format-version: 1.2 date: 02:05:2012 11:08 saved-by: kareneilbeck auto-generated-by: OBO-Edit 2.1.1-beta7 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 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: 1.253 $ 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: "An extent of biological sequence." [SO:ke] subset: SOFA synonym: "located sequence feature" RELATED [] synonym: "located_sequence_feature" EXACT [] synonym: "sequence feature" EXACT [] disjoint_from: SO:0000240 ! chromosome_variation 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 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_C 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 [] is_a: SO:0000306 ! methylated_base_feature [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 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 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:. 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 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 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 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 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 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 [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_A def: "A modified RNA 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 [] is_a: SO:0000306 ! methylated_base_feature [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 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 [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 [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." [SO:ke] subset: DBVAR synonym: "transchr" RELATED [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "translocated sequence" EXACT [] is_a: SO:0001059 ! sequence_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 def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (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:12592000] subset: SOFA synonym: "micro RNA" EXACT [] synonym: "microRNA" EXACT [] xref: http://en.wikipedia.org/wiki/MiRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA relationship: derives_from SO:0000647 ! miRNA_primary_transcript [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 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 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 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 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 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 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 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 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 relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000289 name: microsatellite def: "A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem." [http://www.informatics.jax.org/silver/glossary.shtml] 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 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_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:. subset: SOFA synonym: "modified base site" EXACT [] is_a: SO:0001720 ! epigenetically_modified_region [Term] id: SO:0000306 name: methylated_base_feature def: "A nucleotide modified by methylation." [SO:ke] subset: SOFA synonym: "methylated base feature" EXACT [] is_a: SO:0000305 ! modified_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: 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-----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 [] 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 [] 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 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 is_a: 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 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: "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 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 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: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 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 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 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 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 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 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: "ca_bind" RELATED BS [uniprot:feature_type] synonym: "DNA_bind" RELATED BS [uniprot:feature_type] synonym: "domain" BROAD BS [uniprot:feature_type] synonym: "np_bind" RELATED BS [uniprot:feature_type] synonym: "polypeptide domain" EXACT [] synonym: "polypeptide_structural_domain" EXACT BS [] synonym: "structural domain" BROAD BS [] synonym: "zn_fing" RELATED BS [uniprot:feature_type] 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 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 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 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 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 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 descendent 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 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 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 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 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-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 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 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 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 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 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 def: "A primary transcript encoding a micro RNA." [SO:ke] synonym: "micro RNA primary transcript" EXACT [] synonym: "miRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000648 name: stRNA_primary_transcript def: "A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke] synonym: "small temporal RNA primary transcript" EXACT [] synonym: "stRNA primary transcript" EXACT [] is_a: SO:0000647 ! miRNA_primary_transcript [Term] id: SO:0000649 name: stRNA def: "Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512] subset: SOFA synonym: "small temporal RNA" EXACT [] xref: http://en.wikipedia.org/wiki/StRNA "wiki" is_a: SO:0000655 ! ncRNA [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 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 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 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 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 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 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 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 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 adjcent 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 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 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 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 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 intergenomic 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 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 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 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 more than 1 TF_binding_site together are regulatorily active." [SO:SG] comment: Requested by Stepen Grossmann Dec 2004. subset: SOFA synonym: "cis regulatory module" EXACT [] synonym: "TF module" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region 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 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 maxi circles, 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 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 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 descendent 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 occured 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 recognised 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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:1000002 ! substitution [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 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 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 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 [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 moblity, 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 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 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." [SO:regcreative] subset: SOFA 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: "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: "sequence variant" EXACT [] [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_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 corersponds 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 occuring events such as polymorphisms and altermatve 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 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 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 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 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 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 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 relationship: has_quality SO:0000781 ! transgenic [Term] id: SO:0001219 name: retrogene is_a: SO:0000704 ! gene 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 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 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 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 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 sructure." [SO:ke] synonym: "pre-miRNA" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region relationship: part_of SO:0000647 ! miRNA_primary_transcript [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 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 relationship: has_quality SO:0000979 ! gRNA_encoding [Term] id: SO:0001265 name: miRNA_gene synonym: "miRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000571 ! miRNA_encoding [Term] id: SO:0001266 name: scRNA_gene synonym: "scRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000575 ! scRNA_encoding [Term] id: SO:0001267 name: snoRNA_gene synonym: "snoRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000578 ! snoRNA_encoding [Term] id: SO:0001268 name: snRNA_gene synonym: "snRNA gene" EXACT [] is_a: 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 relationship: has_quality SO:0000642 ! SRP_RNA_encoding [Term] id: SO:0001270 name: stRNA_gene synonym: "stRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000656 ! stRNA_encoding [Term] id: SO:0001271 name: tmRNA_gene synonym: "tmRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000659 ! tmRNA_encoding [Term] id: SO:0001272 name: tRNA_gene synonym: "tRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene 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 insosine." [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 moddified 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 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 histidie 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 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 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 basepairs 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 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] 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. synonym: "X element" RELATED [] 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 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 relationship: 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 [] 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: "stop retained variant" EXACT [] 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:0001564 ! gene_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 def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke] synonym: "exon loss" EXACT [] is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-22T02:31:09Z [Term] id: SO:0001573 name: intron_gain 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 [] 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: "splice acceptor variant" EXACT [] 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 the2 base region at the 5' end of an intron." [SO:ke] synonym: "splice donor variant" EXACT [] 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: "transcript variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:32:41Z [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: "stop codon lost" EXACT [] synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001590 ! terminator_codon_variant is_a: SO:0001650 ! inframe_variant is_a: SO:0001907 ! feature_elongation 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 [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001791 ! exon_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] 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:0001650 ! inframe_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, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid." [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: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "missense codon" EXACT [] synonym: "non synonymous codon" EXACT [] synonym: "non synonymous variant" EXACT [] synonym: "non_synonymous_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] 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:0001650 ! inframe_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: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "nonsense codon" EXACT [] synonym: "stop codon gained" RELATED [] synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] xref: loinc:LA6699-8 "Nonsense" is_a: SO:0001650 ! inframe_variant is_a: SO:0001906 ! feature_truncation 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: "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] 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:0001598 ! translational_product_structure_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:0001598 ! translational_product_structure_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 [] 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: nc_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: "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 ! nc_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:0001576 ! 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: "five prime UTR variant" EXACT [] synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] 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: "three prime UTR variant" EXACT [] synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] 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: "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] 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: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "intergenic variant" EXACT [] 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: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: "splice region variant" EXACT [] synonym: "splice_region_variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] 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: "upstream gene variant" EXACT [] is_a: SO:0001878 ! feature_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: "downstream gene variant" EXACT [] is_a: SO:0001878 ! feature_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: "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 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: "cds-indel" EXACT dbsnp [] synonym: "inframe variant" EXACT [] 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: "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 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:0001411 ! biological_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:0001411 ! biological_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 mis-matches 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 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 acetylatoin 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:0001702 ! histone_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:0001702 ! histone_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 H34histone 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:0001702 ! histone_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:0001702 ! histone_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 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:0001702 ! histone_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