format-version: 1.2 date: 17:01:2008 20:43 saved-by: kareneilbeck auto-generated-by: OBO-Edit 1.101 subsetdef: biosapiens "biosapiens protein feature ontology" subsetdef: SOFA "SO feature annotation" default-namespace: sequence remark: autogenerated-by\: DAG-Edit version 1.417\nsaved-by\: eilbeck\ndate\: Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $ [Term] id: SO:0000000 name: Sequence_Ontology subset: SOFA [Term] id: SO:0000001 name: region def: "A sequence_feature with an extent greater than zero." [SO:ke] subset: SOFA synonym: "sequence" EXACT [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0000002 name: sequence_secondary_structure def: "A folded sequence." [SO:ke] is_a: SO:0000001 ! 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.library.csi.cuny.edu/~davis/molbiol/lecture_notes/post-transcriptional_processes/RNACapping.pdf] synonym: "G-quadruplex" EXACT [] synonym: "G-quartet" EXACT [] synonym: "G_quadruplex" EXACT [] is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000004 name: interior_coding_exon subset: SOFA 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] is_a: SO:0000657 ! repeat_region [Term] id: SO:0000006 name: PCR_product def: "A region amplified by a PCR reaction." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "amplicon" RELATED [] synonym: "PCR product" EXACT [] is_a: SO:0000695 ! reagent [Term] id: SO:0000007 name: read_pair def: "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 is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000149 ! contig [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 is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000011 name: non_protein_coding 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 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: "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] 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] synonym: "DMp2" RELATED [] synonym: "initiator" EXACT [] synonym: "initiator motif" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [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] synonym: "CRWMGCGWKCGCTTS" NARROW [] synonym: "downstream core promoter element" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [Term] id: SO:0000016 name: BRE_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] synonym: " transcription factor B-recognition element" EXACT [] synonym: "B-recognition element" EXACT [] synonym: "TFIIB recognition element" RELATED [] is_a: SO:0000844 ! RNApol_II_promoter_region [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 [] is_a: SO:0000844 ! RNApol_II_promoter_region [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] is_a: SO:0000001 ! 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] 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] 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] 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" EXACT [] synonym: "kink turn" EXACT [] synonym: "kink-turn motif" EXACT [] 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://proton.chem.yale.edu/pdf/7897662.pdf] synonym: " sarcin/ricin RNA domain" EXACT [] synonym: "sarcin/ricin domain" EXACT [] synonym: "sarcin/ricin loop" 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] is_a: SO:0000020 ! RNA_internal_loop [Term] id: SO:0000026 name: RNA_junction_loop is_a: SO:0000715 ! RNA_motif [Term] id: SO:0000027 name: RNA_hook_turn synonym: "hook turn" RELATED [] synonym: "hook-turn motif" EXACT [] is_a: SO:0000026 ! RNA_junction_loop [Term] id: SO:0000028 name: base_pair 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 [] 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] 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] 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] 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] 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/Morpholinos/morpholinos.HTML] synonym: "morpholino oligo" EXACT [] is_a: SO:0000696 ! implied link automatically realized ! oligo intersection_of: SO:0000696 ! oligo intersection_of: has_quality SO:0001183 ! morpholino relationship: has_quality SO:0001183 ! implied link automatically realized ! morpholino [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 [] 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: "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 [] 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 [] 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 isa match_part." [SO:ke] subset: SOFA is_a: SO:0000001 ! region 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] is_a: SO:0000151 ! implied link automatically realized ! clone intersection_of: SO:0000151 ! clone intersection_of: has_quality SO:0000991 ! genomic_DNA relationship: has_quality SO:0000991 ! implied link automatically realized ! genomic_DNA [Term] id: SO:0000041 name: operation def: "An operation that can be applied to a sequence, that results in a change." [SO:ke] is_a: SO:0000000 ! Sequence_Ontology disjoint_from: SO:0000110 ! sequence_feature disjoint_from: SO:0000240 ! chromosome_variation disjoint_from: SO:0000400 ! sequence_attribute disjoint_from: SO:0000968 ! replication_mode disjoint_from: SO:0001026 ! genome disjoint_from: SO:0001060 ! sequence_variant disjoint_from: SO:1000132 ! mutation [Term] id: SO:0000042 name: pseudogene_attribute def: "An attribute of a pseudogene (SO:0000336)." [SO:ma] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000043 name: processed_pseudogene def: "A pseudogene that is processed." [SO:xp] synonym: "pseudogene by reverse transcription" RELATED [] is_a: SO:0000336 ! implied link automatically realized ! pseudogene intersection_of: SO:0000336 ! pseudogene intersection_of: has_quality SO:0000900 ! processed relationship: has_quality SO:0000900 ! implied link automatically realized ! processed [Term] id: SO:0000044 name: pseudogene_by_unequal_crossing_over def: "A pseudogene caused by unequal crossing over at recombination." [SO:ke] is_a: SO:0000336 ! implied link automatically realized ! pseudogene intersection_of: SO:0000336 ! pseudogene intersection_of: has_quality SO:0000901 ! unequally_crossed_over relationship: has_quality SO:0000901 ! implied link automatically realized ! unequally_crossed_over [Term] id: SO:0000045 name: delete def: "To remove a subsection of sequence." [SO:ke] is_a: