term]
id: SO:0000717
name: reading_frame
def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]
comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
subset: SOFA
synonym: "reading frame" EXACT []
xref: http://en.wikipedia.org/wiki/Reading_frame "wiki"
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0000718
name: blocked_reading_frame
def: "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb]
comment: Term requested by Rama from SGD.
synonym: "blocked reading frame" EXACT []
is_a: SO:0000717 ! reading_frame

[Term]
id: SO:0000719
name: ultracontig
def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]
subset: SOFA
synonym: "superscaffold" RELATED []
is_a: SO:0001876 ! partial_genomic_sequence_assembly

[Term]
id: SO:0000720
name: foreign_transposable_element
def: "A transposable element that is foreign." [SO:ke]
comment: requested by Michael on 19 Nov 2004.
synonym: "foreign transposable element" EXACT []
is_a: SO:0000101 ! transposable_element
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000784 ! foreign
relationship: has_quality SO:0000784 ! foreign

[Term]
id: SO:0000721
name: gene_with_dicistronic_primary_transcript
def: "A gene that encodes a dicistronic primary transcript." [SO:xp]
comment: Requested by Michael, 19 nov 2004.
synonym: "gene with dicistronic primary transcript" EXACT []
is_a: SO:0000692 ! gene_with_dicistronic_transcript
intersection_of: SO:0000692 ! gene_with_dicistronic_transcript
intersection_of: transcribed_to SO:1001197 ! dicistronic_primary_transcript
relationship: transcribed_to SO:1001197 ! dicistronic_primary_transcript

[Term]
id: SO:0000722
name: gene_with_dicistronic_mRNA
def: "A gene that encodes a polycistronic mRNA." [SO:xp]
comment: Requested by MA nov 19 2004.
synonym: "gene with dicistronic mRNA" EXACT []
synonym: "gene with dicistronic processed transcript" EXACT []
is_a: SO:0000692 ! gene_with_dicistronic_transcript
intersection_of: SO:0000692 ! gene_with_dicistronic_transcript
intersection_of: transcribed_to SO:0000716 ! dicistronic_mRNA
relationship: transcribed_to SO:0000716 ! dicistronic_mRNA

[Term]
id: SO:0000723
name: iDNA
def: "Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]
synonym: "intervening DNA" EXACT []
xref: http://en.wikipedia.org/wiki/IDNA "wiki"
is_a: SO:0000298 ! recombination_feature

[Term]
id: SO:0000724
name: oriT
def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "origin of transfer" EXACT []
xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki"
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000725
name: transit_peptide
alt_id: BS:00055
def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
subset: biosapiens
subset: SOFA
synonym: "signal" RELATED []
synonym: "transit" RELATED [uniprot:feature_type]
synonym: "transit peptide" EXACT []
is_a: SO:0001527 ! peptide_localization_signal

[Term]
id: SO:0000726
name: repeat_unit
def: "The simplest repeated component of a repeat region. A single repeat." [SO:ke]
comment: Added to comply with the feature table. A single repeat.
synonym: "repeat unit" EXACT []
xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000727
name: CRM
def: "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]
comment: Requested by Stephen Grossmann Dec 2004.
subset: SOFA
synonym: "cis regulatory module" EXACT []
synonym: "TF module" EXACT []
synonym: "transcription factor module" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region
intersection_of: SO:0001055 ! transcriptional_cis_regulatory_region
intersection_of: has_part SO:0000235 ! TF_binding_site
relationship: has_part SO:0000235 ! TF_binding_site

[Term]
id: SO:0000728
name: intein
def: "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]
comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein.
synonym: "protein intron" RELATED []
xref: http://en.wikipedia.org/wiki/Intein "wiki"
is_a: SO:0100011 ! cleaved_peptide_region

[Term]
id: SO:0000729
name: intein_containing
def: "An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke]
synonym: "intein containing" EXACT []
is_a: SO:0000010 ! protein_coding

[Term]
id: SO:0000730
name: gap
def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000353 ! sequence_assembly

[Term]
id: SO:0000731
name: fragmentary
def: "An attribute to describe a feature that is incomplete." [SO:ke]
comment: Term added because of request by MO people.
synonym: "fragment" EXACT []
is_a: SO:0000905 ! status

[Term]
id: SO:0000732
name: predicted
def: "An attribute describing an unverified region." [SO:ke]
xref: http://en.wikipedia.org/wiki/Predicted "wiki"
is_a: SO:0000905 ! status

[Term]
id: SO:0000733
name: feature_attribute
def: "An attribute describing a located_sequence_feature." [SO:ke]
synonym: "feature attribute" EXACT []
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000734
name: exemplar_mRNA
def: "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
comment: Added for the MO people.
synonym: "exemplar mRNA" EXACT []
is_a: SO:0000234 ! mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000864 ! exemplar
relationship: has_quality SO:0000864 ! exemplar

[Term]
id: SO:0000735
name: sequence_location
synonym: "sequence location" EXACT []
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000736
name: organelle_sequence
synonym: "organelle sequence" EXACT []
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000737
name: mitochondrial_sequence
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "mitochondrial sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence

[Term]
id: SO:0000738
name: nuclear_sequence
synonym: "nuclear sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence

[Term]
id: SO:0000739
name: nucleomorphic_sequence
synonym: "nucleomorphic sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence

[Term]
id: SO:0000740
name: plastid_sequence
synonym: "plastid sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence

[Term]
id: SO:0000741
name: kinetoplast
alt_id: SO:0000826
def: "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055]
synonym: "kinetoplast_chromosome" EXACT []
xref: http://en.wikipedia.org/wiki/Kinetoplast "wiki"
is_a: SO:0001026 ! genome
intersection_of: SO:0001260 ! sequence_collection
intersection_of: has_part SO:0000742 ! maxicircle
intersection_of: has_part SO:0000980 ! minicircle
relationship: has_part SO:0000742 ! maxicircle
relationship: has_part SO:0000980 ! minicircle

[Term]
id: SO:0000742
name: maxicircle
alt_id: SO:0000827
def: "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]
synonym: "maxicircle_chromosome" EXACT []
is_a: SO:0001235 ! replicon

[Term]
id: SO:0000743
name: apicoplast_sequence
synonym: "apicoplast sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000744
name: chromoplast_sequence
synonym: "chromoplast sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000745
name: chloroplast_sequence
synonym: "chloroplast sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000746
name: cyanelle_sequence
synonym: "cyanelle sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000747
name: leucoplast_sequence
synonym: "leucoplast sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000748
name: proplastid_sequence
synonym: "proplastid sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000749
name: plasmid_location
synonym: "plasmid location" EXACT []
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000750
name: amplification_origin
def: "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]
synonym: "amplification origin" EXACT []
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000751
name: proviral_location
synonym: "proviral location" EXACT []
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000752
name: gene_group_regulatory_region
subset: SOFA
synonym: "gene group regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
relationship: member_of SO:0005855 ! gene_group

[Term]
id: SO:0000753
name: clone_insert
def: "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]
subset: SOFA
synonym: "clone insert" EXACT []
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000151 ! clone

[Term]
id: SO:0000754
name: lambda_vector
def: "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]
synonym: "lambda vector" EXACT []
is_a: SO:0000440 ! vector_replicon

[Term]
id: SO:0000755
name: plasmid_vector
synonym: "plasmid vector" EXACT []
xref: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors "wiki"
is_a: SO:0000440 ! vector_replicon
intersection_of: SO:0001235 ! replicon
intersection_of: derives_from SO:0000155 ! plasmid
relationship: derives_from SO:0000155 ! plasmid

[Term]
id: SO:0000756
name: cDNA
def: "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]
synonym: "complementary DNA" EXACT []
xref: http://en.wikipedia.org/wiki/CDNA "wiki"
is_a: SO:0000352 ! DNA

[Term]
id: SO:0000757
name: single_stranded_cDNA
synonym: "single strand cDNA" EXACT []
synonym: "single stranded cDNA" EXACT []
synonym: "single-strand cDNA" RELATED []
is_a: SO:0000756 ! cDNA

[Term]
id: SO:0000758
name: double_stranded_cDNA
synonym: "double strand cDNA" RELATED []
synonym: "double stranded cDNA" EXACT []
synonym: "double-strand cDNA" RELATED []
is_a: SO:0000756 ! cDNA

[Term]
id: SO:0000759
name: plasmid_clone
is_obsolete: true

[Term]
id: SO:0000760
name: YAC_clone
is_obsolete: true

[Term]
id: SO:0000761
name: phagemid_clone
is_obsolete: true

[Term]
id: SO:0000762
name: PAC_clone
synonym: "P1_clone" RELATED []
is_obsolete: true

[Term]
id: SO:0000763
name: fosmid_clone
is_obsolete: true

[Term]
id: SO:0000764
name: BAC_clone
is_obsolete: true

[Term]
id: SO:0000765
name: cosmid_clone
is_obsolete: true

[Term]
id: SO:0000766
name: pyrrolysyl_tRNA
def: "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]
synonym: "pyrrolysyl tRNA" EXACT []
synonym: "pyrrolysyl-transfer ribonucleic acid" EXACT []
synonym: "pyrrolysyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0001178 ! pyrrolysine_tRNA_primary_transcript

[Term]
id: SO:0000767
name: clone_insert_start
is_obsolete: true

[Term]
id: SO:0000768
name: episome
def: "A plasmid that may integrate with a chromosome." [SO:ma]
is_a: SO:0000155 ! plasmid

[Term]
id: SO:0000769
name: tmRNA_coding_piece
def: "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]
comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005.
synonym: "tmRNA coding piece" EXACT []
is_a: SO:0000847 ! tmRNA_region

[Term]
id: SO:0000770
name: tmRNA_acceptor_piece
def: "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]
comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005.
synonym: "tmRNA acceptor piece" EXACT []
is_a: SO:0000847 ! tmRNA_region

[Term]
id: SO:0000771
name: QTL
def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/]
comment: Added in respose to request by Simon Twigger November 14th 2005.
synonym: "quantitative trait locus" EXACT []
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0000772
name: genomic_island
def: "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]
comment: Genomic islands are transmissible elements characterized by large size (>10kb).
synonym: "genomic island" EXACT []
xref: http://en.wikipedia.org/wiki/Genomic_island "wiki"
is_a: SO:0001039 ! integrated_mobile_genetic_element

[Term]
id: SO:0000773
name: pathogenic_island
def: "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]
comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
synonym: "pathogenic island" EXACT []
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0000774
name: metabolic_island
def: "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]
comment: Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.
synonym: "metabolic island" EXACT []
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0000775
name: adaptive_island
def: "An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]
comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
synonym: "adaptive island" EXACT []
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0000776
name: symbiosis_island
def: "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]
comment: Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149.
synonym: "symbiosis island" EXACT []
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0000777
name: pseudogenic_rRNA
def: "A non functional descendant of an rRNA." [SO:ke]
comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
subset: SOFA
synonym: "pseudogenic rRNA" EXACT []
is_a: SO:0000462 ! pseudogenic_region

[Term]
id: SO:0000778
name: pseudogenic_tRNA
def: "A non functional descendent of a tRNA." [SO:ke]
comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
subset: SOFA
synonym: "pseudogenic tRNA" EXACT []
is_a: SO:0000462 ! pseudogenic_region

[Term]
id: SO:0000779
name: engineered_episome
def: "An episome that is engineered." [SO:xp]
comment: Requested by Lynn Crosby Jan 2006.
synonym: "engineered episome" EXACT []
is_a: SO:0000637 ! engineered_plasmid
is_a: SO:0000768 ! episome
intersection_of: SO:0000768 ! episome
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000780
name: transposable_element_attribute
comment: Added by KE Jan 2006 to capture the kinds of attributes of TEs
is_obsolete: true

[Term]
id: SO:0000781
name: transgenic
def: "Attribute describing sequence that has been integrated with foreign sequence." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000782
name: natural
def: "An attribute describing a feature that occurs in nature." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000783
name: engineered
def: "An attribute to describe a region that was modified in vitro." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000784
name: foreign
def: "An attribute to describe a region from another species." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000785
name: cloned_region
comment: Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.
synonym: "cloned region" EXACT []
synonym: "cloned segment" EXACT []
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000753 ! clone_insert

[Term]
id: SO:0000786
name: reagent_attribute
comment: Added jan 2006 by KE.
synonym: "reagent attribute" EXACT []
is_obsolete: true

[Term]
id: SO:0000787
name: clone_attribute
is_obsolete: true

[Term]
id: SO:0000788
name: cloned
is_obsolete: true

[Term]
id: SO:0000789
name: validated
def: "An attribute to describe a feature that has been proven." [SO:ke]
is_a: SO:0000905 ! status

[Term]
id: SO:0000790
name: invalidated
def: "An attribute describing a feature that is invalidated." [SO:ke]
is_a: SO:0000905 ! status

[Term]
id: SO:0000791
name: cloned_genomic
is_obsolete: true

[Term]
id: SO:0000792
name: cloned_cDNA
is_obsolete: true

[Term]
id: SO:0000793
name: engineered_DNA
is_obsolete: true

[Term]
id: SO:0000794
name: engineered_rescue_region
def: "A rescue region that is engineered." [SO:xp]
synonym: "engineered rescue fragment" EXACT []
synonym: "engineered rescue region" EXACT []
synonym: "engineered rescue segment" EXACT []
is_a: SO:0000411 ! rescue_region
is_a: SO:0000804 ! engineered_region
intersection_of: SO:0000411 ! rescue_region
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000795
name: rescue_mini_gene
def: "A mini_gene that rescues." [SO:xp]
synonym: "rescue mini gene" EXACT []
synonym: "rescue mini-gene" EXACT []
is_a: SO:0000815 ! mini_gene
intersection_of: SO:0000815 ! mini_gene
intersection_of: has_quality SO:0000814 ! rescue
relationship: has_quality SO:0000814 ! rescue

[Term]
id: SO:0000796
name: transgenic_transposable_element
def: "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]
comment: Modified as requested by Lynn - FB. May 2007.
synonym: "transgenic transposable element" EXACT []
is_a: SO:0000101 ! transposable_element
intersection_of: SO:0000101 ! transposable_element
intersection_of: derives_from SO:0000151 ! clone
intersection_of: has_quality SO:0000781 ! transgenic
relationship: derives_from SO:0000151 ! clone
relationship: has_quality SO:0000781 ! transgenic

[Term]
id: SO:0000797
name: natural_transposable_element
def: "TE that exists (or existed) in nature." [FB:mc]
synonym: "natural transposable element" EXACT []
is_a: SO:0000101 ! transposable_element
is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000782 ! natural
relationship: has_quality SO:0000782 ! natural

[Term]
id: SO:0000798
name: engineered_transposable_element
def: "TE that has been modified by manipulations in vitro." [FB:mc]
synonym: "engineered transposable element" EXACT []
is_a: SO:0000101 ! transposable_element
is_a: SO:0000804 ! engineered_region
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000799
name: engineered_foreign_transposable_element
def: "A transposable_element that is engineered and foreign." [FB:mc]
synonym: "engineered foreign transposable element" EXACT []
is_a: SO:0000720 ! foreign_transposable_element
is_a: SO:0000798 ! engineered_transposable_element
is_a: SO:0000805 ! engineered_foreign_region
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000783 ! engineered
intersection_of: has_quality SO:0000784 ! foreign
relationship: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000784 ! foreign

[Term]
id: SO:0000800
name: assortment_derived_duplication
def: "A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]
synonym: "assortment derived duplication" EXACT []
is_a: SO:0001504 ! assortment_derived_variation

[Term]
id: SO:0000801
name: assortment_derived_deficiency_plus_duplication
def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]
synonym: "assortment derived deficiency plus duplication" EXACT []
is_a: SO:0001504 ! assortment_derived_variation

[Term]
id: SO:0000802
name: assortment_derived_deficiency
def: "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]
synonym: "assortment-derived deficiency" EXACT []
is_a: SO:0001504 ! assortment_derived_variation

[Term]
id: SO:0000803
name: assortment_derived_aneuploid
def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]
synonym: "assortment derived aneuploid" EXACT []
is_a: SO:0001504 ! assortment_derived_variation

[Term]
id: SO:0000804
name: engineered_region
def: "A region that is engineered." [SO:xp]
synonym: "construct" EXACT []
synonym: "engineered region" EXACT []
synonym: "engineered sequence" EXACT []
is_a: SO:0001409 ! biomaterial_region
intersection_of: SO:0000001 ! region
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000805
name: engineered_foreign_region
def: "A region that is engineered and foreign." [SO:xp]
synonym: "engineered foreign region" EXACT []
is_a: SO:0000804 ! engineered_region
intersection_of: SO:0000001 ! region
intersection_of: has_quality SO:0000783 ! engineered
intersection_of: has_quality SO:0000784 ! foreign
relationship: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000784 ! foreign

[Term]
id: SO:0000806
name: fusion
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000807
name: engineered_tag
def: "A tag that is engineered." [SO:xp]
synonym: "engineered tag" EXACT []
is_a: SO:0000324 ! tag
is_a: SO:0000804 ! engineered_region
intersection_of: SO:0000324 ! tag
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000808
name: validated_cDNA_clone
def: "A cDNA clone that has been validated." [SO:xp]
synonym: "validated cDNA clone" EXACT []
is_a: SO:0000317 ! cDNA_clone
intersection_of: SO:0000317 ! cDNA_clone
intersection_of: has_quality SO:0000789 ! validated
relationship: has_quality SO:0000789 ! validated

[Term]
id: SO:0000809
name: invalidated_cDNA_clone
def: "A cDNA clone that is invalid." [SO:xp]
synonym: "invalidated cDNA clone" EXACT []
is_a: SO:0000317 ! cDNA_clone
intersection_of: SO:0000317 ! cDNA_clone
intersection_of: has_quality SO:0000790 ! invalidated
relationship: has_quality SO:0000790 ! invalidated

[Term]
id: SO:0000810
name: chimeric_cDNA_clone
def: "A cDNA clone invalidated because it is chimeric." [SO:xp]
synonym: "chimeric cDNA clone" EXACT []
is_a: SO:0000809 ! invalidated_cDNA_clone
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA
relationship: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA

[Term]
id: SO:0000811
name: genomically_contaminated_cDNA_clone
def: "A cDNA clone invalidated by genomic contamination." [SO:xp]
synonym: "genomically contaminated cDNA clone" EXACT []
is_a: SO:0000809 ! invalidated_cDNA_clone
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000414 ! invalidated_by_genomic_contamination
relationship: has_quality SO:0000414 ! invalidated_by_genomic_contamination

[Term]
id: SO:0000812
name: polyA_primed_cDNA_clone
def: "A cDNA clone invalidated by polyA priming." [SO:xp]
synonym: "polyA primed cDNA clone" EXACT []
is_a: SO:0000809 ! invalidated_cDNA_clone
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA
relationship: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA

[Term]
id: SO:0000813
name: partially_processed_cDNA_clone
def: "A cDNA invalidated clone by partial processing." [SO:xp]
synonym: "partially processed cDNA clone" EXACT []
is_a: SO:0000809 ! invalidated_cDNA_clone
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000416 ! invalidated_by_partial_processing
relationship: has_quality SO:0000416 ! invalidated_by_partial_processing

[Term]
id: SO:0000814
name: rescue
def: "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000815
name: mini_gene
def: "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]
synonym: "mini gene" EXACT []
is_a: SO:0000236 ! ORF

[Term]
id: SO:0000816
name: rescue_gene
def: "A gene that rescues." [SO:xp]
synonym: "rescue gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000814 ! rescue
relationship: has_quality SO:0000814 ! rescue

[Term]
id: SO:0000817
name: wild_type
def: "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke]
synonym: "wild type" EXACT []
xref: http://en.wikipedia.org/wiki/Wild_type "wiki"
xref: loinc:LA9658-1 "wild type"
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000818
name: wild_type_rescue_gene
def: "A gene that rescues." [SO:xp]
synonym: "wild type rescue gene" EXACT []
is_a: SO:0000816 ! rescue_gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000817 ! wild_type
relationship: has_quality SO:0000817 ! wild_type

[Term]
id: SO:0000819
name: mitochondrial_chromosome
def: "A chromosome originating in a mitochondria." [SO:xp]
synonym: "mitochondrial chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000737 ! mitochondrial_sequence
relationship: has_origin SO:0000737 ! mitochondrial_sequence

[Term]
id: SO:0000820
name: chloroplast_chromosome
def: "A chromosome originating in a chloroplast." [SO:xp]
synonym: "chloroplast chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000745 ! chloroplast_sequence
relationship: has_origin SO:0000745 ! chloroplast_sequence

[Term]
id: SO:0000821
name: chromoplast_chromosome
def: "A chromosome originating in a chromoplast." [SO:xp]
synonym: "chromoplast chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000744 ! chromoplast_sequence
relationship: has_origin SO:0000744 ! chromoplast_sequence

[Term]
id: SO:0000822
name: cyanelle_chromosome
def: "A chromosome originating in a cyanelle." [SO:xp]
synonym: "cyanelle chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000746 ! cyanelle_sequence
relationship: has_origin SO:0000746 ! cyanelle_sequence

[Term]
id: SO:0000823
name: leucoplast_chromosome
def: "A chromosome with origin in a leucoplast." [SO:xp]
synonym: "leucoplast chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000747 ! leucoplast_sequence
relationship: has_origin SO:0000747 ! leucoplast_sequence

[Term]
id: SO:0000824
name: macronuclear_chromosome
def: "A chromosome originating in a macronucleus." [SO:xp]
synonym: "macronuclear chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000083 ! macronuclear_sequence
relationship: has_origin SO:0000083 ! macronuclear_sequence

[Term]
id: SO:0000825
name: micronuclear_chromosome
def: "A chromosome originating in a micronucleus." [SO:xp]
synonym: "micronuclear chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000084 ! micronuclear_sequence
relationship: has_origin SO:0000084 ! micronuclear_sequence

[Term]
id: SO:0000828
name: nuclear_chromosome
def: "A chromosome originating in a nucleus." [SO:xp]
synonym: "nuclear chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000738 ! nuclear_sequence
relationship: has_origin SO:0000738 ! nuclear_sequence

[Term]
id: SO:0000829
name: nucleomorphic_chromosome
def: "A chromosome originating in a nucleomorph." [SO:xp]
synonym: "nucleomorphic chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000739 ! nucleomorphic_sequence
relationship: has_origin SO:0000739 ! nucleomorphic_sequence

[Term]
id: SO:0000830
name: chromosome_part
def: "A region of a chromosome." [SO:ke]
comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
subset: SOFA
synonym: "chromosome part" EXACT []
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000831
name: gene_member_region
def: "A region of a gene." [SO:ke]
comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root.
subset: SOFA
synonym: "gene member region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: member_of SO:0000704 ! gene

[Term]
id: SO:0000832
name: promoter_region
def: "A region of sequence which is part of a promoter." [SO:ke]
comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.
is_obsolete: true

[Term]
id: SO:0000833
name: transcript_region
def: "A region of a transcript." [SO:ke]
comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
subset: SOFA
synonym: "transcript region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000673 ! transcript

[Term]
id: SO:0000834
name: mature_transcript_region
def: "A region of a mature transcript." [SO:ke]
comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
subset: SOFA
synonym: "mature transcript region" EXACT []
is_a: SO:0000833 ! transcript_region

[Term]
id: SO:0000835
name: primary_transcript_region
def: "A part of a primary transcript." [SO:ke]
comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
subset: SOFA
synonym: "primary transcript region" EXACT []
is_a: SO:0000833 ! transcript_region
relationship: part_of SO:0000185 ! primary_transcript

[Term]
id: SO:0000836
name: mRNA_region
def: "A region of an mRNA." [SO:cb]
comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
subset: SOFA
synonym: "mRNA region" EXACT []
is_a: SO:0000834 ! mature_transcript_region
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000837
name: UTR_region
def: "A region of UTR." [SO:ke]
comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
subset: SOFA
synonym: "UTR region" EXACT []
is_a: SO:0000836 ! mRNA_region

[Term]
id: SO:0000838
name: rRNA_primary_transcript_region
def: "A region of an rRNA primary transcript." [SO:ke]
comment: To allow transcribed_spacer_region to have a path to the root.
synonym: "rRNA primary transcript region" EXACT []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000209 ! rRNA_primary_transcript

[Term]
id: SO:0000839
name: polypeptide_region
alt_id: BS:00124
alt_id: BS:00331
def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]
comment: Added to allow the polypeptide regions to have is_a paths back to the root.
subset: biosapiens
subset: SOFA
synonym: "positional" RELATED []
synonym: "positional polypeptide feature" RELATED []
synonym: "region" NARROW [uniprot:feature_type]
synonym: "region or site annotation" RELATED []
synonym: "site" NARROW [uniprot:feature_type]
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000840
name: repeat_component
def: "A region of a repeated sequence." [SO:ke]
comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root.
synonym: "repeat component" EXACT []
is_a: SO:0001412 ! topologically_defined_region

[Term]
id: SO:0000841
name: spliceosomal_intron_region
def: "A region within an intron." [SO:ke]
comment: A terms added to allow the parts of introns to have is_a paths to the root.
subset: SOFA
synonym: "spliceosomal intron region" EXACT []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000842
name: gene_component_region
subset: SOFA
synonym: "gene component region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000704 ! gene

[Term]
id: SO:0000843
name: bacterial_RNApol_promoter_region
def: "A region which is part of a bacterial RNA polymerase promoter." [SO:ke]
comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.
is_obsolete: true

[Term]
id: SO:0000844
name: RNApol_II_promoter_region
def: "A region of sequence which is a promoter for RNA polymerase II." [SO:ke]
comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.
is_obsolete: true

[Term]
id: SO:0000845
name: RNApol_III_promoter_type_1_region
def: "A region of sequence which is a promoter for RNA polymerase III type 1." [SO:ke]
comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.
is_obsolete: true

[Term]
id: SO:0000846
name: RNApol_III_promoter_type_2_region
def: "A region of sequence which is a promoter for RNA polymerase III type 2." [SO:ke]
comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.
is_obsolete: true

[Term]
id: SO:0000847
name: tmRNA_region
def: "A region of a tmRNA." [SO:cb]
comment: This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.
synonym: "tmRNA region" EXACT []
is_a: SO:0000834 ! mature_transcript_region
relationship: part_of SO:0000584 ! tmRNA

[Term]
id: SO:0000848
name: LTR_component
synonym: "long term repeat component" EXACT []
synonym: "LTR component" EXACT []
is_a: SO:0000840 ! repeat_component
relationship: part_of SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000849
name: three_prime_LTR_component
synonym: "3' long terminal repeat component" EXACT []
synonym: "three prime LTR component" EXACT []
is_a: SO:0000848 ! LTR_component
relationship: part_of SO:0000426 ! three_prime_LTR

[Term]
id: SO:0000850
name: five_prime_LTR_component
synonym: "5' long term repeat component" EXACT []
synonym: "five prime LTR component" EXACT []
is_a: SO:0000848 ! LTR_component
relationship: part_of SO:0000425 ! five_prime_LTR

[Term]
id: SO:0000851
name: CDS_region
def: "A region of a CDS." [SO:cb]
subset: SOFA
synonym: "CDS region" EXACT []
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000316 ! CDS

[Term]
id: SO:0000852
name: exon_region
def: "A region of an exon." [RSC:cb]
subset: SOFA
synonym: "exon region" EXACT []
is_a: SO:0000833 ! transcript_region
relationship: part_of SO:0000147 ! exon

[Term]
id: SO:0000853
name: homologous_region
def: "A region that is homologous to another region." [SO:ke]
synonym: "homolog" EXACT []
synonym: "homologous region" EXACT []
synonym: "homologue" EXACT []
xref: http://en.wikipedia.org/wiki/Homology_(biology) "wiki"
is_a: SO:0000330 ! conserved_region
intersection_of: SO:0000330 ! conserved_region
intersection_of: has_quality SO:0000857 ! homologous
relationship: has_quality SO:0000857 ! homologous

[Term]
id: SO:0000854
name: paralogous_region
def: "A homologous_region that is paralogous to another region." [SO:ke]
comment: A term to be used in conjunction with the paralogous_to relationship.
synonym: "paralog" EXACT []
synonym: "paralogous region" EXACT []
synonym: "paralogue" EXACT []
xref: http://en.wikipedia.org/wiki/Paralog#Paralogy "wiki"
is_a: SO:0000853 ! homologous_region
intersection_of: SO:0000853 ! homologous_region
intersection_of: has_quality SO:0000859 ! paralogous
relationship: has_quality SO:0000859 ! paralogous

[Term]
id: SO:0000855
name: orthologous_region
def: "A homologous_region that is orthologous to another region." [SO:ke]
comment: This term should be used in conjunction with the similarity relationships defined in SO.
synonym: "ortholog" EXACT []
synonym: "orthologous region" EXACT []
synonym: "orthologue" EXACT []
xref: http://en.wikipedia.org/wiki/Ortholog#Orthology "wiki"
is_a: SO:0000853 ! homologous_region
intersection_of: SO:0000853 ! homologous_region
intersection_of: has_quality SO:0000858 ! orthologous
relationship: has_quality SO:0000858 ! orthologous

[Term]
id: SO:0000856
name: conserved
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000857
name: homologous
def: "Similarity due to common ancestry." [SO:ke]
is_a: SO:0000856 ! conserved

[Term]
id: SO:0000858
name: orthologous
def: "An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]
is_a: SO:0000857 ! homologous

[Term]
id: SO:0000859
name: paralogous
def: "An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke]
is_a: SO:0000857 ! homologous

[Term]
id: SO:0000860
name: syntenic
def: "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke]
xref: http://en.wikipedia.org/wiki/Syntenic "wiki"
is_a: SO:0000856 ! conserved

[Term]
id: SO:0000861
name: capped_primary_transcript
def: "A primary transcript that is capped." [SO:xp]
synonym: "capped primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript
intersection_of: SO:0000185 ! primary_transcript
intersection_of: adjacent_to SO:0000581 ! cap
intersection_of: has_quality SO:0000146 ! capped
relationship: adjacent_to SO:0000581 ! cap
relationship: has_quality SO:0000146 ! capped

[Term]
id: SO:0000862
name: capped_mRNA
def: "An mRNA that is capped." [SO:xp]
synonym: "capped mRNA" EXACT []
is_a: SO:0000234 ! mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: adjacent_to SO:0000581 ! cap
intersection_of: has_quality SO:0000146 ! capped
relationship: adjacent_to SO:0000581 ! cap
relationship: has_quality SO:0000146 ! capped

[Term]
id: SO:0000863
name: mRNA_attribute
def: "An attribute describing an mRNA feature." [SO:ke]
synonym: "mRNA attribute" EXACT []
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000864
name: exemplar
def: "An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute

[Term]
id: SO:0000865
name: frameshift
def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]
xref: http://en.wikipedia.org/wiki/Frameshift "wiki"
is_a: SO:0000863 ! mRNA_attribute

[Term]
id: SO:0000866
name: minus_1_frameshift
def: "A frameshift caused by deleting one base." [SO:ke]
synonym: "minus 1 frameshift" EXACT []
is_a: SO:0000865 ! frameshift

[Term]
id: SO:0000867
name: minus_2_frameshift
def: "A frameshift caused by deleting two bases." [SO:ke]
synonym: "minus 2 frameshift" EXACT []
is_a: SO:0000865 ! frameshift

[Term]
id: SO:0000868
name: plus_1_frameshift
def: "A frameshift caused by inserting one base." [SO:ke]
synonym: "plus 1 frameshift" EXACT []
is_a: SO:0000865 ! frameshift

[Term]
id: SO:0000869
name: plus_2_framshift
def: "A frameshift caused by inserting two bases." [SO:ke]
synonym: "plus 2 framshift" EXACT []
is_a: SO:0000865 ! frameshift

[Term]
id: SO:0000870
name: trans_spliced
def: "An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke]
synonym: "trans-spliced" EXACT []
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000871
name: polyadenylated_mRNA
def: "An mRNA that is polyadenylated." [SO:xp]
synonym: "polyadenylated mRNA" EXACT []
is_a: SO:0000234 ! mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: adjacent_to SO:0000610 ! polyA_sequence
intersection_of: has_quality SO:0000246 ! polyadenylated
relationship: adjacent_to SO:0000610 ! polyA_sequence
relationship: has_quality SO:0000246 ! polyadenylated

[Term]
id: SO:0000872
name: trans_spliced_mRNA
def: "An mRNA that is trans-spliced." [SO:xp]
synonym: "trans-spliced mRNA" EXACT []
is_a: SO:0000234 ! mRNA
is_a: SO:0000479 ! trans_spliced_transcript
intersection_of: SO:0000234 ! mRNA
intersection_of: adjacent_to SO:0000636 ! spliced_leader_RNA
intersection_of: has_quality SO:0000870 ! trans_spliced
relationship: adjacent_to SO:0000636 ! spliced_leader_RNA
relationship: has_quality SO:0000870 ! trans_spliced

[Term]
id: SO:0000873
name: edited_transcript
def: "A transcript that is edited." [SO:ke]
synonym: "edited transcript" EXACT []
is_a: SO:0000673 ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000116 ! edited
relationship: guided_by SO:0000602 ! guide_RNA
relationship: has_part SO:0000977 ! anchor_binding_site
relationship: has_quality SO:0000116 ! edited

[Term]
id: SO:0000874
name: edited_transcript_by_A_to_I_substitution
def: "A transcript that has been edited by A to I substitution." [SO:ke]
synonym: "edited transcript by A to I substitution" EXACT []
is_a: SO:0000873 ! edited_transcript

[Term]
id: SO:0000875
name: bound_by_protein
def: "An attribute describing a sequence that is bound by a protein." [SO:ke]
synonym: "bound by protein" EXACT []
is_a: SO:0000277 ! bound_by_factor

[Term]
id: SO:0000876
name: bound_by_nucleic_acid
def: "An attribute describing a sequence that is bound by a nucleic acid." [SO:ke]
synonym: "bound by nucleic acid" EXACT []
is_a: SO:0000277 ! bound_by_factor

[Term]
id: SO:0000877
name: alternatively_spliced
def: "An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke]
synonym: "alternatively spliced" EXACT []
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000878
name: monocistronic
def: "An attribute describing a sequence that contains the code for one gene product." [SO:ke]
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000879
name: dicistronic
def: "An attribute describing a sequence that contains the code for two gene products." [SO:ke]
is_a: SO:0000880 ! polycistronic

[Term]
id: SO:0000880
name: polycistronic
def: "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000881
name: recoded
def: "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute

[Term]
id: SO:0000882
name: codon_redefined
def: "An attribute describing the alteration of codon meaning." [SO:ke]
synonym: "codon redefined" EXACT []
is_a: SO:0000881 ! recoded

[Term]
id: SO:0000883
name: stop_codon_read_through
def: "A stop codon redefined to be a new amino acid." [SO:ke]
synonym: "stop codon read through" EXACT []
synonym: "stop codon readthrough" RELATED []
is_a: SO:0000145 ! recoded_codon

[Term]
id: SO:0000884
name: stop_codon_redefined_as_pyrrolysine
def: "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]
synonym: "stop codon redefined as pyrrolysine" EXACT []
is_a: SO:0000883 ! stop_codon_read_through

[Term]
id: SO:0000885
name: stop_codon_redefined_as_selenocysteine
def: "A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]
synonym: "stop codon redefined as selenocysteine" EXACT []
is_a: SO:0000883 ! stop_codon_read_through

[Term]
id: SO:0000886
name: recoded_by_translational_bypass
def: "Recoded mRNA where a block of nucleotides is not translated." [SO:ke]
synonym: "recoded by translational bypass" EXACT []
is_a: SO:0000881 ! recoded

[Term]
id: SO:0000887
name: translationally_frameshifted
def: "Recoding by frameshifting a particular site." [SO:ke]
synonym: "translationally frameshifted" EXACT []
is_a: SO:0000881 ! recoded

[Term]
id: SO:0000888
name: maternally_imprinted_gene
def: "A gene that is maternally_imprinted." [SO:xp]
synonym: "maternally imprinted gene" EXACT []
is_a: SO:0000898 ! epigenetically_modified_gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000135 ! maternally_imprinted
relationship: has_quality SO:0000135 ! maternally_imprinted

[Term]
id: SO:0000889
name: paternally_imprinted_gene
def: "A gene that is paternally imprinted." [SO:xp]
synonym: "paternally imprinted gene" EXACT []
is_a: SO:0000898 ! epigenetically_modified_gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000136 ! paternally_imprinted
relationship: has_quality SO:0000136 ! paternally_imprinted

[Term]
id: SO:0000890
name: post_translationally_regulated_gene
def: "A gene that is post translationally regulated." [SO:xp]
synonym: "post translationally regulated gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000130 ! post_translationally_regulated
relationship: has_quality SO:0000130 ! post_translationally_regulated

[Term]
id: SO:0000891
name: negatively_autoregulated_gene
def: "A gene that is negatively autoreguated." [SO:xp]
synonym: "negatively autoregulated gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000473 ! negatively_autoregulated
relationship: has_quality SO:0000473 ! negatively_autoregulated

[Term]
id: SO:0000892
name: positively_autoregulated_gene
def: "A gene that is positively autoregulated." [SO:xp]
synonym: "positively autoregulated gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000475 ! positively_autoregulated
relationship: has_quality SO:0000475 ! positively_autoregulated

[Term]
id: SO:0000893
name: silenced
def: "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]
xref: http://en.wikipedia.org/wiki/Silenced "wiki"
is_a: SO:0000126 ! transcriptionally_repressed

[Term]
id: SO:0000894
name: silenced_by_DNA_modification
def: "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]
synonym: "silenced by DNA modification" EXACT []
is_a: SO:0000893 ! silenced

[Term]
id: SO:0000895
name: silenced_by_DNA_methylation
def: "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]
synonym: "silenced by DNA methylation" EXACT []
is_a: SO:0000894 ! silenced_by_DNA_modification

[Term]
id: SO:0000896
name: translationally_regulated_gene
def: "A gene that is translationally regulated." [SO:xp]
synonym: "translationally regulated gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000131 ! translationally_regulated
relationship: has_quality SO:0000131 ! translationally_regulated

[Term]
id: SO:0000897
name: allelically_excluded_gene
def: "A gene that is allelically_excluded." [SO:xp]
synonym: "allelically excluded gene" EXACT []
is_a: SO:0000898 ! epigenetically_modified_gene
intersection_of: SO:0000898 ! epigenetically_modified_gene
intersection_of: has_quality SO:0000137 ! allelically_excluded
relationship: has_quality SO:0000137 ! allelically_excluded

[Term]
id: SO:0000898
name: epigenetically_modified_gene
def: "A gene that is epigenetically modified." [SO:ke]
synonym: "epigenetically modified gene" EXACT []
is_a: SO:0000704 ! gene
is_a: SO:0001720 ! epigenetically_modified_region
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000133 ! epigenetically_modified
relationship: has_quality SO:0000133 ! epigenetically_modified

[Term]
id: SO:0000899
name: nuclear_mitochondrial
def: "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke]
synonym: "nuclear mitochondrial" EXACT []
is_obsolete: true

[Term]
id: SO:0000900
name: processed
def: "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail." [SO:ke]
is_obsolete: true

[Term]
id: SO:0000901
name: unequally_crossed_over
def: "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." [SO:ke]
synonym: "unequally crossed over" EXACT []
is_obsolete: true

[Term]
id: SO:0000902
name: transgene
def: "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp]
xref: http://en.wikipedia.org/wiki/Transgene "wiki"
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000781 ! transgenic
relationship: has_quality SO:0000781 ! transgenic

[Term]
id: SO:0000903
name: endogenous_retroviral_sequence
synonym: "endogenous retroviral sequence" EXACT []
is_a: SO:0000751 ! proviral_location

[Term]
id: SO:0000904
name: rearranged_at_DNA_level
def: "An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]
synonym: "rearranged at DNA level" EXACT []
is_a: SO:0000133 ! epigenetically_modified

[Term]
id: SO:0000905
name: status
def: "An attribute describing the status of a feature, based on the available evidence." [SO:ke]
comment: This term is the hypernym of attributes and should not be annotated to.
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000906
name: independently_known
def: "Attribute to describe a feature that is independently known - not predicted." [SO:ke]
synonym: "independently known" EXACT []
is_a: SO:0000905 ! status

[Term]
id: SO:0000907
name: supported_by_sequence_similarity
def: "An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]
synonym: "supported by sequence similarity" EXACT []
is_a: SO:0000732 ! predicted

[Term]
id: SO:0000908
name: supported_by_domain_match
def: "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]
synonym: "supported by domain match" EXACT []
is_a: SO:0000907 ! supported_by_sequence_similarity

[Term]
id: SO:0000909
name: supported_by_EST_or_cDNA
def: "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]
synonym: "supported by EST or cDNA" EXACT []
is_a: SO:0000907 ! supported_by_sequence_similarity

[Term]
id: SO:0000910
name: orphan
is_a: SO:0000732 ! predicted

[Term]
id: SO:0000911
name: predicted_by_ab_initio_computation
def: "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]
synonym: "predicted by ab initio computation" EXACT []
is_a: SO:0000732 ! predicted

[Term]
id: SO:0000912
name: asx_turn
alt_id: BS:00203
def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif

[Term]
id: SO:0000913
name: cloned_cDNA_insert
def: "A clone insert made from cDNA." [SO:xp]
synonym: "cloned cDNA insert" EXACT []
is_a: SO:0000753 ! clone_insert
intersection_of: SO:0000753 ! clone_insert
intersection_of: has_quality SO:0000756 ! cDNA
relationship: has_quality SO:0000756 ! cDNA

[Term]
id: SO:0000914
name: cloned_genomic_insert
def: "A clone insert made from genomic DNA." [SO:xp]
synonym: "cloned genomic insert" EXACT []
is_a: SO:0000753 ! clone_insert
intersection_of: SO:0000753 ! clone_insert
intersection_of: has_quality SO:0000991 ! genomic_DNA
relationship: has_quality SO:0000991 ! genomic_DNA

[Term]
id: SO:0000915
name: engineered_insert
def: "A clone insert that is engineered." [SO:xp]
synonym: "engineered insert" EXACT []
is_a: SO:0000753 ! clone_insert
is_a: SO:0000804 ! engineered_region
intersection_of: SO:0000753 ! clone_insert
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000916
name: edit_operation
synonym: "edit operation" EXACT []
is_obsolete: true

[Term]
id: SO:0000917
name: insert_U
def: "An edit to insert a U." [SO:ke]
comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
synonym: "insert U" EXACT []
is_obsolete: true

[Term]
id: SO:0000918
name: delete_U
def: "An edit to delete a uridine." [SO:ke]
comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
synonym: "delete U" EXACT []
is_obsolete: true

[Term]
id: SO:0000919
name: substitute_A_to_I
def: "An edit to substitute an I for an A." [SO:ke]
synonym: "substitute A to I" EXACT []
is_obsolete: true

[Term]
id: SO:0000920
name: insert_C
def: "An edit to insert a cytidine." [SO:ke]
synonym: "insert C" EXACT []
is_obsolete: true

[Term]
id: SO:0000921
name: insert_dinucleotide
def: "An edit to insert a dinucleotide." [SO:ke]
synonym: "insert dinucleotide" EXACT []
is_obsolete: true

[Term]
id: SO:0000922
name: substitute_C_to_U
def: "An edit to substitute an U for a C." [SO:ke]
synonym: "substitute C to U" EXACT []
is_obsolete: true

[Term]
id: SO:0000923
name: insert_G
def: "An edit to insert a G." [SO:ke]
synonym: "insert G" EXACT []
is_obsolete: true

[Term]
id: SO:0000924
name: insert_GC
def: "An edit to insert a GC dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
synonym: "insert GC" EXACT []
is_obsolete: true

[Term]
id: SO:0000925
name: insert_GU
def: "An edit to insert a GU dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
synonym: "insert GU" EXACT []
is_obsolete: true

[Term]
id: SO:0000926
name: insert_CU
def: "An edit to insert a CU dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
synonym: "insert CU" EXACT []
is_obsolete: true

[Term]
id: SO:0000927
name: insert_AU
def: "An edit to insert a AU dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
synonym: "insert AU" EXACT []
is_obsolete: true

[Term]
id: SO:0000928
name: insert_AA
def: "An edit to insert a AA dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
synonym: "insert AA" EXACT []
is_obsolete: true

[Term]
id: SO:0000929
name: edited_mRNA
def: "An mRNA that is edited." [SO:xp]
synonym: "edited mRNA" EXACT []
is_a: SO:0000234 ! mRNA
is_a: SO:0000873 ! edited_transcript
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000116 ! edited
relationship: has_quality SO:0000116 ! edited

[Term]
id: SO:0000930
name: guide_RNA_region
def: "A region of guide RNA." [SO:ma]
synonym: "guide RNA region" EXACT []
is_a: SO:0000834 ! mature_transcript_region
relationship: part_of SO:0000602 ! guide_RNA

[Term]
id: SO:0000931
name: anchor_region
def: "A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]
synonym: "anchor region" EXACT []
is_a: SO:0000930 ! guide_RNA_region

[Term]
id: SO:0000932
name: pre_edited_mRNA
synonym: "pre-edited mRNA" EXACT []
is_a: SO:0000120 ! protein_coding_primary_transcript

[Term]
id: SO:0000933
name: intermediate
def: "An attribute to describe a feature between stages of processing." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000934
name: miRNA_target_site
def: "A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]
synonym: "miRNA target site" EXACT []
is_a: SO:0001655 ! nucleotide_binding_site

[Term]
id: SO:0000935
name: edited_CDS
def: "A CDS that is edited." [SO:xp]
synonym: "edited CDS" EXACT []
is_a: SO:0000316 ! CDS
intersection_of: SO:0000316 ! CDS
intersection_of: has_quality SO:0000116 ! edited
relationship: has_quality SO:0000116 ! edited

[Term]
id: SO:0000936
name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
synonym: "vertebrate immunoglobulin T cell receptor rearranged segment" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000937
name: vertebrate_immune_system_feature
is_obsolete: true

[Term]
id: SO:0000938
name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
synonym: "vertebrate immunoglobulin T cell receptor rearranged gene cluster" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000939
name: vertebrate_immune_system_gene_recombination_signal_feature
synonym: "vertebrate immune system gene recombination signal feature" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000940
name: recombinationally_rearranged
synonym: "recombinationally rearranged" EXACT []
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000941
name: recombinationally_rearranged_vertebrate_immune_system_gene
def: "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]
synonym: "recombinationally rearranged vertebrate immune system gene" EXACT []
is_a: SO:0000456 ! recombinationally_rearranged_gene

[Term]
id: SO:0000942
name: attP_site
def: "An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]
synonym: "attP site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0001042 ! phage_sequence

[Term]
id: SO:0000943
name: attB_site
def: "An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]
synonym: "attB site" EXACT []
is_a: SO:0000946 ! integration_excision_site

[Term]
id: SO:0000944
name: attL_site
def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]
synonym: "attBP'" RELATED []
synonym: "attL site" RELATED []
is_a: SO:0000946 ! integration_excision_site

[Term]
id: SO:0000945
name: attR_site
def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]
synonym: "attPB'" RELATED []
synonym: "attR site" EXACT []
is_a: SO:0000946 ! integration_excision_site

[Term]
id: SO:0000946
name: integration_excision_site
def: "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]
synonym: "attachment site" RELATED []
synonym: "integration excision site" EXACT []
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000947
name: resolution_site
def: "A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]
synonym: "res site" EXACT []
synonym: "resolution site" EXACT []
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000948
name: inversion_site
def: "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]
comment: A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
synonym: "inversion site" EXACT []
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000949
name: dif_site
def: "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]
synonym: "dif site" EXACT []
is_a: SO:0000947 ! resolution_site

[Term]
id: SO:0000950
name: attC_site
def: "An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]
synonym: "attC site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0000365 ! integron

[Term]
id: SO:0000951
name: eukaryotic_terminator
synonym: "eukaryotic terminator" EXACT []
is_a: SO:0000141 ! terminator

[Term]
id: SO:0000952
name: oriV
def: "An origin of vegetative replication in plasmids and phages." [SO:as]
synonym: "origin of vegetative replication" EXACT []
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000953
name: oriC
def: "An origin of bacterial chromosome replication." [SO:as]
synonym: "origin of bacterial chromosome replication" EXACT []
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000954
name: DNA_chromosome
def: "Structural unit composed of a self-replicating, DNA molecule." [SO:ma]
synonym: "DNA chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_quality SO:0000352 ! DNA
relationship: has_quality SO:0000352 ! DNA

[Term]
id: SO:0000955
name: double_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]
synonym: "double stranded DNA chromosome" EXACT []
is_a: SO:0000954 ! DNA_chromosome
intersection_of: SO:0000954 ! DNA_chromosome
intersection_of: has_quality SO:0000985 ! double
relationship: has_quality SO:0000985 ! double

[Term]
id: SO:0000956
name: single_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]
synonym: "single stranded DNA chromosome" EXACT []
is_a: SO:0000954 ! DNA_chromosome
intersection_of: SO:0000954 ! DNA_chromosome
intersection_of: has_quality SO:0000984 ! single
relationship: has_quality SO:0000984 ! single

[Term]
id: SO:0000957
name: linear_double_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]
synonym: "linear double stranded DNA chromosome" EXACT []
is_a: SO:0000955 ! double_stranded_DNA_chromosome
intersection_of: SO:0000955 ! double_stranded_DNA_chromosome
intersection_of: has_quality SO:0000987 ! linear
relationship: has_quality SO:0000987 ! linear

[Term]
id: SO:0000958
name: circular_double_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]
synonym: "circular double stranded DNA chromosome" EXACT []
is_a: SO:0000955 ! double_stranded_DNA_chromosome
intersection_of: SO:0000955 ! double_stranded_DNA_chromosome
intersection_of: has_quality SO:0000988 ! circular
relationship: has_quality SO:0000988 ! circular

[Term]
id: SO:0000959
name: linear_single_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]
synonym: "linear single stranded DNA chromosome" EXACT []
is_a: SO:0000956 ! single_stranded_DNA_chromosome
intersection_of: SO:0000956 ! single_stranded_DNA_chromosome
intersection_of: has_quality SO:0000987 ! linear
relationship: has_quality SO:0000987 ! linear

[Term]
id: SO:0000960
name: circular_single_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]
synonym: "circular single stranded DNA chromosome" EXACT []
is_a: SO:0000956 ! single_stranded_DNA_chromosome
intersection_of: SO:0000956 ! single_stranded_DNA_chromosome
intersection_of: has_quality SO:0000988 ! circular
relationship: has_quality SO:0000988 ! circular

[Term]
id: SO:0000961
name: RNA_chromosome
def: "Structural unit composed of a self-replicating, RNA molecule." [SO:ma]
synonym: "RNA chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_quality SO:0000356 ! RNA
relationship: has_quality SO:0000356 ! RNA

[Term]
id: SO:0000962
name: single_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]
synonym: "single stranded RNA chromosome" EXACT []
is_a: SO:0000961 ! RNA_chromosome
intersection_of: SO:0000961 ! RNA_chromosome
intersection_of: has_quality SO:0000984 ! single
relationship: has_quality SO:0000984 ! single

[Term]
id: SO:0000963
name: linear_single_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]
synonym: "linear single stranded RNA chromosome" EXACT []
is_a: SO:0000962 ! single_stranded_RNA_chromosome
intersection_of: SO:0000962 ! single_stranded_RNA_chromosome
intersection_of: has_quality SO:0000987 ! linear
relationship: has_quality SO:0000987 ! linear

[Term]
id: SO:0000964
name: linear_double_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]
synonym: "linear double stranded RNA chromosome" EXACT []
is_a: SO:0000965 ! double_stranded_RNA_chromosome
intersection_of: SO:0000965 ! double_stranded_RNA_chromosome
intersection_of: has_quality SO:0000987 ! linear
relationship: has_quality SO:0000987 ! linear

[Term]
id: SO:0000965
name: double_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]
synonym: "double stranded RNA chromosome" EXACT []
is_a: SO:0000961 ! RNA_chromosome
intersection_of: SO:0000961 ! RNA_chromosome
intersection_of: has_quality SO:0000985 ! double
relationship: has_quality SO:0000985 ! double

[Term]
id: SO:0000966
name: circular_single_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]
synonym: "circular single stranded RNA chromosome" EXACT []
is_a: SO:0000962 ! single_stranded_RNA_chromosome
intersection_of: SO:0000962 ! single_stranded_RNA_chromosome
intersection_of: has_quality SO:0000988 ! circular
relationship: has_quality SO:0000988 ! circular

[Term]
id: SO:0000967
name: circular_double_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]
synonym: "circular double stranded RNA chromosome" EXACT []
is_a: SO:0000965 ! double_stranded_RNA_chromosome
intersection_of: SO:0000965 ! double_stranded_RNA_chromosome
intersection_of: has_quality SO:0000988 ! circular
relationship: has_quality SO:0000988 ! circular

[Term]
id: SO:0000968
name: sequence_replication_mode
comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
synonym: "sequence replication mode" EXACT []
is_obsolete: true

[Term]
id: SO:0000969
name: rolling_circle
comment: This has been obsoleted as it represents a process. replaced_by: GO:0070581.
synonym: "rolling circle" EXACT []
xref: http://en.wikipedia.org/wiki/Rolling_circle "wiki"
is_obsolete: true

[Term]
id: SO:0000970
name: theta_replication
comment: This has been obsoleted as it represents a process. replaced_by: GO:0070582
synonym: "theta replication" EXACT []
is_obsolete: true

[Term]
id: SO:0000971
name: DNA_replication_mode
comment: This has been obsoleted as it represents a process. replaced_by: GO:0006260.
synonym: "DNA replication mode" EXACT []
is_obsolete: true

[Term]
id: SO:0000972
name: RNA_replication_mode
comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
synonym: "RNA replication mode" EXACT []
is_obsolete: true

[Term]
id: SO:0000973
name: insertion_sequence
def: "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]
synonym: "insertion sequence" EXACT []
synonym: "IS" RELATED []
xref: http://en.wikipedia.org/wiki/Insertion_sequence "wiki"
is_a: SO:0000208 ! terminal_inverted_repeat_element

[Term]
id: SO:0000975
name: minicircle_gene
synonym: "minicircle gene" EXACT []
is_a: SO:0000089 ! kinetoplast_gene
intersection_of: SO:0000089 ! kinetoplast_gene
intersection_of: part_of SO:0000980 ! minicircle
relationship: part_of SO:0000980 ! minicircle

[Term]
id: SO:0000976
name: cryptic
def: "A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000977
name: anchor_binding_site
comment: Part of an edited transcript only.
synonym: "anchor binding site" EXACT []
is_a: SO:0000833 ! transcript_region

[Term]
id: SO:0000978
name: template_region
def: "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]
synonym: "information region" EXACT []
synonym: "template region" EXACT []
is_a: SO:0000930 ! guide_RNA_region

[Term]
id: SO:0000979
name: gRNA_encoding
def: "A non-protein_coding gene that encodes a guide_RNA." [SO:ma]
synonym: "gRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000980
name: minicircle
alt_id: SO:0000974
def: "A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]
synonym: "minicircle_chromosome" EXACT []
xref: http://en.wikipedia.org/wiki/Minicircle "wiki"
is_a: SO:0001235 ! replicon

[Term]
id: SO:0000981
name: rho_dependent_bacterial_terminator
synonym: "rho dependent bacterial terminator" EXACT []
is_a: SO:0000614 ! bacterial_terminator

[Term]
id: SO:0000982
name: rho_independent_bacterial_terminator
synonym: "rho independent bacterial terminator" EXACT []
is_a: SO:0000614 ! bacterial_terminator

[Term]
id: SO:0000983
name: strand_attribute
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
synonym: "strand attribute" EXACT []
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000984
name: single
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
is_a: SO:0000983 ! strand_attribute

[Term]
id: SO:0000985
name: double
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
is_a: SO:0000983 ! strand_attribute

[Term]
id: SO:0000986
name: topology_attribute
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
synonym: "topology attribute" EXACT []
is_a: SO:0000443 ! polymer_attribute

[Term]
id: SO:0000987
name: linear
def: "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb]
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
synonym: "two-ended" RELATED []
is_a: SO:0000986 ! topology_attribute
disjoint_from: SO:0000988 ! circular

[Term]
id: SO:0000988
name: circular
def: "A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb]
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
synonym: "zero-ended" RELATED []
is_a: SO:0000986 ! topology_attribute

[Term]
id: SO:0000989
name: class_II_RNA
def: "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]
synonym: "class II RNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000990
name: class_I_RNA
def: "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]
comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.
synonym: "class I RNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000991
name: genomic_DNA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "genomic DNA" EXACT []
is_a: SO:0000352 ! DNA

[Term]
id: SO:0000992
name: BAC_cloned_genomic_insert
comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006.
synonym: "BAC cloned genomic insert" EXACT []
is_a: SO:0000914 ! cloned_genomic_insert
intersection_of: SO:0000914 ! cloned_genomic_insert
intersection_of: derives_from SO:0000153 ! BAC
relationship: derives_from SO:0000153 ! BAC

[Term]
id: SO:0000993
name: consensus
comment: Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.
is_a: SO:0000905 ! status

[Term]
id: SO:0000994
name: consensus_region
comment: DO not obsolete without considering MGED mapping.
synonym: "consensus region" EXACT []
is_a: SO:0001410 ! experimental_feature
intersection_of: SO:0000001 ! region
intersection_of: has_quality SO:0000993 ! consensus
relationship: has_quality SO:0000993 ! consensus

[Term]
id: SO:0000995
name: consensus_mRNA
comment: DO not obsolete without considering MGED mapping.
synonym: "consensus mRNA" EXACT []
is_a: SO:0000234 ! mRNA
is_a: SO:0000994 ! consensus_region
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000993 ! consensus
relationship: has_quality SO:0000993 ! consensus

[Term]
id: SO:0000996
name: predicted_gene
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "predicted gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000732 ! predicted
relationship: has_quality SO:0000732 ! predicted

[Term]
id: SO:0000997
name: gene_fragment
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "gene fragment" EXACT []
is_a: SO:0000842 ! gene_component_region
intersection_of: SO:0000842 ! gene_component_region
intersection_of: has_quality SO:0000731 ! fragmentary
relationship: has_quality SO:0000731 ! fragmentary

[Term]
id: SO:0000998
name: recursive_splice_site
def: "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]
synonym: "recursive splice site" EXACT []
is_a: SO:0001419 ! cis_splice_site

[Term]
id: SO:0000999
name: BAC_end
def: "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]
comment: Requested by Keith Boroevich December, 2006.
synonym: "BAC end" EXACT []
synonym: "BAC end sequence" EXACT []
synonym: "BES" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000153 ! BAC

[Term]
id: SO:0001000
name: rRNA_16S
def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "16S ribosomal RNA" EXACT []
synonym: "16S rRNA" RELATED []
synonym: "16S SSU RNA" EXACT []
synonym: "rRNA 16S" EXACT []
xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki"
is_a: SO:0000650 ! small_subunit_rRNA

[Term]
id: SO:0001001
name: rRNA_23S
def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "23S LSU rRNA" EXACT []
synonym: "23S ribosomal RNA" RELATED []
synonym: "23S rRNA" EXACT []
synonym: "rRNA 23S" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0001002
name: rRNA_25S
def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]
subset: SOFA
synonym: "25S LSU rRNA" EXACT []
synonym: "25S ribosomal RNA" EXACT []
synonym: "25S rRNA" EXACT []
synonym: "rRNA 25S" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0001003
name: solo_LTR
def: "A recombination product between the 2 LTR of the same element." [SO:ke]
comment: Requested by Hadi Quesneville January 2007.
synonym: "solo LTR" EXACT []
is_a: SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0001004
name: low_complexity
synonym: "low complexity" EXACT []
is_a: SO:0000905 ! status

[Term]
id: SO:0001005
name: low_complexity_region
synonym: "low complexity region" EXACT []
is_a: SO:0001410 ! experimental_feature
intersection_of: SO:0000001 ! region
intersection_of: has_quality SO:0001004 ! low_complexity
relationship: has_quality SO:0001004 ! low_complexity

[Term]
id: SO:0001006
name: prophage
def: "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\"." [GOC:jl]
xref: http://en.wikipedia.org/wiki/Prophage "wiki"
is_a: SO:0000113 ! proviral_region

[Term]
id: SO:0001007
name: cryptic_prophage
def: "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes." [GOC:jl]
comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site.
synonym: "cryptic prophage" EXACT []
xref: http://ecoliwiki.net/colipedia/index.php/Category\:Cryptic_Prophage.w
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0001008
name: tetraloop
def: "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]
xref: http://en.wikipedia.org/wiki/Tetraloop "wiki"
is_a: SO:0000313 ! stem_loop

[Term]
id: SO:0001009
name: DNA_constraint_sequence
def: "A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\]&dispmax=50]
synonym: "DNA constraint" EXACT []
synonym: "DNA constraint sequence" EXACT []
is_a: SO:0000442 ! ds_oligo

[Term]
id: SO:0001010
name: i_motif
def: "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]
synonym: "i motif" EXACT []
synonym: "short intercalated motif" EXACT []
is_a: SO:0000142 ! DNA_sequence_secondary_structure

[Term]
id: SO:0001011
name: PNA_oligo
def: "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]
synonym: "peptide nucleic acid" EXACT []
synonym: "PNA oligo" EXACT []
xref: http://en.wikipedia.org/wiki/Peptide_nucleic_acid "wiki"
is_a: SO:0001247 ! synthetic_oligo
intersection_of: SO:0001247 ! synthetic_oligo
intersection_of: has_quality SO:0001184 ! PNA
relationship: has_quality SO:0001184 ! PNA

[Term]
id: SO:0001012
name: DNAzyme
def: "A DNA sequence with catalytic activity." [SO:cb]
comment: Added by request from Colin Batchelor.
synonym: "catalytic DNA" EXACT []
synonym: "deoxyribozyme" RELATED []
synonym: "DNA enzyme" EXACT []
is_a: SO:0000696 ! oligo
intersection_of: SO:0000696 ! oligo
intersection_of: has_quality SO:0001185 ! enzymatic
relationship: has_quality SO:0001185 ! enzymatic

[Term]
id: SO:0001013
name: MNP
def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]
synonym: "multiple nucleotide polymorphism" RELATED []
is_a: SO:0002007 ! MNV

[Term]
id: SO:0001014
name: intron_domain
comment: Requested by Colin Batchelor, Feb 2007.
synonym: "intron domain" EXACT []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000188 ! intron

[Term]
id: SO:0001015
name: wobble_base_pair
def: "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]
synonym: "wobble base pair" EXACT []
synonym: "wobble pair" EXACT []
xref: http://en.wikipedia.org/wiki/Wobble_base_pair "wiki"
is_a: SO:0000028 ! base_pair

[Term]
id: SO:0001016
name: internal_guide_sequence
def: "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]
synonym: "IGS" EXACT []
synonym: "internal guide sequence" EXACT []
is_a: SO:0001014 ! intron_domain
relationship: part_of SO:0000587 ! group_I_intron

[Term]
id: SO:0001017
name: silent_mutation
def: "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke]
comment: Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc.
synonym: "silent mutation" EXACT []
xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki"
xref: loinc:LA6700-4 "Silent"
is_a: SO:0001878 ! feature_variant

[Term]
id: SO:0001018
name: epitope
def: "A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb]
comment: Requested by Trish Whetzel.
xref: http://en.wikipedia.org/wiki/Epitope "wiki"
is_a: SO:0000409 ! binding_site

[Term]
id: SO:0001019
name: copy_number_variation
def: "A variation that increases or decreases the copy number of a given region." [SO:ke]
subset: SOFA
synonym: "CNP" EXACT []
synonym: "CNV" EXACT []
synonym: "copy number polymorphism" EXACT []
synonym: "copy number variation" EXACT []
xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki"
is_a: SO:0001059 ! sequence_alteration

[Term]
id: SO:0001020
name: sequence_variant_affecting_copy_number
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting copy number" EXACT []
synonym: "sequence variant affecting copy number" EXACT []
is_obsolete: true
replaced_by: SO:0001563

[Term]
id: SO:0001021
name: chromosome_breakpoint
alt_id: SO:0001242
synonym: "aberration breakpoint" EXACT []
synonym: "aberration_junction" EXACT []
synonym: "chromosome breakpoint" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0001022
name: inversion_breakpoint
def: "The point within a chromosome where an inversion begins or ends." [SO:cb]
synonym: "inversion breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint

[Term]
id: SO:0001023
name: allele
def: "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop]
synonym: "allelomorph" EXACT []
xref: http://en.wikipedia.org/wiki/Allele "wiki"
is_a: SO:0001507 ! variant_collection
relationship: variant_of SO:0000704 ! gene

[Term]
id: SO:0001024
name: haplotype
def: "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop]
xref: http://en.wikipedia.org/wiki/Haplotype "wiki"
is_a: SO:0001507 ! variant_collection
relationship: variant_of SO:0000355 ! haplotype_block

[Term]
id: SO:0001025
name: polymorphic_sequence_variant
def: "A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop]
synonym: "polymorphic sequence variant" EXACT []
is_a: SO:0001023 ! allele

[Term]
id: SO:0001026
name: genome
def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]
xref: http://en.wikipedia.org/wiki/Genome "wiki"
is_a: SO:0001260 ! sequence_collection
intersection_of: SO:0001260 ! sequence_collection
intersection_of: has_part SO:0001235 ! replicon
relationship: has_part SO:0001235 ! replicon

[Term]
id: SO:0001027
name: genotype
def: "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop]
xref: http://en.wikipedia.org/wiki/Genotype "wiki"
is_a: SO:0001507 ! variant_collection
relationship: variant_of SO:0001026 ! genome

[Term]
id: SO:0001028
name: diplotype
def: "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop]
is_a: SO:0001507 ! variant_collection

[Term]
id: SO:0001029
name: direction_attribute
synonym: "direction attribute" EXACT []
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0001030
name: forward
def: "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke]
is_a: SO:0001029 ! direction_attribute

[Term]
id: SO:0001031
name: reverse
def: "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke]
is_a: SO:0001029 ! direction_attribute

[Term]
id: SO:0001032
name: mitochondrial_DNA
comment: This terms is used by MO.
synonym: "mitochondrial DNA" EXACT []
synonym: "mtDNA" EXACT []
xref: http://en.wikipedia.org/wiki/Mitochondrial_DNA "wiki"
is_a: SO:0000737 ! mitochondrial_sequence
intersection_of: SO:0000737 ! mitochondrial_sequence
intersection_of: has_quality SO:0000352 ! DNA
relationship: has_quality SO:0000352 ! DNA

[Term]
id: SO:0001033
name: chloroplast_DNA
comment: This term is used by MO.
synonym: "chloroplast DNA" EXACT []
is_a: SO:0000745 ! chloroplast_sequence
intersection_of: SO:0000745 ! chloroplast_sequence
intersection_of: has_quality SO:0000352 ! DNA
relationship: has_quality SO:0000352 ! DNA

[Term]
id: SO:0001034
name: miRtron
def: "A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]
comment: Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns.
is_a: SO:0001014 ! intron_domain
relationship: has_part SO:0001244 ! pre_miRNA

[Term]
id: SO:0001035
name: piRNA
def: "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]
synonym: "piwi-associated RNA" EXACT []
xref: http://en.wikipedia.org/wiki/PiRNA "wiki"
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0001036
name: arginyl_tRNA
def: "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]
synonym: "arginyl tRNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000212 ! arginine_tRNA_primary_transcript

[Term]
id: SO:0001037
name: mobile_genetic_element
def: "A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]
subset: SOFA
synonym: "MGE" EXACT []
synonym: "mobile genetic element" EXACT []
xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki"
is_a: SO:0001411 ! biological_region
intersection_of: SO:0000001 ! region
intersection_of: has_quality SO:0001234 ! mobile
relationship: has_quality SO:0001234 ! mobile

[Term]
id: SO:0001038
name: extrachromosomal_mobile_genetic_element
def: "An MGE that is not integrated into the host chromosome." [SO:ke]
synonym: "extrachromosomal mobile genetic element" EXACT []
is_a: SO:0001037 ! mobile_genetic_element

[Term]
id: SO:0001039
name: integrated_mobile_genetic_element
def: "An MGE that is integrated into the host chromosome." [SO:ke]
subset: SOFA
synonym: "integrated mobile genetic element" EXACT []
is_a: SO:0001037 ! mobile_genetic_element

[Term]
id: SO:0001040
name: integrated_plasmid
def: "A plasmid sequence that is integrated within the host chromosome." [SO:ke]
synonym: "integrated plasmid" EXACT []
is_a: SO:0001039 ! integrated_mobile_genetic_element
intersection_of: SO:0001039 ! integrated_mobile_genetic_element
intersection_of: derives_from SO:0000155 ! plasmid
relationship: derives_from SO:0000155 ! plasmid

[Term]
id: SO:0001041
name: viral_sequence
def: "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]
comment: The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.
synonym: "viral sequence" EXACT []
synonym: "virus sequence" EXACT []
is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
is_a: SO:0001235 ! replicon

[Term]
id: SO:0001042
name: phage_sequence
def: "The nucleotide sequence of a virus that infects bacteria." [SO:ke]
synonym: "bacteriophage" EXACT []
synonym: "phage" EXACT []
synonym: "phage sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Bacteriophage "wiki"
is_a: SO:0001041 ! viral_sequence

[Term]
id: SO:0001043
name: attCtn_site
def: "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]
synonym: "attCtn site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0000371 ! conjugative_transposon

[Term]
id: SO:0001044
name: nuclear_mt_pseudogene
def: "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]
comment: Definition change requested by Val, 3172757.
synonym: "nuclear mitochondrial pseudogene" EXACT []
synonym: "nuclear mt pseudogene" EXACT []
synonym: "NUMT" EXACT []
xref: http://en.wikipedia.org/wiki/Numt "wikipedia"
is_a: SO:0001760 ! non_processed_pseudogene

[Term]
id: SO:0001045
name: cointegrated_plasmid
def: "A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]
synonym: "cointegrated plasmid" EXACT []
synonym: "cointegrated replicon" EXACT []
is_a: SO:0001039 ! integrated_mobile_genetic_element

[Term]
id: SO:0001046
name: IRLinv_site
def: "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]
synonym: "IRLinv site" EXACT []
is_a: SO:0001048 ! inversion_site_part
relationship: part_of SO:0000948 ! inversion_site

[Term]
id: SO:0001047
name: IRRinv_site
def: "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]
synonym: "IRRinv site" EXACT []
is_a: SO:0001048 ! inversion_site_part
relationship: part_of SO:0000948 ! inversion_site

[Term]
id: SO:0001048
name: inversion_site_part
def: "A region located within an inversion site." [SO:ke]
comment: A term created to allow the parts of an inversion site have an is_a path back to the root.
synonym: "inversion site part" EXACT []
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0001049
name: defective_conjugative_transposon
def: "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]
synonym: "defective conjugative transposon" EXACT []
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0001050
name: repeat_fragment
def: "A portion of a repeat, interrupted by the insertion of another element." [SO:ke]
comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats.
synonym: "repeat fragment" EXACT []
is_a: SO:0000840 ! repeat_component
relationship: part_of SO:0001649 ! nested_repeat

[Term]
id: SO:0001051
name: nested_region
is_obsolete: true

[Term]
id: SO:0001052
name: nested_repeat
is_obsolete: true

[Term]
id: SO:0001053
name: nested_transposon
is_obsolete: true

[Term]
id: SO:0001054
name: transposon_fragment
def: "A portion of a transposon, interrupted by the insertion of another element." [SO:ke]
synonym: "transposon fragment" EXACT []
is_a: SO:0000840 ! repeat_component
relationship: part_of SO:0001648 ! nested_transposon

[Term]
id: SO:0001055
name: transcriptional_cis_regulatory_region
def: "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]
subset: SOFA
synonym: "transcription-control region" EXACT []
synonym: "transcriptional cis regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region

[Term]
id: SO:0001056
name: splicing_regulatory_region
def: "A regulatory_region that modulates splicing." [SO:ke]
subset: SOFA
synonym: "splicing regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region

[Term]
id: SO:0001057
name: enhanceosome
is_obsolete: true

[Term]
id: SO:0001058
name: promoter_targeting_sequence
def: "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]
synonym: "promoter targeting sequence" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region

[Term]
id: SO:0001059
name: sequence_alteration
alt_id: SO:1000004
alt_id: SO:1000007
def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]
comment: Merged with partially characterized change in nucleotide sequence.
subset: SOFA
synonym: "partially characterised change in DNA sequence" NARROW []
synonym: "partially_characterised_change_in_DNA_sequence" NARROW []
synonym: "sequence alteration" EXACT []
synonym: "sequence variation" RELATED []
synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW []
is_a: SO:0000110 ! sequence_feature

[Term]
id: SO:0001060
name: sequence_variant
def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
synonym: "ANNOVAR:unknown" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "sequence variant" EXACT []
synonym: "VAAST:sequence_variant" EXACT VAR []

[Term]
id: SO:0001061
name: propeptide_cleavage_site
alt_id: BS:00063
def: "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]
comment: Discrete.
subset: biosapiens
synonym: "propeptide cleavage site" EXACT []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0001062 ! propeptide

[Term]
id: SO:0001062
name: propeptide
alt_id: BS:00077
def: "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "propep" RELATED [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Propeptide "wiki"
is_a: SO:0100011 ! cleaved_peptide_region

[Term]
id: SO:0001063
name: immature_peptide_region
alt_id: BS:00129
def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]
comment: Range.
subset: biosapiens
subset: SOFA
synonym: "immature peptide region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001064
name: active_peptide
alt_id: BS:00076
def: "Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]
comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.
subset: biosapiens
synonym: "active peptide" EXACT []
synonym: "peptide" BROAD [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Peptide "wiki"
is_a: SO:0000419 ! mature_protein_region

[Term]
id: SO:0001066
name: compositionally_biased_region_of_peptide
alt_id: BS:00068
def: "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "compbias" RELATED [uniprot:feature_type]
synonym: "compositional bias" RELATED []
synonym: "compositionally biased" RELATED []
synonym: "compositionally biased region of peptide" RELATED []
synonym: "compositionally_biased_region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001067
name: polypeptide_motif
alt_id: BS:00032
def: "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "motif" BROAD [uniprot:feature_type]
synonym: "polypeptide motif" EXACT []
is_a: SO:0100021 ! polypeptide_conserved_region

[Term]
id: SO:0001068
name: polypeptide_repeat
alt_id: BS:00070
def: "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "polypeptide repeat" EXACT []
synonym: "repeat" RELATED [uniprot:feature_type]
is_a: SO:0100021 ! polypeptide_conserved_region

[Term]
id: SO:0001070
name: polypeptide_structural_region
alt_id: BS:00337
def: "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]
comment: Range.
subset: biosapiens
synonym: "polypeptide structural region" EXACT []
synonym: "structural_region" RELATED []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001071
name: membrane_structure
alt_id: BS:00128
def: "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "membrane structure" EXACT []
is_a: SO:0001070 ! polypeptide_structural_region

[Term]
id: SO:0001072
name: extramembrane_polypeptide_region
alt_id: BS:00154
def: "Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]
comment: Range.
subset: biosapiens
synonym: "extramembrane" RELATED BS []
synonym: "extramembrane polypeptide region" EXACT []
synonym: "extramembrane_region" RELATED BS []
synonym: "topo_dom" RELATED BS [uniprot:feature_type]
is_a: SO:0001070 ! polypeptide_structural_region
relationship: part_of SO:0001071 ! membrane_structure

[Term]
id: SO:0001073
name: cytoplasmic_polypeptide_region
alt_id: BS:00145
def: "Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "cytoplasm_location" EXACT BS []
synonym: "cytoplasmic polypeptide region" EXACT []
synonym: "inside" RELATED BS []
is_a: SO:0001072 ! extramembrane_polypeptide_region

[Term]
id: SO:0001074
name: non_cytoplasmic_polypeptide_region
alt_id: BS:00144
def: "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]
comment: This could be inside an organelle within the cell.
subset: biosapiens
synonym: "non cytoplasmic polypeptide region" EXACT []
synonym: "non_cytoplasm_location" EXACT BS []
synonym: "outside" RELATED BS []
is_a: SO:0001072 ! extramembrane_polypeptide_region

[Term]
id: SO:0001075
name: intramembrane_polypeptide_region
alt_id: BS:00156
def: "Polypeptide region present in the lipid bilayer." [EBIBS:GAR]
subset: biosapiens
synonym: "intramembrane" RELATED BS []
synonym: "intramembrane polypeptide region" EXACT []
is_a: SO:0001070 ! polypeptide_structural_region
relationship: part_of SO:0001071 ! membrane_structure

[Term]
id: SO:0001076
name: membrane_peptide_loop
alt_id: BS:00155
def: "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "membrane peptide loop" EXACT []
synonym: "membrane_loop" RELATED BS []
is_a: SO:0001075 ! intramembrane_polypeptide_region

[Term]
id: SO:0001077
name: transmembrane_polypeptide_region
alt_id: BS:00158
def: "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]
subset: biosapiens
synonym: "transmem" RELATED BS [uniprot:feature_type]
synonym: "transmembrane" RELATED BS []
synonym: "transmembrane polypeptide region" EXACT []
is_a: SO:0001075 ! intramembrane_polypeptide_region

[Term]
id: SO:0001078
name: polypeptide_secondary_structure
alt_id: BS:00003
def: "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]
comment: Biosapien term was secondary_structure.
subset: biosapiens
synonym: "2nary structure" RELATED BS []
synonym: "polypeptide secondary structure" EXACT []
synonym: "secondary structure" RELATED BS []
synonym: "secondary structure region" RELATED BS []
synonym: "secondary_structure" RELATED BS []
xref: http://en.wikipedia.org/wiki/Secondary_structure "wiki"
is_a: SO:0001070 ! polypeptide_structural_region

[Term]
id: SO:0001079
name: polypeptide_structural_motif
alt_id: BS:0000338
def: "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]
subset: biosapiens
synonym: "polypeptide structural motif" RELATED []
synonym: "structural_motif" RELATED BS []
xref: http://en.wikipedia.org/wiki/Structural_motif "wiki"
is_a: SO:0001070 ! polypeptide_structural_region

[Term]
id: SO:0001080
name: coiled_coil
alt_id: BS:00041
def: "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "coiled" RELATED BS [uniprot:feature_type]
synonym: "coiled coil" EXACT []
xref: http://en.wikipedia.org/wiki/Coiled_coil "wiki"
is_a: SO:0001079 ! polypeptide_structural_motif

[Term]
id: SO:0001081
name: helix_turn_helix
alt_id: BS:00147
def: "A motif comprising two helices separated by a turn." [EBIBS:GAR]
subset: biosapiens
synonym: "helix turn helix" EXACT []
synonym: "helix-turn-helix" EXACT []
synonym: "HTH" RELATED BS []
is_a: SO:0001079 ! polypeptide_structural_motif
relationship: has_part SO:0001114 ! peptide_helix
relationship: has_part SO:0001128 ! polypeptide_turn_motif

[Term]
id: SO:0001082
name: polypeptide_sequencing_information
alt_id: BS:00125
def: "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "sequencing_information" EXACT []
is_a: SO:0000700 ! remark

[Term]
id: SO:0001083
name: non_adjacent_residues
alt_id: BS:00182
def: "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "non consecutive" EXACT []
synonym: "non_cons" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001084
name: non_terminal_residue
alt_id: BS:00072
def: "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "non terminal" EXACT []
synonym: "non_ter" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001085
name: sequence_conflict
alt_id: BS:00069
def: "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "conflict" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001086
name: sequence_uncertainty
alt_id: BS:00181
def: "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "unsure" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001087
name: cross_link
alt_id: BS:00178
def: "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "cross link" EXACT []
synonym: "crosslink" RELATED []
is_obsolete: true

[Term]
id: SO:0001088
name: disulfide_bond
alt_id: BS:00028
def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." [EBIBS:GAR, UniProt:curation_manual]
comment: 2 discreet & joined.
subset: biosapiens
synonym: "disulfid" RELATED []
synonym: "disulfide" RELATED []
synonym: "disulfide bond" RELATED []
synonym: "disulphide" EXACT []
synonym: "disulphide bond" RELATED []
is_obsolete: true

[Term]
id: SO:0001089
name: post_translationally_modified_region
alt_id: BS:00052
def: "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "mod_res" EXACT [uniprot:feature_type]
synonym: "modified residue" EXACT []
synonym: "post_translational_modification" EXACT []
xref: http://en.wikipedia.org/wiki/Post_translational_modification "wiki"
is_a: SO:0100001 ! biochemical_region_of_peptide

[Term]
id: SO:0001090
name: covalent_binding_site
alt_id: BS:00246
def: "Binding involving a covalent bond." [EBIBS:GAR]
subset: biosapiens
synonym: "covalent binding site" EXACT []
is_obsolete: true

[Term]
id: SO:0001091
name: non_covalent_binding_site
alt_id: BS:00029
def: "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR]
comment: Discrete.
subset: biosapiens
synonym: "binding" RELATED [uniprot:curation]
synonym: "binding site" RELATED []
synonym: "non covalent binding site" EXACT []
is_obsolete: true

[Term]
id: SO:0001092
name: polypeptide_metal_contact
alt_id: BS:00027
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]
comment: Residue is part of a binding site for a metal ion.
subset: biosapiens
synonym: "metal_binding" RELATED []
is_a: SO:0001656 ! metal_binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0001093
name: protein_protein_contact
alt_id: BS:00131
def: "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]
subset: biosapiens
synonym: "protein protein contact" EXACT []
synonym: "protein protein contact site" EXACT []
synonym: "protein_protein_interaction" RELATED []
xref: http://en.wikipedia.org/wiki/Protein_protein_interaction "wiki"
is_a: SO:0000410 ! protein_binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0001094
name: polypeptide_calcium_ion_contact_site
alt_id: BS:00186
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]
comment: Residue involved in contact with calcium.
subset: biosapiens
synonym: "ca bind" RELATED []
synonym: "ca_bind" EXACT BS [uniprot:feature_type]
synonym: "Ca_contact_site" EXACT []
synonym: "polypeptide calcium ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001095
name: polypeptide_cobalt_ion_contact_site
alt_id: BS:00136
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Co_contact_site" EXACT []
synonym: "polypeptide cobalt ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001096
name: polypeptide_copper_ion_contact_site
alt_id: BS:00146
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Cu_contact_site" EXACT []
synonym: "polypeptide copper ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001097
name: polypeptide_iron_ion_contact_site
alt_id: BS:00137
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Fe_contact_site" EXACT []
synonym: "polypeptide iron ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001098
name: polypeptide_magnesium_ion_contact_site
alt_id: BS:00187
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Mg_contact_site" EXACT []
synonym: "polypeptide magnesium ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001099
name: polypeptide_manganese_ion_contact_site
alt_id: BS:00140
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Mn_contact_site" EXACT []
synonym: "polypeptide manganese ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001100
name: polypeptide_molybdenum_ion_contact_site
alt_id: BS:00141
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Mo_contact_site" EXACT []
synonym: "polypeptide molybdenum ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001101
name: polypeptide_nickel_ion_contact_site
alt_id: BS:00142
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]
subset: biosapiens
synonym: "Ni_contact_site" EXACT []
synonym: "polypeptide nickel ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001102
name: polypeptide_tungsten_ion_contact_site
alt_id: BS:00143
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "polypeptide tungsten ion contact site" EXACT []
synonym: "W_contact_site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001103
name: polypeptide_zinc_ion_contact_site
alt_id: BS:00185
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "polypeptide zinc ion contact site" EXACT []
synonym: "Zn_contact_site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001104
name: catalytic_residue
alt_id: BS:00026
def: "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "act_site" RELATED [uniprot:feature_type]
synonym: "active site residue" EXACT []
synonym: "catalytic residue" EXACT []
is_a: SO:0001237 ! amino_acid
relationship: part_of SO:0100019 ! polypeptide_catalytic_motif

[Term]
id: SO:0001105
name: polypeptide_ligand_contact
alt_id: BS:00157
def: "Residues which interact with a ligand." [EBIBS:GAR]
subset: biosapiens
synonym: "polypeptide ligand contact" EXACT []
synonym: "protein-ligand interaction" RELATED []
is_a: SO:0001657 ! ligand_binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0001106
name: asx_motif
alt_id: BS:00202
def: "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001107
name: beta_bulge
alt_id: BS:00208
def: "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge" EXACT []
xref: http://en.wikipedia.org/wiki/Beta_bulge "wiki"
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001108
name: beta_bulge_loop
alt_id: BS:00209
def: "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge loop" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001109
name: beta_bulge_loop_five
alt_id: BS:00210
def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge loop five" EXACT []
is_a: SO:0001108 ! beta_bulge_loop

[Term]
id: SO:0001110
name: beta_bulge_loop_six
alt_id: BS:00211
def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge loop six" EXACT []
is_a: SO:0001108 ! beta_bulge_loop

[Term]
id: SO:0001111
name: beta_strand
alt_id: BS:00042
def: "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "strand" RELATED BS [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Beta_sheet "wiki"
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001112
name: antiparallel_beta_strand
alt_id: BS:0000341
def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "antiparallel beta strand" EXACT []
is_a: SO:0001111 ! beta_strand

[Term]
id: SO:0001113
name: parallel_beta_strand
alt_id: BS:00151
def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "parallel beta strand" EXACT []
is_a: SO:0001111 ! beta_strand

[Term]
id: SO:0001114
name: peptide_helix
alt_id: BS:00152
def: "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "helix" RELATED BS []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001115
name: left_handed_peptide_helix
alt_id: BS:00222
def: "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]
subset: biosapiens
synonym: "helix-l" RELATED []
synonym: "left handed helix" EXACT []
is_a: SO:0001114 ! peptide_helix

[Term]
id: SO:0001116
name: right_handed_peptide_helix
alt_id: BS:0000339
def: "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]
subset: biosapiens
synonym: "helix" RELATED BS []
synonym: "right handed helix" EXACT []
is_a: SO:0001114 ! peptide_helix

[Term]
id: SO:0001117
name: alpha_helix
alt_id: BS:00040
def: "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "a-helix" RELATED BS []
synonym: "helix" RELATED BS [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Alpha_helix "wiki"
is_a: SO:0001116 ! right_handed_peptide_helix

[Term]
id: SO:0001118
name: pi_helix
alt_id: BS:00153
def: "The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "pi helix" EXACT []
xref: http://en.wikipedia.org/wiki/Pi_helix "wiki"
is_a: SO:0001116 ! right_handed_peptide_helix

[Term]
id: SO:0001119
name: three_ten_helix
alt_id: BS:0000340
def: "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "3(10) helix" EXACT []
synonym: "3-10 helix" EXACT []
synonym: "310 helix" EXACT []
synonym: "three ten helix" EXACT []
xref: http://en.wikipedia.org/wiki/310_helix "wiki"
is_a: SO:0001116 ! right_handed_peptide_helix

[Term]
id: SO:0001120
name: polypeptide_nest_motif
alt_id: BS:00223
def: "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest" RELATED BS []
synonym: "nest_motif" EXACT []
synonym: "polypeptide nest motif" RELATED []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001121
name: polypeptide_nest_left_right_motif
alt_id: BS:00224
def: "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest_left_right" EXACT []
synonym: "nest_lr" EXACT []
synonym: "polypeptide nest left right motif" EXACT []
is_a: SO:0001120 ! polypeptide_nest_motif

[Term]
id: SO:0001122
name: polypeptide_nest_right_left_motif
alt_id: BS:00225
def: "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest_right_left" EXACT []
synonym: "nest_rl" EXACT []
synonym: "polypeptide nest right left motif" EXACT []
is_a: SO:0001120 ! polypeptide_nest_motif

[Term]
id: SO:0001123
name: schellmann_loop
alt_id: BS:00226
def: "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "paperclip" RELATED BS []
synonym: "paperclip loop" RELATED []
synonym: "schellmann loop" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001124
name: schellmann_loop_seven
alt_id: BS:00228
def: "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "schellmann loop seven" EXACT []
synonym: "seven-residue schellmann loop" EXACT []
is_a: SO:0001123 ! schellmann_loop

[Term]
id: SO:0001125
name: schellmann_loop_six
alt_id: BS:00227
def: "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "schellmann loop six" EXACT []
synonym: "six-residue schellmann loop" EXACT []
is_a: SO:0001123 ! schellmann_loop

[Term]
id: SO:0001126
name: serine_threonine_motif
alt_id: BS:00229
def: "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "serine/threonine motif" EXACT []
synonym: "st motif" EXACT []
synonym: "st_motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001127
name: serine_threonine_staple_motif
alt_id: BS:00230
def: "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "serine threonine staple motif" EXACT []
synonym: "st_staple" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001128
name: polypeptide_turn_motif
alt_id: BS:00148
def: "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]
comment: Range.
subset: biosapiens
synonym: "turn" RELATED BS []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001129
name: asx_turn_left_handed_type_one
alt_id: BS:00206
def: "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn left handed type one" EXACT []
synonym: "asx_turn_il" RELATED []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001130
name: asx_turn_left_handed_type_two
alt_id: BS:00204
def: "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn left handed type two" EXACT []
synonym: "asx_turn_iil" EXACT []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001131
name: asx_turn_right_handed_type_two
alt_id: BS:00205
def: "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn right handed type two" EXACT []
synonym: "asx_turn_iir" EXACT []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001132
name: asx_turn_right_handed_type_one
alt_id: BS:00207
def: "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn type right handed type one" EXACT []
synonym: "asx_turn_ir" EXACT []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001133
name: beta_turn
alt_id: BS:00212
def: "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif

[Term]
id: SO:0001134
name: beta_turn_left_handed_type_one
alt_id: BS:00215
def: "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn left handed type one" EXACT []
synonym: "beta_turn_il" EXACT []
synonym: "type I' beta turn" EXACT []
synonym: "type I' turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001135
name: beta_turn_left_handed_type_two
alt_id: BS:00213
def: "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn left handed type two" EXACT []
synonym: "beta_turn_iil" EXACT []
synonym: "type II' beta turn" EXACT []
synonym: "type II' turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001136
name: beta_turn_right_handed_type_one
alt_id: BS:00216
def: "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn right handed type one" EXACT []
synonym: "beta_turn_ir" EXACT []
synonym: "type I beta turn" EXACT []
synonym: "type I turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001137
name: beta_turn_right_handed_type_two
alt_id: BS:00214
def: "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn right handed type two" EXACT []
synonym: "beta_turn_iir" EXACT []
synonym: "type II beta turn" EXACT []
synonym: "type II turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001138
name: gamma_turn
alt_id: BS:00219
def: "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "gamma turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif

[Term]
id: SO:0001139
name: gamma_turn_classic
alt_id: BS:00220
def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "classic gamma turn" EXACT []
synonym: "gamma turn classic" EXACT []
is_a: SO:0001138 ! gamma_turn

[Term]
id: SO:0001140
name: gamma_turn_inverse
alt_id: BS:00221
def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "gamma turn inverse" EXACT []
is_a: SO:0001138 ! gamma_turn

[Term]
id: SO:0001141
name: serine_threonine_turn
alt_id: BS:00231
def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "serine/threonine turn" EXACT []
synonym: "st_turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif

[Term]
id: SO:0001142
name: st_turn_left_handed_type_one
alt_id: BS:00234
def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn left handed type one" EXACT []
synonym: "st_turn_il" EXACT []
is_a: SO:0001141 ! serine_threonine_turn

[Term]
id: SO:0001143
name: st_turn_left_handed_type_two
alt_id: BS:00232
def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn left handed type two" EXACT []
synonym: "st_turn_iil" EXACT []
is_a: SO:0001141 ! serine_threonine_turn

[Term]
id: SO:0001144
name: st_turn_right_handed_type_one
alt_id: BS:00235
def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn right handed type one" EXACT []
synonym: "st_turn_ir" EXACT []
is_a: SO:0001141 ! serine_threonine_turn

[Term]
id: SO:0001145
name: st_turn_right_handed_type_two
alt_id: BS:00233
def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn right handed type two" EXACT []
synonym: "st_turn_iir" EXACT []
is_a: SO:0001141 ! serine_threonine_turn

[Term]
id: SO:0001146
name: polypeptide_variation_site
alt_id: BS:00336
def: "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]
comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
subset: biosapiens
synonym: "sequence_variations" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001147
name: natural_variant_site
alt_id: BS:00071
def: "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "natural_variant" BROAD []
synonym: "sequence variation" BROAD []
synonym: "variant" BROAD [uniprot:feature_type]
is_a: SO:0001146 ! polypeptide_variation_site

[Term]
id: SO:0001148
name: mutated_variant_site
alt_id: BS:00036
def: "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "mutagen" EXACT BS [uniprot:feature_type]
synonym: "mutagenesis" EXACT []
synonym: "mutated_site" EXACT []
is_a: SO:0001146 ! polypeptide_variation_site

[Term]
id: SO:0001149
name: alternate_sequence_site
alt_id: BS:00073
alt_id: SO:0001065
def: "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "alternative_sequence" EXACT []
synonym: "isoform" NARROW []
synonym: "sequence variation" NARROW []
synonym: "var_seq" EXACT [uniprot:feature_type]
synonym: "varsplic" NARROW []
is_a: SO:0001146 ! polypeptide_variation_site

[Term]
id: SO:0001150
name: beta_turn_type_six
def: "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]
subset: biosapiens
synonym: "beta turn type six" EXACT []
synonym: "cis-proline loop" EXACT []
synonym: "type VI beta turn" EXACT []
synonym: "type VI turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001151
name: beta_turn_type_six_a
def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]
subset: biosapiens
synonym: "beta turn type six a" EXACT []
synonym: "type VIa beta turn" EXACT []
synonym: "type VIa turn" EXACT []
is_a: SO:0001150 ! beta_turn_type_six

[Term]
id: SO:0001152
name: beta_turn_type_six_a_one
subset: biosapiens
synonym: "beta turn type six a one" EXACT []
synonym: "type VIa1 beta turn" EXACT []
synonym: "type VIa1 turn" EXACT []
is_a: SO:0001151 ! beta_turn_type_six_a

[Term]
id: SO:0001153
name: beta_turn_type_six_a_two
subset: biosapiens
synonym: "beta turn type six a two" EXACT []
synonym: "type VIa2 beta turn" EXACT []
synonym: "type VIa2 turn" EXACT []
is_a: SO:0001151 ! beta_turn_type_six_a

[Term]
id: SO:0001154
name: beta_turn_type_six_b
def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]
subset: biosapiens
synonym: "beta turn type six b" EXACT []
synonym: "type VIb beta turn" EXACT []
synonym: "type VIb turn" EXACT []
is_a: SO:0001150 ! beta_turn_type_six

[Term]
id: SO:0001155
name: beta_turn_type_eight
def: "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]
subset: biosapiens
synonym: "beta turn type eight" EXACT []
synonym: "type VIII beta turn" EXACT []
synonym: "type VIII turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001156
name: DRE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]
comment: This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183.  Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.
synonym: "DRE motif" EXACT []
synonym: "NDM4" EXACT []
synonym: "WATCGATW_motif" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001157
name: DMv4_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941\:12537576]
synonym: "directional motif v4" EXACT []
synonym: "DMv4" EXACT []
synonym: "DMv4 motif" EXACT []
synonym: "motif 1 element" EXACT []
synonym: "promoter motif 1" EXACT []
synonym: "YGGTCACATR" NARROW []
is_a: SO:0001659 ! promoter_element

[Term]
id: SO:0001158
name: E_box_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576\:16827941]
synonym: "AWCAGCTGWT" NARROW []
synonym: "E box motif" EXACT []
synonym: "generic E box motif" EXACT []
synonym: "NDM5" RELATED []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001159
name: DMv5_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576\:16827941]
synonym: "directional motif v5" EXACT []
synonym: "DMv5" EXACT []
synonym: "DMv5 motif" EXACT []
synonym: "KTYRGTATWTTT" NARROW []
synonym: "promoter motif 6" RELATED []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001160
name: DMv3_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576\:16827941]
synonym: "directional motif v3" EXACT []
synonym: "DMv3" EXACT []
synonym: "DMv3 motif" EXACT []
synonym: "KNNCAKCNCTRNY" NARROW []
synonym: "promoter motif 7" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001161
name: DMv2_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576\:16827941]
synonym: "directional motif v2" EXACT []
synonym: "DMv2" EXACT []
synonym: "DMv2 motif" EXACT []
synonym: "MKSYGGCARCGSYSS" NARROW []
synonym: "promoter motif 8" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001162
name: MTE
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576\:15231738, PMID:16858867]
synonym: "CSARCSSAACGS" NARROW []
synonym: "motif ten element" EXACT []
synonym: "motif_ten_element" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter

[Term]
id: SO:0001163
name: INR1_motif
def: "A promoter motif with consensus sequence TCATTCG." [PMID:16827941]
synonym: "directional motif p3" EXACT []
synonym: "directional promoter motif 3" EXACT []
synonym: "DMp3" EXACT []
synonym: "INR1 motif" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001164
name: DPE1_motif
def: "A promoter motif with consensus sequence CGGACGT." [PMID:16827941]
synonym: "directional motif 5" EXACT []
synonym: "directional promoter motif 5" RELATED []
synonym: "DMp5" EXACT []
synonym: "DPE1 motif" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001165
name: DMv1_motif
def: "A promoter motif with consensus sequence CARCCCT." [PMID:16827941]
synonym: "directional promoter motif v1" RELATED []
synonym: "DMv1" RELATED []
synonym: "DMv1 motif" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001166
name: GAGA_motif
def: "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]
synonym: "GAGA" EXACT []
synonym: "GAGA motif" EXACT []
synonym: "NDM1" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001167
name: NDM2_motif
def: "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]
synonym: "NDM2" EXACT []
synonym: "NDM2 motif" EXACT []
synonym: "non directional promoter motif 2" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001168
name: NDM3_motif
def: "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]
synonym: "NDM3" EXACT []
synonym: "NDM3 motif" EXACT []
synonym: "non directional motif 3" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001169
name: ds_RNA_viral_sequence
def: "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]
synonym: "double stranded RNA virus sequence" EXACT []
synonym: "ds RNA viral sequence" EXACT []
is_a: SO:0001041 ! viral_sequence

[Term]
id: SO:0001170
name: polinton
def: "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]
synonym: "maverick element" RELATED []
is_a: SO:0000208 ! terminal_inverted_repeat_element

[Term]
id: SO:0001171
name: rRNA_21S
def: "A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]
synonym: "21S LSU rRNA" EXACT []
synonym: "21S ribosomal RNA" EXACT []
synonym: "21S rRNA" EXACT []
synonym: "rRNA 21S" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0001172
name: tRNA_region
def: "A region of a tRNA." [RSC:cb]
synonym: "tRNA region" EXACT []
is_a: SO:0000834 ! mature_transcript_region
relationship: part_of SO:0000253 ! tRNA

[Term]
id: SO:0001173
name: anticodon_loop
def: "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]
synonym: "anti-codon loop" EXACT []
synonym: "anticodon loop" EXACT []
is_a: SO:0001172 ! tRNA_region

[Term]
id: SO:0001174
name: anticodon
def: "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]
synonym: "anti-codon" EXACT []
xref: http://en.wikipedia.org/wiki/Anticodon "wiki"
is_a: SO:0001172 ! tRNA_region
relationship: part_of SO:0001173 ! anticodon_loop

[Term]
id: SO:0001175
name: CCA_tail
def: "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]
synonym: "CCA sequence" EXACT []
synonym: "CCA tail" EXACT []
is_a: SO:0001172 ! tRNA_region

[Term]
id: SO:0001176
name: DHU_loop
def: "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]
synonym: "D loop" RELATED []
synonym: "DHU loop" EXACT []
is_a: SO:0001172 ! tRNA_region

[Term]
id: SO:0001177
name: T_loop
def: "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]
synonym: "T loop" EXACT []
synonym: "TpsiC loop" EXACT []
is_a: SO:0001172 ! tRNA_region

[Term]
id: SO:0001178
name: pyrrolysine_tRNA_primary_transcript
def: "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]
synonym: "pyrrolysine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0001179
name: U3_snoRNA
def: "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]
comment: The definition is most of the old definition for snoRNA (SO:0000275).
synonym: "small nucleolar RNA U3" EXACT []
synonym: "snoRNA U3" EXACT []
synonym: "U3 small nucleolar RNA" EXACT []
synonym: "U3 snoRNA" EXACT []
xref: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3 "wiki"
is_a: SO:0000593 ! C_D_box_snoRNA

[Term]
id: SO:0001180
name: AU_rich_element
def: "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]
synonym: "ARE" RELATED []
synonym: "AU rich element" EXACT []
synonym: "AU-rich element" EXACT []
xref: http://en.wikipedia.org/wiki/AU-rich_element "wiki"
is_a: SO:0000837 ! UTR_region
relationship: part_of SO:0000205 ! three_prime_UTR

[Term]
id: SO:0001181
name: Bruno_response_element
def: "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]
comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.
synonym: "BRE" RELATED []
synonym: "Bruno response element" EXACT []
is_a: SO:0000837 ! UTR_region
relationship: part_of SO:0000205 ! three_prime_UTR

[Term]
id: SO:0001182
name: iron_responsive_element
def: "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]
synonym: "IRE" EXACT []
synonym: "iron responsive element" EXACT []
xref: http://en.wikipedia.org/wiki/Iron_responsive_element "wiki"
is_a: SO:0000837 ! UTR_region
relationship: part_of SO:0000203 ! UTR

[Term]
id: SO:0001183
name: morpholino_backbone
def: "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb]
comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.
synonym: "morpholino backbone" EXACT []
xref: http://en.wikipedia.org/wiki/Morpholino "wiki"
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0001184
name: PNA
def: "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb]
comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.
synonym: "peptide nucleic acid" RELATED []
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0001185
name: enzymatic
def: "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]
comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0001186
name: ribozymic
def: "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb]
comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.
is_a: SO:0001185 ! enzymatic

[Term]
id: SO:0001187
name: pseudouridylation_guide_snoRNA
def: "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]
comment: Has RNA pseudouridylation guide activity (GO:0030558).
synonym: "pseudouridylation guide snoRNA" EXACT []
is_a: SO:0000594 ! H_ACA_box_snoRNA

[Term]
id: SO:0001188
name: LNA
def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010]
comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0001189
name: LNA_oligo
def: "An oligo composed of LNA residues." [RSC:cb]
synonym: "LNA oligo" EXACT []
synonym: "locked nucleic acid" EXACT []
xref: http://en.wikipedia.org/wiki/Locked_nucleic_acid "wiki"
is_a: SO:0001247 ! synthetic_oligo
intersection_of: SO:0001247 ! synthetic_oligo
intersection_of: has_quality SO:0001188 ! LNA
relationship: has_quality SO:0001188 ! LNA

[Term]
id: SO:0001190
name: TNA
def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019]
comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0001191
name: TNA_oligo
def: "An oligo composed of TNA residues." [RSC:cb]
synonym: "threose nucleic acid" EXACT []
synonym: "TNA oligo" EXACT []
xref: http://en.wikipedia.org/wiki/Threose_nucleic_acid "wiki"
is_a: SO:0001247 ! synthetic_oligo
intersection_of: SO:0001247 ! synthetic_oligo
intersection_of: has_quality SO:0001190 ! TNA
relationship: has_quality SO:0001190 ! TNA

[Term]
id: SO:0001192
name: GNA
def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]
comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0001193
name: GNA_oligo
def: "An oligo composed of GNA residues." [RSC:cb]
synonym: "glycerol nucleic acid" EXACT []
synonym: "glycol nucleic acid" EXACT []
synonym: "GNA oligo" EXACT []
xref: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid "wiki"
is_a: SO:0001247 ! synthetic_oligo
intersection_of: SO:0001247 ! synthetic_oligo
intersection_of: has_quality SO:0001192 ! GNA
relationship: has_quality SO:0001192 ! GNA

[Term]
id: SO:0001194
name: R_GNA
def: "An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]
comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.
synonym: "R GNA" EXACT []
is_a: SO:0001192 ! GNA

[Term]
id: SO:0001195
name: R_GNA_oligo
def: "An oligo composed of (R)-GNA residues." [RSC:cb]
synonym: "(R)-glycerol nucleic acid" EXACT []
synonym: "(R)-glycol nucleic acid" EXACT []
synonym: "R GNA oligo" EXACT []
is_a: SO:0001193 ! GNA_oligo
intersection_of: SO:0001193 ! GNA_oligo
intersection_of: has_quality SO:0001194 ! R_GNA
relationship: has_quality SO:0001194 ! R_GNA

[Term]
id: SO:0001196
name: S_GNA
def: "An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]
comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.
synonym: "S GNA" EXACT []
is_a: SO:0001192 ! GNA

[Term]
id: SO:0001197
name: S_GNA_oligo
def: "An oligo composed of (S)-GNA residues." [RSC:cb]
synonym: "(S)-glycerol nucleic acid" EXACT []
synonym: "(S)-glycol nucleic acid" EXACT []
synonym: "S GNA oligo" EXACT []
is_a: SO:0001193 ! GNA_oligo
intersection_of: SO:0001193 ! GNA_oligo
intersection_of: has_quality SO:0001196 ! S_GNA
relationship: has_quality SO:0001196 ! S_GNA

[Term]
id: SO:0001198
name: ds_DNA_viral_sequence
def: "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]
synonym: "double stranded DNA virus" EXACT []
synonym: "ds DNA viral sequence" EXACT []
is_a: SO:0001041 ! viral_sequence

[Term]
id: SO:0001199
name: ss_RNA_viral_sequence
def: "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]
synonym: "single strand RNA virus" EXACT []
synonym: "ss RNA viral sequence" EXACT []
is_a: SO:0001041 ! viral_sequence

[Term]
id: SO:0001200
name: negative_sense_ssRNA_viral_sequence
def: "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]
synonym: "negative sense single stranded RNA virus" RELATED []
synonym: "negative sense ssRNA viral sequence" EXACT []
is_a: SO:0001199 ! ss_RNA_viral_sequence

[Term]
id: SO:0001201
name: positive_sense_ssRNA_viral_sequence
def: "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]
synonym: "positive sense single stranded RNA virus" RELATED []
synonym: "positive sense ssRNA viral sequence" EXACT []
is_a: SO:0001199 ! ss_RNA_viral_sequence

[Term]
id: SO:0001202
name: ambisense_ssRNA_viral_sequence
def: "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]
synonym: "ambisense single stranded RNA virus" EXACT []
synonym: "ambisense ssRNA viral sequence" EXACT []
is_a: SO:0001199 ! ss_RNA_viral_sequence

[Term]
id: SO:0001203
name: RNA_polymerase_promoter
def: "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]
synonym: "RNA polymerase promoter" EXACT []
is_a: SO:0000167 ! promoter

[Term]
id: SO:0001204
name: Phage_RNA_Polymerase_Promoter
def: "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]
synonym: "Phage RNA Polymerase Promoter" EXACT []
is_a: SO:0001203 ! RNA_polymerase_promoter

[Term]
id: SO:0001205
name: SP6_RNA_Polymerase_Promoter
def: "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]
synonym: "SP6 RNA Polymerase Promoter" EXACT []
is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter

[Term]
id: SO:0001206
name: T3_RNA_Polymerase_Promoter
def: "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]
synonym: "T3 RNA Polymerase Promoter" EXACT []
is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter

[Term]
id: SO:0001207
name: T7_RNA_Polymerase_Promoter
def: "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]
synonym: "T7 RNA Polymerase Promoter" EXACT []
is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter

[Term]
id: SO:0001208
name: five_prime_EST
def: "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]
synonym: "5' EST" EXACT []
synonym: "five prime EST" EXACT []
is_a: SO:0000345 ! EST

[Term]
id: SO:0001209
name: three_prime_EST
def: "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]
synonym: "3' EST" EXACT []
synonym: "three prime EST" EXACT []
is_a: SO:0000345 ! EST

[Term]
id: SO:0001210
name: translational_frameshift
def: "The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]
synonym: "ribosomal frameshift" EXACT []
synonym: "translational frameshift" EXACT []
xref: http://en.wikipedia.org/wiki/Translational_frameshift "wiki"
is_a: SO:0000836 ! mRNA_region

[Term]
id: SO:0001211
name: plus_1_translational_frameshift
def: "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]
synonym: "plus 1 ribosomal frameshift" EXACT []
synonym: "plus 1 translational frameshift" EXACT []
is_a: SO:0001210 ! translational_frameshift

[Term]
id: SO:0001212
name: plus_2_translational_frameshift
def: "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]
synonym: "plus 2 ribosomal frameshift" EXACT []
synonym: "plus 2 translational frameshift" EXACT []
is_a: SO:0001210 ! translational_frameshift

[Term]
id: SO:0001213
name: group_III_intron
def: "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]
comment: GO:0000374.
synonym: "group III intron" EXACT []
xref: http://en.wikipedia.org/wiki/Group_III_intron "wiki"
is_a: SO:0000588 ! autocatalytically_spliced_intron

[Term]
id: SO:0001214
name: noncoding_region_of_exon
def: "The maximal intersection of exon and UTR." [SO:ke]
comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.
subset: SOFA
synonym: "noncoding region of exon" EXACT []
is_a: SO:0000852 ! exon_region

[Term]
id: SO:0001215
name: coding_region_of_exon
def: "The region of an exon that encodes for protein sequence." [SO:ke]
comment: An exon containing either a start or stop codon will be partially coding and partially non coding.
subset: SOFA
synonym: "coding region of exon" EXACT []
is_a: SO:0000852 ! exon_region

[Term]
id: SO:0001216
name: endonuclease_spliced_intron
def: "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]
synonym: "endonuclease spliced intron" EXACT []
is_a: SO:0000188 ! intron

[Term]
id: SO:0001217
name: protein_coding_gene
synonym: "protein coding gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000010 ! protein_coding
relationship: has_quality SO:0000010 ! protein_coding

[Term]
id: SO:0001218
name: transgenic_insertion
def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]
synonym: "transgenic insertion" EXACT []
is_a: SO:0000667 ! insertion
intersection_of: SO:0000667 ! insertion
intersection_of: has_quality SO:0000781 ! transgenic
relationship: has_quality SO:0000781 ! transgenic

[Term]
id: SO:0001219
name: retrogene
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000569 ! retrotransposed
relationship: has_quality SO:0000569 ! retrotransposed

[Term]
id: SO:0001220
name: silenced_by_RNA_interference
def: "An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]
comment: RNA interference is GO:0016246.
synonym: "silenced by RNA interference" EXACT []
is_a: SO:0000893 ! silenced

[Term]
id: SO:0001221
name: silenced_by_histone_modification
def: "An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]
comment: Histone modification is GO:0016570.
synonym: "silenced by histone modification" EXACT []
is_a: SO:0000893 ! silenced

[Term]
id: SO:0001222
name: silenced_by_histone_methylation
def: "An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]
comment: Histone methylation is GO:0016571.
synonym: "silenced by histone methylation" EXACT []
is_a: SO:0001221 ! silenced_by_histone_modification

[Term]
id: SO:0001223
name: silenced_by_histone_deacetylation
def: "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]
comment: Histone deacetylation is GO:0016573.
synonym: "silenced by histone deacetylation" EXACT []
is_a: SO:0001221 ! silenced_by_histone_modification

[Term]
id: SO:0001224
name: gene_silenced_by_RNA_interference
def: "A gene that is silenced by RNA interference." [SO:xp]
synonym: "gene silenced by RNA interference" EXACT []
synonym: "RNA interference silenced gene" EXACT []
synonym: "RNAi silenced gene" EXACT []
is_a: SO:0000127 ! silenced_gene
intersection_of: SO:0000127 ! silenced_gene
intersection_of: has_quality SO:0001220 ! silenced_by_RNA_interference
relationship: has_quality SO:0001220 ! silenced_by_RNA_interference

[Term]
id: SO:0001225
name: gene_silenced_by_histone_modification
def: "A gene that is silenced by histone modification." [SO:xp]
synonym: "gene silenced by histone modification" EXACT []
is_a: SO:0000127 ! silenced_gene
intersection_of: SO:0000127 ! silenced_gene
intersection_of: has_quality SO:0001221 ! silenced_by_histone_modification
relationship: has_quality SO:0001221 ! silenced_by_histone_modification

[Term]
id: SO:0001226
name: gene_silenced_by_histone_methylation
def: "A gene that is silenced by histone methylation." [SO:xp]
synonym: "gene silenced by histone methylation" EXACT []
is_a: SO:0001225 ! gene_silenced_by_histone_modification
intersection_of: SO:0001225 ! gene_silenced_by_histone_modification
intersection_of: has_quality SO:0001222 ! silenced_by_histone_methylation
relationship: has_quality SO:0001222 ! silenced_by_histone_methylation

[Term]
id: SO:0001227
name: gene_silenced_by_histone_deacetylation
def: "A gene that is silenced by histone deacetylation." [SO:xp]
synonym: "gene silenced by histone deacetylation" EXACT []
is_a: SO:0001225 ! gene_silenced_by_histone_modification
intersection_of: SO:0001225 ! gene_silenced_by_histone_modification
intersection_of: has_quality SO:0001223 ! silenced_by_histone_deacetylation
relationship: has_quality SO:0001223 ! silenced_by_histone_deacetylation

[Term]
id: SO:0001228
name: dihydrouridine
def: "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]
synonym: " D" EXACT RNAMOD []
xref: http://en.wikipedia.org/wiki/Dihydrouridine "wiki"
xref: RNAMOD:051
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001229
name: pseudouridine
def: "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]
comment: The free molecule is CHEBI:17802.
synonym: " Y" EXACT RNAMOD []
xref: http://en.wikipedia.org/wiki/Pseudouridine "wiki"
xref: RNAMOD:050
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001230
name: inosine
def: "A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]
comment: The free molecule is CHEBI:17596.
synonym: "I" RELATED []
synonym: "RNAMOD:017" RELATED []
xref: http://en.wikipedia.org/wiki/Inosine "wiki"
is_a: SO:0000250 ! modified_RNA_base_feature

[Term]
id: SO:0001231
name: seven_methylguanine
def: "A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]
comment: The free molecule is CHEBI:2274.
synonym: "7-methylguanine" EXACT []
synonym: "seven methylguanine" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature

[Term]
id: SO:0001232
name: ribothymidine
def: "A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]
comment: The free molecule is CHEBI:30832.
is_a: SO:0000250 ! modified_RNA_base_feature

[Term]
id: SO:0001233
name: methylinosine
def: "A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]
is_a: SO:0001274 ! modified_inosine

[Term]
id: SO:0001234
name: mobile
def: "An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb]
xref: http://en.wikipedia.org/wiki/Mobile "wiki"
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0001235
name: replicon
def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0001236
name: base
def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Nucleobase "wiki"
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0001237
name: amino_acid
def: "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]
comment: Probably in the future this will cross reference to Chebi.
synonym: "amino acid" EXACT []
xref: http://en.wikipedia.org/wiki/Amino_acid "wiki"
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0001238
name: major_TSS
synonym: "major transcription start site" EXACT []
synonym: "major TSS" EXACT []
is_a: SO:0000315 ! TSS

[Term]
id: SO:0001239
name: minor_TSS
synonym: "minor TSS" EXACT []
is_a: SO:0000315 ! TSS

[Term]
id: SO:0001240
name: TSS_region
def: "The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]
synonym: "TSS region" EXACT []
is_a: SO:0000842 ! gene_component_region
relationship: has_part SO:0000315 ! TSS

[Term]
id: SO:0001241
name: encodes_alternate_transcription_start_sites
synonym: "encodes alternate transcription start sites" EXACT []
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0001243
name: miRNA_primary_transcript_region
def: "A part of an miRNA primary_transcript." [SO:ke]
synonym: "miRNA primary transcript region" EXACT []
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0001244
name: pre_miRNA
def: "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]
synonym: "pre-miRNA" EXACT []
is_a: SO:0001243 ! miRNA_primary_transcript_region

[Term]
id: SO:0001245
name: miRNA_stem
def: "The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]
synonym: "miRNA stem" EXACT []
is_a: SO:0001243 ! miRNA_primary_transcript_region
relationship: part_of SO:0001244 ! pre_miRNA

[Term]
id: SO:0001246
name: miRNA_loop
def: "The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]
synonym: "miRNA loop" EXACT []
is_a: SO:0001243 ! miRNA_primary_transcript_region
relationship: part_of SO:0001244 ! pre_miRNA

[Term]
id: SO:0001247
name: synthetic_oligo
def: "An oligo composed of synthetic nucleotides." [SO:ke]
synonym: "synthetic oligo" EXACT []
is_a: SO:0000696 ! oligo

[Term]
id: SO:0001248
name: assembly
def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki"
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0001249
name: fragment_assembly
def: "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]
synonym: "fragment assembly" EXACT []
synonym: "physical map" EXACT []
is_a: SO:0001248 ! assembly

[Term]
id: SO:0001250
name: fingerprint_map
def: "A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]
synonym: "BACmap" EXACT []
synonym: "fingerprint map" EXACT []
synonym: "FPC" EXACT []
synonym: "FPCmap" EXACT []
synonym: "restriction map" EXACT []
is_a: SO:0001249 ! fragment_assembly
relationship: has_part SO:0000412 ! restriction_fragment

[Term]
id: SO:0001251
name: STS_map
def: "An STS map is a physical map organized by the unique STS landmarks." [SO:ke]
synonym: "STS map" EXACT []
is_a: SO:0001249 ! fragment_assembly
relationship: has_part SO:0000331 ! STS

[Term]
id: SO:0001252
name: RH_map
def: "A radiation hybrid map is a physical map." [SO:ke]
synonym: "radiation hybrid map" EXACT []
synonym: "RH map" EXACT []
is_a: SO:0001249 ! fragment_assembly
relationship: has_part SO:0000331 ! STS

[Term]
id: SO:0001253
name: sonicate_fragment
def: "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke]
synonym: "sonicate fragment" EXACT []
is_a: SO:0000143 ! assembly_component

[Term]
id: SO:0001254
name: polyploid
def: "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]
xref: http://en.wikipedia.org/wiki/Polyploid "wiki"
is_a: SO:1000182 ! chromosome_number_variation

[Term]
id: SO:0001255
name: autopolyploid
def: "A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]
xref: http://en.wikipedia.org/wiki/Autopolyploid "wiki"
is_a: SO:0001254 ! polyploid

[Term]
id: SO:0001256
name: allopolyploid
def: "A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]
xref: http://en.wikipedia.org/wiki/Allopolyploid "wiki"
is_a: SO:0001254 ! polyploid

[Term]
id: SO:0001257
name: homing_endonuclease_binding_site
def: "The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]
synonym: "homing endonuclease binding site" EXACT []
is_a: SO:0000059 ! nuclease_binding_site

[Term]
id: SO:0001258
name: octamer_motif
def: "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]
comment: Nature. 1986 Oct 16-22;323(6089):640-3.
synonym: "octamer motif" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0001259
name: apicoplast_chromosome
def: "A chromosome originating in an apicoplast." [SO:xp]
synonym: "apicoplast chromosome" EXACT []
is_a: SO:0000340 ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000743 ! apicoplast_sequence
relationship: has_origin SO:0000743 ! apicoplast_sequence

[Term]
id: SO:0001260
name: sequence_collection
def: "A collection of discontinuous sequences." [SO:ke]
synonym: "sequence collection" EXACT []

[Term]
id: SO:0001261
name: overlapping_feature_set
def: "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]
comment: This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA.
synonym: "overlapping feature set" EXACT []
is_a: SO:0000703 ! experimental_result_region

[Term]
id: SO:0001262
name: overlapping_EST_set
def: "A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]
synonym: "overlapping EST set" EXACT []
is_a: SO:0001261 ! overlapping_feature_set
relationship: has_part SO:0000345 ! EST

[Term]
id: SO:0001263
name: ncRNA_gene
synonym: "ncRNA gen" EXACT []
synonym: "ncRNA gene" EXACT []
synonym: "non-coding RNA gene" RELATED []
is_a: SO:0000704 ! gene

[Term]
id: SO:0001264
name: gRNA_gene
synonym: "gRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
intersection_of: SO:0001263 ! ncRNA_gene
intersection_of: has_quality SO:0000979 ! gRNA_encoding
relationship: has_quality SO:0000979 ! gRNA_encoding

[Term]
id: SO:0001265
name: miRNA_gene
alt_id: SO:0001270
synonym: "miRNA gene" EXACT []
synonym: "stRNA gene" EXACT []
synonym: "stRNA_gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
intersection_of: SO:0001263 ! ncRNA_gene
intersection_of: has_quality SO:0000571 ! miRNA_encoding
intersection_of: has_quality SO:0000656 ! stRNA_encoding
relationship: has_quality SO:0000571 ! miRNA_encoding
relationship: has_quality SO:0000656 ! stRNA_encoding

[Term]
id: SO:0001266
name: scRNA_gene
synonym: "scRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
intersection_of: SO:0001263 ! ncRNA_gene
intersection_of: has_quality SO:0000575 ! scRNA_encoding
relationship: has_quality SO:0000575 ! scRNA_encoding

[Term]
id: SO:0001267
name: snoRNA_gene
synonym: "snoRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
intersection_of: SO:0001263 ! ncRNA_gene
intersection_of: has_quality SO:0000578 ! snoRNA_encoding
relationship: has_quality SO:0000578 ! snoRNA_encoding

[Term]
id: SO:0001268
name: snRNA_gene
synonym: "snRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
intersection_of: SO:0001263 ! ncRNA_gene
intersection_of: has_quality SO:0001263 ! ncRNA_gene
relationship: has_quality SO:0001263 ! ncRNA_gene

[Term]
id: SO:0001269
name: SRP_RNA_gene
synonym: "SRP RNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
intersection_of: SO:0001263 ! ncRNA_gene
intersection_of: has_quality SO:0000642 ! SRP_RNA_encoding
relationship: has_quality SO:0000642 ! SRP_RNA_encoding

[Term]
id: SO:0001271
name: tmRNA_gene
synonym: "tmRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
intersection_of: SO:0001263 ! ncRNA_gene
intersection_of: has_quality SO:0000659 ! tmRNA_encoding
relationship: has_quality SO:0000659 ! tmRNA_encoding

[Term]
id: SO:0001272
name: tRNA_gene
synonym: "tRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
intersection_of: SO:0001263 ! ncRNA_gene
intersection_of: has_quality SO:0000663 ! tRNA_encoding
relationship: has_quality SO:0000663 ! tRNA_encoding

[Term]
id: SO:0001273
name: modified_adenosine
def: "A modified adenine is an adenine base feature that has been altered." [SO:ke]
synonym: "modified adenosine" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature

[Term]
id: SO:0001274
name: modified_inosine
def: "A modified inosine is an inosine base feature that has been altered." [SO:ke]
synonym: "modified inosine" EXACT []
is_a: SO:0001230 ! inosine

[Term]
id: SO:0001275
name: modified_cytidine
def: "A modified cytidine is a cytidine base feature which has been altered." [SO:ke]
synonym: "modified cytidine" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature

[Term]
id: SO:0001276
name: modified_guanosine
synonym: "modified guanosine" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature

[Term]
id: SO:0001277
name: modified_uridine
synonym: "modified uridine" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature

[Term]
id: SO:0001278
name: one_methylinosine
def: "1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
synonym: "1-methylinosine" EXACT []
synonym: "m1I" EXACT RNAMOD []
synonym: "one methylinosine" EXACT []
xref: RNAMOD:018
is_a: SO:0001274 ! modified_inosine

[Term]
id: SO:0001279
name: one_two_prime_O_dimethylinosine
def: "1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
synonym: "1,2'-O-dimethylinosine" EXACT []
synonym: "m'Im" EXACT RNAMOD []
synonym: "one two prime O dimethylinosine" EXACT []
xref: RNAMOD:019
is_a: SO:0001274 ! modified_inosine

[Term]
id: SO:0001280
name: two_prime_O_methylinosine
def: "2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methylinosine" EXACT []
synonym: "Im" EXACT RNAMOD []
synonym: "two prime O methylinosine" EXACT []
xref: RNAMOD:081
is_a: SO:0001274 ! modified_inosine

[Term]
id: SO:0001281
name: three_methylcytidine
def: "3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "3-methylcytidine" EXACT []
synonym: "m3C" EXACT RNAMOD []
synonym: "three methylcytidine" EXACT []
xref: RNAMOD:020
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001282
name: five_methylcytidine
def: "5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methylcytidine" EXACT []
synonym: "five methylcytidine" EXACT []
synonym: "m5C" EXACT RNAMOD []
xref: RNAMOD:021
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001283
name: two_prime_O_methylcytidine
def: "2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methylcytidine" EXACT []
synonym: "Cm" EXACT RNAMOD []
synonym: "two prime O methylcytidine" EXACT []
xref: RNAMOD:022
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001284
name: two_thiocytidine
def: "2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-thiocytidine" EXACT []
synonym: "s2C" EXACT RNAMOD []
synonym: "two thiocytidine" EXACT []
xref: RNAMOD:023
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001285
name: N4_acetylcytidine
def: "N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "ac4C" EXACT RNAMOD []
synonym: "N4 acetylcytidine" EXACT []
synonym: "N4-acetylcytidine" EXACT []
xref: RNAMOD:024
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001286
name: five_formylcytidine
def: "5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "5-formylcytidine" EXACT []
synonym: "f5C" EXACT RNAMOD []
synonym: "five formylcytidine" EXACT []
xref: RNAMOD:025
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001287
name: five_two_prime_O_dimethylcytidine
def: "5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "5,2'-O-dimethylcytidine" EXACT []
synonym: "five two prime O dimethylcytidine" EXACT []
synonym: "m5Cm" EXACT RNAMOD []
xref: RNAMOD:026
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001288
name: N4_acetyl_2_prime_O_methylcytidine
def: "N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "ac4Cm" EXACT RNAMOD []
synonym: "N4 acetyl 2 prime O methylcytidine" EXACT []
synonym: "N4-acetyl-2'-O-methylcytidine" EXACT []
xref: RNAMOD:027
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001289
name: lysidine
def: "Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "k2C" EXACT RNAMOD []
xref: http://en.wikipedia.org/wiki/Lysidine "wiki"
xref: RNAMOD:028
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001290
name: N4_methylcytidine
def: "N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "m4C" EXACT RNAMOD []
synonym: "N4 methylcytidine" EXACT []
synonym: "N4-methylcytidine" EXACT []
xref: RNAMOD:082
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001291
name: N4_2_prime_O_dimethylcytidine
def: "N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "m4Cm" EXACT RNAMOD []
synonym: "N4 2 prime O dimethylcytidine" EXACT []
synonym: "N4,2'-O-dimethylcytidine" EXACT []
xref: RNAMOD:083
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001292
name: five_hydroxymethylcytidine
def: "5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "5-hydroxymethylcytidine" EXACT []
synonym: "five hydroxymethylcytidine" EXACT []
synonym: "hm5C" EXACT RNAMOD []
xref: RNAMOD:084
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001293
name: five_formyl_two_prime_O_methylcytidine
def: "5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "5-formyl-2'-O-methylcytidine" EXACT []
synonym: "f5Cm" EXACT RNAMOD []
synonym: "five formyl two prime O methylcytidine" EXACT []
xref: RNAMOD:095
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001294
name: N4_N4_2_prime_O_trimethylcytidine
def: "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "m42Cm" EXACT RNAMOD []
synonym: "N4,N4,2'-O-trimethylcytidine" EXACT []
xref: RNAMOD:107
is_a: SO:0001275 ! modified_cytidine

[Term]
id: SO:0001295
name: one_methyladenosine
def: "1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "1-methyladenosine" EXACT []
synonym: "m1A" EXACT RNAMOD []
synonym: "one methyladenosine" EXACT []
xref: RNAMOD:001
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001296
name: two_methyladenosine
def: "2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methyladenosine" EXACT []
synonym: "m2A" EXACT RNAMOD []
synonym: "two methyladenosine" EXACT []
xref: RNAMOD:002
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001297
name: N6_methyladenosine
def: "N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "m6A" EXACT RNAMOD []
synonym: "N6 methyladenosine" EXACT []
synonym: "N6-methyladenosine" EXACT []
xref: RNAMOD:003
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001298
name: two_prime_O_methyladenosine
def: "2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methyladenosine" EXACT []
synonym: "Am" EXACT RNAMOD []
synonym: "two prime O methyladenosine" EXACT []
xref: RNAMOD:004
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001299
name: two_methylthio_N6_methyladenosine
def: "2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methylthio-N6-methyladenosine" EXACT []
synonym: "ms2m6A" EXACT RNAMOD []
synonym: "two methylthio N6 methyladenosine" EXACT []
xref: RNAMOD:005
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001300
name: N6_isopentenyladenosine
def: "N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "i6A" EXACT RNAMOD []
synonym: "N6 isopentenyladenosine" EXACT []
synonym: "N6-isopentenyladenosine" EXACT []
xref: RNAMOD:006
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001301
name: two_methylthio_N6_isopentenyladenosine
def: "2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methylthio-N6-isopentenyladenosine" EXACT []
synonym: "ms2i6A" EXACT RNAMOD []
synonym: "two methylthio N6 isopentenyladenosine" EXACT []
xref: RNAMOD:007
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001302
name: N6_cis_hydroxyisopentenyl_adenosine
def: "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "io6A" EXACT RNAMOD []
synonym: "N6 cis hydroxyisopentenyl adenosine" EXACT []
synonym: "N6-(cis-hydroxyisopentenyl)adenosine" EXACT []
xref: RNAMOD:008
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001303
name: two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
def: "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine" EXACT []
synonym: "ms2io6A" EXACT RNAMOD []
synonym: "two methylthio N6 cis hydroxyisopentenyl adenosine" EXACT []
xref: RNAMOD:009
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001304
name: N6_glycinylcarbamoyladenosine
def: "N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "g6A" EXACT RNAMOD []
synonym: "N6 glycinylcarbamoyladenosine" EXACT []
synonym: "N6-glycinylcarbamoyladenosine" EXACT []
xref: RNAMOD:010
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001305
name: N6_threonylcarbamoyladenosine
def: "N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "N6 threonylcarbamoyladenosine" EXACT []
synonym: "N6-threonylcarbamoyladenosine" EXACT []
synonym: "t6A" EXACT RNAMOD []
xref: RNAMOD:011
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001306
name: two_methylthio_N6_threonyl_carbamoyladenosine
def: "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methylthio-N6-threonyl carbamoyladenosine" EXACT []
synonym: "ms2t6A" EXACT RNAMOD []
synonym: "two methylthio N6 threonyl carbamoyladenosine" EXACT []
xref: RNAMOD:012
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001307
name: N6_methyl_N6_threonylcarbamoyladenosine
def: "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "m6t6A" EXACT RNAMOD []
synonym: "N6 methyl N6 threonylcarbamoyladenosine" EXACT []
synonym: "N6-methyl-N6-threonylcarbamoyladenosine" EXACT []
xref: RNAMOD:013
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001308
name: N6_hydroxynorvalylcarbamoyladenosine
def: "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "hn6A" EXACT RNAMOD []
synonym: "N6 hydroxynorvalylcarbamoyladenosine" EXACT []
synonym: "N6-hydroxynorvalylcarbamoyladenosine" EXACT []
xref: RNAMOD:014
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001309
name: two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
def: "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methylthio-N6-hydroxynorvalyl carbamoyladenosine" EXACT []
synonym: "ms2hn6A" EXACT RNAMOD []
synonym: "two methylthio N6 hydroxynorvalyl carbamoyladenosine" EXACT []
xref: RNAMOD:015
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001310
name: two_prime_O_ribosyladenosine_phosphate
def: "2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-ribosyladenosine (phosphate)" EXACT []
synonym: "Ar(p)" EXACT RNAMOD []
synonym: "two prime O ribosyladenosine phosphate" EXACT []
xref: RNAMOD:016
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001311
name: N6_N6_dimethyladenosine
def: "N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "m62A" EXACT RNAMOD []
synonym: "N6,N6-dimethyladenosine" EXACT []
xref: RNAMOD:080
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001312
name: N6_2_prime_O_dimethyladenosine
def: "N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "m6Am" EXACT RNAMOD []
synonym: "N6 2 prime O dimethyladenosine" EXACT []
synonym: "N6,2'-O-dimethyladenosine" EXACT []
xref: RNAMOD:088
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001313
name: N6_N6_2_prime_O_trimethyladenosine
def: "N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "m62Am" EXACT RNAMOD []
synonym: "N6,N6,2'-O-trimethyladenosine" EXACT []
xref: RNAMOD:089
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001314
name: one_two_prime_O_dimethyladenosine
def: "1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "1,2'-O-dimethyladenosine" EXACT []
synonym: "m1Am" EXACT RNAMOD []
synonym: "one two prime O dimethyladenosine" EXACT []
xref: RNAMOD:097
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001315
name: N6_acetyladenosine
def: "N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "ac6A" EXACT RNAMOD []
synonym: "N6 acetyladenosine" EXACT []
synonym: "N6-acetyladenosine" EXACT []
xref: RNAMOD:102
is_a: SO:0001273 ! modified_adenosine

[Term]
id: SO:0001316
name: seven_deazaguanosine
def: "7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "7-deazaguanosine" RELATED []
synonym: "seven deazaguanosine" EXACT []
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001317
name: queuosine
def: "Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: " Q" EXACT RNAMOD []
xref: http://en.wikipedia.org/wiki/Queuosine "wiki"
xref: RNAMOD:043
is_a: SO:0001316 ! seven_deazaguanosine

[Term]
id: SO:0001318
name: epoxyqueuosine
def: "Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "eQ" EXACT RNAMOD []
xref: RNAMOD:044
is_a: SO:0001316 ! seven_deazaguanosine

[Term]
id: SO:0001319
name: galactosyl_queuosine
def: "Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "galactosyl queuosine" EXACT []
synonym: "galactosyl-queuosine" EXACT []
synonym: "galQ" EXACT RNAMOD []
xref: RNAMOD:045
is_a: SO:0001316 ! seven_deazaguanosine

[Term]
id: SO:0001320
name: mannosyl_queuosine
def: "Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "mannosyl queuosine" EXACT []
synonym: "mannosyl-queuosine" EXACT []
synonym: "manQ" EXACT RNAMOD []
xref: RNAMOD:046
is_a: SO:0001316 ! seven_deazaguanosine

[Term]
id: SO:0001321
name: seven_cyano_seven_deazaguanosine
def: "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "7-cyano-7-deazaguanosine" EXACT []
synonym: "preQ0" EXACT RNAMOD []
synonym: "seven cyano seven deazaguanosine" EXACT []
xref: RNAMOD:047
is_a: SO:0001316 ! seven_deazaguanosine

[Term]
id: SO:0001322
name: seven_aminomethyl_seven_deazaguanosine
def: "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "7-aminomethyl-7-deazaguanosine" EXACT []
synonym: "preQ1" EXACT RNAMOD []
synonym: "seven aminomethyl seven deazaguanosine" EXACT []
xref: RNAMOD:048
is_a: SO:0001316 ! seven_deazaguanosine

[Term]
id: SO:0001323
name: archaeosine
def: "Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "G+" EXACT RNAMOD []
xref: RNAMOD:049
is_a: SO:0001316 ! seven_deazaguanosine

[Term]
id: SO:0001324
name: one_methylguanosine
def: "1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "1-methylguanosine" EXACT []
synonym: "m1G" EXACT RNAMOD []
synonym: "one methylguanosine" EXACT []
xref: RNAMOD:029
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001325
name: N2_methylguanosine
def: "N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m2G" EXACT RNAMOD []
synonym: "N2 methylguanosine" EXACT []
synonym: "N2-methylguanosine" EXACT []
xref: RNAMOD:030
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001326
name: seven_methylguanosine
def: "7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "7-methylguanosine" EXACT []
synonym: "m7G" EXACT RNAMOD []
synonym: "seven methylguanosine" EXACT []
xref: RNAMOD:031
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001327
name: two_prime_O_methylguanosine
def: "2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methylguanosine" EXACT []
synonym: "Gm" EXACT RNAMOD []
synonym: "two prime O methylguanosine" EXACT []
xref: RNAMOD:032
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001328
name: N2_N2_dimethylguanosine
def: "N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m22G" EXACT RNAMOD []
synonym: "N2,N2-dimethylguanosine" EXACT []
xref: RNAMOD:033
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001329
name: N2_2_prime_O_dimethylguanosine
def: "N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m2Gm" EXACT RNAMOD []
synonym: "N2 2 prime O dimethylguanosine" EXACT []
synonym: "N2,2'-O-dimethylguanosine" EXACT []
xref: RNAMOD:034
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001330
name: N2_N2_2_prime_O_trimethylguanosine
def: "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m22Gmv" EXACT RNAMOD []
synonym: "N2,N2,2'-O-trimethylguanosine" EXACT []
xref: RNAMOD:035
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001331
name: two_prime_O_ribosylguanosine_phosphate
def: "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-ribosylguanosine (phosphate)" EXACT []
synonym: "Gr(p)" EXACT RNAMOD []
synonym: "two prime O ribosylguanosine phosphate" EXACT []
xref: RNAMOD:036
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001332
name: wybutosine
def: "Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "yW" EXACT RNAMOD []
xref: RNAMOD:037
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001333
name: peroxywybutosine
def: "Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "o2yW" EXACT RNAMOD []
xref: RNAMOD:038
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001334
name: hydroxywybutosine
def: "Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "OHyW" EXACT RNAMOD []
xref: RNAMOD:039
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001335
name: undermodified_hydroxywybutosine
def: "Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "OHyW*" EXACT RNAMOD []
synonym: "undermodified hydroxywybutosine" EXACT []
xref: RNAMOD:040
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001336
name: wyosine
def: "Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "IMG" EXACT RNAMOD []
xref: RNAMOD:041
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001337
name: methylwyosine
def: "Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "mimG" EXACT RNAMOD []
xref: RNAMOD:042
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001338
name: N2_7_dimethylguanosine
def: "N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m2,7G" EXACT RNAMOD []
synonym: "N2 7 dimethylguanosine" EXACT []
synonym: "N2,7-dimethylguanosine" EXACT []
xref: RNAMOD:090
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001339
name: N2_N2_7_trimethylguanosine
def: "N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m2,2,7G" EXACT RNAMOD []
synonym: "N2,N2,7-trimethylguanosine" EXACT []
xref: RNAMOD:091
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001340
name: one_two_prime_O_dimethylguanosine
def: "1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "1,2'-O-dimethylguanosine" EXACT []
synonym: "m1Gm" EXACT RNAMOD []
synonym: "one two prime O dimethylguanosine" EXACT []
xref: RNAMOD:096
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001341
name: four_demethylwyosine
def: "4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "4-demethylwyosine" EXACT []
synonym: "four demethylwyosine" EXACT []
synonym: "imG-14" EXACT RNAMOD []
xref: RNAMOD:100
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001342
name: isowyosine
def: "Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "imG2" EXACT RNAMOD []
xref: RNAMOD:101
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001343
name: N2_7_2prirme_O_trimethylguanosine
def: "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m2,7Gm" EXACT RNAMOD []
synonym: "N2 7 2prirme O trimethylguanosine" EXACT []
synonym: "N2,7,2'-O-trimethylguanosine" EXACT []
xref: RNAMOD:106
is_a: SO:0001276 ! modified_guanosine

[Term]
id: SO:0001344
name: five_methyluridine
def: "5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methyluridine" EXACT []
synonym: "five methyluridine" EXACT []
synonym: "m5U" EXACT RNAMOD []
xref: http://en.wikipedia.org/wiki/5-methyluridine "wiki"
xref: RNAMOD:052
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001345
name: two_prime_O_methyluridine
def: "2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methyluridine" EXACT []
synonym: "two prime O methyluridine" EXACT []
synonym: "Um" EXACT RNAMOD []
xref: RNAMOD:053
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001346
name: five_two_prime_O_dimethyluridine
def: "5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5,2'-O-dimethyluridine" EXACT []
synonym: "five two prime O dimethyluridine" EXACT []
synonym: "m5Um" EXACT RNAMOD []
xref: RNAMOD:054
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001347
name: one_methylpseudouridine
def: "1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "1-methylpseudouridine" EXACT []
synonym: "m1Y" EXACT RNAMOD []
synonym: "one methylpseudouridine" EXACT []
xref: RNAMOD:055
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001348
name: two_prime_O_methylpseudouridine
def: "2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methylpseudouridine" EXACT []
synonym: "two prime O methylpseudouridine" EXACT []
synonym: "Ym" EXACT RNAMOD []
xref: RNAMOD:056
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001349
name: two_thiouridine
def: "2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2-thiouridine" EXACT []
synonym: "s2U" EXACT RNAMOD []
synonym: "two thiouridine" EXACT []
xref: RNAMOD:057
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001350
name: four_thiouridine
def: "4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "4-thiouridine" EXACT []
synonym: "four thiouridine" EXACT []
synonym: "s4U" EXACT RNAMOD []
xref: RNAMOD:058
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001351
name: five_methyl_2_thiouridine
def: "5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methyl-2-thiouridine" EXACT []
synonym: "five methyl 2 thiouridine" EXACT []
synonym: "m5s2U" EXACT RNAMOD []
xref: RNAMOD:059
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001352
name: two_thio_two_prime_O_methyluridine
def: "2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2-thio-2'-O-methyluridine" EXACT []
synonym: "s2Um" EXACT RNAMOD []
synonym: "two thio two prime O methyluridine" EXACT []
xref: RNAMOD:060
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001353
name: three_three_amino_three_carboxypropyl_uridine
def: "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "3-(3-amino-3-carboxypropyl)uridine" EXACT []
synonym: "acp3U" EXACT RNAMOD []
xref: RNAMOD:061
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001354
name: five_hydroxyuridine
def: "5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-hydroxyuridine" EXACT []
synonym: "five hydroxyuridine" EXACT []
synonym: "ho5U" EXACT RNAMOD []
xref: RNAMOD:060
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001355
name: five_methoxyuridine
def: "5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methoxyuridine" EXACT []
synonym: "five methoxyuridine" EXACT []
synonym: "mo5U" EXACT RNAMOD []
xref: RNAMOD:063
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001356
name: uridine_five_oxyacetic_acid
def: "Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "cmo5U" EXACT RNAMOD []
synonym: "uridine 5-oxyacetic acid" EXACT []
synonym: "uridine five oxyacetic acid" EXACT []
xref: RNAMOD:064
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001357
name: uridine_five_oxyacetic_acid_methyl_ester
def: "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "mcmo5U" EXACT RNAMOD []
synonym: "uridine 5-oxyacetic acid methyl ester" EXACT []
synonym: "uridine five oxyacetic acid methyl ester" EXACT []
xref: RNAMOD:065
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001358
name: five_carboxyhydroxymethyl_uridine
def: "5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-(carboxyhydroxymethyl)uridine" EXACT []
synonym: "chm5U" EXACT RNAMOD []
synonym: "five carboxyhydroxymethyl uridine" EXACT []
xref: RNAMOD:066
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001359
name: five_carboxyhydroxymethyl_uridine_methyl_ester
def: "5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-(carboxyhydroxymethyl)uridine methyl ester" EXACT []
synonym: "five carboxyhydroxymethyl uridine methyl ester" EXACT []
synonym: "mchm5U" EXACT RNAMOD []
xref: RNAMOD:067
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001360
name: five_methoxycarbonylmethyluridine
def: "Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methoxycarbonylmethyluridine" EXACT []
synonym: "five methoxycarbonylmethyluridine" EXACT []
synonym: "mcm5U" EXACT RNAMOD []
xref: RNAMOD:068
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001361
name: five_methoxycarbonylmethyl_two_prime_O_methyluridine
def: "Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methoxycarbonylmethyl-2'-O-methyluridine" EXACT []
synonym: "five methoxycarbonylmethyl two prime O methyluridine" EXACT []
synonym: "mcm5Um" EXACT RNAMOD []
xref: RNAMOD:069
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001362
name: five_methoxycarbonylmethyl_two_thiouridine
def: "5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methoxycarbonylmethyl-2-thiouridine" EXACT []
synonym: "five methoxycarbonylmethyl two thiouridine" EXACT []
synonym: "mcm5s2U" EXACT RNAMOD []
xref: RNAMOD:070
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001363
name: five_aminomethyl_two_thiouridine
def: "5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-aminomethyl-2-thiouridine" EXACT []
synonym: "five aminomethyl two thiouridine" EXACT []
synonym: "nm5s2U" EXACT RNAMOD []
xref: RNAMOD:071
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001364
name: five_methylaminomethyluridine
def: "5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methylaminomethyluridine" EXACT []
synonym: "five methylaminomethyluridine" EXACT []
synonym: "mnm5U" EXACT RNAMOD []
xref: RNAMOD:072
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001365
name: five_methylaminomethyl_two_thiouridine
def: "5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methylaminomethyl-2-thiouridine" EXACT []
synonym: "five methylaminomethyl two thiouridine" EXACT []
synonym: "mnm5s2U" EXACT RNAMOD []
xref: RNAMOD:073
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001366
name: five_methylaminomethyl_two_selenouridine
def: "5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methylaminomethyl-2-selenouridine" EXACT []
synonym: "five methylaminomethyl two selenouridine" EXACT []
synonym: "mnm5se2U" EXACT RNAMOD []
xref: RNAMOD:074
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001367
name: five_carbamoylmethyluridine
def: "5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carbamoylmethyluridine" EXACT []
synonym: "five carbamoylmethyluridine" EXACT []
synonym: "ncm5U" EXACT RNAMOD []
xref: RNAMOD:075
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001368
name: five_carbamoylmethyl_two_prime_O_methyluridine
def: "5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carbamoylmethyl-2'-O-methyluridine" EXACT []
synonym: "five carbamoylmethyl two prime O methyluridine" EXACT []
synonym: "ncm5Um" EXACT RNAMOD []
xref: RNAMOD:076
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001369
name: five_carboxymethylaminomethyluridine
def: "5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carboxymethylaminomethyluridine" EXACT []
synonym: "cmnm5U" EXACT RNAMOD []
synonym: "five carboxymethylaminomethyluridine" EXACT []
xref: RNAMOD:077
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001370
name: five_carboxymethylaminomethyl_two_prime_O_methyluridine
def: "5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carboxymethylaminomethyl- 2'-O-methyluridine" EXACT []
synonym: "cmnm5Um" EXACT RNAMOD []
synonym: "five carboxymethylaminomethyl two prime O methyluridine" EXACT []
xref: RNAMOD:078
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001371
name: five_carboxymethylaminomethyl_two_thiouridine
def: "5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carboxymethylaminomethyl-2-thiouridine" EXACT []
synonym: "cmnm5s2U" EXACT RNAMOD []
synonym: "five carboxymethylaminomethyl two thiouridine" EXACT []
xref: RNAMOD:079
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001372
name: three_methyluridine
def: "3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "3-methyluridine" EXACT []
synonym: "m3U" EXACT RNAMOD []
synonym: "three methyluridine" EXACT []
xref: RNAMOD:085
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001373
name: one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
def: "1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine" EXACT []
synonym: "m1acp3Y" EXACT RNAMOD []
xref: RNAMOD:086
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001374
name: five_carboxymethyluridine
def: "5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carboxymethyluridine" EXACT []
synonym: "cm5U" EXACT RNAMOD []
synonym: "five carboxymethyluridine" EXACT []
xref: RNAMOD:087
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001375
name: three_two_prime_O_dimethyluridine
def: "3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "3,2'-O-dimethyluridine" EXACT []
synonym: "m3Um" EXACT RNAMOD []
synonym: "three two prime O dimethyluridine" EXACT []
xref: RNAMOD:092
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001376
name: five_methyldihydrouridine
def: "5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methyldihydrouridine" EXACT []
synonym: "five methyldihydrouridine" EXACT []
synonym: "m5D" EXACT RNAMOD []
xref: RNAMOD:093
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001377
name: three_methylpseudouridine
def: "3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "3-methylpseudouridine" EXACT []
synonym: "m3Y" EXACT RNAMOD []
synonym: "three methylpseudouridine" EXACT []
xref: RNAMOD:094
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001378
name: five_taurinomethyluridine
def: "5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-taurinomethyluridine" EXACT []
synonym: "five taurinomethyluridine" EXACT []
synonym: "tm5U" EXACT RNAMOD []
xref: RNAMOD:098
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001379
name: five_taurinomethyl_two_thiouridine
def: "5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-taurinomethyl-2-thiouridine" EXACT []
synonym: "five taurinomethyl two thiouridine" EXACT []
synonym: "tm5s2U" EXACT RNAMOD []
xref: RNAMOD:099
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001380
name: five_isopentenylaminomethyl_uridine
def: "5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-(isopentenylaminomethyl)uridine" EXACT []
synonym: "five isopentenylaminomethyl uridine" EXACT []
synonym: "inm5U" EXACT RNAMOD []
xref: RNAMOD:103
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001381
name: five_isopentenylaminomethyl_two_thiouridine
def: "5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-(isopentenylaminomethyl)- 2-thiouridine" EXACT []
synonym: "five isopentenylaminomethyl two thiouridine" EXACT []
synonym: "inm5s2U" EXACT RNAMOD []
xref: RNAMOD:104
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001382
name: five_isopentenylaminomethyl_two_prime_O_methyluridine
def: "5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-(isopentenylaminomethyl)- 2'-O-methyluridine" EXACT []
synonym: "five isopentenylaminomethyl two prime O methyluridine" EXACT []
synonym: "inm5Um" EXACT RNAMOD []
xref: RNAMOD:105
is_a: SO:0001277 ! modified_uridine

[Term]
id: SO:0001383
name: histone_binding_site
def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]
synonym: "histone binding site" EXACT []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site

[Term]
id: SO:0001384
name: CDS_fragment
synonym: "CDS fragment" EXACT []
synonym: "incomplete CDS" EXACT []
is_a: SO:0000316 ! CDS
intersection_of: SO:0000316 ! CDS
intersection_of: has_quality SO:0000731 ! fragmentary
relationship: has_quality SO:0000731 ! fragmentary

[Term]
id: SO:0001385
name: modified_amino_acid_feature
def: "A post translationally modified amino acid feature." [SO:ke]
synonym: "modified amino acid feature" EXACT []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001386
name: modified_glycine
def: "A post translationally modified glycine amino acid feature." [SO:ke]
synonym: "ModGly" EXACT AAMOD []
synonym: "modified glycine" EXACT []
xref: MOD:00908
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001387
name: modified_L_alanine
def: "A post translationally modified alanine amino acid feature." [SO:ke]
synonym: "ModAla" EXACT AAMOD []
synonym: "modified L alanine" EXACT []
synonym: "modified L-alanine" EXACT []
xref: MOD:00901
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001388
name: modified_L_asparagine
def: "A post translationally modified asparagine amino acid feature." [SO:ke]
synonym: "ModAsn" EXACT AAMOD []
synonym: "modified L asparagine" EXACT []
synonym: "modified L-asparagine" EXACT []
xref: MOD:00903
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001389
name: modified_L_aspartic_acid
def: "A post translationally modified aspartic acid amino acid feature." [SO:ke]
synonym: "ModAsp" EXACT AAMOD []
synonym: "modified L aspartic acid" EXACT []
synonym: "modified L-aspartic acid" EXACT []
xref: MOD:00904
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001390
name: modified_L_cysteine
def: "A post translationally modified cysteine amino acid feature." [SO:ke]
synonym: "ModCys" EXACT AAMOD []
synonym: "modified L cysteine" EXACT []
synonym: "modified L-cysteine" EXACT []
xref: MOD:00905
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001391
name: modified_L_glutamic_acid
synonym: "ModGlu" EXACT AAMOD []
synonym: "modified L glutamic acid" EXACT []
synonym: "modified L-glutamic acid" EXACT []
xref: MOD:00906
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001392
name: modified_L_threonine
def: "A post translationally modified threonine amino acid feature." [SO:ke]
synonym: "modified L threonine" EXACT []
synonym: "modified L-threonine" EXACT []
synonym: "ModThr" EXACT AAMOD []
xref: MOD:00917
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001393
name: modified_L_tryptophan
def: "A post translationally modified tryptophan amino acid feature." [SO:ke]
synonym: "modified L tryptophan" EXACT []
synonym: "modified L-tryptophan" EXACT []
synonym: "ModTrp" EXACT AAMOD []
xref: MOD:00918
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001394
name: modified_L_glutamine
def: "A post translationally modified glutamine amino acid feature." [SO:ke]
synonym: "ModGln" EXACT []
synonym: "modified L glutamine" EXACT []
synonym: "modified L-glutamine" EXACT []
xref: MOD:00907
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001395
name: modified_L_methionine
def: "A post translationally modified methionine amino acid feature." [SO:ke]
synonym: "modified L methionine" EXACT []
synonym: "modified L-methionine" EXACT []
synonym: "ModMet" EXACT AAMOD []
xref: MOD:00913
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001396
name: modified_L_isoleucine
def: "A post translationally modified isoleucine amino acid feature." [SO:ke]
synonym: "modified L isoleucine" EXACT []
synonym: "modified L-isoleucine" EXACT []
synonym: "ModIle" EXACT AAMOD []
xref: MOD:00910
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001397
name: modified_L_phenylalanine
def: "A post translationally modified phenylalanine amino acid feature." [SO:ke]
synonym: "modified L phenylalanine" EXACT []
synonym: "modified L-phenylalanine" EXACT []
synonym: "ModPhe" EXACT AAMOD []
xref: MOD:00914
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001398
name: modified_L_histidine
def: "A post translationally modified histidine amino acid feature." [SO:ke]
synonym: "ModHis" EXACT []
synonym: "modified L histidine" EXACT []
synonym: "modified L-histidine" EXACT []
xref: MOD:00909
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001399
name: modified_L_serine
def: "A post translationally modified serine amino acid feature." [SO:ke]
synonym: "modified L serine" EXACT []
synonym: "modified L-serine" EXACT []
synonym: "MosSer" EXACT AAMOD []
xref: MOD:00916 "http://www.psidev.info/index.php?q=node/104"
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001400
name: modified_L_lysine
def: "A post translationally modified lysine amino acid feature." [SO:ke]
synonym: "modified L lysine" EXACT []
synonym: "modified L-lysine" EXACT []
synonym: "ModLys" EXACT AAMOD []
xref: MOD:00912
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001401
name: modified_L_leucine
def: "A post translationally modified leucine amino acid feature." [SO:ke]
synonym: "modified L leucine" EXACT []
synonym: "modified L-leucine " EXACT []
synonym: "ModLeu" EXACT AAMOD []
xref: MOD:00911
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001402
name: modified_L_selenocysteine
def: "A post translationally modified selenocysteine amino acid feature." [SO:ke]
synonym: "modified L selenocysteine" EXACT []
synonym: "modified L-selenocysteine" EXACT []
xref: MOD:01158
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001403
name: modified_L_valine
def: "A post translationally modified valine amino acid feature." [SO:ke]
synonym: "modified L valine" EXACT []
synonym: "modified L-valine" EXACT []
synonym: "ModVal" EXACT AAMOD []
xref: MOD:00920
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001404
name: modified_L_proline
def: "A post translationally modified proline amino acid feature." [SO:ke]
synonym: "modified L proline" EXACT []
synonym: "modified L-proline " EXACT []
synonym: "ModPro" EXACT AAMOD []
xref: MOD:00915
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001405
name: modified_L_tyrosine
def: "A post translationally modified tyrosine amino acid feature." [SO:ke]
synonym: "modified L tyrosine" EXACT []
synonym: "modified L-tyrosine" EXACT []
synonym: "ModTry" EXACT AAMOD []
xref: MOD:00919
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001406
name: modified_L_arginine
def: "A post translationally modified arginine amino acid feature." [SO:ke]
synonym: "ModArg" EXACT AAMOD []
synonym: "modified L arginine" EXACT []
synonym: "modified L-arginine" EXACT []
xref: MOD:00902
is_a: SO:0001385 ! modified_amino_acid_feature

[Term]
id: SO:0001407
name: peptidyl
def: "An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke]
is_a: SO:0000443 ! polymer_attribute

[Term]
id: SO:0001408
name: cleaved_for_gpi_anchor_region
def: "The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]
synonym: "cleaved for gpi anchor region" EXACT []
is_a: SO:0100011 ! cleaved_peptide_region

[Term]
id: SO:0001409
name: biomaterial_region
def: "A region which is intended for use in an experiment." [SO:cb]
subset: SOFA
synonym: "biomaterial region" EXACT []
is_a: SO:0000001 ! region

[Term]
id: SO:0001410
name: experimental_feature
def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]
subset: SOFA
synonym: "analysis feature" RELATED []
synonym: "experimental output artefact" EXACT []
synonym: "experimental_output_artefact" EXACT []
is_a: SO:0000001 ! region

[Term]
id: SO:0001411
name: biological_region
def: "A region defined by its disposition to be involved in a biological process." [SO:cb]
subset: SOFA
synonym: "biological region" EXACT []
is_a: SO:0000001 ! region

[Term]
id: SO:0001412
name: topologically_defined_region
def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb]
subset: SOFA
synonym: "topologically defined region" EXACT []
is_a: SO:0000001 ! region

[Term]
id: SO:0001413
name: translocation_breakpoint
def: "The point within a chromosome where a translocation begins or ends." [SO:cb]
synonym: "translocation breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint

[Term]
id: SO:0001414
name: insertion_breakpoint
def: "The point within a chromosome where a insertion begins or ends." [SO:cb]
synonym: "insertion breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint

[Term]
id: SO:0001415
name: deletion_breakpoint
def: "The point within a chromosome where a deletion begins or ends." [SO:cb]
synonym: "deletion breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint

[Term]
id: SO:0001416
name: five_prime_flanking_region
def: "A flanking region located five prime of a specific region." [SO:chado]
synonym: "5' flanking region" RELATED []
synonym: "five prime flanking region" EXACT []
is_a: SO:0000239 ! flanking_region

[Term]
id: SO:0001417
name: three_prime_flanking_region
def: "A flanking region located three prime of a specific region." [SO:chado]
synonym: "3' flanking region" RELATED []
synonym: "three prime flanking region" EXACT []
is_a: SO:0000239 ! flanking_region

[Term]
id: SO:0001418
name: transcribed_fragment
def: "An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke]
comment: Term requested by the MODencode group.
synonym: "transcribed fragment" EXACT []
synonym: "transfrag" RELATED []
is_a: SO:0001410 ! experimental_feature

[Term]
id: SO:0001419
name: cis_splice_site
def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]
subset: SOFA
synonym: "cis splice site" EXACT []
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0001420
name: trans_splice_site
def: "Primary transcript region bordering trans-splice junction." [SO:ke]
subset: SOFA
synonym: "trans splice site" EXACT []
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0001421
name: splice_junction
def: "The boundary between an intron and an exon." [SO:ke]
synonym: "splice boundary" EXACT []
synonym: "splice junction" EXACT []
is_a: SO:0000699 ! junction

[Term]
id: SO:0001422
name: conformational_switch
def: "A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]
comment: MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999.
synonym: "polypeptide conformational switch" EXACT []
is_a: SO:0100001 ! biochemical_region_of_peptide

[Term]
id: SO:0001423
name: dye_terminator_read
def: "A read produced by the dye terminator method of sequencing." [SO:ke]
synonym: "dye terminator read" RELATED []
is_a: SO:0000150 ! read

[Term]
id: SO:0001424
name: pyrosequenced_read
def: "A read produced by pyrosequencing technology." [SO:ke]
comment: An example is a read produced by Roche 454 technology.
synonym: "pyorsequenced read" RELATED []
is_a: SO:0000150 ! read

[Term]
id: SO:0001425
name: ligation_based_read
def: "A read produced by ligation based sequencing technologies." [SO:ke]
comment: An example of this kind of read is one produced by ABI SOLiD.
synonym: "ligation based read" RELATED []
is_a: SO:0000150 ! read

[Term]
id: SO:0001426
name: polymerase_synthesis_read
def: "A read produced by the polymerase based sequence by synthesis method." [SO:ke]
comment: An example is a read produced by Illumina technology.
synonym: "polymerase synthesis read" RELATED []
is_a: SO:0000150 ! read

[Term]
id: SO:0001427
name: cis_regulatory_frameshift_element
def: "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]
synonym: "cis regulatory frameshift element" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region

[Term]
id: SO:0001428
name: expressed_sequence_assembly
def: "A sequence assembly derived from expressed sequences." [SO:ke]
comment: From tracker [ 2372385 ] expressed_sequence_assembly.
synonym: "expressed sequence assembly" EXACT []
is_a: SO:0000353 ! sequence_assembly

[Term]
id: SO:0001429
name: DNA_binding_site
def: "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]
synonym: "DNA binding site" EXACT []
is_a: SO:0001655 ! nucleotide_binding_site

[Term]
id: SO:0001431
name: cryptic_gene
def: "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]
synonym: "cryptic gene" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000976 ! cryptic
relationship: has_quality SO:0000976 ! cryptic

[Term]
id: SO:0001432
name: sequence_variant_affecting_polyadenylation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting polyadenylation" RELATED []
synonym: "sequence variant affecting polyadenylation" EXACT []
is_obsolete: true
replaced_by: SO:0001545

[Term]
id: SO:0001433
name: three_prime_RACE_clone
def: "A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]
synonym: "3' RACE clone" RELATED []
is_a: SO:0000317 ! cDNA_clone

[Term]
id: SO:0001434
name: cassette_pseudogene
def: "A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke]
comment: Requested by the Trypanosome community.
synonym: "cassette pseudogene" EXACT []
synonym: "cassette type psedogene" RELATED []
is_a: SO:0001760 ! non_processed_pseudogene

[Term]
id: SO:0001435
name: alanine
comment: A place holder for a cross product with chebi.
synonym: "A" EXACT aa1 []
synonym: "Ala" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001436
name: valine
comment: A place holder for a cross product with chebi.
synonym: "V" EXACT aa1 []
synonym: "Val" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001437
name: leucine
comment: A place holder for a cross product with chebi.
synonym: "L" EXACT aa1 []
synonym: "Leu" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001438
name: isoleucine
comment: A place holder for a cross product with chebi.
synonym: "I" EXACT aa1 []
synonym: "Ile" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001439
name: proline
comment: A place holder for a cross product with chebi.
synonym: "P" EXACT aa1 []
synonym: "Pro" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001440
name: tryptophan
comment: A place holder for a cross product with chebi.
synonym: "Trp" EXACT aa3 []
synonym: "W" EXACT aa1 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001441
name: phenylalanine
comment: A place holder for a cross product with chebi.
synonym: "F" EXACT aa1 []
synonym: "Phe" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001442
name: methionine
comment: A place holder for a cross product with chebi.
synonym: "M" EXACT aa1 []
synonym: "Met" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001443
name: glycine
comment: A place holder for a cross product with chebi.
synonym: "G" EXACT aa1 []
synonym: "Gly" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001444
name: serine
comment: A place holder for a cross product with chebi.
synonym: "S" EXACT aa1 []
synonym: "Ser" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001445
name: threonine
comment: A place holder for a cross product with chebi.
synonym: "T" EXACT aa1 []
synonym: "Thr" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001446
name: tyrosine
comment: A place holder for a cross product with chebi.
synonym: "Tyr" EXACT aa3 []
synonym: "Y" EXACT aa1 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001447
name: cysteine
comment: A place holder for a cross product with chebi.
synonym: "C" EXACT aa1 []
synonym: "Cys" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001448
name: glutamine
comment: A place holder for a cross product with chebi.
synonym: "Gln" EXACT aa3 []
synonym: "Q" EXACT aa1 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001449
name: asparagine
comment: A place holder for a cross product with chebi.
synonym: "Asn" EXACT aa3 []
synonym: "N" EXACT aa1 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001450
name: lysine
comment: A place holder for a cross product with chebi.
synonym: "K" EXACT aa1 []
synonym: "Lys" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001451
name: arginine
comment: A place holder for a cross product with chebi.
synonym: "Arg" EXACT aa3 []
synonym: "R" EXACT aa1 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001452
name: histidine
comment: A place holder for a cross product with chebi.
synonym: "H" EXACT aa1 []
synonym: "His" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001453
name: aspartic_acid
comment: A place holder for a cross product with chebi.
synonym: "Asp" EXACT aa3 []
synonym: "aspartic acid" EXACT []
synonym: "D" EXACT aa1 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001454
name: glutamic_acid
comment: A place holder for a cross product with chebi.
synonym: "E" EXACT aa1 []
synonym: "Glu" EXACT aa3 []
synonym: "glutamic acid" EXACT []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001455
name: selenocysteine
comment: A place holder for a cross product with chebi.
synonym: "Sec" EXACT aa3 []
synonym: "U" EXACT aa1 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001456
name: pyrrolysine
comment: A place holder for a cross product with chebi.
synonym: "O" EXACT aa1 []
synonym: "Pyl" EXACT aa3 []
is_a: SO:0001237 ! amino_acid

[Term]
id: SO:0001457
name: transcribed_cluster
def: "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke]
comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
synonym: "transcribed cluster" EXACT []
synonym: "unigene cluster" RELATED []
is_a: SO:0001410 ! experimental_feature
relationship: has_part SO:0000695 ! reagent

[Term]
id: SO:0001458
name: unigene_cluster
def: "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke]
comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
synonym: "unigene cluster" RELATED []
is_a: SO:0001457 ! transcribed_cluster

[Term]
id: SO:0001459
name: CRISPR
def: "Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]
synonym: "Clustered_Regularly_Interspaced_Short_Palindromic_Repeat" EXACT []
synonym: "CRISPR element" EXACT []
xref: http:en.wikipedia.org/wiki/CRISPR
is_a: SO:0000314 ! direct_repeat

[Term]
id: SO:0001460
name: insulator_binding_site
def: "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
comment: See tracker ID 2060908.
synonym: "insulator binding site" RELATED []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site
relationship: part_of SO:0000627 ! insulator

[Term]
id: SO:0001461
name: enhancer_binding_site
def: "A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
synonym: "enhancer binding site" RELATED []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site
relationship: part_of SO:0000165 ! enhancer

[Term]
id: SO:0001462
name: contig_collection
def: "A collection of contigs." [SO:ke]
comment: See tracker ID: 2138359.
synonym: "contig collection" EXACT []
is_a: SO:0001085 ! sequence_conflict
is_a: SO:0001260 ! sequence_collection
intersection_of: SO:0001085 ! sequence_conflict
intersection_of: has_part SO:0000149 ! contig
relationship: has_part SO:0000149 ! contig

[Term]
id: SO:0001463
name: lincRNA
def: "A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]
synonym: "large intervening non-coding RNA" EXACT []
synonym: "long intergenic non-coding RNA" EXACT []
is_a: SO:0001877 ! lnc_RNA

[Term]
id: SO:0001464
name: UST
def: "An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]
synonym: "UTR sequence tag" EXACT []
is_a: SO:0000345 ! EST

[Term]
id: SO:0001465
name: three_prime_UST
def: "A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]
synonym: "3' UST" RELATED []
is_a: SO:0001464 ! UST

[Term]
id: SO:0001466
name: five_prime_UST
def: "An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]
synonym: "5' UST" RELATED []
is_a: SO:0001464 ! UST

[Term]
id: SO:0001467
name: RST
def: "A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]
synonym: "RACE sequence tag" EXACT []
is_a: SO:0000345 ! EST

[Term]
id: SO:0001468
name: three_prime_RST
def: "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]
synonym: "3' RST" EXACT []
is_a: SO:0001467 ! RST

[Term]
id: SO:0001469
name: five_prime_RST
def: "A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]
synonym: "5' RST" RELATED []
is_a: SO:0001467 ! RST

[Term]
id: SO:0001470
name: UST_match
def: "A match against an UST sequence." [SO:nlw]
synonym: "UST match" EXACT []
is_a: SO:0000102 ! expressed_sequence_match

[Term]
id: SO:0001471
name: RST_match
def: "A match against an RST sequence." [SO:nlw]
synonym: "RST match" EXACT []
is_a: SO:0000102 ! expressed_sequence_match

[Term]
id: SO:0001472
name: primer_match
def: "A nucleotide match to a primer sequence." [SO:nlw]
synonym: "primer match" EXACT []
is_a: SO:0000347 ! nucleotide_match

[Term]
id: SO:0001473
name: miRNA_antiguide
def: "A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]
synonym: "miRNA antiguide " EXACT []
synonym: "miRNA passenger strand" EXACT []
synonym: "miRNA star" EXACT []
is_a: SO:0001243 ! miRNA_primary_transcript_region
created_by: kareneilbeck
creation_date: 2009-05-27T03:35:43Z

[Term]
id: SO:0001474
name: trans_splice_junction
def: "The boundary between the spliced leader and the first exon of the mRNA." [SO:ke]
synonym: "trans-splice junction" EXACT []
is_a: SO:0000699 ! junction
created_by: kareneilbeck
creation_date: 2009-07-13T04:50:49Z

[Term]
id: SO:0001475
name: outron
def: "A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]
is_a: SO:0000835 ! primary_transcript_region
created_by: kareneilbeck
creation_date: 2009-07-14T11:36:08Z

[Term]
id: SO:0001476
name: natural_plasmid
def: "A plasmid that occurs naturally." [SO:xp]
synonym: "natural plasmid" EXACT []
is_a: SO:0000155 ! plasmid
is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
intersection_of: SO:0000155 ! plasmid
intersection_of: has_quality SO:0000782 ! natural
relationship: has_quality SO:0000782 ! natural
created_by: kareneilbeck
creation_date: 2009-09-01T03:43:06Z

[Term]
id: SO:0001477
name: gene_trap_construct
def: "A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]
synonym: "gene trap construct" EXACT []
is_a: SO:0000637 ! engineered_plasmid
created_by: kareneilbeck
creation_date: 2009-09-01T03:49:09Z

[Term]
id: SO:0001478
name: promoter_trap_construct
def: "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]
synonym: "promoter trap construct" EXACT []
is_a: SO:0000637 ! engineered_plasmid
created_by: kareneilbeck
creation_date: 2009-09-01T03:52:01Z

[Term]
id: SO:0001479
name: enhancer_trap_construct
def: "An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]
synonym: "enhancer trap construct" EXACT []
is_a: SO:0000637 ! engineered_plasmid
created_by: kareneilbeck
creation_date: 2009-09-01T03:53:26Z

[Term]
id: SO:0001480
name: PAC_end
def: "A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]
synonym: "PAC end" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000154 ! PAC
created_by: kareneilbeck
creation_date: 2009-09-09T05:18:12Z

[Term]
id: SO:0001481
name: RAPD
def: "RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]
synonym: "Random Amplification Polymorphic DNA" EXACT []
is_a: SO:0000006 ! PCR_product
created_by: kareneilbeck
creation_date: 2009-09-09T05:26:10Z

[Term]
id: SO:0001482
name: shadow_enhancer
synonym: "shadow enhancer" EXACT []
is_a: SO:0000165 ! enhancer
created_by: kareneilbeck
creation_date: 2009-09-09T05:29:29Z

[Term]
id: SO:0001483
name: SNV
def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]
subset: SOFA
synonym: "single nucleotide variant" EXACT []
is_a: SO:1000002 ! substitution
created_by: kareneilbeck
creation_date: 2009-10-08T11:37:49Z

[Term]
id: SO:0001484
name: X_element_combinatorial_repeat
def: "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]
comment: X element combinatorial repeats contain Tbf1p binding sites,\nand possible functions include a role in telomerase-independent telomere\nmaintenance via recombination or as a barrier against transcriptional\nsilencing. These are usually present as a combination of one or more of\nseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
synonym: "X element combinatorial repeat" EXACT []
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000624 ! telomere
created_by: kareneilbeck
creation_date: 2009-11-10T11:03:37Z

[Term]
id: SO:0001485
name: Y_prime_element
def: "A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http\://www.yeastgenome.org/help/glossary.html]
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
synonym: "Y' element" EXACT []
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000624 ! telomere
created_by: kareneilbeck
creation_date: 2009-11-10T12:08:57Z

[Term]
id: SO:0001486
name: standard_draft
def: "The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126]
synonym: "standard draft" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T12:48:32Z

[Term]
id: SO:0001487
name: high_quality_draft
def: "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126]
synonym: "high quality draft" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T12:52:36Z

[Term]
id: SO:0001488
name: improved_high_quality_draft
def: "The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126]
synonym: "improved high quality draft" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T12:54:35Z

[Term]
id: SO:0001489
name: annotation_directed_improved_draft
def: "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126]
synonym: "annotation directed improvement" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T12:57:10Z

[Term]
id: SO:0001490
name: noncontiguous_finished
def: "The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126]
synonym: "non contiguous finished" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T01:01:07Z

[Term]
id: SO:0001491
name: finished_genome
def: "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126]
synonym: "finished" EXACT []
synonym: "finished genome" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T01:04:43Z

[Term]
id: SO:0001492
name: intronic_regulatory_region
def: "A regulatory region that is part of an intron." [SO:ke]
synonym: "intronic regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
relationship: part_of SO:0000188 ! intron
created_by: kareneilbeck
creation_date: 2009-11-08T02:48:02Z

[Term]
id: SO:0001493
name: centromere_DNA_Element_I
def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
synonym: "CDEI" EXACT []
synonym: "Centromere DNA Element I" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0001794 ! point_centromere
created_by: kareneilbeck
creation_date: 2009-11-09T05:47:23Z

[Term]
id: SO:0001494
name: centromere_DNA_Element_II
def: "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
synonym: "CDEII" EXACT []
synonym: "centromere DNA Element II" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0001794 ! point_centromere
created_by: kareneilbeck
creation_date: 2009-11-09T05:51:26Z

[Term]
id: SO:0001495
name: centromere_DNA_Element_III
def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
synonym: "CDEIII" EXACT []
synonym: "centromere DNA Element III" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0001794 ! point_centromere
created_by: kareneilbeck
creation_date: 2009-11-09T05:54:47Z

[Term]
id: SO:0001496
name: telomeric_repeat
def: "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]
comment: The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739.
synonym: "telomeric repeat" EXACT []
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000624 ! telomere
created_by: kareneilbeck
creation_date: 2009-11-09T06:00:42Z

[Term]
id: SO:0001497
name: X_element
def: "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]
comment: Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. \n\nFrom Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1.
synonym: "X element" RELATED []
synonym: "X element core sequence" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0000624 ! telomere
created_by: kareneilbeck
creation_date: 2009-11-10T10:56:54Z

[Term]
id: SO:0001498
name: YAC_end
def: "A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]
synonym: "YAC end" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000152 ! YAC
created_by: kareneilbeck
creation_date: 2009-11-19T11:07:18Z

[Term]
id: SO:0001499
name: whole_genome_sequence_status
def: "The status of whole genome sequence." [DOI:10.1126]
comment: This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms.
synonym: "whole genome sequence status" EXACT []
is_a: SO:0000905 ! status
created_by: kareneilbeck
creation_date: 2009-10-23T12:47:47Z

[Term]
id: SO:0001500
name: heritable_phenotypic_marker
def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene]
synonym: "heritable phenotypic marker" EXACT []
synonym: "phenotypic marker" EXACT []
is_a: SO:0001645 ! genetic_marker
created_by: kareneilbeck
creation_date: 2009-12-07T01:50:55Z

[Term]
id: SO:0001501
name: peptide_collection
def: "A collection of peptide sequences." [BBOP:nlw]
comment: Term requested via tracker ID: 2910829.
synonym: "peptide collection" EXACT []
synonym: "peptide set" EXACT []
is_a: SO:0001260 ! sequence_collection
intersection_of: SO:0001260 ! sequence_collection
intersection_of: has_part SO:0000104 ! polypeptide
relationship: has_part SO:0000104 ! polypeptide
created_by: kareneilbeck
creation_date: 2009-12-11T10:58:58Z

[Term]
id: SO:0001502
name: high_identity_region
def: "An experimental feature with high sequence identity to another sequence." [SO:ke]
comment: Requested by tracker ID: 2902685.
synonym: "high identity region" EXACT []
is_a: SO:0001410 ! experimental_feature
created_by: kareneilbeck
creation_date: 2009-12-11T11:06:05Z

[Term]
id: SO:0001503
name: processed_transcript
def: "A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]
comment: Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.
synonym: "processed transcript" EXACT []
is_a: SO:0000673 ! transcript
created_by: kareneilbeck
creation_date: 2009-12-21T05:37:14Z

[Term]
id: SO:0001504
name: assortment_derived_variation
def: "A chromosome variation derived from an event during meiosis." [SO:ke]
synonym: "assortment derived variation" RELATED []
is_a: SO:0000240 ! chromosome_variation
created_by: kareneilbeck
creation_date: 2010-03-02T05:03:18Z

[Term]
id: SO:0001505
name: reference_genome
def: "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke]
synonym: "reference genome" RELATED []
is_a: SO:0001026 ! genome
created_by: kareneilbeck
creation_date: 2010-03-03T02:10:03Z

[Term]
id: SO:0001506
name: variant_genome
def: "A collection of sequences (often chromosomes) of an individual." [SO:ke]
synonym: "variant genome" RELATED []
is_a: SO:0001026 ! genome
created_by: kareneilbeck
creation_date: 2010-03-03T02:11:25Z

[Term]
id: SO:0001507
name: variant_collection
def: "A collection of one or more sequences of an individual." [SO:ke]
synonym: "variant collection" RELATED []
is_a: SO:0001260 ! sequence_collection
intersection_of: SO:0001260 ! sequence_collection
intersection_of: has_part SO:0001059 ! sequence_alteration
created_by: kareneilbeck
creation_date: 2010-03-03T02:13:28Z

[Term]
id: SO:0001508
name: alteration_attribute
synonym: "alteration attribute" EXACT []
is_a: SO:0000733 ! feature_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:53:23Z

[Term]
id: SO:0001509
name: chromosomal_variation_attribute
synonym: "chromosomal variation attribute" EXACT []
is_a: SO:0001508 ! alteration_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:54:30Z

[Term]
id: SO:0001510
name: intrachromosomal
is_a: SO:0001509 ! chromosomal_variation_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:55:25Z

[Term]
id: SO:0001511
name: interchromosomal
is_a: SO:0001509 ! chromosomal_variation_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:55:43Z

[Term]
id: SO:0001512
name: insertion_attribute
def: "A quality of a chromosomal insertion,." [SO:ke]
synonym: "insertion attribute" EXACT []
is_a: SO:0001508 ! alteration_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:55:56Z

[Term]
id: SO:0001513
name: tandem
is_a: SO:0001512 ! insertion_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:56:37Z

[Term]
id: SO:0001514
name: direct
def: "A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke]
is_a: SO:0001512 ! insertion_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:56:49Z

[Term]
id: SO:0001515
name: inverted
def: "A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke]
is_a: SO:0001512 ! insertion_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:57:40Z

[Term]
id: SO:0001516
name: free
def: "The quality of a duplication where the new region exists independently of the original." [SO:ke]
is_a: SO:0001523 ! duplication_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:57:51Z

[Term]
id: SO:0001517
name: inversion_attribute
synonym: "inversion attribute" EXACT []
is_a: SO:0001508 ! alteration_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:58:10Z

[Term]
id: SO:0001518
name: pericentric
is_a: SO:0001517 ! inversion_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:58:24Z

[Term]
id: SO:0001519
name: paracentric
is_a: SO:0001517 ! inversion_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:58:35Z

[Term]
id: SO:0001520
name: translocaton_attribute
synonym: "translocation attribute" EXACT []
is_a: SO:0001508 ! alteration_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:58:47Z

[Term]
id: SO:0001521
name: reciprocal
is_a: SO:0001520 ! translocaton_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:59:34Z

[Term]
id: SO:0001522
name: insertional
is_a: SO:0001520 ! translocaton_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:59:51Z

[Term]
id: SO:0001523
name: duplication_attribute
synonym: "duplication attribute" RELATED []
is_a: SO:0001508 ! alteration_attribute
created_by: kareneilbeck
creation_date: 2010-03-05T01:56:33Z

[Term]
id: SO:0001524
name: chromosomally_aberrant_genome
synonym: "chromosomally aberrant genome" RELATED []
is_a: SO:0001506 ! variant_genome
created_by: kareneilbeck
creation_date: 2010-03-05T02:21:00Z

[Term]
id: SO:0001525
name: assembly_error_correction
def: "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke]
synonym: "assembly error correction" RELATED []
is_a: SO:0000413 ! sequence_difference
created_by: kareneilbeck
creation_date: 2010-03-09T02:16:31Z

[Term]
id: SO:0001526
name: base_call_error_correction
def: "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke]
synonym: "base call error correction" RELATED []
is_a: SO:0000413 ! sequence_difference
created_by: kareneilbeck
creation_date: 2010-03-09T02:18:07Z

[Term]
id: SO:0001527
name: peptide_localization_signal
def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]
subset: SOFA
synonym: "localization signal" RELATED []
synonym: "peptide localization signal" EXACT []
is_a: SO:0000839 ! polypeptide_region
created_by: kareneilbeck
creation_date: 2010-03-11T02:15:05Z

[Term]
id: SO:0001528
name: nuclear_localization_signal
def: "A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]
synonym: "NLS" EXACT []
xref: http://en.wikipedia.org/wiki/Nuclear_localization_signal "wikipedia"
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2010-03-11T02:16:38Z

[Term]
id: SO:0001529
name: endosomal_localization_signal
def: "A polypeptide region that targets a polypeptide to the endosome." [SO:ke]
synonym: "endosomal localization signal" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2010-03-11T02:20:58Z

[Term]
id: SO:0001530
name: lysosomal_localization_signal
def: "A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]
synonym: "lysosomal localization signal" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2010-03-11T02:24:10Z

[Term]
id: SO:0001531
name: nuclear_export_signal
def: "A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]
synonym: "NES" EXACT []
synonym: "nuclear export signal" EXACT []
xref: http://en.wikipedia.org/wiki/Nuclear_export_signal
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2010-03-11T02:25:25Z

[Term]
id: SO:0001532
name: recombination_signal_sequence
def: "A region recognized by a recombinase." [SO:ke]
synonym: "recombination signal sequence" RELATED []
xref: http://en.wikipedia.org/wiki/Recombination_Signal_Sequences "wikipedia"
is_a: SO:0000299 ! specific_recombination_site
created_by: kareneilbeck
creation_date: 2010-03-11T03:16:47Z

[Term]
id: SO:0001533
name: cryptic_splice_site
def: "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]
synonym: "cryptic splice signal" RELATED []
synonym: "cryptic splice site" EXACT []
is_a: SO:0000162 ! splice_site
created_by: kareneilbeck
creation_date: 2010-03-11T03:25:06Z

[Term]
id: SO:0001534
name: nuclear_rim_localization_signal
def: "A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]
synonym: "nuclear rim localization signal" RELATED []
xref: PMID:16027110
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2010-03-11T03:31:30Z

[Term]
id: SO:0001535
name: p_element
def: "A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]
synonym: "P element" RELATED []
is_a: SO:0000182 ! DNA_transposon
created_by: kareneilbeck
creation_date: 2010-03-12T03:40:33Z

[Term]
id: SO:0001536
name: functional_variant
def: "A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]
synonym: "functional variant" EXACT []
is_a: SO:0001060 ! sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:30:25Z

[Term]
id: SO:0001537
name: structural_variant
def: "A sequence variant that changes one or more sequence features." [SO:ke]
synonym: "structural variant" RELATED []
is_a: SO:0001060 ! sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:31:01Z

[Term]
id: SO:0001538
name: transcript_function_variant
def: "A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]
synonym: "transcript function variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:32:58Z

[Term]
id: SO:0001539
name: translational_product_function_variant
def: "A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]
synonym: "translational product variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:46:15Z

[Term]
id: SO:0001540
name: level_of_transcript_variant
def: "A sequence variant which alters the level of a transcript." [SO:ke]
synonym: "level of transcript variant" EXACT []
is_a: SO:0001538 ! transcript_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:47:07Z

[Term]
id: SO:0001541
name: decreased_transcript_level_variant
def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]
synonym: "decreased transcript level" EXACT []
is_a: SO:0001540 ! level_of_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:47:47Z

[Term]
id: SO:0001542
name: increased_transcript_level_variant
def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]
synonym: "increased transcript level variant" EXACT []
is_a: SO:0001540 ! level_of_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:48:17Z

[Term]
id: SO:0001543
name: transcript_processing_variant
def: "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]
synonym: "transcript processing variant" EXACT []
is_a: SO:0001538 ! transcript_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:48:48Z

[Term]
id: SO:0001544
name: editing_variant
def: "A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke]
synonym: "editing variant" EXACT []
is_a: SO:0001543 ! transcript_processing_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:49:25Z

[Term]
id: SO:0001545
name: polyadenylation_variant
def: "A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]
synonym: "polyadenylation variant" EXACT []
is_a: SO:0001543 ! transcript_processing_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:49:40Z

[Term]
id: SO:0001546
name: transcript_stability_variant
def: "A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]
synonym: "transcript stability variant" EXACT []
is_a: SO:0001538 ! transcript_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:50:01Z

[Term]
id: SO:0001547
name: decreased_transcript_stability_variant
def: "A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke]
synonym: "decrease transcript stability variant" EXACT []
is_a: SO:0001546 ! transcript_stability_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:50:23Z

[Term]
id: SO:0001548
name: increased_transcript_stability_variant
def: "A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke]
synonym: "increased transcript stability variant" EXACT []
is_a: SO:0001546 ! transcript_stability_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:50:39Z

[Term]
id: SO:0001549
name: transcription_variant
def: "A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]
synonym: "transcription variant" EXACT []
is_a: SO:0001538 ! transcript_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:51:26Z

[Term]
id: SO:0001550
name: rate_of_transcription_variant
def: "A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]
synonym: "rate of transcription variant" EXACT []
is_a: SO:0001549 ! transcription_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:51:50Z

[Term]
id: SO:0001551
name: increased_transcription_rate_variant
def: "A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]
synonym: "increased transcription rate variant" EXACT []
is_a: SO:0001550 ! rate_of_transcription_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:52:17Z

[Term]
id: SO:0001552
name: decreased_transcription_rate_variant
def: "A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]
synonym: "decreased transcription rate variant" EXACT []
is_a: SO:0001550 ! rate_of_transcription_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:52:43Z

[Term]
id: SO:0001553
name: translational_product_level_variant
def: "A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]
synonym: "translational product level variant" EXACT []
is_a: SO:0001539 ! translational_product_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:53:32Z

[Term]
id: SO:0001554
name: polypeptide_function_variant
def: "A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]
synonym: "polypeptide function variant" EXACT []
is_a: SO:0001539 ! translational_product_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:53:54Z

[Term]
id: SO:0001555
name: decreased_translational_product_level
def: "A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke]
synonym: "decrease translational product level" EXACT []
is_a: SO:0001553 ! translational_product_level_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:54:25Z

[Term]
id: SO:0001556
name: increased_translational_product_level
def: "A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke]
synonym: "increase translational product level" EXACT []
is_a: SO:0001553 ! translational_product_level_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:55:25Z

[Term]
id: SO:0001557
name: polypeptide_gain_of_function_variant
def: "A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke]
synonym: "polypeptide gain of function variant" EXACT []
is_a: SO:0001554 ! polypeptide_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:56:12Z

[Term]
id: SO:0001558
name: polypeptide_localization_variant
def: "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke]
synonym: "polypeptide localization variant" EXACT []
is_a: SO:0001554 ! polypeptide_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:56:37Z

[Term]
id: SO:0001559
name: polypeptide_loss_of_function_variant
def: "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]
synonym: "polypeptide loss of function variant" EXACT []
is_a: SO:0001554 ! polypeptide_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:56:58Z

[Term]
id: SO:0001560
name: inactive_ligand_binding_site
def: "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]
synonym: "inactive ligand binding site" EXACT []
is_a: SO:0001559 ! polypeptide_loss_of_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:58:00Z

[Term]
id: SO:0001561
name: polypeptide_partial_loss_of_function
def: "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]
synonym: "polypeptide partial loss of function" EXACT []
is_a: SO:0001559 ! polypeptide_loss_of_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:58:32Z

[Term]
id: SO:0001562
name: polypeptide_post_translational_processing_variant
def: "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke]
synonym: "polypeptide post translational processing variant" EXACT []
is_a: SO:0001554 ! polypeptide_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:59:06Z

[Term]
id: SO:0001563
name: copy_number_change
def: "A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke]
synonym: "copy number change" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:27:33Z

[Term]
id: SO:0001564
name: gene_variant
def: "A sequence variant where the structure of the gene is changed." [SO:ke]
synonym: "gene structure variant" EXACT []
synonym: "snpEff:GENE" EXACT VAR []
synonym: "VAAST:gene_variant" EXACT VAR []
is_a: SO:0001878 ! feature_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:28:01Z

[Term]
id: SO:0001565
name: gene_fusion
def: "A sequence variant whereby a two genes have become joined." [SO:ke]
synonym: "gene fusion" EXACT []
is_a: SO:0001564 ! gene_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:28:28Z

[Term]
id: SO:0001566
name: regulatory_region_variant
def: "A sequence variant located within a regulatory region." [SO:ke]
comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.
synonym: "regulatory region variant" EXACT []
synonym: "regulatory_region_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001878 ! feature_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:28:48Z

[Term]
id: SO:0001567
name: stop_retained_variant
def: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]
synonym: "snpEff:SYNONYMOUS_STOP" EXACT VAR []
synonym: "stop retained variant" EXACT []
synonym: "VAAST:stop_retained" EXACT VAR []
is_a: SO:0001590 ! terminator_codon_variant
is_a: SO:0001819 ! synonymous_variant
created_by: kareneilbeck
creation_date: 2010-04-19T05:02:30Z

[Term]
id: SO:0001568
name: splicing_variant
def: "A sequence variant that changes the process of splicing." [SO:ke]
synonym: "splicing variant" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:29:22Z

[Term]
id: SO:0001569
name: cryptic_splice_site_variant
def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "cryptic splice site activation" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001568 ! splicing_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:29:41Z

[Term]
id: SO:0001570
name: cryptic_splice_acceptor
def: "A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]
synonym: "cryptic splice acceptor" EXACT []
is_a: SO:0001569 ! cryptic_splice_site_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:30:11Z

[Term]
id: SO:0001571
name: cryptic_splice_donor
def: "A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]
synonym: "cryptic splice donor" EXACT []
is_a: SO:0001569 ! cryptic_splice_site_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:30:35Z

[Term]
id: SO:0001572
name: exon_loss_variant
def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke]
synonym: "exon loss" EXACT []
synonym: "snpEff:EXON_DELETED" EXACT VAR []
is_a: SO:0001568 ! splicing_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:31:09Z

[Term]
id: SO:0001573
name: intron_gain_variant
def: "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "intron gain" EXACT []
synonym: "intron gain variant" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001568 ! splicing_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:31:25Z

[Term]
id: SO:0001574
name: splice_acceptor_variant
def: "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]
synonym: "snpEff:SPLICE_SITE_ACCEPTOR" EXACT VAR []
synonym: "splice acceptor variant" EXACT []
synonym: "VAAST:splice_acceptor_variant" EXACT VAR []
is_a: SO:0001629 ! splice_site_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:31:52Z

[Term]
id: SO:0001575
name: splice_donor_variant
def: "A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]
synonym: "snpEff:SPLICE_SITE_DONOR" EXACT VAR []
synonym: "splice donor variant" EXACT []
synonym: "VAAST:splice_donor_variant" EXACT VAR []
is_a: SO:0001629 ! splice_site_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:32:10Z

[Term]
id: SO:0001576
name: transcript_variant
def: "A sequence variant that changes the structure of the transcript." [SO:ke]
synonym: "snpEff:TRANSCRIPT" EXACT VAR []
synonym: "transcript variant" EXACT []
synonym: "VAAST:transcript_variant" EXACT VAR []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001564 ! gene_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:32:41Z

[Term]
id: SO:0001577
name: complex_transcript_variant
def: "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html]
comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
synonym: "complex transcript variant" EXACT []
synonym: "complex_indel" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "complext change in transcript" EXACT []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:33:03Z

[Term]
id: SO:0001578
name: stop_lost
def: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]
comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.
synonym: "ANNOVAR:stoploss" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "snpEff:STOP_LOST" EXACT VAR []
synonym: "stop codon lost" EXACT []
synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "VAAST:stop_lost" EXACT VAR []
is_a: SO:0001590 ! terminator_codon_variant
is_a: SO:0001907 ! feature_elongation
is_a: SO:0001992 ! nonsynonymous_variant
created_by: kareneilbeck
creation_date: 2010-03-23T03:46:42Z

[Term]
id: SO:0001579
name: transcript_sequence_variant
synonym: "transcript sequence variant" EXACT []
is_obsolete: true

[Term]
id: SO:0001580
name: coding_sequence_variant
alt_id: SO:0001581
def: "A sequence variant that changes the coding sequence." [SO:ke]
synonym: "coding sequence variant" EXACT []
synonym: "coding variant" EXACT []
synonym: "codon variant" EXACT []
synonym: "codon_variant" EXACT []
synonym: "snpEff:CDS" EXACT VAR []
synonym: "snpEff:CODON_CHANGE" RELATED VAR []
synonym: "VAAST:coding_sequence_variant" EXACT VAR []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001791 ! exon_variant
is_a: SO:0001968 ! coding_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:34:36Z

[Term]
id: SO:0001582
name: initiator_codon_variant
def: "A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]
comment: This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called.
synonym: "initiatior codon variant" EXACT []
synonym: "initiator codon change" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
xref: loinc:LA6695-6 "Initiating Methionine"
is_a: SO:0001580 ! coding_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:35:18Z

[Term]
id: SO:0001583
name: missense_variant
alt_id: SO:0001584
alt_id: SO:0001783
def: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]
comment: EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution.
synonym: "ANNOVAR:nonsynonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "missense codon" EXACT []
synonym: "snpEff:NON_SYSNONYMOUS_CODING" EXACT VAR []
synonym: "VAAST:non_synonymous_codon" RELATED VAR []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
xref: http://en.wikipedia.org/wiki/Missense_mutation
xref: loinc:LA6698-0 "Missense"
is_a: SO:0001992 ! nonsynonymous_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:35:49Z

[Term]
id: SO:0001585
name: conservative_missense_variant
def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]
synonym: "conservative missense codon" EXACT []
synonym: "conservative missense variant" EXACT []
synonym: "neutral missense codon" RELATED []
synonym: "quiet missense codon" RELATED []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001583 ! missense_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:36:40Z

[Term]
id: SO:0001586
name: non_conservative_missense_variant
def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]
synonym: "non conservative missense codon" EXACT []
synonym: "non conservative missense variant" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001583 ! missense_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:37:16Z

[Term]
id: SO:0001587
name: stop_gained
def: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]
comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
synonym: "ANNOVAR:stopgain" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "nonsense codon" EXACT []
synonym: "snpEFF:STOP_GAINED" EXACT VAR []
synonym: "stop codon gained" RELATED []
synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "VAAST:stop_gained" EXACT VAR []
xref: loinc:LA6699-8 "Nonsense"
is_a: SO:0001906 ! feature_truncation
is_a: SO:0001992 ! nonsynonymous_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:37:52Z

[Term]
id: SO:0001589
name: frameshift_variant
def: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]
comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
synonym: "ANNOVAR:frameshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "frameshift variant" EXACT []
synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "frameshift_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "snpEff:FRAME_SHIFT" EXACT VAR []
synonym: "VAAST:frameshift_variant" EXACT VAR []
xref: loinc:LA6694-9 "Frameshift"
is_a: SO:0001818 ! protein_altering_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:40:19Z

[Term]
id: SO:0001590
name: terminator_codon_variant
alt_id: SO:0001625
def: "A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]
comment: The terminal codon may be the terminator, or in an incomplete transcript the last available codon.
synonym: "terminal codon variant" EXACT []
synonym: "terminal_codon_variant" EXACT []
synonym: "terminator codon variant" EXACT []
xref: loinc:LA6700-2 "Stop Codon Mutation"
is_a: SO:0001580 ! coding_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:40:37Z

[Term]
id: SO:0001591
name: frame_restoring_variant
def: "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]
synonym: "frame restoring variant" EXACT []
is_a: SO:0001589 ! frameshift_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:41:09Z

[Term]
id: SO:0001592
name: minus_1_frameshift_variant
def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]
synonym: "-1 frameshift variant" EXACT []
synonym: "minus 1 frameshift variant" EXACT []
is_a: SO:0001589 ! frameshift_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:41:30Z

[Term]
id: SO:0001593
name: minus_2_frameshift_variant
synonym: "-2 frameshift variant" EXACT []
synonym: "minus 2 frameshift variant" EXACT []
is_a: SO:0001589 ! frameshift_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:41:52Z

[Term]
id: SO:0001594
name: plus_1_frameshift_variant
def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]
synonym: "+1 frameshift variant" EXACT []
synonym: "plus 1 frameshift variant" EXACT []
is_a: SO:0001589 ! frameshift_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:42:06Z

[Term]
id: SO:0001595
name: plus_2_frameshift_variant
synonym: "+2 frameshift variant" EXACT []
synonym: "plus 2 frameshift variant" EXACT []
is_a: SO:0001589 ! frameshift_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:42:23Z

[Term]
id: SO:0001596
name: transcript_secondary_structure_variant
def: "A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]
synonym: "transcript secondary structure variant" EXACT []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:43:18Z

[Term]
id: SO:0001597
name: compensatory_transcript_secondary_structure_variant
def: "A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]
synonym: "compensatory transcript secondary structure variant" EXACT []
is_a: SO:0001596 ! transcript_secondary_structure_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:43:54Z

[Term]
id: SO:0001598
name: translational_product_structure_variant
def: "A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]
synonym: "translational product structure variant" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001564 ! gene_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:44:17Z

[Term]
id: SO:0001599
name: 3D_polypeptide_structure_variant
def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke]
synonym: "3D polypeptide structure variant" EXACT []
is_a: SO:0001539 ! translational_product_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:44:46Z

[Term]
id: SO:0001600
name: complex_3D_structural_variant
def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke]
synonym: "complex 3D structural variant" EXACT []
is_a: SO:0001599 ! 3D_polypeptide_structure_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:45:13Z

[Term]
id: SO:0001601
name: conformational_change_variant
def: "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke]
synonym: "conformational change variant" EXACT []
is_a: SO:0001599 ! 3D_polypeptide_structure_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:45:48Z

[Term]
id: SO:0001602
name: complex_change_of_translational_product_variant
synonym: "complex change of translational product variant" EXACT []
is_a: SO:0001539 ! translational_product_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:46:54Z

[Term]
id: SO:0001603
name: polypeptide_sequence_variant
def: "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]
synonym: "polypeptide sequence variant" EXACT []
is_a: SO:0001598 ! translational_product_structure_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:47:13Z

[Term]
id: SO:0001604
name: amino_acid_deletion
def: "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]
synonym: "amino acid deletion" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:47:36Z

[Term]
id: SO:0001605
name: amino_acid_insertion
def: "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]
synonym: "amino acid insertion" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:47:56Z

[Term]
id: SO:0001606
name: amino_acid_substitution
def: "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]
synonym: "amino acid substitution" EXACT []
synonym: "VAAST:amino_acid_substitution" EXACT VAR []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:48:17Z

[Term]
id: SO:0001607
name: conservative_amino_acid_substitution
def: "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]
synonym: "conservative amino acid substitution" EXACT []
is_a: SO:0001606 ! amino_acid_substitution
created_by: kareneilbeck
creation_date: 2010-03-22T02:48:57Z

[Term]
id: SO:0001608
name: non_conservative_amino_acid_substitution
def: "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]
synonym: "non conservative amino acid substitution" EXACT []
is_a: SO:0001606 ! amino_acid_substitution
created_by: kareneilbeck
creation_date: 2010-03-22T02:49:23Z

[Term]
id: SO:0001609
name: elongated_polypeptide
def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]
synonym: "elongated polypeptide" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:49:52Z

[Term]
id: SO:0001610
name: elongated_polypeptide_C_terminal
def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
synonym: "elongated polypeptide C terminal" EXACT []
is_a: SO:0001609 ! elongated_polypeptide
created_by: kareneilbeck
creation_date: 2010-03-22T02:50:20Z

[Term]
id: SO:0001611
name: elongated_polypeptide_N_terminal
def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
synonym: "elongated polypeptide N terminal" EXACT []
is_a: SO:0001609 ! elongated_polypeptide
created_by: kareneilbeck
creation_date: 2010-03-22T02:50:31Z

[Term]
id: SO:0001612
name: elongated_in_frame_polypeptide_C_terminal
def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
synonym: "elongated in frame polypeptide C terminal" EXACT []
is_a: SO:0001610 ! elongated_polypeptide_C_terminal
created_by: kareneilbeck
creation_date: 2010-03-22T02:51:05Z

[Term]
id: SO:0001613
name: elongated_out_of_frame_polypeptide_C_terminal
def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
synonym: "elongated polypeptide out of frame C terminal" EXACT []
is_a: SO:0001610 ! elongated_polypeptide_C_terminal
created_by: kareneilbeck
creation_date: 2010-03-22T02:51:20Z

[Term]
id: SO:0001614
name: elongated_in_frame_polypeptide_N_terminal_elongation
def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
synonym: "elongated in frame polypeptide N terminal" EXACT []
is_a: SO:0001611 ! elongated_polypeptide_N_terminal
created_by: kareneilbeck
creation_date: 2010-03-22T02:51:49Z

[Term]
id: SO:0001615
name: elongated_out_of_frame_polypeptide_N_terminal
def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
synonym: "elongated out of frame N terminal" EXACT []
is_a: SO:0001611 ! elongated_polypeptide_N_terminal
created_by: kareneilbeck
creation_date: 2010-03-22T02:52:05Z

[Term]
id: SO:0001616
name: polypeptide_fusion
def: "A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]
synonym: "polypeptide fusion" EXACT []
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:52:43Z

[Term]
id: SO:0001617
name: polypeptide_truncation
def: "A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]
synonym: "polypeptide truncation" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:53:07Z

[Term]
id: SO:0001618
name: inactive_catalytic_site
def: "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]
synonym: "inactive catalytic site" EXACT []
is_a: SO:0001560 ! inactive_ligand_binding_site
created_by: kareneilbeck
creation_date: 2010-03-22T03:06:14Z

[Term]
id: SO:0001619
name: non_coding_transcript_variant
def: "A transcript variant of a non coding RNA gene." [SO:ke]
comment: Within non-coding gene - Located within a gene that does not code for a protein.
synonym: "ANNOVAR:ncRNA" RELATED VAR [http:http\://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "nc transcript variant" EXACT []
synonym: "non coding transcript variant" EXACT []
synonym: "within_non_coding_gene" EXACT dbsnp [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:16:23Z

[Term]
id: SO:0001620
name: mature_miRNA_variant
def: "A transcript variant located with the sequence of the mature miRNA." [SO:ke]
comment: EBI term: Within mature miRNA - Located within a microRNA.
synonym: "mature miRNA variant" EXACT []
synonym: "within_mature_miRNA" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001619 ! non_coding_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:16:58Z

[Term]
id: SO:0001621
name: NMD_transcript_variant
def: "A variant in a transcript that is the target of NMD." [SO:ke]
synonym: "NMD transcript variant" EXACT []
synonym: "NMD_transcript" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:20:40Z

[Term]
id: SO:0001622
name: UTR_variant
def: "A transcript variant that is located within the UTR." [SO:ke]
synonym: "UTR variant" EXACT []
synonym: "UTR_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001791 ! exon_variant
is_a: SO:0001968 ! coding_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:22:58Z

[Term]
id: SO:0001623
name: 5_prime_UTR_variant
def: "A UTR variant of the 5' UTR." [SO:ke]
comment: EBI term: 5prime UTR variations - In 5prime UTR (untranslated region).
synonym: "5'UTR variant" EXACT []
synonym: "5PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "ANNOVAR:UTR5" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "five prime UTR variant" EXACT []
synonym: "snpEff:UTR_5_PRIME" EXACT VAR []
synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "VAAST:five_prime_UTR_variant" EXACT VAR []
is_a: SO:0001622 ! UTR_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:23:29Z

[Term]
id: SO:0001624
name: 3_prime_UTR_variant
def: "A UTR variant of the 3' UTR." [SO:ke]
comment: EBI term 3prime UTR variations - In 3prime UTR.
synonym: "3'UTR variant" EXACT []
synonym: "3PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "ANNOVAR:UTR3" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "snpEff:UTR_3_PRIME" EXACT VAR []
synonym: "three prime UTR variant" EXACT []
synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "VAAST:three_prime_UTR_variant" EXACT VAR []
is_a: SO:0001622 ! UTR_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:23:54Z

[Term]
id: SO:0001626
name: incomplete_terminal_codon_variant
def: "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]
comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.
synonym: "incomplete terminal codon variant" EXACT []
synonym: "partial_codon" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001590 ! terminator_codon_variant
is_a: SO:0001650 ! inframe_variant
created_by: kareneilbeck
creation_date: 2010-03-23T03:51:15Z

[Term]
id: SO:0001627
name: intron_variant
def: "A transcript variant occurring within an intron." [SO:ke]
comment: EBI term: Intronic variations - In intron.
synonym: "ANNOVAR:intronic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "intron variant" EXACT []
synonym: "intron_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "intronic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "snpEff:INTRON" EXACT VAR []
synonym: "VAAST:intron_variant" EXACT VAR []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T03:52:38Z

[Term]
id: SO:0001628
name: intergenic_variant
def: "A sequence variant located in the intergenic region, between genes." [SO:ke]
comment: EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript.
synonym: "ANNOVAR:intergenic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "intergenic variant" EXACT []
synonym: "snpEff:INTERGENIC" EXACT VAR []
is_a: SO:0001878 ! feature_variant
created_by: kareneilbeck
creation_date: 2010-03-23T05:07:37Z

[Term]
id: SO:0001629
name: splice_site_variant
def: "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]
comment: EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger.
synonym: "essential_splice_site" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "splice site variant" EXACT []
is_a: SO:0001568 ! splicing_variant
is_a: SO:0001627 ! intron_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:42:00Z

[Term]
id: SO:0001630
name: splice_region_variant
def: "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]
comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.
synonym: "ANNOVAR:splicing" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "splice region variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "VAAST:splice_region_variant" EXACT VAR []
is_a: SO:0001568 ! splicing_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:46:02Z

[Term]
id: SO:0001631
name: upstream_gene_variant
def: "A sequence variant located 5' of a gene." [SO:ke]
comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
synonym: "ANNOVAR:upstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "snpEff:UPSTREAM" EXACT VAR []
synonym: "upstream gene variant" EXACT []
is_a: SO:0001628 ! intergenic_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:49:13Z

[Term]
id: SO:0001632
name: downstream_gene_variant
def: "A sequence variant located 3' of a gene." [SO:ke]
comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
synonym: "ANNOVAR:downstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "downstream gene variant" EXACT []
synonym: "snpEff:DOWNSTREAM" EXACT VAR []
is_a: SO:0001628 ! intergenic_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:49:38Z

[Term]
id: SO:0001633
name: 5KB_downstream_variant
def: "A sequence variant located within 5 KB of the end of a gene." [SO:ke]
comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
synonym: "5KB downstream variant" EXACT []
synonym: "downstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "within 5KB downstream" RELATED []
is_a: SO:0001632 ! downstream_gene_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:50:16Z

[Term]
id: SO:0001634
name: 500B_downstream_variant
def: "A sequence variant located within a half KB of the end of a gene." [SO:ke]
synonym: "500B downstream variant" EXACT []
synonym: "near-gene-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
is_a: SO:0001633 ! 5KB_downstream_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:50:42Z

[Term]
id: SO:0001635
name: 5KB_upstream_variant
def: "A sequence variant located within 5KB 5' of a gene." [SO:ke]
comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
synonym: "5kb upstream variant" EXACT []
synonym: "upstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001631 ! upstream_gene_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:51:06Z

[Term]
id: SO:0001636
name: 2KB_upstream_variant
def: "A sequence variant located within 2KB 5' of a gene." [SO:ke]
synonym: "2KB upstream variant" EXACT []
synonym: "near-gene-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
is_a: SO:0001635 ! 5KB_upstream_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:51:22Z

[Term]
id: SO:0001637
name: rRNA_gene
def: "A gene that encodes for ribosomal RNA." [SO:ke]
synonym: "rDNA" EXACT []
synonym: "rRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-04-21T10:10:32Z

[Term]
id: SO:0001638
name: piRNA_gene
def: "A gene that encodes for an piwi associated RNA." [SO:ke]
synonym: "piRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-04-21T10:11:36Z

[Term]
id: SO:0001639
name: RNase_P_RNA_gene
def: "A gene that encodes an RNase P RNA." [SO:ke]
synonym: "RNase P RNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-04-21T10:13:23Z

[Term]
id: SO:0001640
name: RNase_MRP_RNA_gene
def: "A gene that encodes a RNase_MRP_RNA." [SO:ke]
synonym: "RNase MRP RNA gene" RELATED []
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-04-21T10:13:58Z

[Term]
id: SO:0001641
name: lincRNA_gene
def: "A gene that encodes large intervening non-coding RNA." [SO:ke]
synonym: "lincRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-04-21T10:14:24Z

[Term]
id: SO:0001642
name: mathematically_defined_repeat
def: "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill]
comment: Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.).
synonym: "mathematically defined repeat" EXACT []
is_a: SO:0001410 ! experimental_feature
created_by: kareneilbeck
creation_date: 2010-05-03T11:50:14Z

[Term]
id: SO:0001643
name: telomerase_RNA_gene
def: "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]
synonym: "Telomerase RNA component" EXACT []
synonym: "telomerase RNA gene" EXACT []
synonym: "TERC" EXACT []
xref: http:http\://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia"
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-05-18T05:26:38Z

[Term]
id: SO:0001644
name: targeting_vector
def: "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]
synonym: "targeting vector" RELATED []
is_a: SO:0000440 ! vector_replicon
is_a: SO:0000804 ! engineered_region
intersection_of: SO:0000440 ! vector_replicon
intersection_of: has_part SO:0000853 ! homologous_region
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_part SO:0000853 ! homologous_region
relationship: has_quality SO:0000783 ! engineered
created_by: kareneilbeck
creation_date: 2010-05-28T02:05:25Z

[Term]
id: SO:0001645
name: genetic_marker
def: "A measurable sequence feature that varies within a population." [SO:db]
synonym: "genetic marker" RELATED []
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2010-05-28T02:33:07Z

[Term]
id: SO:0001646
name: DArT_marker
def: "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke]
synonym: "DArT marker" EXACT []
is_a: SO:0001645 ! genetic_marker
created_by: kareneilbeck
creation_date: 2010-05-28T02:34:43Z

[Term]
id: SO:0001647
name: kozak_sequence
def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]
subset: SOFA
synonym: "kozak consensus" EXACT []
synonym: "kozak consensus sequence" EXACT []
synonym: "kozak sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia"
is_a: SO:0000139 ! ribosome_entry_site
created_by: kareneilbeck
creation_date: 2010-06-07T03:12:20Z

[Term]
id: SO:0001648
name: nested_transposon
def: "A transposon that is disrupted by the insertion of another element." [SO:ke]
synonym: "nested transposon" EXACT []
is_a: SO:0000101 ! transposable_element
created_by: kareneilbeck
creation_date: 2010-06-23T03:22:57Z

[Term]
id: SO:0001649
name: nested_repeat
def: "A repeat that is disrupted by the insertion of another element." [SO:ke]
synonym: "nested repeat" RELATED []
is_a: SO:0000657 ! repeat_region
created_by: kareneilbeck
creation_date: 2010-06-23T03:24:55Z

[Term]
id: SO:0001650
name: inframe_variant
def: "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]
synonym: "ANNOVAR:nonframeshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "cds-indel" EXACT dbsnp []
synonym: "inframe variant" EXACT []
synonym: "VAAST:inframe_variant" EXACT VAR []
is_a: SO:0001818 ! protein_altering_variant
created_by: kareneilbeck
creation_date: 2010-07-19T01:24:44Z

[Term]
id: SO:0001653
name: retinoic_acid_responsive_element
def: "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]
synonym: "RARE" EXACT []
synonym: "retinoic acid responsive element" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000167 ! promoter
created_by: kareneilbeck
creation_date: 2010-08-03T10:46:12Z

[Term]
id: SO:0001654
name: nucleotide_to_protein_binding_site
def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
subset: SOFA
synonym: "nucleotide to protein binding site" RELATED []
is_a: SO:0000410 ! protein_binding_site
created_by: kareneilbeck
creation_date: 2010-08-03T12:26:05Z

[Term]
id: SO:0001655
name: nucleotide_binding_site
def: "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]
comment: See GO:0000166 : nucleotide binding.
synonym: "np_bind" EXACT BS [uniprot:feature]
synonym: "nucleotide binding site" EXACT []
is_a: SO:0000409 ! binding_site
created_by: kareneilbeck
creation_date: 2010-08-03T12:30:04Z

[Term]
id: SO:0001656
name: metal_binding_site
def: "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]
comment: See GO:0046872 : metal ion binding.
synonym: "metal binding site" RELATED []
is_a: SO:0000409 ! binding_site
created_by: kareneilbeck
creation_date: 2010-08-03T12:31:42Z

[Term]
id: SO:0001657
name: ligand_binding_site
def: "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke]
synonym: "ligand binding site" EXACT []
is_a: SO:0000409 ! binding_site
created_by: kareneilbeck
creation_date: 2010-08-03T12:32:58Z

[Term]
id: SO:0001658
name: nested_tandem_repeat
def: "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]
comment: Tracker ID: 3052459.
synonym: "nested tandem repeat" EXACT []
synonym: "NTR" EXACT []
is_a: SO:0001649 ! nested_repeat
created_by: kareneilbeck
creation_date: 2010-08-26T09:36:16Z

[Term]
id: SO:0001659
name: promoter_element
synonym: "promoter element" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: overlaps SO:0000235 ! TF_binding_site
created_by: kareneilbeck
creation_date: 2010-10-01T11:48:32Z

[Term]
id: SO:0001660
name: core_promoter_element
synonym: "core promoter element" EXACT []
synonym: "general transcription factor binding site" RELATED []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2010-10-01T11:49:03Z

[Term]
id: SO:0001661
name: RNA_polymerase_II_TATA_box
def: "A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]
synonym: "RNA polymerase II TATA box" EXACT []
is_a: SO:0000174 ! TATA_box
relationship: part_of SO:0001669 ! RNApol_II_core_promoter
created_by: kareneilbeck
creation_date: 2010-10-01T02:42:12Z

[Term]
id: SO:0001662
name: RNA_polymerase_III_TATA_box
def: "A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]
synonym: "RNA polymerase III TATA box" EXACT []
is_a: SO:0000174 ! TATA_box
relationship: part_of SO:0000171 ! RNApol_III_promoter
created_by: kareneilbeck
creation_date: 2010-10-01T02:43:16Z

[Term]
id: SO:0001663
name: BREd_motif
def: "A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]
synonym: "BREd" EXACT []
synonym: "BREd motif" RELATED []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter
created_by: kareneilbeck
creation_date: 2010-10-01T02:49:55Z

[Term]
id: SO:0001664
name: DCE
def: "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]
synonym: "downstream core element" RELATED []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter
created_by: kareneilbeck
creation_date: 2010-10-01T02:56:41Z

[Term]
id: SO:0001665
name: DCE_SI
def: "A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]
synonym: "DCE SI" RELATED []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001664 ! DCE
created_by: kareneilbeck
creation_date: 2010-10-01T03:00:10Z

[Term]
id: SO:0001666
name: DCE_SII
def: "A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]
synonym: "DCE SII" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001664 ! DCE
created_by: kareneilbeck
creation_date: 2010-10-01T03:00:30Z

[Term]
id: SO:0001667
name: DCE_SIII
def: "A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]
synonym: "DCE SIII" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001664 ! DCE
created_by: kareneilbeck
creation_date: 2010-10-01T03:00:44Z

[Term]
id: SO:0001668
name: proximal_promoter_element
def: "DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]
synonym: "proximal promoter element" RELATED []
synonym: "specific transcription factor binding site" RELATED []
is_a: SO:0001678 ! regulatory_promoter_element
created_by: kareneilbeck
creation_date: 2010-10-01T03:10:23Z

[Term]
id: SO:0001669
name: RNApol_II_core_promoter
def: "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]
synonym: "RNApol II core promoter" EXACT []
is_a: SO:0000170 ! RNApol_II_promoter
created_by: kareneilbeck
creation_date: 2010-10-01T03:13:41Z

[Term]
id: SO:0001670
name: distal_promoter_element
synonym: "distal promoter element" RELATED []
is_a: SO:0001678 ! regulatory_promoter_element
created_by: kareneilbeck
creation_date: 2010-10-01T03:21:08Z

[Term]
id: SO:0001671
name: bacterial_RNApol_promoter_sigma_70
synonym: "bacterial RNA polymerase promoter sigma 70" EXACT []
is_a: SO:0000613 ! bacterial_RNApol_promoter
created_by: kareneilbeck
creation_date: 2010-10-06T01:41:34Z

[Term]
id: SO:0001672
name: bacterial_RNApol_promoter_sigma54
synonym: "bacterial RNA polymerase promoter sigma54" EXACT []
is_a: SO:0000613 ! bacterial_RNApol_promoter
created_by: kareneilbeck
creation_date: 2010-10-06T01:42:37Z

[Term]
id: SO:0001673
name: minus_12_signal
def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]
synonym: "minus 12 signal" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54
created_by: kareneilbeck
creation_date: 2010-10-06T01:44:57Z

[Term]
id: SO:0001674
name: minus_24_signal
def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]
synonym: "minus 24 signal" RELATED []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54
created_by: kareneilbeck
creation_date: 2010-10-06T01:45:24Z

[Term]
id: SO:0001675
name: A_box_type_1
def: "An A box within an RNA polymerase III type 1 promoter." [SO:ke]
comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
synonym: "A box type 1" RELATED []
is_a: SO:0000619 ! A_box
relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
created_by: kareneilbeck
creation_date: 2010-10-06T05:43:43Z

[Term]
id: SO:0001676
name: A_box_type_2
def: "An A box within an RNA polymerase III type 2 promoter." [SO:ke]
comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
synonym: "A box type 2" RELATED []
is_a: SO:0000619 ! A_box
relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2
created_by: kareneilbeck
creation_date: 2010-10-06T05:44:18Z

[Term]
id: SO:0001677
name: intermediate_element
def: "A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]
synonym: "IE" EXACT []
synonym: "intermediate element" RELATED []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
created_by: kareneilbeck
creation_date: 2010-10-06T05:52:03Z

[Term]
id: SO:0001678
name: regulatory_promoter_element
def: "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]
synonym: "regulatory promoter element" RELATED []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2010-10-07T04:39:48Z

[Term]
id: SO:0001679
name: transcription_regulatory_region
def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke]
subset: SOFA
synonym: "transcription regulatory region" EXACT []
is_a: SO:0005836 ! regulatory_region
created_by: kareneilbeck
creation_date: 2010-10-12T03:49:35Z

[Term]
id: SO:0001680
name: translation_regulatory_region
def: "A regulatory region that is involved in the control of the process of translation." [SO:ke]
synonym: "translation regulatory region" EXACT []
is_a: SO:0005836 ! regulatory_region
created_by: kareneilbeck
creation_date: 2010-10-12T03:52:45Z

[Term]
id: SO:0001681
name: recombination_regulatory_region
def: "A regulatory region that is involved in the control of the process of recombination." [SO:ke]
synonym: "recombination regulatory region" EXACT []
is_a: SO:0005836 ! regulatory_region
created_by: kareneilbeck
creation_date: 2010-10-12T03:53:35Z

[Term]
id: SO:0001682
name: replication_regulatory_region
def: "A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]
synonym: "replication regulatory region" RELATED []
is_a: SO:0005836 ! regulatory_region
created_by: kareneilbeck
creation_date: 2010-10-12T03:54:09Z

[Term]
id: SO:0001683
name: sequence_motif
def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]
subset: SOFA
synonym: "sequence motif" RELATED []
xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia"
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2010-10-14T04:13:22Z

[Term]
id: SO:0001684
name: experimental_feature_attribute
def: "An attribute of an experimentally derived feature." [SO:ke]
synonym: "experimental feature attribute" RELATED []
is_a: SO:0000733 ! feature_attribute
created_by: kareneilbeck
creation_date: 2010-10-28T02:22:23Z

[Term]
id: SO:0001685
name: score
def: "The score of an experimentally derived feature such as a p-value." [SO:ke]
is_a: SO:0001684 ! experimental_feature_attribute
created_by: kareneilbeck
creation_date: 2010-10-28T02:23:16Z

[Term]
id: SO:0001686
name: quality_value
def: "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke]
synonym: "quality value" RELATED []
is_a: SO:0001684 ! experimental_feature_attribute
created_by: kareneilbeck
creation_date: 2010-10-28T02:24:11Z

[Term]
id: SO:0001687
name: restriction_enzyme_recognition_site
def: "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]
synonym: "restriction endonuclease recognition site" EXACT []
synonym: "restriction enzyme recognition site" EXACT []
is_a: SO:0001954 ! restriction_enzyme_region
created_by: kareneilbeck
creation_date: 2010-10-29T12:29:57Z

[Term]
id: SO:0001688
name: restriction_enzyme_cleavage_junction
def: "The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]
synonym: "restriction enzyme cleavage junction" EXACT []
is_a: SO:0000699 ! junction
created_by: kareneilbeck
creation_date: 2010-10-29T12:35:02Z

[Term]
id: SO:0001689
name: five_prime_restriction_enzyme_junction
def: "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]
synonym: "5' restriction enzyme junction" EXACT []
is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site
relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:36:24Z

[Term]
id: SO:0001690
name: three_prime_restriction_enzyme_junction
synonym: "3' restriction enzyme junction" EXACT []
is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site
relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:37:52Z

[Term]
id: SO:0001691
name: blunt_end_restriction_enzyme_cleavage_site
synonym: "blunt end restriction enzyme cleavage site" EXACT []
is_a: SO:0001687 ! restriction_enzyme_recognition_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:39:53Z

[Term]
id: SO:0001692
name: sticky_end_restriction_enzyme_cleavage_site
synonym: "sticky end restriction enzyme cleavage site" RELATED []
is_a: SO:0001687 ! restriction_enzyme_recognition_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:40:50Z

[Term]
id: SO:0001693
name: blunt_end_restriction_enzyme_cleavage_junction
def: "A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]
synonym: "blunt end restriction enzyme cleavage site" RELATED []
is_a: SO:0001688 ! restriction_enzyme_cleavage_junction
relationship: part_of SO:0001691 ! blunt_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:43:14Z

[Term]
id: SO:0001694
name: single_strand_restriction_enzyme_cleavage_site
def: "A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]
synonym: "single strand restriction enzyme cleavage site" RELATED []
is_a: SO:0001688 ! restriction_enzyme_cleavage_junction
created_by: kareneilbeck
creation_date: 2010-10-29T12:44:48Z

[Term]
id: SO:0001695
name: restriction_enzyme_single_strand_overhang
def: "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]
synonym: "single strand overhang" EXACT []
synonym: "sticky end" RELATED []
is_a: SO:0001954 ! restriction_enzyme_region
relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:48:35Z

[Term]
id: SO:0001696
name: experimentally_defined_binding_region
def: "A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke]
synonym: "experimentally defined binding region" RELATED []
is_a: SO:0001410 ! experimental_feature
created_by: kareneilbeck
creation_date: 2010-11-02T11:39:59Z

[Term]
id: SO:0001697
name: ChIP_seq_region
def: "A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke]
synonym: "ChIP seq region" RELATED []
is_a: SO:0001696 ! experimentally_defined_binding_region
relationship: contains SO:0000410 ! protein_binding_site
created_by: kareneilbeck
creation_date: 2010-11-02T11:43:07Z

[Term]
id: SO:0001698
name: ASPE_primer
def: "\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]
synonym: "allele specific primer extension primer" EXACT []
synonym: "ASPE primer" EXACT []
is_a: SO:0000112 ! primer
created_by: kareneilbeck
creation_date: 2010-11-11T03:25:21Z

[Term]
id: SO:0001699
name: dCAPS_primer
def: "A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]
synonym: "dCAPS primer" EXACT []
synonym: "derived cleaved amplified polymorphic primer" EXACT []
is_a: SO:0000112 ! primer
created_by: kareneilbeck
creation_date: 2010-11-11T03:27:09Z

[Term]
id: SO:0001700
name: histone_modification
def: "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]
synonym: "histone modification" EXACT []
synonym: "histone modification site" RELATED []
is_a: SO:0001089 ! post_translationally_modified_region
is_a: SO:0001720 ! epigenetically_modified_region
intersection_of: SO:0001089 ! post_translationally_modified_region
intersection_of: has_quality SO:0000133 ! epigenetically_modified
relationship: has_quality SO:0000133 ! epigenetically_modified
created_by: kareneilbeck
creation_date: 2010-03-31T10:22:08Z

[Term]
id: SO:0001701
name: histone_methylation_site
def: "A histone modification site where the modification is the methylation of the residue." [SO:ke]
synonym: "histone methylation" EXACT []
synonym: "histone methylation site" EXACT []
is_a: SO:0001700 ! histone_modification
created_by: kareneilbeck
creation_date: 2010-03-31T10:23:02Z

[Term]
id: SO:0001702
name: histone_acetylation_site
def: "A histone modification where the modification is the acylation of the residue." [SO:ke]
synonym: "histone acetylation" EXACT []
synonym: "histone acetylation site" EXACT []
is_a: SO:0001700 ! histone_modification
created_by: kareneilbeck
creation_date: 2010-03-31T10:23:27Z

[Term]
id: SO:0001703
name: H3K9_acetylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K9 acetylation site" EXACT []
synonym: "H3K9Ac" RELATED []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:25:05Z

[Term]
id: SO:0001704
name: H3K14_acetylation_site
def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K14 acetylation site" EXACT []
synonym: "H3K14Ac" RELATED []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:25:53Z

[Term]
id: SO:0001705
name: H3K4_monomethylation_site
def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K4 mono-methylation site" EXACT []
synonym: "H3K4me1" RELATED []
is_a: SO:0001734 ! H3K4_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:28:14Z

[Term]
id: SO:0001706
name: H3K4_trimethylation
def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K4 tri-methylation" EXACT []
synonym: "H3K4me3" RELATED []
is_a: SO:0001734 ! H3K4_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:29:12Z

[Term]
id: SO:0001707
name: H3K9_trimethylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K9 tri-methylation site" EXACT []
synonym: "H3K9Me3" RELATED []
is_a: SO:0001736 ! H3K9_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:30:34Z

[Term]
id: SO:0001708
name: H3K27_monomethylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H2K27 mono-methylation site" EXACT []
synonym: "H2K27Me1" RELATED []
is_a: SO:0001732 ! H3K27_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:31:54Z

[Term]
id: SO:0001709
name: H3K27_trimethylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K27 tri-methylation site" EXACT []
synonym: "H3K27Me3" RELATED []
is_a: SO:0001732 ! H3K27_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:32:41Z

[Term]
id: SO:0001710
name: H3K79_monomethylation_site
def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K79 mono-methylation site" EXACT []
synonym: "H3K79me1" RELATED []
is_a: SO:0001735 ! H3K79_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:33:42Z

[Term]
id: SO:0001711
name: H3K79_dimethylation_site
def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K79 di-methylation site" EXACT []
synonym: "H3K79Me2" RELATED []
is_a: SO:0001735 ! H3K79_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:34:39Z

[Term]
id: SO:0001712
name: H3K79_trimethylation_site
def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K79 tri-methylation site" EXACT []
synonym: "H3K79Me3" RELATED []
is_a: SO:0001735 ! H3K79_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:35:30Z

[Term]
id: SO:0001713
name: H4K20_monomethylation_site
def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H4K20 mono-methylation site" EXACT []
synonym: "H4K20Me1" RELATED []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:36:43Z

[Term]
id: SO:0001714
name: H2BK5_monomethylation_site
def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H2BK5 mono-methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:38:12Z

[Term]
id: SO:0001715
name: ISRE
def: "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]
comment: Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term.
synonym: "interferon stimulated response element" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region
created_by: kareneilbeck
creation_date: 2010-04-05T11:15:08Z

[Term]
id: SO:0001716
name: histone_ubiqitination_site
def: "A histone modification site where ubiquitin may be added." [SO:ke]
synonym: "histone ubiquitination site" RELATED []
is_a: SO:0001700 ! histone_modification
created_by: kareneilbeck
creation_date: 2010-04-13T10:12:18Z

[Term]
id: SO:0001717
name: H2B_ubiquitination_site
def: "A histone modification site on H2B where ubiquitin may be added." [SO:ke]
synonym: "H2BUbiq" RELATED []
is_a: SO:0001716 ! histone_ubiqitination_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:13:28Z

[Term]
id: SO:0001718
name: H3K18_acetylation_site
def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
synonym: "H3K18 acetylation site" EXACT []
synonym: "H3K18Ac" RELATED []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:39:35Z

[Term]
id: SO:0001719
name: H3K23_acylation_site
def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
synonym: "H3K23 acylation site" RELATED []
synonym: "H3K23Ac" RELATED []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:42:45Z

[Term]
id: SO:0001720
name: epigenetically_modified_region
def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]
subset: SOFA
synonym: "epigenetically modified region" RELATED []
is_a: SO:0001411 ! biological_region
intersection_of: SO:0001411 ! biological_region
intersection_of: has_quality SO:0000133 ! epigenetically_modified
relationship: has_quality SO:0000133 ! epigenetically_modified
created_by: kareneilbeck
creation_date: 2010-03-27T12:02:29Z

[Term]
id: SO:0001721
name: H3K27_acylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
synonym: "H3K27 acylation site" EXACT []
synonym: "H3K27Ac" RELATED []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:44:09Z

[Term]
id: SO:0001722
name: H3K36_monomethylation_site
def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]
synonym: "H3K36 mono-methylation site" EXACT []
synonym: "H3K36<Me1" RELATED []
is_a: SO:0001733 ! H3K36_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:46:32Z

[Term]
id: SO:0001723
name: H3K36_dimethylation_site
def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]
synonym: "H3K36 di-methylation site" EXACT []
synonym: "H3K36Me2" RELATED []
is_a: SO:0001733 ! H3K36_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:59:35Z

[Term]
id: SO:0001724
name: H3K36_trimethylation_site
def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]
synonym: "H3K36 tri-methylation site" EXACT []
synonym: "H3K36Me3" RELATED []
is_a: SO:0001733 ! H3K36_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:01:58Z

[Term]
id: SO:0001725
name: H3K4_dimethylation_site
def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]
synonym: "H3K4 di-methylation site" EXACT []
synonym: "H3K4Me2" RELATED []
is_a: SO:0001734 ! H3K4_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:03:15Z

[Term]
id: SO:0001726
name: H3K27_dimethylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]
synonym: "H3K27 di-methylation site" EXACT []
synonym: "H3K27Me2" RELATED []
is_a: SO:0001732 ! H3K27_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T01:45:41Z

[Term]
id: SO:0001727
name: H3K9_monomethylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]
synonym: "H3K9 mono-methylation site" EXACT []
synonym: "H3K9Me1" RELATED []
is_a: SO:0001736 ! H3K9_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:06:17Z

[Term]
id: SO:0001728
name: H3K9_dimethylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]
synonym: "H3K9 di-methylation site" EXACT []
synonym: "H3K9Me2" RELATED []
is_a: SO:0001736 ! H3K9_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:08:19Z

[Term]
id: SO:0001729
name: H4K16_acylation_site
def: "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]
synonym: "H4K16 acylation_site" RELATED []
synonym: "H4K16Ac" RELATED []
is_a: SO:0001972 ! histone_4_acylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:09:41Z

[Term]
id: SO:0001730
name: H4K5_acylation_site
def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]
synonym: "H4K5 acylation site" RELATED []
synonym: "H4K5Ac" RELATED []
is_a: SO:0001972 ! histone_4_acylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:13:00Z

[Term]
id: SO:0001731
name: H4K8_acylation_site
def: "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]
synonym: "H4K8 acylation site" RELATED []
synonym: "H4K8Ac" RELATED []
is_a: SO:0001972 ! histone_4_acylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:14:24Z

[Term]
id: SO:0001732
name: H3K27_methylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
synonym: "H3K27 methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:26:22Z

[Term]
id: SO:0001733
name: H3K36_methylation_site
def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
synonym: "H3K36 methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:27:28Z

[Term]
id: SO:0001734
name: H3K4_methylation_site
def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]
synonym: "H3K4 methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:28:14Z

[Term]
id: SO:0001735
name: H3K79_methylation_site
def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
synonym: "H3K79 methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:29:16Z

[Term]
id: SO:0001736
name: H3K9_methylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
synonym: "H3K9 methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:31:37Z

[Term]
id: SO:0001737
name: histone_acylation_region
def: "A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]
synonym: "histone acylation region" RELATED []
is_a: SO:0001700 ! histone_modification
created_by: kareneilbeck
creation_date: 2010-04-13T01:58:21Z

[Term]
id: SO:0001738
name: H4K_acylation_region
def: "A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]
synonym: "H4K acylation region" EXACT []
synonym: "H4KAc" RELATED []
is_a: SO:0001737 ! histone_acylation_region
created_by: kareneilbeck
creation_date: 2010-04-13T02:00:06Z

[Term]
id: SO:0001739
name: gene_with_non_canonical_start_codon
def: "A gene with a start codon other than AUG." [SO:xp]
comment: Requested by flybase, Dec 2010.
synonym: "gene with non canonical start codon" EXACT []
is_a: SO:0000704 ! gene
intersection_of: SO:0000704 ! gene
intersection_of: contains SO:0000680 ! non_canonical_start_codon
relationship: contains SO:0000680 ! non_canonical_start_codon
created_by: kareneilbeck
creation_date: 2011-01-10T01:30:31Z

[Term]
id: SO:0001740
name: gene_with_start_codon_CUG
def: "A gene with a translational start codon of CUG." [SO:mc]
comment: Requested by flybase, Dec 2010.
synonym: "gene with start codon CUG" EXACT []
is_a: SO:0001739 ! gene_with_non_canonical_start_codon
created_by: kareneilbeck
creation_date: 2011-01-10T01:32:35Z

[Term]
id: SO:0001741
name: pseudogenic_gene_segment
def: "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]
synonym: "pseudogenic gene segment" EXACT []
is_a: SO:3000000 ! gene_segment
created_by: batchelorc
creation_date: 2011-02-15T05:07:52Z

[Term]
id: SO:0001742
name: copy_number_gain
def: "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke]
subset: DBVAR
synonym: "copy number gain" EXACT []
synonym: "gain" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
is_a: SO:0001019 ! copy_number_variation
created_by: kareneilbeck
creation_date: 2011-02-28T01:54:09Z

[Term]
id: SO:0001743
name: copy_number_loss
def: "A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke]
subset: DBVAR
synonym: "copy number loss" EXACT []
synonym: "loss" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
is_a: SO:0001019 ! copy_number_variation
created_by: kareneilbeck
creation_date: 2011-02-28T01:55:02Z

[Term]
id: SO:0001744
name: UPD
def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM]
subset: DBVAR
synonym: "uniparental disomy" EXACT []
synonym: "UPD" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
xref: http:http\://en.wikipedia.org/wiki/Uniparental_disomy "wikipedia"
is_a: SO:0001059 ! sequence_alteration
created_by: kareneilbeck
creation_date: 2011-02-28T02:01:05Z

[Term]
id: SO:0001745
name: maternal_uniparental_disomy
def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm]
synonym: "maternal uniparental disomy" EXACT []
is_a: SO:0001744 ! UPD
created_by: kareneilbeck
creation_date: 2011-02-28T02:03:01Z

[Term]
id: SO:0001746
name: paternal_uniparental_disomy
def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm]
synonym: "paternal uniparental disomy" EXACT []
is_a: SO:0001744 ! UPD
created_by: kareneilbeck
creation_date: 2011-02-28T02:03:30Z

[Term]
id: SO:0001747
name: open_chromatin_region
def: "A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb]
comment: Requested by John Calley 3125900.
synonym: "open chromatin region" EXACT []
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2011-02-28T02:21:52Z

[Term]
id: SO:0001748
name: SL3_acceptor_site
def: "A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL3 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T02:58:40Z

[Term]
id: SO:0001749
name: SL4_acceptor_site
def: "A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL4 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:08:47Z

[Term]
id: SO:0001750
name: SL5_acceptor_site
def: "A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL5 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:09:36Z

[Term]
id: SO:0001751
name: SL6_acceptor_site
def: "A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL6 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:10:14Z

[Term]
id: SO:0001752
name: SL7_acceptor_site
def: "A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL37 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:13:20Z

[Term]
id: SO:0001753
name: SL8_acceptor_site
def: "A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL8 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:15:26Z

[Term]
id: SO:0001754
name: SL9_acceptor_site
def: "A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL9 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:15:57Z

[Term]
id: SO:0001755
name: SL10_acceptor_site
def: "A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL10 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:16:31Z

[Term]
id: SO:0001756
name: SL11_acceptor_site
def: "A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL11 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:16:54Z

[Term]
id: SO:0001757
name: SL12_acceptor_site
def: "A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL12 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:17:23Z

[Term]
id: SO:0001758
name: duplicated_pseudogene
def: "A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene]
synonym: "duplicated pseudogene" RELATED []
is_a: SO:0001760 ! non_processed_pseudogene
created_by: kareneilbeck
creation_date: 2011-03-09T09:58:04Z

[Term]
id: SO:0001759
name: unitary_pseudogene
def: "A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]
comment: This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates.
synonym: "disabled gene" RELATED []
synonym: "unitary pseudogene" RELATED []
is_a: SO:0001760 ! non_processed_pseudogene
created_by: kareneilbeck
creation_date: 2011-03-09T10:04:04Z

[Term]
id: SO:0001760
name: non_processed_pseudogene
def: "A pseudogene that arose from a means other than retrotransposition." [SO:ke]
synonym: "non processed pseudogene" RELATED []
is_a: SO:0000336 ! pseudogene
created_by: kareneilbeck
creation_date: 2011-03-09T10:54:47Z

[Term]
id: SO:0001761
name: variant_quality
def: "A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]
synonym: "variant quality" EXACT []
is_a: SO:0000400 ! sequence_attribute
created_by: kareneilbeck
creation_date: 2011-03-15T03:40:35Z

[Term]
id: SO:0001762
name: variant_origin
def: "A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]
synonym: "variant origin" EXACT []
is_a: SO:0001761 ! variant_quality
created_by: kareneilbeck
creation_date: 2011-03-15T03:42:13Z

[Term]
id: SO:0001763
name: variant_frequency
def: "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]
synonym: "variant frequency" EXACT []
is_a: SO:0001761 ! variant_quality
created_by: kareneilbeck
creation_date: 2011-03-15T03:44:39Z

[Term]
id: SO:0001764
name: unique_variant
def: "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke]
synonym: "unique variant" EXACT []
is_a: SO:0001763 ! variant_frequency
created_by: kareneilbeck
creation_date: 2011-03-15T03:47:20Z

[Term]
id: SO:0001765
name: rare_variant
synonym: "rare variant" EXACT []
is_a: SO:0001763 ! variant_frequency
created_by: kareneilbeck
creation_date: 2011-03-15T03:48:29Z

[Term]
id: SO:0001766
name: polymorphic_variant
synonym: "polymorphic variant" EXACT []
is_a: SO:0001763 ! variant_frequency
created_by: kareneilbeck
creation_date: 2011-03-15T03:48:51Z

[Term]
id: SO:0001767
name: common_variant
synonym: "common variant" EXACT []
is_a: SO:0001763 ! variant_frequency
created_by: kareneilbeck
creation_date: 2011-03-15T03:50:36Z

[Term]
id: SO:0001768
name: fixed_variant
synonym: "fixed variant" EXACT []
is_a: SO:0001763 ! variant_frequency
created_by: kareneilbeck
creation_date: 2011-03-15T03:50:53Z

[Term]
id: SO:0001769
name: variant_phenotype
def: "A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]
synonym: "variant phenotype" EXACT []
is_a: SO:0001761 ! variant_quality
created_by: kareneilbeck
creation_date: 2011-03-15T03:53:15Z

[Term]
id: SO:0001770
name: benign_variant
synonym: "benign variant" EXACT []
is_a: SO:0001769 ! variant_phenotype
created_by: kareneilbeck
creation_date: 2011-03-15T03:55:40Z

[Term]
id: SO:0001771
name: disease_associated_variant
synonym: "disease associated variant" EXACT []
is_a: SO:0001769 ! variant_phenotype
created_by: kareneilbeck
creation_date: 2011-03-15T04:05:16Z

[Term]
id: SO:0001772
name: disease_causing_variant
synonym: "disease causing variant" EXACT []
is_a: SO:0001769 ! variant_phenotype
created_by: kareneilbeck
creation_date: 2011-03-15T04:05:46Z

[Term]
id: SO:0001773
name: lethal_variant
synonym: "lethal variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2011-03-15T04:06:22Z

[Term]
id: SO:0001774
name: quantitative_variant
synonym: "quantitative variant" EXACT []
is_a: SO:0001769 ! variant_phenotype
created_by: kareneilbeck
creation_date: 2011-03-15T04:28:13Z

[Term]
id: SO:0001775
name: maternal_variant
synonym: "maternal variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:30:23Z

[Term]
id: SO:0001776
name: paternal_variant
synonym: "paternal variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:30:47Z

[Term]
id: SO:0001777
name: somatic_variant
synonym: "somatic variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:31:12Z

[Term]
id: SO:0001778
name: germline_variant
synonym: "germline variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:31:46Z

[Term]
id: SO:0001779
name: pedigree_specific_variant
synonym: "pedigree specific variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:32:18Z

[Term]
id: SO:0001780
name: population_specific_variant
synonym: "population specific variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:33:05Z

[Term]
id: SO:0001781
name: de_novo_variant
synonym: "de novo variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:33:34Z

[Term]
id: SO:0001782
name: TF_binding_site_variant
def: "A sequence variant located within a transcription factor binding site." [EBI:fc]
synonym: "TF binding site variant" EXACT []
is_a: SO:0001566 ! regulatory_region_variant
created_by: kareneilbeck
creation_date: 2011-03-17T10:59:20Z

[Term]
id: SO:0001784
name: complex_structural_alteration
alt_id: SO:1000146
def: "A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints." [FB:reference_manual, NCBI:th, SO:ke]
subset: DBVAR
synonym: "complex" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
synonym: "complex chromosomal mutation" EXACT []
synonym: "complex_chromosomal_mutation" EXACT []
is_a: SO:0001785 ! structural_alteration
is_a: SO:1000183 ! chromosome_structure_variation
created_by: kareneilbeck
creation_date: 2011-03-23T03:21:19Z

[Term]
id: SO:0001785
name: structural_alteration
subset: DBVAR
synonym: "structural alteration" EXACT []
is_a: SO:0001059 ! sequence_alteration
created_by: kareneilbeck
creation_date: 2011-03-25T02:27:41Z

[Term]
id: SO:0001786
name: loss_of_heterozygosity
def: "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." [SO:ke]
subset: DBVAR
synonym: "LOH" EXACT []
synonym: "loss of heterozygosity" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2011-03-25T02:32:58Z

[Term]
id: SO:0001787
name: splice_donor_5th_base_variant
def: "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]
synonym: "splice donor 5th base variant" EXACT []
is_a: SO:0001629 ! splice_site_variant
created_by: kareneilbeck
creation_date: 2011-04-05T04:16:28Z

[Term]
id: SO:0001788
name: U_box
def: "An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]
synonym: "U-box" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0000186 ! LTR_retrotransposon
created_by: kareneilbeck
creation_date: 2011-04-08T10:39:14Z

[Term]
id: SO:0001789
name: mating_type_region
def: "A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]
synonym: "mating type region" EXACT []
xref: http://en.wikipedia.org/wiki/Mating-type_region
is_a: SO:0005855 ! gene_group
created_by: kareneilbeck
creation_date: 2011-04-08T11:14:07Z

[Term]
id: SO:0001790
name: paired_end_fragment
def: "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]
subset: SOFA
synonym: "paired end fragment" EXACT []
is_a: SO:0000143 ! assembly_component
created_by: kareneilbeck
creation_date: 2011-04-14T01:48:20Z

[Term]
id: SO:0001791
name: exon_variant
def: "A sequence variant that changes exon sequence." [SO:ke]
synonym: "ANNOVAR:exonic" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "exon variant" EXACT []
synonym: "snpEff:EXON" EXACT VAR []
synonym: "VAAST:exon_variant" EXACT VAR []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2011-05-06T01:51:17Z

[Term]
id: SO:0001792
name: non_coding_transcript_exon_variant
def: "A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]
synonym: "non coding transcript exon variant" EXACT []
is_a: SO:0001619 ! non_coding_transcript_variant
is_a: SO:0001791 ! exon_variant
created_by: kareneilbeck
creation_date: 2011-05-06T01:51:59Z

[Term]
id: SO:0001793
name: clone_end
def: "A read from an end of the clone sequence." [SO:ke]
synonym: "clone end" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000151 ! clone
created_by: kareneilbeck
creation_date: 2011-05-13T11:32:27Z

[Term]
id: SO:0001794
name: point_centromere
def: "A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]
synonym: "point centromere" EXACT []
is_a: SO:0000577 ! centromere
created_by: kareneilbeck
creation_date: 2011-05-31T12:42:35Z

[Term]
id: SO:0001795
name: regional_centromere
def: "A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]
synonym: "regional centromere" EXACT []
is_a: SO:0000577 ! centromere
created_by: kareneilbeck
creation_date: 2011-05-31T12:43:07Z

[Term]
id: SO:0001796
name: regional_centromere_central_core
def: "A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]
synonym: "regional centromere central core" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0001795 ! regional_centromere
created_by: kareneilbeck
creation_date: 2011-05-31T12:56:30Z

[Term]
id: SO:0001797
name: centromeric_repeat
def: "A repeat region found within the modular centromere." [SO:ke]
synonym: "centromeric repeat" EXACT []
is_a: SO:0000657 ! repeat_region
created_by: kareneilbeck
creation_date: 2011-05-31T12:59:27Z

[Term]
id: SO:0001798
name: regional_centromere_inner_repeat_region
def: "The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]
synonym: "lmr repeat" EXACT []
synonym: "lmr1L" EXACT []
synonym: "lmr1R" EXACT []
synonym: "regional centromere inner repeat region" EXACT []
is_a: SO:0001797 ! centromeric_repeat
relationship: part_of SO:0001796 ! regional_centromere_central_core
created_by: kareneilbeck
creation_date: 2011-05-31T01:01:08Z

[Term]
id: SO:0001799
name: regional_centromere_outer_repeat_region
def: "The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]
synonym: "regional centromere outer repeat region" EXACT []
is_a: SO:0001797 ! centromeric_repeat
relationship: part_of SO:0001795 ! regional_centromere
created_by: kareneilbeck
creation_date: 2011-05-31T01:03:23Z

[Term]
id: SO:0001800
name: tasiRNA
def: "The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]
synonym: "trans acting small interfering RNA" RELATED []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0001801 ! tasiRNA_primary_transcript
created_by: kareneilbeck
creation_date: 2011-05-31T03:24:06Z

[Term]
id: SO:0001801
name: tasiRNA_primary_transcript
def: "A primary transcript encoding a tasiRNA." [PMID:16145017]
synonym: "tasiRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
created_by: kareneilbeck
creation_date: 2011-05-31T03:27:35Z

[Term]
id: SO:0001802
name: increased_polyadenylation_variant
def: "A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]
comment: Term requested by M. Dumontier, June 1 2011.
synonym: "increased polyadenylation variant" EXACT []
is_a: SO:0001545 ! polyadenylation_variant
created_by: kareneilbeck
creation_date: 2011-06-01T10:53:12Z

[Term]
id: SO:0001803
name: decreased_polyadenylation_variant
def: "A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]
comment: Term requested by M. Dumontier, June 1 2011.
synonym: "decreased polyadenylation variant" EXACT []
is_a: SO:0001545 ! polyadenylation_variant
created_by: kareneilbeck
creation_date: 2011-06-01T10:53:40Z

[Term]
id: SO:0001804
name: DDB_box
def: "A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]
comment: Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence.
synonym: "DDB box" EXACT []
synonym: "DDB-box" EXACT []
is_a: SO:0001093 ! protein_protein_contact
created_by: kareneilbeck
creation_date: 2011-06-17T12:10:44Z

[Term]
id: SO:0001805
name: destruction_box
def: "A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]
synonym: "D-box" EXACT []
synonym: "destruction box" EXACT []
is_a: SO:0100017 ! polypeptide_conserved_motif
created_by: kareneilbeck
creation_date: 2011-06-17T12:16:02Z

[Term]
id: SO:0001806
name: ER_retention_signal
def: "A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]
synonym: "endoplasmic reticulum retention signal" EXACT []
synonym: "ER retention signal" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2011-06-17T12:19:49Z

[Term]
id: SO:0001807
name: KEN_box
def: "A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]
synonym: "KEN box" EXACT []
is_a: SO:0100017 ! polypeptide_conserved_motif
created_by: kareneilbeck
creation_date: 2011-06-17T12:24:14Z

[Term]
id: SO:0001808
name: mitochondrial_targeting_signal
def: "A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]
synonym: "mitochondrial signal sequence" EXACT []
synonym: "mitochondrial targeting signal" EXACT []
synonym: "MTS" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2011-06-17T12:26:35Z

[Term]
id: SO:0001809
name: signal_anchor
def: "A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]
synonym: "signal anchor" EXACT []
synonym: "uncleaved signal peptide" EXACT []
is_a: SO:0000418 ! signal_peptide
created_by: kareneilbeck
creation_date: 2011-06-17T12:28:53Z

[Term]
id: SO:0001810
name: PIP_box
def: "A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]
synonym: "PIP box" EXACT []
is_a: SO:0001093 ! protein_protein_contact
created_by: kareneilbeck
creation_date: 2011-06-17T12:33:25Z

[Term]
id: SO:0001811
name: phosphorylation_site
def: "A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]
synonym: "phosphorylation site" EXACT []
is_a: SO:0001089 ! post_translationally_modified_region
created_by: kareneilbeck
creation_date: 2011-06-17T12:36:20Z

[Term]
id: SO:0001812
name: transmembrane_helix
def: "A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]
synonym: "transmembrane helix" EXACT []
is_a: SO:0001114 ! peptide_helix
relationship: part_of SO:0001077 ! transmembrane_polypeptide_region
created_by: kareneilbeck
creation_date: 2011-06-17T12:39:46Z

[Term]
id: SO:0001813
name: vacuolar_sorting_signal
def: "A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]
synonym: "vacuolar sorting signal" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2011-06-17T12:42:48Z

[Term]
id: SO:0001814
name: coding_variant_quality
synonym: "coding variant quality" EXACT []
is_a: SO:0001761 ! variant_quality
created_by: kareneilbeck
creation_date: 2011-06-24T03:32:25Z

[Term]
id: SO:0001815
name: synonymous
is_a: SO:0001814 ! coding_variant_quality
created_by: kareneilbeck
creation_date: 2011-06-24T03:33:16Z

[Term]
id: SO:0001816
name: non_synonymous
synonym: "non synonymous" RELATED []
is_a: SO:0001814 ! coding_variant_quality
created_by: kareneilbeck
creation_date: 2011-06-24T03:33:36Z

[Term]
id: SO:0001817
name: inframe
def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute
created_by: kareneilbeck
creation_date: 2011-06-24T03:34:03Z

[Term]
id: SO:0001818
name: protein_altering_variant
def: "A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]
synonym: "protein altering variant" EXACT []
is_a: SO:0001580 ! coding_sequence_variant
created_by: kareneilbeck
creation_date: 2011-06-24T03:38:02Z

[Term]
id: SO:0001819
name: synonymous_variant
alt_id: SO:0001588
def: "A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]
comment: EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).\nThis term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term.
synonym: "ANNOVAR:synonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "coding-synon" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "silent mutation" RELATED []
synonym: "silent substitution" RELATED []
synonym: "silent_mutation" RELATED []
synonym: "snpEff:SYNONYMOUS_CODING" EXACT VAR []
synonym: "synonymous codon" EXACT []
synonym: "synonymous_coding" EXACT []
synonym: "synonymous_codon" EXACT []
synonym: "VAAST:synonymous_codon" EXACT VAR []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki"
xref: http://en.wikipedia.org/wiki/Synonymous_mutation
is_a: SO:0001580 ! coding_sequence_variant
created_by: kareneilbeck
creation_date: 2011-06-24T03:38:30Z

[Term]
id: SO:0001820
name: inframe_indel
def: "A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]
synonym: "inframe change in CDS length" EXACT []
synonym: "inframe indel" EXACT []
is_a: SO:0001650 ! inframe_variant
created_by: kareneilbeck
creation_date: 2011-06-27T11:25:33Z

[Term]
id: SO:0001821
name: inframe_insertion
alt_id: SO:0001651
def: "An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]
synonym: "ANNOVAR:nonframeshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "inframe codon gain" RELATED []
synonym: "inframe increase in CDS length" EXACT []
synonym: "inframe insertion" EXACT []
synonym: "inframe_codon_gain" EXACT []
synonym: "snpEFF:CODON_INSERTION" EXACT VAR []
is_a: SO:0001820 ! inframe_indel
is_a: SO:0001908 ! internal_feature_elongation
created_by: kareneilbeck
creation_date: 2011-06-27T11:26:22Z

[Term]
id: SO:0001822
name: inframe_deletion
alt_id: SO:0001652
def: "An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]
synonym: "ANNOVAR:nonframeshift deletion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "inframe codon loss" RELATED []
synonym: "inframe decrease in CDS length" EXACT []
synonym: "inframe deletion" RELATED []
synonym: "inframe_codon_loss" EXACT []
synonym: "snpEff:CODON_DELETION" RELATED VAR []
is_a: SO:0001820 ! inframe_indel
is_a: SO:0001906 ! feature_truncation
created_by: kareneilbeck
creation_date: 2011-06-27T11:27:10Z

[Term]
id: SO:0001823
name: conservative_inframe_insertion
def: "An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]
synonym: "conservative increase in CDS length" EXACT []
synonym: "conservative inframe insertion" EXACT []
is_a: SO:0001821 ! inframe_insertion
created_by: kareneilbeck
creation_date: 2011-06-27T11:28:02Z

[Term]
id: SO:0001824
name: disruptive_inframe_insertion
def: "An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]
synonym: "disruptive increase in CDS length" EXACT []
synonym: "disruptive inframe insertion" EXACT []
synonym: "snpEff:CODON_CHANGE_PLUS_CODON_INSERTION" EXACT VAR []
is_a: SO:0001821 ! inframe_insertion
created_by: kareneilbeck
creation_date: 2011-06-27T11:28:37Z

[Term]
id: SO:0001825
name: conservative_inframe_deletion
def: "An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]
synonym: "conservative decrease in CDS length" RELATED []
synonym: "conservative inframe deletion" EXACT []
is_a: SO:0001822 ! inframe_deletion
created_by: kareneilbeck
creation_date: 2011-06-27T11:30:43Z

[Term]
id: SO:0001826
name: disruptive_inframe_deletion
def: "An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]
synonym: "disruptive decrease in CDS length" EXACT []
synonym: "disruptive inframe deletion" EXACT []
synonym: "snpEff:CODON_CHANGE_PLUS_CODON_DELETION" EXACT VAR []
is_a: SO:0001822 ! inframe_deletion
created_by: kareneilbeck
creation_date: 2011-06-27T11:31:31Z

[Term]
id: SO:0001827
name: mRNA_read
def: "A sequencer read of an mRNA substrate." [SO:ke]
comment: Requested by Bayer Cropscience June, 2011.
synonym: "mRNA read" EXACT []
is_a: SO:0000150 ! read
created_by: kareneilbeck
creation_date: 2011-06-28T04:04:32Z

[Term]
id: SO:0001828
name: genomic_DNA_read
def: "A sequencer read of a genomic DNA substrate." [SO:ke]
synonym: "genomic DNA read" EXACT []
is_a: SO:0000150 ! read
created_by: kareneilbeck
creation_date: 2011-06-28T04:06:10Z

[Term]
id: SO:0001829
name: mRNA_contig
def: "A contig composed of mRNA_reads." [SO:ke]
comment: Requested by Bayer Cropscience June, 2011.
synonym: "mRNA contig" RELATED []
is_a: SO:0000149 ! contig
created_by: kareneilbeck
creation_date: 2011-06-28T04:07:09Z

[Term]
id: SO:0001830
name: AFLP_fragment
def: "A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea]
comment: Requested by Bayer Cropscience June, 2011.
synonym: "AFLP" EXACT []
synonym: "AFLP fragment" EXACT []
synonym: "AFLP-PCR" EXACT []
synonym: "amplified fragment length polymorphism" EXACT []
synonym: "amplified fragment length polymorphism PCR" EXACT []
xref: http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism "wiki"
is_a: SO:0000006 ! PCR_product
created_by: kareneilbeck
creation_date: 2011-07-14T12:12:35Z

[Term]
id: SO:0001831
name: protein_hmm_match
def: "A match to a protein HMM such as pfam." [SO:ke]
synonym: "protein hmm match" EXACT []
is_a: SO:0000349 ! protein_match
created_by: kareneilbeck
creation_date: 2011-08-11T03:20:27Z

[Term]
id: SO:0001832
name: immunoglobulin_region
def: "A region of immunoglobulin sequence, either constant or variable." [SO:ke]
synonym: "immunoglobulin region" EXACT []
is_a: SO:0000839 ! polypeptide_region
created_by: kareneilbeck
creation_date: 2011-09-01T03:27:20Z

[Term]
id: SO:0001833
name: V_region
def: "The variable region of an immunoglobulin polypeptide sequence." [SO:ke]
synonym: "V region" EXACT []
is_a: SO:0001832 ! immunoglobulin_region
created_by: kareneilbeck
creation_date: 2011-09-01T03:28:40Z

[Term]
id: SO:0001834
name: C_region
def: "The constant region of an immunoglobulin polypeptide sequence." [SO:ke]
synonym: "C region" EXACT []
is_a: SO:0001832 ! immunoglobulin_region
created_by: kareneilbeck
creation_date: 2011-09-01T03:29:41Z

[Term]
id: SO:0001835
name: N_region
def: "Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]
synonym: "N-region" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
created_by: kareneilbeck
creation_date: 2011-09-01T03:50:16Z

[Term]
id: SO:0001836
name: S_region
def: "The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]
synonym: "S region" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
created_by: kareneilbeck
creation_date: 2011-09-01T03:52:05Z

[Term]
id: SO:0001837
name: mobile_element_insertion
def: "A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]
comment: Requested by the EBI.
synonym: "mobile element insertion" EXACT []
is_a: SO:0000667 ! insertion
intersection_of: SO:0000667 ! insertion
intersection_of: contains SO:0001037 ! mobile_genetic_element
relationship: contains SO:0001037 ! mobile_genetic_element
created_by: kareneilbeck
creation_date: 2011-10-04T12:36:52Z

[Term]
id: SO:0001838
name: novel_sequence_insertion
def: "An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]
comment: Requested by the NCBI.
synonym: "novel sequence insertion" EXACT []
is_a: SO:0000667 ! insertion
created_by: kareneilbeck
creation_date: 2011-10-04T01:14:50Z

[Term]
id: SO:0001839
name: CSL_response_element
def: "A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]
synonym: "CSL response element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T03:37:43Z

[Term]
id: SO:0001840
name: GATA_box
def: "A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]
synonym: "GATA box" EXACT []
synonym: "GATA element" RELATED []
is_a: SO:0001660 ! core_promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T03:42:05Z

[Term]
id: SO:0001841
name: polymorphic_pseudogene
def: "Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]
comment: This terms is used by Ensembl and Vega.
synonym: "polymorphic psuedogene" EXACT []
is_a: SO:0000336 ! pseudogene
created_by: kareneilbeck
creation_date: 2011-10-07T03:46:57Z

[Term]
id: SO:0001842
name: AP_1_binding_site
def: "A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]
synonym: "AP-1 binding site" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T03:54:52Z

[Term]
id: SO:0001843
name: CRE
def: "A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]
synonym: "ATF/CRE site" EXACT [PMID:11483993]
synonym: "cyclic AMP response element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T03:58:48Z

[Term]
id: SO:0001844
name: CuRE
def: "A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]
synonym: "copper-response element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:02:51Z

[Term]
id: SO:0001845
name: DRE
def: "A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]
synonym: "DNA damage response element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:17:25Z

[Term]
id: SO:0001846
name: FLEX_element
def: "A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]
synonym: "FLEX element" RELATED []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:20:01Z

[Term]
id: SO:0001847
name: forkhead_motif
def: "A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]
synonym: "forkhead motif" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:22:06Z

[Term]
id: SO:0001848
name: homol_D_box
def: "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]
synonym: "homol D box" EXACT []
is_a: SO:0001660 ! core_promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:24:14Z

[Term]
id: SO:0001849
name: homol_E_box
def: "A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]
synonym: "homol E box" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:26:09Z

[Term]
id: SO:0001850
name: HSE
def: "A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]
synonym: "heat shock element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:29:10Z

[Term]
id: SO:0001851
name: iron_repressed_GATA_element
def: "A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]
comment: The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes.
synonym: "IDP (GATA)" EXACT []
synonym: "iron repressed GATA element" EXACT []
is_a: SO:0001840 ! GATA_box
created_by: kareneilbeck
creation_date: 2011-10-07T04:32:42Z

[Term]
id: SO:0001852
name: mating_type_M_box
def: "A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]
comment: Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF.
synonym: "mating type M-box" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:39:43Z

[Term]
id: SO:0001853
name: androgen_response_element
def: "A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]
synonym: "androgen response element" EXACT []
synonym: "ARE" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2011-10-10T04:52:44Z

[Term]
id: SO:0001854
name: smFISH_probe
def: "A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]
synonym: "single molecule fish probe" EXACT []
synonym: "smFISH probe" RELATED []
is_a: SO:0000051 ! probe
created_by: kareneilbeck
creation_date: 2011-10-10T05:00:30Z

[Term]
id: SO:0001855
name: MCB
def: "A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]
synonym: "MluI cell cycle box" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-10T05:09:45Z

[Term]
id: SO:0001856
name: CCAAT_motif
def: "A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]
synonym: "CCAAT motif" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-10T05:13:54Z

[Term]
id: SO:0001857
name: Ace2_UAS
def: "A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]
synonym: "Ace2 upstream activating sequence" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-10T05:19:10Z

[Term]
id: SO:0001858
name: TR_box
def: "A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]
synonym: "TR box" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-10T05:22:13Z

[Term]
id: SO:0001859
name: STREP_motif
def: "A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]
synonym: "STREP motif" RELATED []
synonym: "stress-starvation response element of Schizosaccharomyces pombe" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-14T10:25:02Z

[Term]
id: SO:0001860
name: rDNA_intergenic_spacer_element
def: "A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]
synonym: "rDIS" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2011-10-19T11:23:09Z

[Term]
id: SO:0001861
name: sterol_regulatory_element
def: "A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]
synonym: "SRE" BROAD [GO:mah]
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-19T03:02:05Z

[Term]
id: SO:0001862
name: GT_dinucleotide_repeat
def: "A dinucleotide repeat region composed of GT repeating elements." [SO:ke]
comment: paper:PMID:16043634.
synonym: "d(GT)n" EXACT []
is_a: SO:0000290 ! dinucleotide_repeat_microsatellite_feature
created_by: kareneilbeck
creation_date: 2011-10-19T03:54:37Z

[Term]
id: SO:0001863
name: GTT_trinucleotide_repeat
def: "A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]
synonym: "d(GTT)" EXACT []
is_a: SO:0000291 ! trinucleotide_repeat_microsatellite_feature
created_by: kareneilbeck
creation_date: 2011-10-19T03:56:54Z

[Term]
id: SO:0001864
name: Sap1_recognition_motif
def: "A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]
synonym: "Sap1 recognitions site" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2011-10-19T04:24:16Z

[Term]
id: SO:0001865
name: CDRE_motif
def: "An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]
synonym: "calcineurin-dependent response element" EXACT [PMID:16928959]
synonym: "CDRE motif" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-20T10:12:19Z

[Term]
id: SO:0001866
name: BAC_read_contig
def: "A contig of BAC reads." [GMOD:ea]
comment: Requested by Bayer Cropscience December, 2011.
synonym: "BAC read contig" EXACT []
is_a: SO:0000149 ! contig
intersection_of: SO:0000149 ! contig
intersection_of: has_origin SO:0000153 ! BAC
relationship: has_origin SO:0000153 ! BAC
relationship: part_of SO:0000153 ! BAC
created_by: kareneilbeck
creation_date: 2012-01-17T02:45:04Z

[Term]
id: SO:0001867
name: candidate_gene
def: "A gene suspected of being involved in the expression of a trait." [GMOD:ea]
comment: Requested by Bayer Cropscience December, 2011.
synonym: "candidate gene" EXACT []
synonym: "target gene" EXACT []
is_a: SO:0000704 ! gene
created_by: kareneilbeck
creation_date: 2012-01-17T02:53:03Z

[Term]
id: SO:0001868
name: positional_candidate_gene
def: "A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]
comment: Requested by Bayer Cropscience December, 2011.
synonym: "positional candidate gene" EXACT []
synonym: "positional target gene" RELATED []
is_a: SO:0001867 ! candidate_gene
created_by: kareneilbeck
creation_date: 2012-01-17T02:54:42Z

[Term]
id: SO:0001869
name: functional_candidate_gene
def: "A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]
comment: Requested by Bayer Cropscience December, 2011.
synonym: "functional candidate gene" EXACT []
synonym: "functional target gene" EXACT []
is_a: SO:0001867 ! candidate_gene
created_by: kareneilbeck
creation_date: 2012-01-17T02:57:30Z

[Term]
id: SO:0001870
name: enhancerRNA
def: "A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]
synonym: "eRNA" EXACT []
is_a: SO:0000655 ! ncRNA
intersection_of: SO:0000655 ! ncRNA
intersection_of: transcribed_from SO:0000165 ! enhancer
relationship: transcribed_from SO:0000165 ! enhancer
created_by: kareneilbeck
creation_date: 2012-01-17T03:09:35Z

[Term]
id: SO:0001871
name: PCB
def: "A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2012-01-17T03:14:02Z

[Term]
id: SO:0001872
name: rearrangement_region
def: "A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]
comment: NCBI definition: An orphan rearrangement between chromosomal location observed in isolation.
synonym: "rearrangement region" EXACT []
is_a: SO:0001411 ! biological_region
is_a: SO:0001785 ! structural_alteration
created_by: kareneilbeck
creation_date: 2012-02-03T04:38:35Z

[Term]
id: SO:0001873
name: interchromosomal_breakpoint
def: "A rearrangement breakpoint between two different chromosomes." [NCBI:th]
synonym: "interchromosomal breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint
created_by: kareneilbeck
creation_date: 2012-02-03T04:43:45Z

[Term]
id: SO:0001874
name: intrachromosomal_breakpoint
def: "A rearrangement breakpoint within the same chromosome." [NCBI:th]
synonym: "intrachromosomal breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint
created_by: kareneilbeck
creation_date: 2012-02-03T04:44:53Z

[Term]
id: SO:0001875
name: unassigned_supercontig
def: "A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]
comment: Requested by Bayer Cropscience January, 2012.
synonym: "unassigned scaffold" RELATED []
synonym: "unassigned supercontig" EXACT []
is_a: SO:0000148 ! supercontig
created_by: kareneilbeck
creation_date: 2012-02-14T05:02:20Z

[Term]
id: SO:0001876
name: partial_genomic_sequence_assembly
def: "A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]
comment: Requested by Bayer Cropscience January, 2012.
synonym: "partial genomic sequence assembly" EXACT []
synonym: "pseudomolecule" BROAD []
synonym: "sequence assembly with N-gaps" EXACT []
is_a: SO:0000353 ! sequence_assembly
created_by: kareneilbeck
creation_date: 2012-02-14T05:05:32Z

[Term]
id: SO:0001877
name: lnc_RNA
def: "A non-coding RNA over 200nucleotides in length." [HGNC:mw]
synonym: "long non-coding RNA" EXACT []
is_a: SO:0000655 ! ncRNA
created_by: kareneilbeck
creation_date: 2012-02-14T05:18:01Z

[Term]
id: SO:0001878
name: feature_variant
def: "A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]
comment: Created in conjunction with the EBI.
synonym: "feature alteration" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2012-04-03T11:27:27Z

[Term]
id: SO:0001879
name: feature_ablation
def: "A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "feature ablation" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2012-04-03T11:36:48Z

[Term]
id: SO:0001880
name: feature_amplification
def: "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "feature amplification" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2012-04-03T11:37:48Z

[Term]
id: SO:0001881
name: feature_translocation
def: "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "feature translocation" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2012-04-03T11:38:52Z

[Term]
id: SO:0001882
name: feature_fusion
def: "A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "feature fusion" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2012-04-03T11:39:20Z

[Term]
id: SO:0001883
name: transcript_translocation
def: "A feature translocation where the region contains a transcript." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "transcript translocation" EXACT []
is_a: SO:0001881 ! feature_translocation
created_by: kareneilbeck
creation_date: 2012-04-03T12:29:52Z

[Term]
id: SO:0001884
name: regulatory_region_translocation
def: "A feature translocation where the region contains a regulatory region." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "regulatory region translocation" EXACT []
is_a: SO:0001881 ! feature_translocation
created_by: kareneilbeck
creation_date: 2012-04-03T12:31:04Z

[Term]
id: SO:0001885
name: TFBS_translocation
def: "A feature translocation where the region contains a transcription factor binding site." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "TFBS binding site translocation" EXACT []
synonym: "transcription factor binding site translocation" EXACT []
is_a: SO:0001884 ! regulatory_region_translocation
created_by: kareneilbeck
creation_date: 2012-04-03T12:31:15Z

[Term]
id: SO:0001886
name: transcript_fusion
def: "A feature fusion where the deletion brings together transcript regions." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "transcript fusion" EXACT []
is_a: SO:0001882 ! feature_fusion
created_by: kareneilbeck
creation_date: 2012-04-03T12:34:56Z

[Term]
id: SO:0001887
name: regulatory_region_fusion
def: "A feature fusion where the deletion brings together regulatory regions." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "regulatory region fusion" EXACT []
is_a: SO:0001882 ! feature_fusion
created_by: kareneilbeck
creation_date: 2012-04-03T12:35:58Z

[Term]
id: SO:0001888
name: TFBS_fusion
def: "A fusion where the deletion brings together transcription factor binding sites." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "TFBS fusion " EXACT []
synonym: "transcription factor binding site fusion" EXACT []
is_a: SO:0001887 ! regulatory_region_fusion
created_by: kareneilbeck
creation_date: 2012-04-03T12:36:42Z

[Term]
id: SO:0001889
name: transcript_amplification
def: "A feature amplification of a region containing a transcript." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "transcript amplification" EXACT []
is_a: SO:0001880 ! feature_amplification
created_by: kareneilbeck
creation_date: 2012-04-03T12:39:23Z

[Term]
id: SO:0001890
name: transcript_regulatory_region_fusion
def: "A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "transcript regulatory region fusion" EXACT []
is_a: SO:0001882 ! feature_fusion
created_by: kareneilbeck
creation_date: 2012-04-03T12:40:17Z

[Term]
id: SO:0001891
name: regulatory_region_amplification
def: "A feature amplification of a region containing a regulatory region." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "regulatory region amplification" EXACT []
is_a: SO:0001880 ! feature_amplification
created_by: kareneilbeck
creation_date: 2012-04-03T12:41:28Z

[Term]
id: SO:0001892
name: TFBS_amplification
def: "A feature amplification of a region containing a transcription factor binding site." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "TFBS amplification " EXACT []
synonym: "transcription factor binding site amplification" EXACT []
is_a: SO:0001891 ! regulatory_region_amplification
created_by: kareneilbeck
creation_date: 2012-04-03T12:42:48Z

[Term]
id: SO:0001893
name: transcript_ablation
def: "A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "transcript ablation" EXACT []
is_a: SO:0001879 ! feature_ablation
created_by: kareneilbeck
creation_date: 2012-04-03T12:44:19Z

[Term]
id: SO:0001894
name: regulatory_region_ablation
def: "A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "regulatory region ablation" EXACT []
is_a: SO:0001879 ! feature_ablation
created_by: kareneilbeck
creation_date: 2012-04-03T12:45:13Z

[Term]
id: SO:0001895
name: TFBS_ablation
def: "A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "TFBS ablation" EXACT []
synonym: "transcription factor binding site ablation" EXACT []
is_a: SO:0001894 ! regulatory_region_ablation
created_by: kareneilbeck
creation_date: 2012-04-03T12:45:56Z

[Term]
id: SO:0001896
name: transposable_element_CDS
def: "A CDS that is part of a transposable element." [SO:ke]
synonym: "transposable element CDS" EXACT []
is_a: SO:0000316 ! CDS
intersection_of: SO:0000316 ! CDS
intersection_of: part_of SO:0000101 ! transposable_element
relationship: part_of SO:0000101 ! transposable_element
created_by: kareneilbeck
creation_date: 2012-04-05T01:57:04Z

[Term]
id: SO:0001897
name: transposable_element_pseudogene
def: "A pseudogene contained within a transposable element." [SO:ke]
synonym: "transposable element pseudogene" EXACT []
is_a: SO:0000336 ! pseudogene
intersection_of: SO:0000336 ! pseudogene
intersection_of: part_of SO:0000101 ! transposable_element
relationship: part_of SO:0000101 ! transposable_element
created_by: kareneilbeck
creation_date: 2012-04-05T04:09:45Z

[Term]
id: SO:0001898
name: dg_repeat
def: "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]
comment: For the S. pombe project - requested by Val Wood.
synonym: "dg repeat" EXACT []
is_a: SO:0001797 ! centromeric_repeat
relationship: part_of SO:0001799 ! regional_centromere_outer_repeat_region
created_by: kareneilbeck
creation_date: 2012-04-06T11:48:48Z

[Term]
id: SO:0001899
name: dh_repeat
def: "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]
comment: For the S. pombe project - requested by Val Wood.
synonym: "dh repeat" EXACT []
is_a: SO:0001797 ! centromeric_repeat
relationship: part_of SO:0001799 ! regional_centromere_outer_repeat_region
created_by: kareneilbeck
creation_date: 2012-04-06T11:50:07Z

[Term]
id: SO:0001900
name: M26_binding_site
def: "A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]
synonym: "m26 site" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2012-04-06T12:02:10Z

[Term]
id: SO:0001901
name: AACCCT_box
def: "A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]
synonym: "AACCCT box" EXACT []
is_a: SO:0001660 ! core_promoter_element
created_by: kareneilbeck
creation_date: 2012-04-06T12:05:24Z

[Term]
id: SO:0001902
name: splice_region
def: "A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]
synonym: "splice region" RELATED []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000185 ! primary_transcript
created_by: kareneilbeck
creation_date: 2012-04-06T12:23:32Z

[Term]
id: SO:0001903
name: intronic_lncRNA
def: "A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]
synonym: "intronic lncRNA" EXACT []
is_a: SO:0001877 ! lnc_RNA
created_by: kareneilbeck
creation_date: 2012-04-06T04:34:17Z

[Term]
id: SO:0001904
name: antisense_lncRNA
def: "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]
synonym: "antisense lncRNA" RELATED []
synonym: "natural antisense transcript" EXACT []
is_a: SO:0001877 ! lnc_RNA
created_by: kareneilbeck
creation_date: 2012-04-06T04:36:44Z

[Term]
id: SO:0001905
name: regional_centromere_outer_repeat_transcript
def: "A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]
synonym: "centromere outer repeat transcript" EXACT []
synonym: "regional centromere outer repeat region transcript" EXACT []
synonym: "regional_centromere_outer_repeat_region_transcript" EXACT []
is_a: SO:0000185 ! primary_transcript
intersection_of: SO:0000185 ! primary_transcript
intersection_of: derives_from SO:0001799 ! regional_centromere_outer_repeat_region
relationship: derives_from SO:0001799 ! regional_centromere_outer_repeat_region
created_by: kareneilbeck
creation_date: 2012-04-11T04:54:22Z

[Term]
id: SO:0001906
name: feature_truncation
def: "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]
synonym: "feature truncation" EXACT []
is_a: SO:0001878 ! feature_variant
created_by: kareneilbeck
creation_date: 2012-04-12T05:05:28Z

[Term]
id: SO:0001907
name: feature_elongation
def: "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]
synonym: "feature elongation" EXACT []
is_a: SO:0001878 ! feature_variant
created_by: kareneilbeck
creation_date: 2012-04-12T05:05:56Z

[Term]
id: SO:0001908
name: internal_feature_elongation
def: "A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]
synonym: "internal feature elongation" EXACT []
is_a: SO:0001907 ! feature_elongation
created_by: kareneilbeck
creation_date: 2012-04-12T05:06:20Z

[Term]
id: SO:0001909
name: frameshift_elongation
def: "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]
synonym: "ANNOVAR:frameshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "frameshift elongation" EXACT []
is_a: SO:0001589 ! frameshift_variant
is_a: SO:0001908 ! internal_feature_elongation
created_by: kareneilbeck
creation_date: 2012-04-12T05:10:05Z

[Term]
id: SO:0001910
name: frameshift_truncation
def: "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]
synonym: "ANNOVAR:frameshit deletion" EXACT ebi_variants [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "frameshft truncation" EXACT []
is_a: SO:0001589 ! frameshift_variant
is_a: SO:0001906 ! feature_truncation
created_by: kareneilbeck
creation_date: 2012-04-12T05:10:45Z

[Term]
id: SO:0001911
name: copy_number_increase
def: "A sequence variant where copies of a feature are increased relative to the reference." [SO:ke]
synonym: "copy number increase" EXACT []
is_a: SO:0001563 ! copy_number_change
created_by: kareneilbeck
creation_date: 2012-04-13T11:26:32Z

[Term]
id: SO:0001912
name: copy_number_decrease
def: "A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke]
is_a: SO:0001563 ! copy_number_change
created_by: kareneilbeck
creation_date: 2012-04-13T11:27:52Z

[Term]
id: SO:0001913
name: bacterial_RNApol_promoter_sigma_ecf
def: "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]
comment: Requested by Kevin Clancy - invitrogen -May 2012.
synonym: "bacterial RNApol promoter sigma ecf " EXACT []
is_a: SO:0000613 ! bacterial_RNApol_promoter
created_by: kareneilbeck
creation_date: 2012-06-11T02:41:33Z

[Term]
id: SO:0001914
name: rDNA_replication_fork_barrier
def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]
comment: Requested by Midori - June 2012.
synonym: "DNA spacer replication fork barrier" EXACT []
synonym: "rDNA replication fork barrier" EXACT []
synonym: "RFB" EXACT []
synonym: "RTS1 barrier" EXACT []
synonym: "RTS1 element" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2012-06-11T02:55:02Z

[Term]
id: SO:0001915
name: transcription_start_cluster
def: "A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson]
synonym: "transcriptional initiation cluster" EXACT []
synonym: "transcriptional start site cluster" EXACT []
synonym: "TSC" EXACT []
synonym: "TSS cluster" EXACT []
is_a: SO:0001410 ! experimental_feature
created_by: kareneilbeck
creation_date: 2012-10-17T12:09:50Z

[Term]
id: SO:0001916
name: CAGE_tag
def: "A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]
synonym: "CAGE tag" EXACT []
is_a: SO:0000324 ! tag
created_by: kareneilbeck
creation_date: 2012-10-17T12:36:58Z

[Term]
id: SO:0001917
name: CAGE_cluster
def: "A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson]
synonym: "CAGE cluster" EXACT []
synonym: "CAGE peak" EXACT []
synonym: "CAGE_peak" EXACT []
is_a: SO:0001915 ! transcription_start_cluster
created_by: kareneilbeck
creation_date: 2012-10-17T12:42:03Z

[Term]
id: SO:0001918
name: 5_methylcytosine
def: "A cytosine methylated at the 5 carbon." [SO:rtapella]
synonym: "5 methylcytosine" EXACT []
synonym: "5-mC" EXACT []
synonym: "m-5C" EXACT []
synonym: "m5c" EXACT []
xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0000114 ! methylated_cytosine
created_by: kareneilbeck
creation_date: 2012-10-17T12:46:10Z

[Term]
id: SO:0001919
name: 4_methylcytosine
def: "A cytosine methylated at the 4 nitrogen." [SO:rtapella]
synonym: "4-mC" EXACT []
synonym: "4-methylcytosine" EXACT []
synonym: "m-4C" EXACT []
synonym: "m4c" EXACT []
synonym: "N4 methylcytosine" EXACT []
synonym: "N4-methylcytosine" EXACT []
synonym: "N4_methylcytosine" EXACT []
xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0000114 ! methylated_cytosine
created_by: kareneilbeck
creation_date: 2012-10-17T12:50:40Z

[Term]
id: SO:0001920
name: N6_methyladenine
def: "An adenine methylated at the 6 nitrogen." [SO:rtapella]
synonym: "6-mA" EXACT []
synonym: "6-methyladenine" EXACT []
synonym: "6mA" EXACT []
synonym: "m-6A" EXACT []
synonym: "m6a" EXACT []
synonym: "N6-methyladenine" EXACT []
xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0000161 ! methylated_adenine
created_by: kareneilbeck
creation_date: 2012-10-17T12:54:23Z

[Term]
id: SO:0001921
name: mitochondrial_contig
def: "A contig of mitochondria derived sequences." [GMOD:ea]
comment: Requested by Bayer Cropscience, October, 2012.
synonym: "mitochondrial contig" EXACT []
is_a: SO:0000149 ! contig
intersection_of: SO:0000149 ! contig
intersection_of: has_origin SO:0000737 ! mitochondrial_sequence
relationship: has_origin SO:0000737 ! mitochondrial_sequence
created_by: kareneilbeck
creation_date: 2012-10-31T12:34:38Z

[Term]
id: SO:0001922
name: mitochondrial_supercontig
def: "A scaffold composed of mitochondrial contigs." [GMOD:ea]
synonym: "mitochondrial scaffold" EXACT []
synonym: "mitochondrial supercontig" EXACT []
synonym: "mitochondrial_scaffold" EXACT []
is_a: SO:0000148 ! supercontig
created_by: kareneilbeck
creation_date: 2012-10-31T12:42:45Z

[Term]
id: SO:0001923
name: TERRA
def: "A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]
comment: Telomeric transcription has been documented in mammals, birds,  fish, plants and  yeast. Requested by Antonia Lock, October 2012.
synonym: "telomeric repeat containing RNA" RELATED []
is_a: SO:0001927 ! telomeric_transcript
created_by: kareneilbeck
creation_date: 2012-10-31T01:06:40Z

[Term]
id: SO:0001924
name: ARRET
def: "A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]
comment: Telomeric transcription has been documented in mammals, birds,  fish, plants and  yeast. Requested by Antonia Lock, October 2012.
is_a: SO:0001927 ! telomeric_transcript
created_by: kareneilbeck
creation_date: 2012-10-31T01:11:49Z

[Term]
id: SO:0001925
name: ARIA
def: "A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats." [PMID:22139915]
comment: Telomeric transcription has been documented in mammals, birds,  fish, plants and  yeast. Requested by Antonia Lock, October 2012.
is_a: SO:0001927 ! telomeric_transcript
created_by: kareneilbeck
creation_date: 2012-10-31T01:24:37Z

[Term]
id: SO:0001926
name: anti_ARRET
def: "A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts." [PMID:22139915]
comment: Telomeric transcription has been documented in mammals, birds,  fish, plants and  yeast. Requested by Antonia Lock, October 2012.
synonym: "anti-ARRET" EXACT []
is_a: SO:0001927 ! telomeric_transcript
created_by: kareneilbeck
creation_date: 2012-10-31T01:40:22Z

[Term]
id: SO:0001927
name: telomeric_transcript
def: "A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]
synonym: "telomeric transcript" EXACT []
is_a: SO:0000655 ! ncRNA
created_by: kareneilbeck
creation_date: 2012-10-31T01:42:15Z

[Term]
id: SO:0001928
name: distal_duplication
def: "A duplication of the distal region of a chromosome." [SO:bm]
comment: This term is used by Complete Genomics in the structural variant analysis files.
synonym: "distal duplication" EXACT []
is_a: SO:1000035 ! duplication
created_by: kareneilbeck
creation_date: 2012-10-31T01:56:44Z

[Term]
id: SO:0001929
name: mitochondrial_DNA_read
def: "A sequencer read of a mitochondrial DNA sample." [GMOD:ea]
comment: Requested by Bayer Cropscience, October, 2012.
synonym: "mitochondrial DNA read" EXACT []
is_a: SO:0000150 ! read
intersection_of: SO:0000150 ! read
intersection_of: has_origin SO:0001032 ! mitochondrial_DNA
relationship: has_origin SO:0001032 ! mitochondrial_DNA
created_by: kareneilbeck
creation_date: 2012-11-14T04:39:56Z

[Term]
id: SO:0001930
name: chloroplast_DNA_read
def: "A sequencer read of a chloroplast DNA sample." [GMOD:ea]
comment: Requested by Bayer Cropscience, October, 2012.
synonym: "chloroplast DNA read" EXACT []
is_a: SO:0000150 ! read
intersection_of: SO:0000150 ! read
intersection_of: has_origin SO:0001033 ! chloroplast_DNA
relationship: has_origin SO:0001033 ! chloroplast_DNA
created_by: kareneilbeck
creation_date: 2012-11-14T04:43:45Z

[Term]
id: SO:0001931
name: consensus_gDNA
def: "Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]
comment: Requested by Bayer Cropscience November, 2012.
synonym: "consensus gDNA" EXACT []
synonym: "consensus genomic DNA" EXACT []
is_a: SO:0000994 ! consensus_region
created_by: kareneilbeck
creation_date: 2012-11-28T12:53:14Z

[Term]
id: SO:0001932
name: restriction_enzyme_five_prime_single_strand_overhang
def: "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]
synonym: "restriction enzyme five prime single strand overhang" EXACT []
is_a: SO:0001695 ! restriction_enzyme_single_strand_overhang
created_by: kareneilbeck
creation_date: 2013-03-06T09:50:44Z

[Term]
id: SO:0001933
name: restriction_enzyme_three_prime_single_strand_overhang
def: "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]
synonym: "restriction enzyme three prime single strand overhang" EXACT []
is_a: SO:0001695 ! restriction_enzyme_single_strand_overhang
created_by: kareneilbeck
creation_date: 2013-03-06T09:52:14Z

[Term]
id: SO:0001934
name: monomeric_repeat
def: "A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]
synonym: "monomeric repeat" EXACT []
is_a: SO:0000705 ! tandem_repeat
created_by: kareneilbeck
creation_date: 2013-03-06T09:59:15Z

[Term]
id: SO:0001935
name: H3K20_trimethylation_site
def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]
synonym: "H3K20 trimethylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:13:48Z

[Term]
id: SO:0001936
name: H3K36_acetylation_site
def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]
synonym: "H3K36 acetylation site" EXACT []
synonym: "H3K36ac" EXACT []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:16:55Z

[Term]
id: SO:0001937
name: H2BK12_acetylation_site
def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]
synonym: "H2BK12 acetylation site" EXACT []
synonym: "H2BK12ac" RELATED []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:19:13Z

[Term]
id: SO:0001938
name: H2AK5_acetylation_site
def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]
synonym: "H2AK5 acetylation site" EXACT []
synonym: "H2AK5ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:20:57Z

[Term]
id: SO:0001939
name: H4K12_acetylation_site
def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]
synonym: "H4K12 acetylation site" EXACT []
synonym: "H4K12ac" EXACT []
is_a: SO:0001972 ! histone_4_acylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:26:15Z

[Term]
id: SO:0001940
name: H2BK120_acetylation_site
def: "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
synonym: "H2BK120 acetylation site" EXACT []
synonym: "H2BK120ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:28:38Z

[Term]
id: SO:0001941
name: H4K91_acetylation_site
def: "A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]
synonym: "H4K91 acetylation site" EXACT []
is_a: SO:0001972 ! histone_4_acylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:41:04Z

[Term]
id: SO:0001942
name: H2BK20_acetylation_site
def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
synonym: "H2BK20 acetylation site" RELATED []
synonym: "H2BK20ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:44:31Z

[Term]
id: SO:0001943
name: H3K4ac_acetylation_site
def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]
synonym: "H3K4ac" EXACT []
synonym: "H3K4ac acetylation site" EXACT []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:46:32Z

[Term]
id: SO:0001944
name: H2AK9_acetylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]
synonym: "H2AK9 acetylation site" EXACT []
synonym: "H2AK9ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:48:11Z

[Term]
id: SO:0001945
name: H3K56_acetylation_site
def: "A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]
synonym: "H3K56 acetylation site" EXACT []
synonym: "H3K56ac" EXACT []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:51:14Z

[Term]
id: SO:0001946
name: H2BK15_acetylation_site
def: "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
synonym: "H2BK15 acetylation site" EXACT []
synonym: "H2BK15ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:53:23Z

[Term]
id: SO:0001947
name: H3R2_monomethylation_site
def: "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]
synonym: " H3R2me1" EXACT []
synonym: "H3R2 monomethylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:57:13Z

[Term]
id: SO:0001948
name: H3R2_dimethylation_site
def: "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]
synonym: "H3R2 dimethylation site" EXACT []
synonym: "H3R2me2" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:59:17Z

[Term]
id: SO:0001949
name: H4R3_dimethylation_site
def: "A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]
synonym: "H4R3 dimethylation site" EXACT []
synonym: "H4R3me2" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T11:01:27Z

[Term]
id: SO:0001950
name: H4K4_trimethylation_site
def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]
synonym: " H4K4me3" EXACT []
synonym: "H4K4 trimethylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T11:03:29Z

[Term]
id: SO:0001951
name: H3K23_dimethylation_site
def: "A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]
synonym: "H3K23 dimethylation site" EXACT []
synonym: "H3K23me2" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T11:05:33Z

[Term]
id: SO:0001952
name: promoter_flanking_region
def: "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]
synonym: "promoter flanking region" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region
created_by: kareneilbeck
creation_date: 2013-03-06T11:36:25Z

[Term]
id: SO:0001953
name: restriction_enzyme_assembly_scar
def: "A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke]
is_a: SO:0001954 ! restriction_enzyme_region
created_by: kareneilbeck
creation_date: 2013-03-06T03:18:11Z

[Term]
id: SO:0001954
name: restriction_enzyme_region
def: "A region related to restriction enzyme function." [SO:ke]
comment: Not a great term for annotation, but used to classify the various regions related to restriction enzymes.
synonym: "restriction enzyme region" RELATED []
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2013-03-06T03:23:34Z

[Term]
id: SO:0001955
name: protein_stability_element
def: "A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]
synonym: "protein stability element" RELATED []
is_a: SO:0000839 ! polypeptide_region
created_by: kareneilbeck
creation_date: 2013-03-06T03:32:47Z

[Term]
id: SO:0001956
name: protease_site
def: "A polypeptide_region that  codes for a protease cleavage site." [SO:ke]
synonym: "protease site" EXACT []
is_a: SO:0000839 ! polypeptide_region
created_by: kareneilbeck
creation_date: 2013-03-06T03:36:28Z

[Term]
id: SO:0001957
name: RNA_stability_element
def: "RNA secondary structure that affects the stability of an RNA molecule." [SO:ke]
synonym: "rna stability element" RELATED []
is_obsolete: true
created_by: kareneilbeck
creation_date: 2013-03-06T03:38:35Z

[Term]
id: SO:0001958
name: lariat_intron
def: "A kind of intron whereby the excision is driven by lariat formation." [SO:ke]
comment: Requested by PomBase 3604508.
synonym: "lariat intron" EXACT []
is_a: SO:0000188 ! intron
created_by: kareneilbeck
creation_date: 2013-03-07T10:58:40Z

[Term]
id: SO:0001959
name: TCT_motif
def: "A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]
synonym: "polypyrimidine initiator" EXACT []
synonym: "TCT element" EXACT []
is_a: SO:0001660 ! core_promoter_element
created_by: kareneilbeck
creation_date: 2013-05-17T04:38:48Z

[Term]
id: SO:0001960
name: 5_hydroxymethylcytosine
def: "A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]
synonym: "5-hmC" EXACT []
synonym: "5-hydroxymethylcytosine" EXACT []
xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0000114 ! methylated_cytosine
created_by: kareneilbeck
creation_date: 2013-05-17T05:05:31Z

[Term]
id: SO:0001961
name: 5_formylcytosine
def: "A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]
synonym: "5-fC" EXACT []
synonym: "5-formylcytosine" EXACT []
xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0001963 ! modified_cytosine
created_by: kareneilbeck
creation_date: 2013-05-17T05:06:13Z

[Term]
id: SO:0001962
name: modified_adenine
def: "A modified adenine DNA base feature." [SO:ke]
is_a: SO:0000305 ! modified_DNA_base
created_by: kareneilbeck
creation_date: 2013-05-20T01:22:30Z

[Term]
id: SO:0001963
name: modified_cytosine
def: "A modified cytosine DNA base feature." [SO:ke]
is_a: SO:0000305 ! modified_DNA_base
created_by: kareneilbeck
creation_date: 2013-05-20T01:23:47Z

[Term]
id: SO:0001964
name: modified_guanine
def: "A modified guanine DNA base feature." [SO:ke]
is_a: SO:0000305 ! modified_DNA_base
created_by: kareneilbeck
creation_date: 2013-05-20T01:25:31Z

[Term]
id: SO:0001965
name: 8_oxoguanine
def: "A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]
synonym: "8-oxoG" EXACT []
synonym: "8-oxoguanine" EXACT []
xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0001964 ! modified_guanine
created_by: kareneilbeck
creation_date: 2013-05-20T01:27:51Z

[Term]
id: SO:0001966
name: 5_carboxylcytosine
def: "A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]
synonym: "5-caC" EXACT []
synonym: "5-carboxycytosine" EXACT []
xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0001963 ! modified_cytosine
created_by: kareneilbeck
creation_date: 2013-05-20T01:30:01Z

[Term]
id: SO:0001967
name: 8_oxoadenine
def: "A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]
synonym: "8-oxoA" EXACT []
synonym: "8-oxoadenine" EXACT []
xref: http:http\://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0001962 ! modified_adenine
created_by: kareneilbeck
creation_date: 2013-05-20T01:31:05Z

[Term]
id: SO:0001968
name: coding_transcript_variant
def: "A transcript variant of a protein coding gene." [SO:ke]
synonym: "coding transcript variant" EXACT []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2013-05-22T04:34:49Z

[Term]
id: SO:0001969
name: coding_transcript_intron_variant
def: "A transcript variant occurring within an intron of a coding transcript." [SO:ke]
synonym: "coding sequence intron variant" EXACT []
is_a: SO:0001627 ! intron_variant
is_a: SO:0001968 ! coding_transcript_variant
created_by: kareneilbeck
creation_date: 2013-05-23T10:54:17Z

[Term]
id: SO:0001970
name: non_coding_transcript_intron_variant
def: "A transcript variant occurring within an intron of a non coding transcript." [SO:ke]
synonym: "non coding transcript intron variant" EXACT []
is_a: SO:0001619 ! non_coding_transcript_variant
is_a: SO:0001627 ! intron_variant
created_by: kareneilbeck
creation_date: 2013-05-23T10:55:03Z

[Term]
id: SO:0001971
name: zinc_finger_binding_site
synonym: "zinc finger binding site" EXACT []
synonym: "zinc_fing" EXACT BS [unirot:features]
is_a: SO:0001429 ! DNA_binding_site
created_by: kareneilbeck
creation_date: 2013-07-29T04:41:53Z

[Term]
id: SO:0001972
name: histone_4_acylation_site
def: "A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
synonym: "H4ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-07-30T10:43:04Z

[Term]
id: SO:0001973
name: histone_3_acetylation_site
def: "A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
synonym: "H3ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-07-30T10:46:42Z

[Term]
id: SO:0001974
name: CTCF_binding_site
def: "A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]
synonym: "CCCTF binding site" EXACT []
synonym: "CTCF binding site" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2013-07-30T10:59:11Z

[Term]
id: SO:0001975
name: five_prime_sticky_end_restriction_enzyme_cleavage_site
def: "A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]
comment: Requested by  Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
synonym: "five prime sticky end restriction enzyme cleavage site" EXACT []
is_a: SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2013-07-30T11:32:16Z

[Term]
id: SO:0001976
name: three_prime_sticky_end_restriction_enzyme_cleavage_site
def: "A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]
comment: Requested by  Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
synonym: "three prime sticky end restriction enzyme cleavage site" EXACT []
is_a: SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2013-07-30T11:37:19Z

[Term]
id: SO:0001977
name: ribonuclease_site
def: "A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]
synonym: "ribonuclease site" EXACT []
is_a: SO:0000833 ! transcript_region
created_by: kareneilbeck
creation_date: 2013-07-30T11:41:06Z

[Term]
id: SO:0001978
name: signature
def: "A region of  sequence where developer information is encoded." [SO:ke]
comment: Requested by Jackie Quinn for use in synthetic biology.
synonym: "DNA signature" EXACT []
is_a: SO:0000804 ! engineered_region
created_by: kareneilbeck
creation_date: 2013-07-30T11:49:22Z

[Term]
id: SO:0001979
name: RNA_stability_element
def: "A motif that affects the stability of RNA." [PMID:22495308, SO:ke]
synonym: "RNA stability element" EXACT []
is_a: SO:0000715 ! RNA_motif
created_by: kareneilbeck
creation_date: 2013-07-30T03:33:53Z

[Term]
id: SO:0001980
name: G_box
def: "A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]
comment: A plant specific region.
synonym: "G-box" EXACT []
synonym: "GBF binding sequence" EXACT []
is_a: SO:0001678 ! regulatory_promoter_element
created_by: kareneilbeck
creation_date: 2013-07-30T04:00:50Z

[Term]
id: SO:0001981
name: L_box
def: "An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]
synonym: "L-box" EXACT []
synonym: "L-box promoter element" EXACT []
is_a: SO:0001678 ! regulatory_promoter_element
created_by: kareneilbeck
creation_date: 2013-07-30T04:12:19Z

[Term]
id: SO:0001982
name: I-box
def: "A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]
synonym: "I-box promoter motif" EXACT []
is_a: SO:0001678 ! regulatory_promoter_element
created_by: kareneilbeck
creation_date: 2013-07-30T04:17:55Z

[Term]
id: SO:0001983
name: 5_prime_UTR_premature_start_codon_variant
def: "A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]
comment: Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia.
synonym: "5' UTR premature start codon variant" EXACT []
synonym: "snpEff:START_GAINED" EXACT VAR []
is_a: SO:0001623 ! 5_prime_UTR_variant
created_by: kareneilbeck
creation_date: 2013-07-30T04:36:25Z

[Term]
id: SO:0001984
name: silent_mating_type_cassette_array
def: "A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]
synonym: "silent mating-type cassette" RELATED []
is_a: SO:0005854 ! gene_cassette_array
created_by: kareneilbeck
creation_date: 2013-07-31T02:40:38Z

[Term]
id: SO:0001985
name: Okazaki_fragment
def: "Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152]
comment: Requested by Midori Harris, 2013.
synonym: "Okazaki fragment" EXACT []
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2013-07-31T02:57:55Z

[Term]
id: SO:0001986
name: upstream_transcript_variant
def: "A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr]
comment: Requested by Graham Ritchie, EBI/Sanger.
synonym: "upstream transcript variant" EXACT []
is_a: SO:0001628 ! intergenic_variant
created_by: kareneilbeck
creation_date: 2013-07-31T03:46:14Z

[Term]
id: SO:0001987
name: downstream_transcript_variant
comment: Requested by Graham Ritchie, EBI/Sanger.
synonym: "downstream transcript variant" EXACT []
is_a: SO:0001628 ! intergenic_variant
created_by: kareneilbeck
creation_date: 2013-07-31T03:47:51Z

[Term]
id: SO:0001988
name: 5_prime_UTR_premature_start_codon_gain_variant
def: "A 5' UTR variant where a premature start codon is gained." [Sanger:am]
synonym: "5 prime UTR premature start codon gain variant" EXACT []
is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
created_by: kareneilbeck
creation_date: 2013-07-31T03:53:06Z

[Term]
id: SO:0001989
name: 5_prime_UTR_premature_start_codon_loss_variant
def: "A 5' UTR variant where a premature start codon is lost." [SANGER:am]
is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
created_by: kareneilbeck
creation_date: 2013-07-31T03:56:48Z

[Term]
id: SO:0001990
name: five_prime_UTR_premature_start_codon_location_variant
def: "A 5' UTR variant where a premature start codon is moved." [SANGER:am]
is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
created_by: kareneilbeck
creation_date: 2013-07-31T03:57:47Z

[Term]
id: SO:0001991
name: consensus_AFLP_fragment
def: "A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]
comment: Requested by Bayer Cropscience September, 2013.
synonym: "consensus AFLP fragment" EXACT []
synonym: "consensus amplified fragment length polymorphism fragment" EXACT []
is_a: SO:0000994 ! consensus_region
created_by: kareneilbeck
creation_date: 2013-09-24T10:43:41Z

[Term]
id: SO:0001992
name: nonsynonymous_variant
def: "A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]
synonym: "non_synonymous_coding" EXACT [http://ensembl.org/info/docs/variation/index.html]
synonym: "nonsynonymous variant" EXACT []
is_a: SO:0001650 ! inframe_variant
created_by: kareneilbeck
creation_date: 2013-10-16T11:47:51Z

[Term]
id: SO:0001993
name: extended_cis_splice_site
def: "Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]
comment: Added by Andy Menzies (Sanger).
synonym: "extended cis splice site" EXACT []
is_a: SO:0001419 ! cis_splice_site
created_by: kareneilbeck
creation_date: 2014-01-04T06:20:00Z

[Term]
id: SO:0001994
name: intron_base_5
def: "Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]
synonym: "intron base 5" EXACT []
is_a: SO:0001014 ! intron_domain
relationship: part_of SO:0001993 ! extended_cis_splice_site
created_by: kareneilbeck
creation_date: 2014-01-04T06:26:02Z

[Term]
id: SO:0001995
name: extended_intronic_splice_region_variant
def: "A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]
comment: Added by Andy Menzies (Sanger).
synonym: "extended intronic splice region variant" EXACT []
is_a: SO:0001568 ! splicing_variant
created_by: kareneilbeck
creation_date: 2014-01-04T06:37:27Z

[Term]
id: SO:0001996
name: extended_intronic_splice_region
def: "Region of intronic sequence within 10 bases of an exon." [SANGER:am]
synonym: "extended intronic splice region " EXACT []
is_a: SO:0001014 ! intron_domain
created_by: kareneilbeck
creation_date: 2014-01-04T06:41:23Z

[Term]
id: SO:0001997
name: subtelomere
def: "A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]
is_a: SO:0000628 ! chromosomal_structural_element
created_by: kareneilbeck
creation_date: 2014-01-05T07:02:01Z

[Term]
id: SO:0001998
name: sgRNA
def: "A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893]
synonym: "gRNA" RELATED []
synonym: "guide RNA" RELATED []
synonym: "small guide RNA" EXACT []
is_a: SO:0000696 ! oligo
created_by: kareneilbeck
creation_date: 2014-01-05T07:25:08Z

[Term]
id: SO:0001999
name: mating_type_region_motif
def: "DNA motif that is a component of a mating type region." [SO:ke]
synonym: "mating type region motif" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001789 ! mating_type_region
created_by: kareneilbeck
creation_date: 2014-01-05T07:30:17Z

[Term]
id: SO:0002001
name: Y_region
def: "A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]
comment: Requested by Janos Demeter, SGD.
synonym: "Y-region" EXACT []
is_a: SO:0001999 ! mating_type_region_motif
created_by: kareneilbeck
creation_date: 2014-01-05T07:33:30Z

[Term]
id: SO:0002002
name: Z1_region
def: "A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]
comment: Requested by Janos Demeter, SGD.
synonym: "Z1-region" EXACT []
is_a: SO:0001999 ! mating_type_region_motif
created_by: kareneilbeck
creation_date: 2014-01-05T07:34:59Z

[Term]
id: SO:0002003
name: Z2_region
def: "A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]
comment: Requested by Janos Demeter, SGD.
synonym: "Z2-segment" EXACT []
is_a: SO:0001999 ! mating_type_region_motif
created_by: kareneilbeck
creation_date: 2014-01-05T07:36:45Z

[Term]
id: SO:0002004
name: ARS_consensus_sequence
def: "The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]
synonym: "ACS" EXACT []
synonym: "ARS consensus sequence" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000436 ! ARS
created_by: kareneilbeck
creation_date: 2014-01-05T07:47:48Z

[Term]
id: SO:0002005
name: DSR_motif
def: "The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]
comment: Requested by Antonia Locke, (Pombe).
synonym: "DSR motif" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2014-01-05T07:51:27Z

[Term]
id: SO:0002006
name: zinc_repressed_element
def: "A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]
comment: This element is bound by Loz1 in S. pombe. The paper does not name the element. This term was requested by Midoris Harris, for Pombe.
synonym: "zinc repressed element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2014-01-05T09:23:27Z

[Term]
id: SO:0002007
name: MNV
def: "An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]
synonym: "multiple nucleotide substitution" EXACT []
synonym: "multiple nucleotide variant" EXACT []
is_a: SO:1000002 ! substitution
created_by: kareneilbeck
creation_date: 2014-01-13T03:48:40Z

[Term]
id: SO:0002008
name: rare_amino_acid_variant
def: "A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]
comment: Request from  Uma Devi Paila, UVA.  Variants in the sites of rare amino acids e.g. Selenocysteine.  These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
synonym: "rare amino acid variant" EXACT []
is_a: SO:0001586 ! non_conservative_missense_variant
created_by: kareneilbeck
creation_date: 2014-03-24T02:24:01Z

[Term]
id: SO:0002009
name: selenocysteine_loss
def: "A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid." [SO:ke]
comment: Request from  Uma Devi Paila, UVA.  Variants in the sites of rare amino acids e.g. Selenocysteine.  These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
synonym: "selenocysteine loss" EXACT []
is_a: SO:0002008 ! rare_amino_acid_variant
created_by: kareneilbeck
creation_date: 2014-03-24T02:29:44Z

[Term]
id: SO:0002010
name: pyrrolysine_loss
def: "A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]
comment: Request from  Uma Devi Paila, UVA.  Variants in the sites of rare amino acids e.g. Selenocysteine.  These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
synonym: "pyrrolysine loss" EXACT []
is_a: SO:0002008 ! rare_amino_acid_variant
created_by: kareneilbeck
creation_date: 2014-03-24T02:30:16Z

[Term]
id: SO:0002011
name: intragenic_variant
def: "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping  sequence." [SO:ke]
comment: Requested by Pablo Cingolani, for use in SnpEff.
synonym: "intragenic variant" EXACT []
synonym: "snpEff:INTRAGENIC" EXACT VAR []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2014-03-24T02:33:13Z

[Term]
id: SO:0002012
name: start_lost
def: "A codon variant that changes at least one base of the canonical start codon." [SO:ke]
comment: Request from  Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts.
synonym: "snpEff:START_LOST" EXACT VAR []
is_a: SO:0001582 ! initiator_codon_variant
is_a: SO:0001992 ! nonsynonymous_variant
created_by: kareneilbeck
creation_date: 2014-03-24T02:41:28Z

[Term]
id: SO:0002013
name: 5_prime_UTR_truncation
def: "A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence." [SO:ke]
synonym: "5 prime UTR truncation" EXACT []
synonym: "snpEff:UTR_5_DELETED" EXACT VAR []
is_a: SO:0001623 ! 5_prime_UTR_variant
created_by: kareneilbeck
creation_date: 2014-03-25T10:46:42Z

[Term]
id: SO:0002014
name: 5_prime_UTR_elongation
def: "A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]
synonym: "5 prime UTR elongation" EXACT []
is_a: SO:0001623 ! 5_prime_UTR_variant
created_by: kareneilbeck
creation_date: 2014-03-25T10:48:26Z

[Term]
id: SO:0002015
name: 3_prime_UTR_truncation
def: "A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence." [SO:ke]
synonym: "3 prime UTR truncation" EXACT []
synonym: "snpEff:UTR_3_DELETED" EXACT VAR []
is_a: SO:0001624 ! 3_prime_UTR_variant
created_by: kareneilbeck
creation_date: 2014-03-25T10:54:50Z

[Term]
id: SO:0002016
name: 3_prime_UTR_elongation
def: "A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]
synonym: "3 prime UTR elongation" EXACT []
is_a: SO:0001624 ! 3_prime_UTR_variant
created_by: kareneilbeck
creation_date: 2014-03-25T10:55:33Z

[Term]
id: SO:0002017
name: conserved_intergenic_variant
def: "A sequence variant located in a conserved intergenic region, between genes." [SO:ke]
comment: Requested by Uma Paila (UVA) for snpEff.
synonym: "conserved intergenic variant" EXACT []
synonym: "snpEff:INTERGENIC_CONSERVED" EXACT VAR []
is_a: SO:0001628 ! intergenic_variant
created_by: kareneilbeck
creation_date: 2014-03-25T02:54:39Z

[Term]
id: SO:0002018
name: conserved_intron_variant
def: "A transcript variant occurring within a conserved region of an intron." [SO:ke]
comment: Requested by Uma Paila (UVA) for snpEff.
synonym: "conserved intron variant" EXACT []
synonym: "snpEff:INTRON_CONSERVED" EXACT VAR []
is_a: SO:0001627 ! intron_variant
created_by: kareneilbeck
creation_date: 2014-03-25T02:58:41Z

[Term]
id: SO:0002019
name: start_retained_variant
def: "A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]
comment: Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation.
is_a: SO:0001582 ! initiator_codon_variant
is_a: SO:0001819 ! synonymous_variant
created_by: kareneilbeck
creation_date: 2014-03-28T10:08:41Z

[Term]
id: SO:0002020
name: boundary_element
def: "Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]
comment: Requested by Antonia Lock.
synonym: "boundary element" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2014-05-30T14:45:37Z

[Term]
id: SO:0002021
name: mating_type_region_replication_fork_barrier
def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]
comment: Requested by Midori Harris.
synonym: "mating type region replication fork barrier" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2014-05-30T14:57:26Z

[Term]
id: SO:0002022
name: priRNA
def: "A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]
synonym: "primal small RNA" EXACT []
is_a: SO:0000655 ! ncRNA
created_by: kareneilbeck
creation_date: 2014-05-30T15:01:24Z

[Term]
id: SO:0002023
name: multiplexing_sequence_identifier
def: "A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]
synonym: "multiplexing sequence identifier" EXACT []
is_a: SO:0000324 ! tag
created_by: kareneilbeck
creation_date: 2014-05-30T15:13:16Z

[Term]
id: SO:0002024
name: W_region
alt_id: SO:0002000
def: "The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR." [SGD:jd]
comment: MERGED COMMENT:\nTARGET COMMENT: Requested by Janos Demeter, SGD.\n--------------------\nSOURCE COMMENT: Requested by Janos Demeter, SGD.
synonym: "W-region" EXACT []
is_a: SO:0001999 ! mating_type_region_motif
created_by: kareneilbeck
creation_date: 2014-07-11T13:20:08Z

[Term]
id: SO:0002025
name: cis_acting_homologous_chromosome_pairing_region
def: "A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]
comment: Comment: An example of this is the Sme2 locus in fission yeast S. pombe, where is coincident with an ribonuclear complex termed the "Mei2 dot". This term was Requested by Val Wood, PomBase.
synonym: "cis-acting homologous chromosome pairing region" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2014-07-14T11:40:34Z

[Term]
id: SO:0002026
name: intein_encoding_region
def: "The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]
comment: Requested by Janos Demeter 2014.
is_a: SO:0000842 ! gene_component_region
created_by: kareneilbeck
creation_date: 2014-07-14T11:53:21Z

[Term]
id: SO:0002027
name: uORF
def: "A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]
synonym: "upstream ORF" EXACT []
is_a: SO:0000236 ! ORF
created_by: kareneilbeck
creation_date: 2014-07-14T11:59:23Z

[Term]
id: SO:0002028
name: sORF
def: "An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]
synonym: "small ORF" EXACT []
synonym: "smORF" EXACT []
is_a: SO:0000236 ! ORF
created_by: kareneilbeck
creation_date: 2014-07-14T12:02:33Z

[Term]
id: SO:0002029
name: tnaORF
def: "A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]
synonym: "translated nested antisense gene" EXACT []
is_a: SO:0000236 ! ORF
created_by: kareneilbeck
creation_date: 2014-07-14T12:04:32Z

[Term]
id: SO:0002030
name: X_region
def: "One of two segments of homology found at all three mating loci (HML, MAT and HMR)." [SGD:jd]
synonym: "x-region" EXACT []
is_a: SO:0001999 ! mating_type_region_motif
created_by: kareneilbeck
creation_date: 2014-07-14T18:43:21Z

[Term]
id: SO:0002031
name: shRNA
def: "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]
synonym: "short hairpin RNA" EXACT []
synonym: "small hairpin RNA" EXACT []
xref: http:http\:en.wikipedia.org/wiki/Small_hairpin_RNA "wikipedia"
is_a: SO:0000655 ! ncRNA
created_by: kareneilbeck
creation_date: 2014-10-23T09:16:29Z

[Term]
id: SO:0002032
name: moR
def: "A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA." [SO:ke]
comment: MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015.
synonym: "microRNA-offset RNA" EXACT []
is_a: SO:0000370 ! small_regulatory_ncRNA
relationship: part_of SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T13:57:43Z

[Term]
id: SO:0002033
name: loR
def: "A short, non coding transcript of loop-derived sequences encoded in precursor miRNA." [SO:ke]
comment: MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015.
synonym: "loop-origin miRs" EXACT []
is_a: SO:0000370 ! small_regulatory_ncRNA
relationship: part_of SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T14:02:02Z

[Term]
id: SO:0002034
name: miR_encoding_snoRNA_primary_transcript
def: "A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:02:13Z

[Term]
id: SO:0002035
name: lncRNA_primary_transcript
def: "A primary transcript encoding a  lncRNA." [SO:ke]
synonym: "lncRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
created_by: kareneilbeck
creation_date: 2015-01-09T15:23:03Z

[Term]
id: SO:0002036
name: miR_encoding_lncRNA_primary_transcript
def: "A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding lncRNA primary transcript" EXACT []
is_a: SO:0002035 ! lncRNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:23:48Z

[Term]
id: SO:0002037
name: miR_encoding_tRNA_primary_transcript
def: "A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:28:23Z

[Term]
id: SO:0002038
name: shRNA_primary_transcript
def: "A primary transcript encoding an shRNA." [SO:ke]
synonym: "shRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
created_by: kareneilbeck
creation_date: 2015-01-09T15:30:43Z

[Term]
id: SO:0002039
name: miR_encoding_shRNA_primary_transcript
def: "A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding shRNA primary transcript" EXACT []
is_a: SO:0002038 ! shRNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:32:00Z

[Term]
id: SO:0002040
name: vaultRNA_primary_transcript
def: "A primary transcript encoding a  vaultRNA." [SO:ke]
synonym: "vaultRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
created_by: kareneilbeck
creation_date: 2015-01-09T15:33:33Z

[Term]
id: SO:0002041
name: miR_encoding_vaultRNA_primary_transcript
def: "A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding vaultRNA primary transcript" EXACT []
is_a: SO:0002040 ! vaultRNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:34:32Z

[Term]
id: SO:0002042
name: Y_RNA_primary_transcript
def: "A primary transcript encoding a  Y-RNA." [SO:ke]
synonym: "Y-RNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
created_by: kareneilbeck
creation_date: 2015-01-09T15:36:51Z

[Term]
id: SO:0002043
name: miR_encoding_Y_RNA_primary_transcript
def: "A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding Y-RNA primary transcript" EXACT []
is_a: SO:0002042 ! Y_RNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:37:46Z

[Term]
id: SO:0002044
name: TCS_element
def: "A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT." [PMID:1489142, PMID:20118212, SO:ke]
comment: Requested by Rama - SGD.
synonym: "TCS element" EXACT []
synonym: "TEA Consensus Sequence " EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2015-02-09T15:02:53Z

[Term]
id: SO:0002045
name: pheromone_response_element
def: "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)]." [PMID:1489142, SO:ke]
comment: Requested by Rama, SGD.
synonym: "pheromone response element" EXACT []
synonym: "PRE" EXACT []
is_a: SO:0000235 ! TF_binding_site
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2015-02-09T15:05:43Z

[Term]
id: SO:0002046
name: FRE
def: "A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae." [PMID:1489142, SO:ke]
comment: Requested by Rama, SGD.
synonym: "filamentation and invasion response element" EXACT []
is_a: SO:0001461 ! enhancer_binding_site
created_by: kareneilbeck
creation_date: 2015-02-09T15:09:47Z

[Term]
id: SO:0002047
name: transcription_pause_site
def: "Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli." [PMID:24789973, SO:ke]
synonym: "transcription pause site" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
created_by: kareneilbeck
creation_date: 2015-02-09T15:32:52Z

[Term]
id: SO:0002048
name: disabled_reading_frame
def: "A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons)." [SGD:se]
synonym: "disabled ORF" EXACT []
synonym: "disabled_reading frame" RELATED []
synonym: "dORF" EXACT []
is_a: SO:0000717 ! reading_frame
created_by: kareneilbeck
creation_date: 2015-02-09T16:15:46Z

[Term]
id: SO:0002049
name: H3K27_acetylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:rs]
comment: Requested by: Sagar Jain, Richard Scheuermann.
synonym: "H3K27 acetylation site" EXACT []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2015-05-14T10:17:11Z

[Term]
id: SO:0002050
name: constitutive_promoter
def: "A promoter that allows for continual transcription of gene." [SO:ke]
synonym: "constitutive promoter" EXACT []
is_a: SO:0000167 ! promoter
created_by: kareneilbeck
creation_date: 2015-05-14T10:39:09Z

[Term]
id: SO:0002051
name: inducible_promoter
def: "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors." [SO:ke]
synonym: "inducible promoter" EXACT []
is_a: SO:0000167 ! promoter
created_by: kareneilbeck
creation_date: 2015-05-14T10:39:56Z

[Term]
id: SO:0002052
name: dominant_negative_variant
def: "A variant where the mutated gene product adversely affects the other (wild type) gene product." [SO:ke]
comment: Requested by Deanna Church.
synonym: "dominant negative" EXACT []
synonym: "dominant negative variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2015-05-14T11:16:28Z

[Term]
id: SO:0002053
name: gain_of_function_variant
def: "A sequence variant whereby new or enhanced function is conferred on the gene product." [SO:ke]
synonym: "gain of function variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2015-05-14T11:20:47Z

[Term]
id: SO:0002054
name: loss_of_function_variant
def: "A sequence variant whereby the gene product has diminished or abolished function." [SO:ke]
synonym: "loss of function variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2015-05-14T11:21:29Z

[Term]
id: SO:0002055
name: null_mutation
def: "A variant whereby the gene product is not functional or the gene product is not produced." [SO:ke]
synonym: "null mutation" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2015-05-14T11:21:57Z

[Term]
id: SO:0002056
name: intronic_splicing_silencer
def: "An intronic  splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." [PMID:23241926, SO:ke]
comment: Requested by Javier Diez Perez.
synonym: "intronic splicing silencer" EXACT []
synonym: "ISS" EXACT []
is_a: SO:0000625 ! silencer
relationship: part_of SO:0000188 ! intron
created_by: kareneilbeck
creation_date: 2015-05-14T12:24:10Z

[Term]
id: SO:0002057
name: intronic_splicing_enhancer
synonym: "ISE" EXACT []
is_obsolete: true
created_by: kareneilbeck
creation_date: 2015-05-14T12:28:31Z

[Term]
id: SO:0002058
name: exonic_splicing_silencer
def: "An exonic  splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." [PMID:23241926, SO:ke]
comment: Requested by Javier Diez Perez.
synonym: "ESS" EXACT []
synonym: "exonic splicing silencer" EXACT []
is_a: SO:0000625 ! silencer
is_a: SO:0000852 ! exon_region
created_by: kareneilbeck
creation_date: 2015-05-14T12:42:12Z

[Term]
id: SO:0002059
name: recombination_enhancer
def: "A regulatory_region that promotes or induces the process of recombination." [PMID:8861911, SGD:se]
synonym: "recombination enhancer" EXACT []
is_a: SO:0001681 ! recombination_regulatory_region
created_by: kareneilbeck
creation_date: 2015-05-14T13:08:58Z

[Term]
id: SO:0002060
name: interchromosomal_translocation
def: "A translocation where the regions involved are from different chromosomes." [NCBI:th]
is_a: SO:1000044 ! chromosomal_translocation
created_by: kareneilbeck
creation_date: 2015-06-18T11:10:30Z

[Term]
id: SO:0002061
name: intrachromosomal_translocation
def: "A translocation where the regions involved are from the same chromosome." [NCBI:th]
is_a: SO:1000044 ! chromosomal_translocation
created_by: kareneilbeck
creation_date: 2015-06-18T11:10:51Z

[Term]
id: SO:0002062
name: complex_chromosomal_rearrangement
def: "A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis." [NCBI:th]
synonym: "complex chromosomal rearrangement" EXACT []
is_a: SO:0001784 ! complex_structural_alteration
created_by: kareneilbeck
creation_date: 2015-06-18T11:24:55Z

[Term]
id: SO:0002063
name: Alu_insertion
def: "An insertion of sequence from the Alu family of mobile elements." [NCBI:th]
synonym: "Alu insertion" EXACT []
is_a: SO:0001837 ! mobile_element_insertion
created_by: kareneilbeck
creation_date: 2015-06-18T11:30:36Z

[Term]
id: SO:0002064
name: LINE1_insertion
def: "An insertion from the Line1 family of mobile elements." [NCBI:th]
synonym: "line1 insertion" RELATED []
is_a: SO:0001837 ! mobile_element_insertion
created_by: kareneilbeck
creation_date: 2015-06-18T11:34:44Z

[Term]
id: SO:0002065
name: SVA_insertion
def: "An insertion of sequence from the SVA family of mobile elements." [NCBI:th]
is_a: SO:0001837 ! mobile_element_insertion
created_by: kareneilbeck
creation_date: 2015-06-18T11:36:12Z

[Term]
id: SO:0002066
name: mobile_element_deletion
def: "A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element)." [NCBI:th]
synonym: "mobile element deletion" EXACT []
is_a: SO:0000159 ! deletion
created_by: kareneilbeck
creation_date: 2015-09-04T13:40:43Z

[Term]
id: SO:0002067
name: HERV_deletion
def: "A deletion of the HERV mobile element with respect to  a reference." [NCBI:th]
synonym: "HERV deletion" EXACT []
is_a: SO:0002066 ! mobile_element_deletion
created_by: kareneilbeck
creation_date: 2015-09-04T13:42:52Z

[Term]
id: SO:0002068
name: SVA_deletion
def: "A deletion of an SVA mobile element." [NCBI:th]
synonym: "SVA deletion" EXACT []
is_a: SO:0002066 ! mobile_element_deletion
created_by: kareneilbeck
creation_date: 2015-09-04T13:45:22Z

[Term]
id: SO:0002069
name: LINE1_deletion
def: "A deletion of a LINE1 mobile element with respect to a reference." [NCBI:th]
synonym: "LINE1 deletion" RELATED []
is_a: SO:0002066 ! mobile_element_deletion
created_by: kareneilbeck
creation_date: 2015-09-04T13:46:26Z

[Term]
id: SO:0002070
name: Alu_deletion
def: "A deletion of an Alu mobile element with respect to a reference." [NCBI:th]
is_a: SO:0002066 ! mobile_element_deletion
created_by: kareneilbeck
creation_date: 2015-09-04T13:47:16Z

[Term]
id: SO:0005836
name: regulatory_region
def: "A region of sequence that is involved in the control of a biological process." [SO:ke]
subset: SOFA
synonym: "regulatory region" EXACT []
xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki"
is_a: SO:0000831 ! gene_member_region

[Term]
id: SO:0005837
name: U14_snoRNA_primary_transcript
def: "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]
synonym: "4.5S snRNA primary transcript" EXACT []
synonym: "U14 snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0005841
name: methylation_guide_snoRNA
def: "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]
comment: Has RNA 2'-O-ribose methylation guide activity (GO:0030561).
synonym: "methylation guide snoRNA" EXACT []
is_a: SO:0000593 ! C_D_box_snoRNA
relationship: derives_from SO:0000580 ! methylation_guide_snoRNA_primary_transcript

[Term]
id: SO:0005843
name: rRNA_cleavage_RNA
def: "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]
synonym: "rRNA cleavage RNA" EXACT []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000582 ! rRNA_cleavage_snoRNA_primary_transcript

[Term]
id: SO:0005845
name: exon_of_single_exon_gene
def: "An exon that is the only exon in a gene." [RSC:cb]
synonym: "exon of single exon gene" EXACT []
synonym: "single_exon" RELATED []
synonym: "singleton exon" EXACT []
is_a: SO:0000147 ! exon

[Term]
id: SO:0005847
name: cassette_array_member
synonym: "cassette array member" EXACT []
is_a: SO:0005848 ! gene_cassette_member

[Term]
id: SO:0005848
name: gene_cassette_member
synonym: "gene cassette member" EXACT []
is_a: SO:0000081 ! gene_array_member

[Term]
id: SO:0005849
name: gene_subarray_member
synonym: "gene subarray member" EXACT []
is_a: SO:0000081 ! gene_array_member

[Term]
id: SO:0005850
name: primer_binding_site
def: "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "primer binding site" EXACT []
xref: http://en.wikipedia.org/wiki/Primer_binding_site "wiki"
is_a: SO:0001655 ! nucleotide_binding_site
relationship: part_of SO:0000186 ! LTR_retrotransposon

[Term]
id: SO:0005851
name: gene_array
def: "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]
comment: This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
synonym: "gene array" EXACT []
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0005852
name: gene_subarray
def: "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]
comment: This would include, for example, a cluster of genes encoding different histones.
synonym: "gene subarray" EXACT []
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0005853
name: gene_cassette
def: "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]
comment: This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid.
synonym: "gene cassette" EXACT []
xref: http://en.wikipedia.org/wiki/Gene_cassette "wiki"
is_a: SO:0000704 ! gene

[Term]
id: SO:0005854
name: gene_cassette_array
def: "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]
comment: This would include, for example, the arrays of non-functional VSG genes of Trypanosomes.
synonym: "gene cassette array" EXACT []
is_a: SO:0005855 ! gene_group
relationship: has_part SO:0005853 ! gene_cassette

[Term]
id: SO:0005855
name: gene_group
def: "A collection of related genes." [SO:ma]
subset: SOFA
synonym: "gene group" EXACT []
is_a: SO:0001411 ! biological_region

[Term]
id: SO:0005856
name: selenocysteine_tRNA_primary_transcript
def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
synonym: "selenocysteine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0005857
name: selenocysteinyl_tRNA
def: "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]
synonym: "selenocysteinyl tRNA" EXACT []
synonym: "selenocysteinyl-transfer ribonucleic acid" EXACT []
synonym: "selenocysteinyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0005856 ! selenocysteine_tRNA_primary_transcript

[Term]
id: SO:0005858
name: syntenic_region
def: "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml]
synonym: "syntenic region" EXACT []
is_a: SO:0000330 ! conserved_region
intersection_of: SO:0000330 ! conserved_region
intersection_of: has_quality SO:0000860 ! syntenic
relationship: has_quality SO:0000860 ! syntenic

[Term]
id: SO:0100001
name: biochemical_region_of_peptide
def: "A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "biochemical motif" EXACT []
synonym: "biochemical region of peptide" EXACT []
synonym: "biochemical_region" RELATED []
is_a: SO:0001067 ! polypeptide_motif

[Term]
id: SO:0100002
name: molecular_contact_region
def: "A region that is involved a contact with another molecule." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "molecular contact region" RELATED []
is_a: SO:0100001 ! biochemical_region_of_peptide

[Term]
id: SO:0100003
name: intrinsically_unstructured_polypeptide_region
def: "A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]
subset: biosapiens
synonym: "disordered region" RELATED BS []
synonym: "intrinsically unstructured polypeptide region" EXACT []
is_a: SO:0001070 ! polypeptide_structural_region

[Term]
id: SO:0100004
name: catmat_left_handed_three
def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-3l" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100005
name: catmat_left_handed_four
def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-4l" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100006
name: catmat_right_handed_three
def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-3r" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100007
name: catmat_right_handed_four
def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-4r" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100008
name: alpha_beta_motif
def: "A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "alpha beta motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100009
name: lipoprotein_signal_peptide
def: "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]
subset: biosapiens
synonym: "lipoprotein signal peptide" EXACT []
synonym: "prokaryotic membrane lipoprotein lipid attachment site" EXACT []
is_a: SO:0100011 ! cleaved_peptide_region

[Term]
id: SO:0100010
name: no_output
def: "An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]
subset: biosapiens
synonym: "no output" EXACT BS []
is_a: SO:0000703 ! experimental_result_region

[Term]
id: SO:0100011
name: cleaved_peptide_region
def: "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]
comment: Range.
subset: biosapiens
subset: SOFA
synonym: "cleaved peptide region" EXACT []
is_a: SO:0000839 ! polypeptide_region
relationship: part_of SO:0001063 ! immature_peptide_region

[Term]
id: SO:0100012
name: peptide_coil
def: "Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]
subset: biosapiens
synonym: "coil" RELATED BS []
synonym: "peptide coil" EXACT []
synonym: "random coil" RELATED BS []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100013
name: hydrophobic_region_of_peptide
def: "Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "hydropathic" RELATED []
synonym: "hydrophobic region of peptide" RELATED []
synonym: "hydrophobic_region" EXACT []
synonym: "hydrophobicity" RELATED []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0100014
name: n_terminal_region
def: "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]
subset: biosapiens
synonym: "N-region" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0000418 ! signal_peptide

[Term]
id: SO:0100015
name: c_terminal_region
def: "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]
subset: biosapiens
synonym: "C-region" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0000418 ! signal_peptide

[Term]
id: SO:0100016
name: central_hydrophobic_region_of_signal_peptide
def: "The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]
subset: biosapiens
synonym: "central hydrophobic region of signal peptide" EXACT []
synonym: "central_hydrophobic_region" RELATED []
synonym: "H-region" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0000418 ! signal_peptide

[Term]
id: SO:0100017
name: polypeptide_conserved_motif
def: "A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]
subset: biosapiens
synonym: "motif" RELATED []
is_a: SO:0001067 ! polypeptide_motif

[Term]
id: SO:0100018
name: polypeptide_binding_motif
def: "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]
subset: biosapiens
synonym: "binding" RELATED [uniprot:feature_type]
synonym: "polypeptide binding motif" EXACT []
is_a: SO:0100001 ! biochemical_region_of_peptide

[Term]
id: SO:0100019
name: polypeptide_catalytic_motif
def: "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]
subset: biosapiens
synonym: "catalytic_motif" RELATED []
synonym: "polypeptide catalytic motif" EXACT []
is_a: SO:0100001 ! biochemical_region_of_peptide

[Term]
id: SO:0100020
name: polypeptide_DNA_contact
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]
subset: biosapiens
synonym: "DNA_bind" EXACT BS [uniprot:feature]
synonym: "polypeptide DNA contact" EXACT []
is_a: SO:0001429 ! DNA_binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0100021
name: polypeptide_conserved_region
def: "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]
subset: biosapiens
synonym: "polypeptide conserved region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:1000002
name: substitution
def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]
subset: SOFA
xref: loinc:LA6690-7 "Substitution"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region

[Term]
id: SO:1000005
name: complex_substitution
def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
synonym: "complex substitution" EXACT []
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000008
name: point_mutation
def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]
subset: SOFA
synonym: "point mutation" EXACT []
xref: http://en.wikipedia.org/wiki/Point_mutation "wiki"
is_a: SO:0001483 ! SNV

[Term]
id: SO:1000009
name: transition
def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:0001483 ! SNV

[Term]
id: SO:1000010
name: pyrimidine_transition
def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]
synonym: "pyrimidine transition" EXACT []
is_a: SO:1000009 ! transition

[Term]
id: SO:1000011
name: C_to_T_transition
def: "A transition of a cytidine to a thymine." [SO:ke]
synonym: "C to T transition" EXACT []
is_a: SO:1000010 ! pyrimidine_transition

[Term]
id: SO:1000012
name: C_to_T_transition_at_pCpG_site
def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "C to T transition at pCpG site" EXACT []
is_a: SO:1000011 ! C_to_T_transition

[Term]
id: SO:1000013
name: T_to_C_transition
synonym: "T to C transition" EXACT []
is_a: SO:1000010 ! pyrimidine_transition

[Term]
id: SO:1000014
name: purine_transition
def: "A substitution of a purine, A or G, for another purine." [SO:ke]
synonym: "purine transition" EXACT []
is_a: SO:1000009 ! transition

[Term]
id: SO:1000015
name: A_to_G_transition
def: "A transition of an adenine to a guanine." [SO:ke]
synonym: "A to G transition" EXACT []
is_a: SO:1000014 ! purine_transition

[Term]
id: SO:1000016
name: G_to_A_transition
def: "A transition of a guanine to an adenine." [SO:ke]
synonym: "G to A transition" EXACT []
is_a: SO:1000014 ! purine_transition

[Term]
id: SO:1000017
name: transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
xref: http://en.wikipedia.org/wiki/Transversion "wiki"
is_a: SO:0001483 ! SNV

[Term]
id: SO:1000018
name: pyrimidine_to_purine_transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]
synonym: "pyrimidine to purine transversion" EXACT []
is_a: SO:1000017 ! transversion

[Term]
id: SO:1000019
name: C_to_A_transversion
def: "A transversion from cytidine to adenine." [SO:ke]
synonym: "C to A transversion" EXACT []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000020
name: C_to_G_transversion
synonym: "C to G transversion" EXACT []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000021
name: T_to_A_transversion
def: "A transversion from T to A." [SO:ke]
synonym: "T to A transversion" EXACT []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000022
name: T_to_G_transversion
def: "A transversion from T to G." [SO:ke]
synonym: "T to G transversion" EXACT []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000023
name: purine_to_pyrimidine_transversion
def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]
synonym: "purine to pyrimidine transversion" EXACT []
is_a: SO:1000017 ! transversion

[Term]
id: SO:1000024
name: A_to_C_transversion
def: "A transversion from adenine to cytidine." [SO:ke]
synonym: "A to C transversion" EXACT []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000025
name: A_to_T_transversion
def: "A transversion from adenine to thymine." [SO:ke]
synonym: "A to T transversion" EXACT []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000026
name: G_to_C_transversion
def: "A transversion from guanine to cytidine." [SO:ke]
synonym: "G to C transversion" EXACT []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000027
name: G_to_T_transversion
def: "A transversion from guanine to thymine." [SO:ke]
synonym: "G to T transversion" EXACT []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000028
name: intrachromosomal_mutation
def: "A chromosomal structure variation within a single chromosome." [SO:ke]
synonym: "intrachromosomal mutation" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation
intersection_of: SO:1000183 ! chromosome_structure_variation
intersection_of: has_quality SO:0001510 ! intrachromosomal
relationship: has_quality SO:0001510 ! intrachromosomal

[Term]
id: SO:1000029
name: chromosomal_deletion
def: "An incomplete chromosome." [SO:ke]
synonym: "(bacteria)&ampDgr;" RELATED []
synonym: "(Drosophila)Df" RELATED []
synonym: "(fungi)D" RELATED []
synonym: "chromosomal deletion" EXACT []
synonym: "deficiency" EXACT []
xref: http://en.wikipedia.org/wiki/Chromosomal_deletion "wiki"
is_a: SO:1000028 ! intrachromosomal_mutation
intersection_of: SO:1000028 ! intrachromosomal_mutation
intersection_of: has_part SO:0000159 ! deletion
relationship: has_part SO:0000159 ! deletion

[Term]
id: SO:1000030
name: chromosomal_inversion
def: "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]
synonym: "(bacteria)IN" RELATED []
synonym: "(Drosophila)In" RELATED []
synonym: "(fungi)In" RELATED []
synonym: "chromosomal inversion" EXACT []
xref: http://en.wikipedia.org/wiki/Chromosomal_inversion "wiki"
is_a: SO:1000028 ! intrachromosomal_mutation
intersection_of: SO:1000028 ! intrachromosomal_mutation
intersection_of: has_part SO:1000036 ! inversion
relationship: has_part SO:1000036 ! inversion

[Term]
id: SO:1000031
name: interchromosomal_mutation
def: "A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]
synonym: "interchromosomal mutation" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation
intersection_of: SO:1000183 ! chromosome_structure_variation
intersection_of: has_quality SO:0001511 ! interchromosomal
relationship: has_quality SO:0001511 ! interchromosomal

[Term]
id: SO:1000032
name: indel
def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, http:http\://www.hgvs.org/mutnomen/recs-DNA.html#indel]
comment: Indels can have a different number of bases than the corresponding reference sequence.
xref: http://en.wikipedia.org/wiki/Indel "wiki"
xref: loinc:LA9659-9 "Insertion and Deletion"
is_a: SO:0001059 ! sequence_alteration

[Term]
id: SO:1000035
name: duplication
def: "An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]
synonym: "nucleotide duplication" EXACT []
synonym: "nucleotide_duplication" RELATED []
xref: loinc:LA6686-5 "Duplication"
is_a: SO:0000667 ! insertion

[Term]
id: SO:1000036
name: inversion
def: "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: DBVAR
subset: SOFA
synonym: "inversion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
xref: loinc:LA6689-9 "Inversion"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region

[Term]
id: SO:1000037
name: chromosomal_duplication
def: "An extra chromosome." [SO:ke]
synonym: "(Drosophila)Dp" RELATED []
synonym: "(fungi)Dp" RELATED []
synonym: "chromosomal duplication" EXACT []
xref: http://en.wikipedia.org/wiki/Chromosomal_duplication "wiki"
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000038
name: intrachromosomal_duplication
def: "A duplication that occurred within a chromosome." [SO:ke]
synonym: "intrachromosomal duplication" EXACT []
is_a: SO:1000028 ! intrachromosomal_mutation
is_a: SO:1000037 ! chromosomal_duplication
intersection_of: SO:1000028 ! intrachromosomal_mutation
intersection_of: has_part SO:1000035 ! duplication
relationship: has_part SO:1000035 ! duplication

[Term]
id: SO:1000039
name: direct_tandem_duplication
def: "A tandem duplication where the individual regions are in the same orientation." [SO:ke]
synonym: "direct tandem duplication" EXACT []
is_a: SO:1000173 ! tandem_duplication

[Term]
id: SO:1000040
name: inverted_tandem_duplication
def: "A tandem duplication where the individual regions are not in the same orientation." [SO:ke]
synonym: "inverted tandem duplication" EXACT []
synonym: "mirror duplication" RELATED []
is_a: SO:1000173 ! tandem_duplication

[Term]
id: SO:1000041
name: intrachromosomal_transposition
def: "A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]
synonym: "(Drosophila)Tp" RELATED []
synonym: "intrachromosomal transposition" EXACT []
is_a: SO:0000453 ! chromosomal_transposition
is_a: SO:1000038 ! intrachromosomal_duplication
intersection_of: SO:1000028 ! intrachromosomal_mutation
intersection_of: has_part SO:0000199 ! translocation
intersection_of: has_part SO:1000035 ! duplication
relationship: has_part SO:1000035 ! duplication

[Term]
id: SO:1000042
name: compound_chromosome
def: "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]
synonym: "compound chromosome" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000043
name: Robertsonian_fusion
def: "A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]
synonym: "centric-fusion translocations" EXACT []
synonym: "Robertsonian fusion" EXACT []
synonym: "whole-arm translocations" EXACT []
xref: http://en.wikipedia.org/wiki/Robertsonian_fusion "wiki"
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000044
name: chromosomal_translocation
def: "A chromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]
synonym: "(Drosophila)T" RELATED []
synonym: "(fungi)T" RELATED []
synonym: "chromosomal translocation" EXACT []
xref: http://en.wikipedia.org/wiki/Chromosomal_translocation "wiki"
is_a: SO:0000199 ! translocation
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000045
name: ring_chromosome
def: "A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]
synonym: "(Drosophila)R" RELATED []
synonym: "(fungi)C" RELATED []
synonym: "ring chromosome" EXACT []
xref: http://en.wikipedia.org/wiki/Ring_chromosome "wiki"
is_a: SO:1000028 ! intrachromosomal_mutation
intersection_of: SO:1000028 ! intrachromosomal_mutation
intersection_of: has_quality SO:0000988 ! circular
relationship: has_quality SO:0000988 ! circular

[Term]
id: SO:1000046
name: pericentric_inversion
def: "A chromosomal inversion that includes the centromere." [FB:reference_manual]
synonym: "pericentric inversion" EXACT []
is_a: SO:1000030 ! chromosomal_inversion
intersection_of: SO:1000030 ! chromosomal_inversion
intersection_of: has_quality SO:0001518 ! pericentric
relationship: has_quality SO:0001518 ! pericentric

[Term]
id: SO:1000047
name: paracentric_inversion
def: "A chromosomal inversion that does not include the centromere." [FB:reference_manual]
synonym: "paracentric inversion" EXACT []
is_a: SO:1000030 ! chromosomal_inversion
intersection_of: SO:1000030 ! chromosomal_inversion
intersection_of: has_quality SO:0001519 ! paracentric
relationship: has_quality SO:0001519 ! paracentric

[Term]
id: SO:1000048
name: reciprocal_chromosomal_translocation
def: "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]
synonym: "reciprocal chromosomal translocation" EXACT []
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000049
name: sequence_variation_affecting_transcript
alt_id: SO:1000177
alt_id: SO:1000179
def: "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcript" EXACT []
synonym: "mutation causing partially characterised change in transcript" RELATED []
synonym: "mutation causing uncharacterised change in transcript" RELATED []
synonym: "sequence variant causing partially characterised change in transcript" EXACT []
synonym: "sequence variant causing uncharacterised change in transcript" EXACT []
synonym: "sequence variation affecting transcript" EXACT []
synonym: "sequence_variant_causing_partially_characterised_change_in_transcript" EXACT []
synonym: "sequence_variant_causing_uncharacterised_change_in_transcript" EXACT []
is_obsolete: true
replaced_by: SO:0001576

[Term]
id: SO:1000050
name: sequence_variant_causing_no_change_in_transcript
def: "No effect on the state of the RNA." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term.
synonym: "mutation causing no change in transcript" RELATED []
synonym: "sequence variant causing no change in transcript" EXACT []
is_obsolete: true

[Term]
id: SO:1000054
name: sequence_variation_affecting_coding_sequence
def: "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting coding sequence" EXACT []
synonym: "sequence variation affecting coding sequence" RELATED []
is_obsolete: true
replaced_by: SO:0001580

[Term]
id: SO:1000055
name: sequence_variant_causing_initiator_codon_change_in_transcript
def: "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing initiator codon change in transcript" RELATED []
synonym: "sequence variant causing initiator codon change in transcript" EXACT []
is_obsolete: true
replaced_by: SO:0001582

[Term]
id: SO:1000056
name: sequence_variant_causing_amino_acid_coding_codon_change_in_transcript
def: "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutaton causing amino acid coding codon change in transcript" RELATED []
synonym: "sequence variant causing amino acid coding codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001606

[Term]
id: SO:1000057
name: sequence_variant_causing_synonymous_codon_change_in_transcript
def: "The changed codon has the same translation product as the original codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing synonymous codon change in transcript" RELATED []
synonym: "sequence variant causing synonymous codon change in transcript" EXACT []
is_obsolete: true
replaced_by: SO:0001819

[Term]
id: SO:1000058
name: sequence_variant_causing_non_synonymous_codon_change_in_transcript
def: "A DNA point mutation that causes a substitution of an amino acid by an other." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing non synonymous codon change in transcript" RELATED []
synonym: "non-synonymous codon change in transcript" EXACT []
synonym: "sequence variant causing non synonymous codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001583

[Term]
id: SO:1000059
name: sequence_variant_causing_missense_codon_change_in_transcript
def: "The nucleotide change in the codon leads to a new codon coding for a new amino acid." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing missense codon change in transcript" RELATED []
synonym: "sequence variant causing missense codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001583

[Term]
id: SO:1000060
name: sequence_variant_causing_conservative_missense_codon_change_in_transcript
def: "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
synonym: "mutation causing conservative missense codon change in transcript" RELATED []
synonym: "sequence variant causing conservative missense codon change in transcript" EXACT []
is_obsolete: true
replaced_by: SO:0001585

[Term]
id: SO:1000061
name: sequence_variant_causing_nonconservative_missense_codon_change_in_transcript
def: "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
synonym: "mutation causing nonconservative missense codon change in transcript" RELATED []
synonym: "sequence variant causing nonconservative missense codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001586

[Term]
id: SO:1000062
name: sequence_variant_causing_nonsense_codon_change_in_transcript
def: "The nucleotide change in the codon triplet creates a terminator codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing nonsense codon change in transcript" RELATED []
synonym: "sequence variant causing nonsense codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001587

[Term]
id: SO:1000063
name: sequence_variant_causing_terminator_codon_change_in_transcript
def: "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing terminator codon change in transcript" RELATED []
synonym: "sequence variant causing terminator codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001590

[Term]
id: SO:1000064
name: sequence_variation_affecting_reading_frame
def: "An umbrella term for terms describing an effect of a sequence variation on the frame of translation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting reading frame" EXACT []
synonym: "sequence variation affecting reading frame" RELATED []
is_obsolete: true

[Term]
id: SO:1000065
name: frameshift_sequence_variation
def: "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]
synonym: "frameshift mutation" EXACT []
synonym: "frameshift sequence variation" RELATED []
synonym: "out of frame mutation" RELATED []
xref: http://en.wikipedia.org/wiki/Frameshift_mutation "wiki"
is_obsolete: true

[Term]
id: SO:1000066
name: sequence_variant_causing_plus_1_frameshift_mutation
def: "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "plus 1 frameshift mutation" EXACT []
synonym: "sequence variant causing plus 1 frameshift mutation" EXACT []
is_obsolete: true
replaced_by: SO:0001594

[Term]
id: SO:1000067
name: sequence_variant_causing_minus_1_frameshift
def: "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "minus 1 frameshift mutation" EXACT []
synonym: "sequence variant causing minus 1 frameshift" EXACT []
is_obsolete: true
replaced_by: SO:0001592

[Term]
id: SO:1000068
name: sequence_variant_causing_plus_2_frameshift
def: "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "plus 2 frameshift mutation" EXACT []
synonym: "sequence variant causing plus 2 frameshift" EXACT []
is_obsolete: true
replaced_by: SO:0001595

[Term]
id: SO:1000069
name: sequence_variant_causing_minus_2_frameshift
def: "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "minus 2 frameshift mutation" EXACT []
synonym: "sequence variant causing minus 2 frameshift" EXACT []
is_obsolete: true
replaced_by: SO:0001593

[Term]
id: SO:1000070
name: sequence_variant_affecting_transcript_processing
def: "Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcript processing" RELATED []
synonym: "sequence variant affecting transcript processing" EXACT []
is_obsolete: true
replaced_by: SO:0001543

[Term]
id: SO:1000071
name: sequence_variant_affecting_splicing
def: "A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting splicing" RELATED []
synonym: "sequence variant affecting splicing" EXACT []
is_obsolete: true
replaced_by: SO:0001568

[Term]
id: SO:1000072
name: sequence_variant_affecting_splice_donor
def: "A sequence_variant_effect that changes the splice donor sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting splice donor" RELATED []
synonym: "sequence variant affecting splice donor" RELATED []
synonym: "splice donor mutation" EXACT []
is_obsolete: true
replaced_by: SO:0001575

[Term]
id: SO:1000073
name: sequence_variant_affecting_splice_acceptor
def: "A sequence_variant_effect that changes the splice acceptor sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting splicing" RELATED []
synonym: "sequence variant affecting splice acceptor" RELATED []
synonym: "splice acceptor mutation" EXACT []
is_obsolete: true
replaced_by: SO:0001574

[Term]
id: SO:1000074
name: sequence_variant_causing_cryptic_splice_activation
def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration.
synonym: "cryptic splice activator sequence variant" EXACT []
synonym: "mutation causing cryptic splice activator" RELATED []
synonym: "sequence variant causing cryptic splice activator" EXACT []
is_obsolete: true
replaced_by: SO:0001569

[Term]
id: SO:1000075
name: sequence_variant_affecting_editing
def: "Sequence variant affects the editing of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting editing" RELATED []
synonym: "sequence variant affecting editing" EXACT []
is_obsolete: true
replaced_by: SO:0001544

[Term]
id: SO:1000076
name: sequence_variant_affecting_transcription
def: "Mutation affects the process of transcription, its initiation, progression or termination." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcription" RELATED []
synonym: "sequence variant affecting transcription" EXACT []
is_obsolete: true
replaced_by: SO:0001549

[Term]
id: SO:1000078
name: sequence_variant_decreasing_rate_of_transcription
def: "A sequence variation that decreases the rate a which transcription of the sequence occurs." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation decreasing rate of transcription" RELATED []
synonym: "sequence variation decreasing rate of transcription" EXACT []
is_obsolete: true

[Term]
id: SO:1000079
name: sequence_variation_affecting_transcript_sequence
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcript sequence" EXACT []
synonym: "sequence variation affecting transcript sequence" EXACT []
is_obsolete: true

[Term]
id: SO:1000080
name: sequence_variant_increasing_rate_of_transcription
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation increasing rate of transcription" RELATED []
synonym: "sequence variation increasing rate of transcription" EXACT []
is_obsolete: true

[Term]
id: SO:1000081
name: sequence_variant_affecting_rate_of_transcription
def: "A mutation that alters the rate a which transcription of the sequence occurs." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting rate of transcription" RELATED []
synonym: "sequence variant affecting rate of transcription" EXACT []
is_obsolete: true
replaced_by: SO:0001550

[Term]
id: SO:1000082
name: sequence variant_affecting_transcript_stability
def: "Sequence variant affects the stability of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcript stability" RELATED []
synonym: "sequence variant affecting transcript stability" EXACT []
is_obsolete: true
replaced_by: SO:0001546

[Term]
id: SO:1000083
name: sequence_variant_increasing_transcript_stability
def: "Sequence variant increases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation increasing transcript stability" RELATED []
synonym: "sequence variant increasing transcript stability" EXACT []
is_obsolete: true

[Term]
id: SO:1000084
name: sequence_variant_decreasing_transcript_stability
def: "Sequence variant decreases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation decreasing transcript stability" RELATED []
synonym: "sequence variant decreasing transcript stability" EXACT []
is_obsolete: true

[Term]
id: SO:1000085
name: sequence_variation_affecting_level_of_transcript
def: "A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting level of transcript" RELATED []
synonym: "sequence variation affecting level of transcript" EXACT []
is_obsolete: true
replaced_by: SO:0001540

[Term]
id: SO:1000086
name: sequence_variation_decreasing_level_of_transcript
def: "A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation decreasing level of transcript" EXACT []
synonym: "sequence variation decreasing level of transcript" RELATED []
is_obsolete: true

[Term]
id: SO:1000087
name: sequence_variation_increasing_level_of_transcript
def: "A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation increasing level of transcript" EXACT []
synonym: "sequence variation increasing level of transcript" EXACT []
is_obsolete: true

[Term]
id: SO:1000088
name: sequence_variant_affecting_translational_product
alt_id: SO:1000090
alt_id: SO:1000091
def: "A sequence variant causing a change in primary translation product of a transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting translational product" RELATED []
synonym: "mutation causing partially characterised change of translational product" RELATED []
synonym: "mutation causing uncharacterised change of translational product" RELATED []
synonym: "sequence variant affecting translational product" EXACT []
synonym: "sequence variant causing partially characterised change of translational product" EXACT []
synonym: "sequence variant causing uncharacterised change of translational product" EXACT []
synonym: "sequence_variant_causing_partially_characterised_change_of_translational_product" EXACT []
synonym: "sequence_variant_causing_uncharacterised_change_of_translational_product" EXACT []
is_obsolete: true
replaced_by: SO:0001553

[Term]
id: SO:1000089
name: sequence_variant_causing_no_change_of_translational_product
def: "The sequence variant at RNA level does not lead to any change in polypeptide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term.
synonym: "mutation causing no change of translational product" RELATED []
synonym: "sequence variant causing no change of translational product" EXACT []
is_obsolete: true

[Term]
id: SO:1000092
name: sequence_variant_causing_complex_change_of_translational_product
def: "Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing complex change of translational product" RELATED []
synonym: "sequence variant causing complex change of translational product" EXACT []
is_obsolete: true
consider: SO:0001539

[Term]
id: SO:1000093
name: sequence_variant_causing_amino_acid_substitution
def: "The replacement of a single amino acid by another." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing amino acid substitution" RELATED []
synonym: "sequence variant causing amino acid substitution" EXACT []
is_obsolete: true
replaced_by: SO:0001606

[Term]
id: SO:1000094
name: sequence_variant_causing_conservative_amino_acid_substitution
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing conservative amino acid substitution" RELATED []
synonym: "sequence variant causing conservative amino acid substitution" EXACT []
is_obsolete: true
replaced_by: SO:0001607

[Term]
id: SO:1000095
name: sequence_variant_causing_nonconservative_amino_acid_substitution
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing nonconservative amino acid substitution" RELATED []
synonym: "sequence variant causing nonconservative amino acid substitution" EXACT []
is_obsolete: true
replaced_by: SO:0001607

[Term]
id: SO:1000096
name: sequence_variant_causing_amino_acid_insertion
def: "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing amino acid insertion" RELATED []
synonym: "sequence variant causing amino acid insertion" EXACT []
is_obsolete: true
replaced_by: SO:0001605

[Term]
id: SO:1000097
name: sequence_variant_causing_amino_acid_deletion
def: "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing amino acid deletion" RELATED []
synonym: "sequence variant causing amino acid deletion" EXACT []
is_obsolete: true
consider: SO:0001825

[Term]
id: SO:1000098
name: sequence_variant_causing_polypeptide_truncation
def: "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide truncation" RELATED []
synonym: "sequence variant causing polypeptide truncation" EXACT []
is_obsolete: true
replaced_by: SO:0001587

[Term]
id: SO:1000099
name: sequence_variant_causing_polypeptide_elongation
def: "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide elongation" RELATED []
synonym: "sequence variant causing polypeptide elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001609

[Term]
id: SO:1000100
name: mutation_causing_polypeptide_N_terminal_elongation
def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide N terminal elongation" EXACT []
synonym: "polypeptide N-terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001611

[Term]
id: SO:1000101
name: mutation_causing_polypeptide_C_terminal_elongation
def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide C terminal elongation" EXACT []
synonym: "polypeptide C-terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001610

[Term]
id: SO:1000102
name: sequence_variant_affecting_level_of_translational_product
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting level of translational product" RELATED []
synonym: "sequence variant affecting level of translational product" EXACT []
is_obsolete: true
replaced_by: SO:0001553

[Term]
id: SO:1000103
name: sequence_variant_decreasing_level_of_translation_product
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutationdecreasing level of translation product" RELATED []
synonym: "sequence variant decreasing level of translation product" EXACT []
is_obsolete: true
replaced_by: SO:0001555

[Term]
id: SO:1000104
name: sequence_variant_increasing_level_of_translation_product
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutationt increasing level of translation product" RELATED []
synonym: "sequence variant increasing level of translation product" EXACT []
is_obsolete: true

[Term]
id: SO:1000105
name: sequence_variant_affecting_polypeptide_amino_acid_sequence
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting polypeptide amino acid sequence" RELATED []
synonym: "sequence variant affecting polypeptide amino acid sequence" EXACT []
is_obsolete: true
replaced_by: SO:0001603

[Term]
id: SO:1000106
name: mutation_causing_inframe_polypeptide_N_terminal_elongation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "inframe polypeptide N-terminal elongation" EXACT []
synonym: "mutation causing inframe polypeptide N terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001614

[Term]
id: SO:1000107
name: mutation_causing_out_of_frame_polypeptide_N_terminal_elongation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing out of frame polypeptide N terminal elongation" EXACT []
synonym: "out of frame polypeptide N-terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001615

[Term]
id: SO:1000108
name: mutaton_causing_inframe_polypeptide_C_terminal_elongation
synonym: "inframe_polypeptide C-terminal elongation" EXACT []
synonym: "mutaton causing inframe polypeptide C terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001612

[Term]
id: SO:1000109
name: mutation_causing_out_of_frame_polypeptide_C_terminal_elongation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing out of frame polypeptide C terminal elongation" EXACT []
synonym: "out of frame polypeptide C-terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001613

[Term]
id: SO:1000110
name: frame_restoring_sequence_variant
def: "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]
synonym: "frame restoring mutation" EXACT []
synonym: "frame restoring sequence variant" EXACT []
is_obsolete: true

[Term]
id: SO:1000111
name: sequence_variant_affecting_3D_structure_of_polypeptide
alt_id: SO:1000113
alt_id: SO:1000114
def: "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting 3D structure of polypeptide" RELATED []
synonym: "mutation causing partially characterised 3D structural change" RELATED []
synonym: "mutation causing uncharacterised 3D structural change" RELATED []
synonym: "sequence variant affecting 3D structure of polypeptide" EXACT []
synonym: "sequence variant affecting 3D-structure of polypeptide" EXACT []
synonym: "sequence variant causing partially characterised 3D structural change" EXACT []
synonym: "sequence variant causing uncharacterised 3D structural change" EXACT []
synonym: "sequence_variant_causing_partially_characterised_3D_structural_change" EXACT []
synonym: "sequence_variant_causing_uncharacterised_3D_structural_change" EXACT []
is_obsolete: true
replaced_by: SO:0001599

[Term]
id: SO:1000112
name: sequence_variant_causing_no_3D_structural_change
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term.
synonym: "mutation causing no 3D structural change" RELATED []
synonym: "sequence variant causing no 3D structural change" EXACT []
is_obsolete: true

[Term]
id: SO:1000115
name: sequence_variant_causing_complex_3D_structural_change
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing complex 3D structural change" RELATED []
synonym: "sequence variant causing complex 3D structural change" EXACT []
is_obsolete: true
replaced_by: SO:0001600

[Term]
id: SO:1000116
name: sequence_variant_causing_conformational_change
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing conformational change" RELATED []
synonym: "sequence variant causing conformational change" EXACT []
is_obsolete: true
replaced_by: SO:0001601

[Term]
id: SO:1000117
name: sequence_variant_affecting_polypeptide_function
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting polypeptide function" RELATED []
synonym: "sequence variant affecting polypeptide function" EXACT []
is_obsolete: true
replaced_by: SO:0001554

[Term]
id: SO:1000118
name: sequence_variant_causing_loss_of_function_of_polypeptide
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "loss of function of polypeptide" RELATED []
synonym: "mutation causing loss of function of polypeptide" RELATED []
synonym: "sequence variant causing loss of function of polypeptide" EXACT []
is_obsolete: true
replaced_by: SO:0001559

[Term]
id: SO:1000119
name: sequence_variant_causing_inactive_ligand_binding_site
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing inactive ligand binding site" RELATED []
synonym: "sequence variant causing inactive ligand binding site" EXACT []
is_obsolete: true
replaced_by: SO:0001560

[Term]
id: SO:1000120
name: sequence_variant_causing_inactive_catalytic_site
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing inactive catalytic site" RELATED []
synonym: "sequence variant causing inactive catalytic site" EXACT []
is_obsolete: true
replaced_by: SO:0001618

[Term]
id: SO:1000121
name: sequence_variant_causing_polypeptide_localization_change
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide localization change" RELATED []
synonym: "sequence variant causing polypeptide localization change" EXACT []
is_obsolete: true
replaced_by: SO:0001558

[Term]
id: SO:1000122
name: sequence_variant_causing_polypeptide_post_translational_processing_change
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide post translational processing change" RELATED []
synonym: "polypeptide post-translational processing affected" EXACT []
synonym: "sequence variant causing polypeptide post translational processing change" EXACT []
is_obsolete: true
replaced_by: SO:0001562

[Term]
id: SO:1000123
name: polypeptide_post_translational_processing_affected
synonym: "polypeptide_post-translational_processing_affected" RELATED []
is_obsolete: true

[Term]
id: SO:1000124
name: sequence_variant_causing_partial_loss_of_function_of_polypeptide
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing partial loss of function of polypeptide" RELATED []
synonym: "partial loss of function of polypeptide" EXACT []
synonym: "sequence variant causing partial loss of function of polypeptide" EXACT []
is_obsolete: true
replaced_by: SO:0001561

[Term]
id: SO:1000125
name: sequence_variant_causing_gain_of_function_of_polypeptide
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "gain of function of polypeptide" EXACT []
synonym: "mutation causing gain of function of polypeptide" RELATED []
synonym: "sequence variant causing gain of function of polypeptide" EXACT []
is_obsolete: true
replaced_by: SO:0001557

[Term]
id: SO:1000126
name: sequence_variant_affecting_transcript_secondary_structure
def: "A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcript secondary structure" RELATED []
synonym: "sequence variant affecting transcript secondary structure" EXACT []
is_obsolete: true
replaced_by: SO:0001596

[Term]
id: SO:1000127
name: sequence_variant_causing_compensatory_transcript_secondary_structure_mutation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing compensatory transcript secondary structure mutation" RELATED []
synonym: "sequence variant causing compensatory transcript secondary structure mutation" EXACT []
is_obsolete: true
replaced_by: SO:0001597

[Term]
id: SO:1000132
name: sequence_variant_effect
def: "The effect of a change in nucleotide sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.\nUpdated after discussion with Peter Taschner - Feb 09.
synonym: "sequence variant effect" RELATED []
is_obsolete: true

[Term]
id: SO:1000134
name: sequence_variant_causing_polypeptide_fusion
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide fusion" RELATED []
synonym: "sequence variant causing polypeptide fusion" EXACT []
is_obsolete: true
replaced_by: SO:0001616

[Term]
id: SO:1000136
name: autosynaptic_chromosome
def: "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]
synonym: "(Drosophila)A" RELATED []
synonym: "autosynaptic chromosome" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000138
name: homo_compound_chromosome
def: "A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]
synonym: "homo compound chromosome" EXACT []
synonym: "homo-compound chromosome" EXACT []
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:1000140
name: hetero_compound_chromosome
def: "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]
synonym: "hetero compound chromosome" EXACT []
synonym: "hetero-compound chromosome" EXACT []
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:1000141
name: chromosome_fission
def: "A chromosome that occurred by the division of a larger chromosome." [SO:ke]
synonym: "chromosome fission" EXACT []
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000142
name: dexstrosynaptic_chromosome
def: "An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]
synonym: "dexstrosynaptic chromosome" EXACT []
is_a: SO:1000136 ! autosynaptic_chromosome

[Term]
id: SO:1000143
name: laevosynaptic_chromosome
def: "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]
synonym: "laevosynaptic chromosome" EXACT []
is_a: SO:1000136 ! autosynaptic_chromosome

[Term]
id: SO:1000144
name: free_duplication
def: "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]
synonym: "free duplication" EXACT []
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000145
name: free_ring_duplication
def: "A ring chromosome which is a copy of another chromosome." [SO:ke]
synonym: "(Drosophila)R" RELATED []
synonym: "free ring duplication" EXACT []
is_a: SO:1000045 ! ring_chromosome
is_a: SO:1000144 ! free_duplication
intersection_of: SO:1000045 ! ring_chromosome
intersection_of: has_quality SO:0001516 ! free
relationship: has_quality SO:0001516 ! free

[Term]
id: SO:1000147
name: deficient_translocation
def: "A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]
synonym: "(Drosophila)Df" RELATED []
synonym: "(Drosophila)DfT" RELATED []
synonym: "deficient translocation" EXACT []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000044 ! chromosomal_translocation
relationship: has_part SO:0000159 ! deletion

[Term]
id: SO:1000148
name: inversion_cum_translocation
def: "A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]
synonym: "(Drosophila)InT" RELATED []
synonym: "(Drosophila)T" RELATED []
synonym: "inversion cum translocation" EXACT []
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000044 ! chromosomal_translocation
relationship: has_part SO:1000036 ! inversion

[Term]
id: SO:1000149
name: bipartite_duplication
def: "An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]
synonym: "(Drosophila)bDp" RELATED []
synonym: "bipartite duplication" EXACT []
is_a: SO:1000031 ! interchromosomal_mutation
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:1000150
name: cyclic_translocation
def: "A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]
synonym: "cyclic translocation" EXACT []
is_a: SO:0002060 ! interchromosomal_translocation

[Term]
id: SO:1000151
name: bipartite_inversion
def: "A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]
synonym: "(Drosophila)bIn" RELATED []
synonym: "bipartite inversion" EXACT []
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000152
name: uninverted_insertional_duplication
def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]
synonym: "(Drosophila)eDp" RELATED []
synonym: "uninverted insertional duplication" EXACT []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000153
name: inverted_insertional_duplication
def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]
synonym: "(Drosophila)iDp" RELATED []
synonym: "inverted insertional duplication" EXACT []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000154
name: insertional_duplication
def: "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]
synonym: "(Drosophila)Dpp" RELATED []
synonym: "insertional duplication" EXACT []
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000155
name: interchromosomal_transposition
def: "A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]
synonym: "(Drosophila)Tp" RELATED []
synonym: "interchromosomal transposition" EXACT []
is_a: SO:0000453 ! chromosomal_transposition
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000156
name: inverted_interchromosomal_transposition
def: "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]
synonym: "(Drosophila)iTp" RELATED []
synonym: "inverted interchromosomal transposition" EXACT []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000157
name: uninverted_interchromosomal_transposition
def: "An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]
synonym: "(Drosophila)eTp" RELATED []
synonym: "uninverted interchromosomal transposition" EXACT []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000158
name: inverted_intrachromosomal_transposition
def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]
synonym: "(Drosophila)iTp" RELATED []
synonym: "inverted intrachromosomal transposition" EXACT []
is_a: SO:1000148 ! inversion_cum_translocation
relationship: has_part SO:1000036 ! inversion

[Term]
id: SO:1000159
name: uninverted_intrachromosomal_transposition
def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]
synonym: "(Drosophila)eTp" RELATED []
synonym: "uninverted intrachromosomal transposition" EXACT []
is_a: SO:1000041 ! intrachromosomal_transposition
intersection_of: SO:1000041 ! intrachromosomal_transposition
intersection_of: has_part SO:0001514 ! direct
relationship: has_part SO:0001514 ! direct

[Term]
id: SO:1000160
name: unoriented_insertional_duplication
def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]
comment: Flag - unknown in the definition.
synonym: "(Drosophila)uDp" RELATED []
synonym: "unoriented insertional duplication" EXACT []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000161
name: unoriented_interchromosomal_transposition
def: "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]
comment: FLAG - term describes an unknown.
synonym: "(Drosophila)uTp" RELATED []
synonym: "unorientated interchromosomal transposition" EXACT []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000162
name: unoriented_intrachromosomal_transposition
def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]
comment: FLAG - definition describes an unknown.
synonym: "(Drosophila)uTp" RELATED []
synonym: "unorientated intrachromosomal transposition" EXACT []
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:1000170
name: uncharacterized_chromosomal_mutation
synonym: "uncharacterized chromosomal mutation" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000171
name: deficient_inversion
def: "A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]
synonym: "(Drosophila)Df" RELATED []
synonym: "(Drosophila)DfIn" RELATED []
synonym: "deficient inversion" EXACT []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000030 ! chromosomal_inversion
relationship: has_part SO:0000159 ! deletion
relationship: has_part SO:1000036 ! inversion

[Term]
id: SO:1000173
name: tandem_duplication
def: "A duplication consisting of 2 identical adjacent regions." [SO:ke]
subset: DBVAR
synonym: "erverted" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
synonym: "tandem duplication" EXACT []
is_a: SO:1000035 ! duplication

[Term]
id: SO:1000175
name: partially_characterized_chromosomal_mutation
synonym: "partially characterized chromosomal mutation" EXACT []
is_a: SO:1000170 ! uncharacterized_chromosomal_mutation

[Term]
id: SO:1000180
name: sequence_variant_affecting_gene_structure
def: "A sequence_variant_effect that changes the gene structure." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting gene structure" RELATED []
synonym: "sequence variant affecting gene structure" EXACT []
is_obsolete: true
replaced_by: SO:0001564

[Term]
id: SO:1000181
name: sequence_variant_causing_gene_fusion
def: "A sequence_variant_effect that changes the gene structure by causing a fusion to another gene." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing gene fusion" RELATED []
synonym: "sequence variant causing gene fusion" EXACT []
is_obsolete: true
replaced_by: SO:0001565

[Term]
id: SO:1000182
name: chromosome_number_variation
def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
synonym: "chromosome number variation" EXACT []
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:1000183
name: chromosome_structure_variation
synonym: "chromosome structure variation" EXACT []
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:1000184
name: sequence_variant_causes_exon_loss
def: "A sequence variant affecting splicing and causes an exon loss." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causes exon loss" RELATED []
synonym: "sequence variant causes exon loss" EXACT []
is_obsolete: true

[Term]
id: SO:1000185
name: sequence_variant_causes_intron_gain
def: "A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causes intron gain" RELATED []
synonym: "sequence variant causes intron gain" EXACT []
is_obsolete: true

[Term]
id: SO:1000186
name: sequence_variant_causing_cryptic_splice_donor_activation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "sequence variant causing cryptic splice donor activation" EXACT []
is_obsolete: true
replaced_by: SO:0001571

[Term]
id: SO:1001186
name: sequence_variant_causing_cryptic_splice_acceptor_activation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "sequence variant causing cryptic splice acceptor activation" EXACT []
is_obsolete: true
replaced_by: SO:0001570

[Term]
id: SO:1001187
name: alternatively_spliced_transcript
def: "A transcript that is alternatively spliced." [SO:xp]
synonym: "alternatively spliced transcript" EXACT []
is_a: SO:0000673 ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000877 ! alternatively_spliced
relationship: has_quality SO:0000877 ! alternatively_spliced

[Term]
id: SO:1001188
name: encodes_1_polypeptide
def: "A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]
synonym: "encodes 1 polypeptide" EXACT []
is_a: SO:0000463 ! encodes_alternately_spliced_transcripts

[Term]
id: SO:1001189
name: encodes_greater_than_1_polypeptide
def: "A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]
synonym: "encodes greater than 1 polypeptide" EXACT []
is_a: SO:0000463 ! encodes_alternately_spliced_transcripts

[Term]
id: SO:1001190
name: encodes_different_polypeptides_different_stop
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]
synonym: "encodes different polypeptides different stop" EXACT []
is_a: SO:1001195 ! encodes_overlapping_peptides

[Term]
id: SO:1001191
name: encodes_overlapping_peptides_different_start
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]
synonym: "encodes overlapping peptides different start" EXACT []
is_a: SO:1001195 ! encodes_overlapping_peptides

[Term]
id: SO:1001192
name: encodes_disjoint_polypeptides
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]
synonym: "encodes disjoint polypeptides" EXACT []
is_a: SO:1001189 ! encodes_greater_than_1_polypeptide

[Term]
id: SO:1001193
name: encodes_overlapping_polypeptides_different_start_and_stop
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]
synonym: "encodes overlapping polypeptides different start and stop" EXACT []
is_a: SO:1001195 ! encodes_overlapping_peptides

[Term]
id: SO:1001194
name: alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping
is_obsolete: true

[Term]
id: SO:1001195
name: encodes_overlapping_peptides
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]
synonym: "encodes overlapping peptides" EXACT []
is_a: SO:1001189 ! encodes_greater_than_1_polypeptide

[Term]
id: SO:1001196
name: cryptogene
def: "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]
is_a: SO:0000654 ! maxicircle_gene
is_a: SO:0001431 ! cryptic_gene
intersection_of: SO:0000654 ! maxicircle_gene
intersection_of: has_quality SO:0000976 ! cryptic
relationship: has_quality SO:0000976 ! cryptic

[Term]
id: SO:1001197
name: dicistronic_primary_transcript
def: "A primary transcript that has the quality dicistronic." [SO:xp]
synonym: "dicistronic primary transcript" EXACT []
is_a: SO:0000079 ! dicistronic_transcript
is_a: SO:0000631 ! polycistronic_primary_transcript
intersection_of: SO:0000185 ! primary_transcript
intersection_of: has_quality SO:0000879 ! dicistronic
relationship: has_quality SO:0000879 ! dicistronic

[Term]
id: SO:1001217
name: member_of_regulon
synonym: "member of regulon" EXACT []
is_a: SO:0000081 ! gene_array_member

[Term]
id: SO:1001244
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
synonym: "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping" RELATED []
is_obsolete: true

[Term]
id: SO:1001246
name: CDS_independently_known
def: "A CDS with the evidence status of being independently known." [SO:xp]
synonym: "CDS independently known" EXACT []
is_a: SO:0000316 ! CDS
intersection_of: SO:0000316 ! CDS
intersection_of: has_quality SO:0000906 ! independently_known
relationship: has_quality SO:0000906 ! independently_known

[Term]
id: SO:1001247
name: orphan_CDS
def: "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]
synonym: "orphan CDS" EXACT []
is_a: SO:1001254 ! CDS_predicted
intersection_of: SO:1001254 ! CDS_predicted
intersection_of: has_origin SO:0000910 ! orphan
relationship: has_origin SO:0000910 ! orphan

[Term]
id: SO:1001249
name: CDS_supported_by_domain_match_data
def: "A CDS that is supported by domain similarity." [SO:xp]
synonym: "CDS supported by domain match data" EXACT []
is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data
intersection_of: SO:1001251 ! CDS_supported_by_sequence_similarity_data
intersection_of: has_quality SO:0000908 ! supported_by_domain_match
relationship: has_quality SO:0000908 ! supported_by_domain_match

[Term]
id: SO:1001251
name: CDS_supported_by_sequence_similarity_data
def: "A CDS that is supported by sequence similarity data." [SO:xp]
synonym: "CDS supported by sequence similarity data" EXACT []
is_a: SO:1001254 ! CDS_predicted
intersection_of: SO:0000316 ! CDS
intersection_of: has_quality SO:0000907 ! supported_by_sequence_similarity
relationship: has_quality SO:0000907 ! supported_by_sequence_similarity

[Term]
id: SO:1001254
name: CDS_predicted
def: "A CDS that is predicted." [SO:ke]
synonym: "CDS predicted" EXACT []
is_a: SO:0000316 ! CDS
intersection_of: SO:0000316 ! CDS
intersection_of: has_quality SO:0000732 ! predicted
relationship: has_quality SO:0000732 ! predicted

[Term]
id: SO:1001255
name: status_of_coding_sequence
is_obsolete: true

[Term]
id: SO:1001259
name: CDS_supported_by_EST_or_cDNA_data
def: "A CDS that is supported by similarity to EST or cDNA data." [SO:xp]
synonym: "CDS supported by EST or cDNA data" EXACT []
is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data
intersection_of: SO:1001251 ! CDS_supported_by_sequence_similarity_data
intersection_of: has_quality SO:0000909 ! supported_by_EST_or_cDNA
relationship: has_quality SO:0000909 ! supported_by_EST_or_cDNA

[Term]
id: SO:1001260
name: internal_Shine_Dalgarno_sequence
def: "A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]
synonym: "internal Shine Dalgarno sequence" EXACT []
synonym: "internal Shine-Dalgarno sequence" EXACT []
is_a: SO:0000243 ! internal_ribosome_entry_site
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001261
name: recoded_mRNA
def: "The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]
synonym: "recoded mRNA" EXACT []
is_a: SO:0000234 ! mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000881 ! recoded
relationship: has_quality SO:0000881 ! recoded

[Term]
id: SO:1001262
name: minus_1_translationally_frameshifted
def: "An attribute describing a translational frameshift of -1." [SO:ke]
synonym: "minus 1 translationally frameshifted" EXACT []
is_a: SO:0000887 ! translationally_frameshifted

[Term]
id: SO:1001263
name: plus_1_translationally_frameshifted
def: "An attribute describing a translational frameshift of +1." [SO:ke]
synonym: "plus 1 translationally frameshifted" EXACT []
is_a: SO:0000887 ! translationally_frameshifted

[Term]
id: SO:1001264
name: mRNA_recoded_by_translational_bypass
def: "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]
synonym: "mRNA recoded by translational bypass" EXACT []
is_a: SO:1001261 ! recoded_mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000886 ! recoded_by_translational_bypass
relationship: has_quality SO:0000886 ! recoded_by_translational_bypass

[Term]
id: SO:1001265
name: mRNA_recoded_by_codon_redefinition
def: "A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]
synonym: "mRNA recoded by codon redefinition" EXACT []
is_a: SO:1001261 ! recoded_mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000882 ! codon_redefined
relationship: has_quality SO:0000882 ! codon_redefined

[Term]
id: SO:1001266
name: stop_codon_redefinition_as_selenocysteine
is_obsolete: true

[Term]
id: SO:1001267
name: stop_codon_readthrough
is_obsolete: true

[Term]
id: SO:1001268
name: recoding_stimulatory_region
def: "A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]
synonym: "recoding stimulatory region" EXACT []
synonym: "recoding stimulatory signal" EXACT []
is_a: SO:0000836 ! mRNA_region

[Term]
id: SO:1001269
name: four_bp_start_codon
def: "A non-canonical start codon with 4 base pairs." [SO:ke]
synonym: "4bp start codon" EXACT []
synonym: "four bp start codon" EXACT []
is_a: SO:0000680 ! non_canonical_start_codon

[Term]
id: SO:1001270
name: stop_codon_redefinition_as_pyrrolysine
is_obsolete: true

[Term]
id: SO:1001271
name: archaeal_intron
def: "An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]
comment: Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism.
synonym: "archaeal intron" EXACT []
is_a: SO:0001216 ! endonuclease_spliced_intron

[Term]
id: SO:1001272
name: tRNA_intron
def: "An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]
comment: Could be a cross product with Gene ontology, GO:0006388.
synonym: "pre-tRNA intron" EXACT []
synonym: "tRNA intron" EXACT []
is_a: SO:0001216 ! endonuclease_spliced_intron

[Term]
id: SO:1001273
name: CTG_start_codon
def: "A non-canonical start codon of sequence CTG." [SO:ke]
synonym: "CTG start codon" EXACT []
is_a: SO:0000680 ! non_canonical_start_codon

[Term]
id: SO:1001274
name: SECIS_element
def: "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]
synonym: "SECIS element" EXACT []
xref: http://en.wikipedia.org/wiki/SECIS_element "wiki"
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001275
name: retron
def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]
is_a: SO:0001411 ! biological_region

[Term]
id: SO:1001277
name: three_prime_recoding_site
def: "The recoding stimulatory signal located downstream of the recoding site." [SO:ke]
synonym: "three prime recoding site" EXACT []
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001279
name: three_prime_stem_loop_structure
def: "A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]
synonym: "three prime stem loop structure" EXACT []
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001280
name: five_prime_recoding_site
def: "The recoding stimulatory signal located upstream of the recoding site." [SO:ke]
synonym: "five prime recoding site" EXACT []
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001281
name: flanking_three_prime_quadruplet_recoding_signal
def: "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]
synonym: "flanking three prime quadruplet recoding signal" EXACT []
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001282
name: UAG_stop_codon_signal
def: "A stop codon signal for a UAG stop codon redefinition." [SO:ke]
synonym: "UAG stop codon signal" EXACT []
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001283
name: UAA_stop_codon_signal
def: "A stop codon signal for a UAA stop codon redefinition." [SO:ke]
synonym: "UAA stop codon signal" EXACT []
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001284
name: regulon
def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Regulon "wiki"
is_a: SO:0005855 ! gene_group

[Term]
id: SO:1001285
name: UGA_stop_codon_signal
def: "A stop codon signal for a UGA stop codon redefinition." [SO:ke]
synonym: "UGA stop codon signal" EXACT []
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001286
name: three_prime_repeat_recoding_signal
def: "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]
synonym: "three prime repeat recoding signal" EXACT []
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001287
name: distant_three_prime_recoding_signal
def: "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]
synonym: "distant three prime recoding signal" EXACT []
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001288
name: stop_codon_signal
def: "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]
comment: This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal.
synonym: "stop codon signal" EXACT []
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:2000061
name: databank_entry
def: "The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]
subset: SOFA
synonym: "accession" RELATED []
synonym: "databank entry" EXACT []
is_a: SO:0000695 ! reagent

[Term]
id: SO:3000000
name: gene_segment
def: "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]
comment: Requested by tracker 2021594, July 2008, by Alex.
synonym: "gene segment" EXACT []
is_a: SO:0000842 ! gene_component_region

[Typedef]
id: adjacent_to
name: adjacent_to
def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap." [PMID:20226267, SO:ke]
subset: SOFA

[Typedef]
id: associated_with
name: associated_with
comment: This relationship is vague and up for discussion.

[Typedef]
id: complete_evidence_for_feature
name: complete_evidence_for_feature
def: "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." [SO:ke]
comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
is_transitive: true
is_a: evidence_for_feature ! evidence_for_feature

[Typedef]
id: connects_on
name: connects_on
def: "X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z." [PMID:20226267]
comment: Example: A splice_junction connects_on exon, exon, mature_transcript.
created_by: kareneilbeck
creation_date: 2010-10-14T01:38:51Z

[Typedef]
id: contained_by
name: contained_by
def: "X contained_by Y iff X starts after start of Y and X ends before end of Y." [PMID:20226267]
comment: The inverse is contains. Example: intein contained_by immature_peptide_region.
is_transitive: true
created_by: kareneilbeck
creation_date: 2010-10-14T01:26:16Z

[Typedef]
id: contains
name: contains
def: "The inverse of contained_by." [PMID:20226267]
comment: Example: pre_miRNA contains miRNA_loop.
is_transitive: true
created_by: kareneilbeck
creation_date: 2010-10-14T01:32:15Z

[Typedef]
id: derives_from
name: derives_from
subset: SOFA
is_transitive: true

[Typedef]
id: disconnected_from
name: disconnected_from
def: "X is disconnected_from Y iff it is not the case that X overlaps Y." [PMID:20226267]
created_by: kareneilbeck
creation_date: 2010-10-14T01:42:10Z

[Typedef]
id: edited_from
name: edited_from
created_by: kareneilbeck
creation_date: 2009-08-19T02:19:45Z

[Typedef]
id: edited_to
name: edited_to
created_by: kareneilbeck
creation_date: 2009-08-19T02:19:11Z

[Typedef]
id: evidence_for_feature
name: evidence_for_feature
def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke]
comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
is_transitive: true

[Typedef]
id: exemplar_of
name: exemplar_of
def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke]
comment: Tracker id: 2594157.

[Typedef]
id: finished_by
name: finished_by
def: "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary." [PMID:20226267]
comment: Example CDS finished_by stop_codon.
created_by: kareneilbeck
creation_date: 2010-10-14T01:45:45Z

[Typedef]
id: finishes
name: finishes
def: "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary." [PMID:20226267]
comment: Example: stop_codon finishes CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T02:17:53Z

[Typedef]
id: gained
name: gained
def: "X gained Y if X is a variant_of X' and Y part of X but not X'." [SO:ke]
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may gain a stop codon not present in the reference sequence.
created_by: kareneilbeck
creation_date: 2011-06-28T12:51:10Z

[Typedef]
id: genome_of
name: genome_of

[Typedef]
id: guided_by
name: guided_by
created_by: kareneilbeck
creation_date: 2009-08-19T02:27:04Z

[Typedef]
id: guides
name: guides
created_by: kareneilbeck
creation_date: 2009-08-19T02:27:24Z

[Typedef]
id: has_integral_part
name: has_integral_part
def: "X has_integral_part Y if and only if: X has_part Y and Y part_of X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: mRNA has_integral_part CDS.
is_a: has_part ! has_part
created_by: kareneilbeck
creation_date: 2009-08-19T12:01:46Z

[Typedef]
id: has_origin
name: has_origin

[Typedef]
id: has_part
name: has_part
def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: operon has_part gene.

[Typedef]
id: has_quality
name: has_quality
comment: The relationship between a feature and an attribute.

[Typedef]
id: homologous_to
name: homologous_to
subset: SOFA
is_symmetric: true
is_a: similar_to ! similar_to

[Typedef]
id: integral_part_of
name: integral_part_of
def: "X integral_part_of Y if and only if: X part_of Y and Y has_part X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: exon integral_part_of transcript.
is_a: part_of ! part_of
created_by: kareneilbeck
creation_date: 2009-08-19T12:03:28Z

[Typedef]
id: is_consecutive_sequence_of
name: is_consecutive_sequence_of
def: "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical)." [PMID:20226267]
comment: Example: region is consecutive_sequence of base.
created_by: kareneilbeck
creation_date: 2010-10-14T02:19:48Z

[Typedef]
id: lost
name: lost
def: "X lost Y if X is a variant_of X' and Y part of X' but not X." [SO:ke]
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence.
created_by: kareneilbeck
creation_date: 2011-06-28T12:53:16Z

[Typedef]
id: maximally_overlaps
name: maximally_overlaps
def: "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y." [PMID:20226267]
comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.
created_by: kareneilbeck
creation_date: 2010-10-14T01:34:48Z

[Typedef]
id: member_of
name: member_of
comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
subset: SOFA
is_transitive: true
is_a: part_of ! part_of

[Typedef]
id: non_functional_homolog_of
name: non_functional_homolog_of
def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]
subset: SOFA
is_a: homologous_to ! homologous_to

[Typedef]
id: orthologous_to
name: orthologous_to
subset: SOFA
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: overlaps
name: overlaps
def: "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y." [PMID:20226267]
comment: Example: coding_exon overlaps CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T01:33:15Z

[Typedef]
id: paralogous_to
name: paralogous_to
subset: SOFA
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: part_of
name: part_of
def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: amino_acid part_of polypeptide.
subset: SOFA
is_transitive: true

[Typedef]
id: partial_evidence_for_feature
name: partial_evidence_for_feature
def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke]
is_a: evidence_for_feature ! evidence_for_feature

[Typedef]
id: position_of
name: position_of

[Typedef]
id: processed_from
name: processed_from
def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: miRNA processed_from miRNA_primary_transcript.
created_by: kareneilbeck
creation_date: 2009-08-19T12:14:00Z

[Typedef]
id: processed_into
name: processed_into
def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: miRNA_primary_transcript processed into miRNA.
created_by: kareneilbeck
creation_date: 2009-08-19T12:15:02Z

[Typedef]
id: recombined_from
name: recombined_from
created_by: kareneilbeck
creation_date: 2009-08-19T02:21:03Z

[Typedef]
id: recombined_to
name: recombined_to
created_by: kareneilbeck
creation_date: 2009-08-19T02:20:07Z

[Typedef]
id: sequence_of
name: sequence_of

[Typedef]
id: similar_to
name: similar_to
subset: SOFA
is_symmetric: true

[Typedef]
id: started_by
name: started_by
def: "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary." [PMID:20226267]
comment: Example: CDS started_by start_codon.
created_by: kareneilbeck
creation_date: 2010-10-14T01:43:55Z

[Typedef]
id: starts
name: starts
def: "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary." [PMID:20226267]
comment: Example: start_codon starts CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T01:47:53Z

[Typedef]
id: trans_spliced_from
name: trans_spliced_from
created_by: kareneilbeck
creation_date: 2009-08-19T02:22:14Z

[Typedef]
id: trans_spliced_to
name: trans_spliced_to
created_by: kareneilbeck
creation_date: 2009-08-19T02:22:00Z

[Typedef]
id: transcribed_from
name: transcribed_from
def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: primary_transcript transcribed_from gene.
created_by: kareneilbeck
creation_date: 2009-08-19T12:05:39Z

[Typedef]
id: transcribed_to
name: transcribed_to
def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: gene transcribed_to primary_transcript.
created_by: kareneilbeck
creation_date: 2009-08-19T12:08:24Z

[Typedef]
id: translates_to
name: translates_to
def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: codon translates_to amino_acid.
created_by: kareneilbeck
creation_date: 2009-08-19T12:11:53Z

[Typedef]
id: translation_of
name: translation_of
def: "X is translation of Y if Y is translated by ribosome to create X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: Polypeptide translation_of CDS.
created_by: kareneilbeck
creation_date: 2009-08-19T12:09:59Z

[Typedef]
id: variant_of
name: variant_of
def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop]
comment: Added to SO during the immunology workshop, June 2007.  This relationship was approved by Barry Smith.