SO:0000041 ! operation [Term] id: SO:0000046 name: insert def: "To insert a subsection of sequence." [SO:ke] is_a: SO:0000041 ! operation [Term] id: SO:0000047 name: invert def: "To invert a subsection of sequence." [SO:ke] is_a: SO:0000041 ! operation [Term] id: SO:0000048 name: substitute def: "To substitute a subsection of sequence for another." [SO:ke] is_a: SO:0000041 ! operation [Term] id: SO:0000049 name: translocate def: "To translocate a subsection of sequence." [SO:ke] is_a: SO:0000041 ! operation [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] is_a: SO:0000695 ! reagent [Term] id: SO:0000052 name: assortment_derived_deficiency synonym: "assortment-derived_deficiency" RELATED [] is_obsolete: true [Term] id: SO:0000053 name: mutation_affecting_regulatory_region def: "A kind of mutation that affects a regulatory region of a gene." [SO:ke] is_a: SO:1000132 ! mutation [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] 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] 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] 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 [] 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 is_a: SO:0000410 ! protein_binding_site [Term] id: SO:0000060 name: compound_chromosome_arm is_a: SO:1000042 ! compound_chromosome [Term] id: SO:0000061 name: restriction_enzyme_binding_site synonym: "restriction endonuclease binding site" EXACT [] synonym: "restriction endonuclease recognition site" RELATED [] synonym: "restriction enzyme recognition site" RELATED [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0000062 name: deficient_intrachromosomal_transposition is_a: SO:1000041 ! intrachromosomal_transposition [Term] id: SO:0000063 name: deficient_interchromosomal_transposition 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 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 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] 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] 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] 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] 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] 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] 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 [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000077 name: antisense is_a: SO:0000068 ! overlapping [Term] id: SO:0000078 name: polycistronic_transcript def: "A transcript that is polycistronic." [SO:xp] is_a: SO:0000673 ! implied link automatically realized ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000880 ! polycistronic relationship: has_quality SO:0000880 ! implied link automatically realized ! polycistronic [Term] id: SO:0000079 name: dicistronic_transcript def: "A transcript that is dicistronic." [SO:ke] is_a: SO:0000078 ! implied link automatically realized ! polycistronic_transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000879 ! dicistronic relationship: has_quality SO:0000879 ! implied link automatically realized ! dicistronic [Term] id: SO:0000080 name: operon_member 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 is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000084 name: micronuclear_sequence 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] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000738 ! nuclear_sequence relationship: has_origin SO:0000738 ! implied link automatically realized ! nuclear_sequence [Term] id: SO:0000088 name: mt_gene def: "A gene located in mitochondrial sequence." [SO:xp] synonym: "mitochondrial gene" EXACT [] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000737 ! mitochondrial_sequence relationship: has_origin SO:0000737 ! implied link automatically realized ! mitochondrial_sequence [Term] id: SO:0000089 name: kinetoplast_gene def: "A gene located in kinetoplast sequence." [SO:xp] is_a: SO:0000088 ! implied link automatically realized ! mt_gene intersection_of: SO:0000088 ! mt_gene intersection_of: has_origin SO:0000741 ! kinetoplast_sequence relationship: has_origin SO:0000741 ! implied link automatically realized ! kinetoplast_sequence [Term] id: SO:0000090 name: plastid_gene def: "A gene from plastid sequence." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000740 ! plastid_sequence relationship: has_origin SO:0000740 ! implied link automatically realized ! plastid_sequence [Term] id: SO:0000091 name: apicoplast_gene def: "A gene from apicoplast sequence." [SO:xp] is_a: SO:0000090 ! implied link automatically realized ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000743 ! apicoplast_sequence relationship: has_origin SO:0000743 ! implied link automatically realized ! apicoplast_sequence [Term] id: SO:0000092 name: ct_gene def: "A gene from chloroplast sequence." [SO:xp] synonym: "chloroplast gene" EXACT [] is_a: SO:0000090 ! implied link automatically realized ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000745 ! chloroplast_sequence relationship: has_origin SO:0000745 ! implied link automatically realized ! chloroplast_sequence [Term] id: SO:0000093 name: chromoplast_gene def: "A gene from chromoplast_sequence." [SO:xp] is_a: SO:0000090 ! implied link automatically realized ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000744 ! chromoplast_sequence relationship: has_origin SO:0000744 ! implied link automatically realized ! chromoplast_sequence [Term] id: SO:0000094 name: cyanelle_gene def: "A gene from cyanelle sequence." [SO:xp] is_a: SO:0000090 ! implied link automatically realized ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000746 ! cyanelle_sequence relationship: has_origin SO:0000746 ! implied link automatically realized ! cyanelle_sequence [Term] id: SO:0000095 name: leucoplast_gene def: "A plastid gene from leucoplast sequence." [SO:xp] is_a: SO:0000090 ! implied link automatically realized ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000747 ! leucoplast_sequence relationship: has_origin SO:0000747 ! implied link automatically realized ! leucoplast_sequence [Term] id: SO:0000096 name: proplastid_gene def: "A gene from proplastid sequence." [SO:ke] is_a: SO:0000090 ! implied link automatically realized ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000748 ! proplastid_sequence relationship: has_origin SO:0000748 ! implied link automatically realized ! proplastid_sequence [Term] id: SO:0000097 name: nucleomorph_gene def: "A gene from nucleomorph sequence." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000739 ! nucleomorphic_sequence relationship: has_origin SO:0000739 ! implied link automatically realized ! nucleomorphic_sequence [Term] id: SO:0000098 name: plasmid_gene def: "A gene from plasmid sequence." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000749 ! plasmid_location relationship: has_origin SO:0000749 ! implied link automatically realized ! plasmid_location [Term] id: SO:0000099 name: proviral_gene def: "A gene from proviral sequence." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000751 ! proviral_location relationship: has_origin SO:0000751 ! implied link automatically realized ! proviral_location [Term] id: SO:0000100 name: endogenous_retroviral_gene def: "A proviral gene with origin endogenous retrovirus." [SO:xp] is_a: SO:0000099 ! implied link automatically realized ! proviral_gene intersection_of: SO:0000099 ! proviral_gene intersection_of: has_origin SO:0000903 ! endogenous_retroviral_sequence relationship: has_origin SO:0000903 ! implied link automatically realized ! 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: " transposon" EXACT [] 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 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 is_a: SO:0000699 ! junction relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000104 name: polypeptide 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. subset: SOFA is_a: SO:0000001 ! 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.exactsciences.com/cic/glossary/_index.htm] 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 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 [] is_a: SO:0000234 ! implied link automatically realized ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000865 ! frameshift relationship: has_quality SO:0000865 ! implied link automatically realized ! 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 [] is_a: SO:0000000 ! Sequence_Ontology disjoint_from: SO:0000041 ! operation disjoint_from: SO:0000240 ! chromosome_variation disjoint_from: SO:0000400 ! sequence_attribute disjoint_from: SO:0000968 ! replication_mode disjoint_from: SO:0001026 ! genome disjoint_from: SO:0001060 ! sequence_variant disjoint_from: SO:1000132 ! mutation [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] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: part_of SO:0000101 ! transposable_element relationship: part_of SO:0000101 ! implied link automatically realized ! transposable_element [Term] id: SO:0000112 name: primer def: "A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase." [http://www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/glossary.html] subset: SOFA synonym: "primer oligonucleotide" EXACT [] synonym: "primer polynucleotide" EXACT [] synonym: "primer sequence" EXACT [] is_a: SO:0000696 ! 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 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] is_a: SO:0000673 ! implied link automatically realized ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000887 ! translational_frameshift relationship: has_quality SO:0000887 ! implied link automatically realized ! translational_frameshift [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 [] 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: "forward primer oligonucleotide" EXACT [] synonym: "forward primer polynucleotide" EXACT [] synonym: "forward primer sequence" EXACT [] is_a: SO:0000112 ! primer [Term] id: SO:0000122 name: RNA_sequence_secondary_structure def: "A folded RNA sequence." [SO:ke] 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:. 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] 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] 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] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000127 name: silenced_gene def: "A gene that is silenced." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000893 ! silenced relationship: has_quality SO:0000893 ! implied link automatically realized ! silenced [Term] id: SO:0000128 name: gene_silenced_by_DNA_modification def: "A gene that is silenced by DNA modification." [SO:xp] is_a: SO:0000127 ! implied link automatically realized ! silenced_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000894 ! silenced_by_DNA_modification relationship: has_quality SO:0000894 ! implied link automatically realized ! 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: "methylation-silenced gene" EXACT [] is_a: SO:0000128 ! implied link automatically realized ! gene_silenced_by_DNA_modification intersection_of: SO:0000128 ! gene_silenced_by_DNA_modification intersection_of: has_quality SO:0000895 ! silenced_by_DNA_methylation relationship: has_quality SO:0000895 ! implied link automatically realized ! 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 [] 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] 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. is_a: SO:0000112 ! primer [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] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000134 name: imprinted def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke] 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] is_a: SO:0000134 ! imprinted [Term] id: SO:0000136 name: paternally_imprinted def: "The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] is_a: SO:0000134 ! imprinted [Term] id: SO:0000137 name: allelically_excluded def: "Allelic exclusion is a process occuring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke] comment: Exapmles are x-innactivation and immunoglobulin formation. 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] is_a: SO:0000898 ! implied link automatically realized ! epigenetically_modified_gene intersection_of: SO:0000898 ! epigenetically_modified_gene intersection_of: has_quality SO:0000904 ! rearranged_at_DNA_level relationship: has_quality SO:0000904 ! implied link automatically realized ! rearranged_at_DNA_level [Term] id: SO:0000139 name: ribosome_entry_site def: "Region in mRNA where ribosome assembles." [SO:ke] comment: Gene:. subset: SOFA is_a: SO:0000837 ! UTR_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 [] is_a: SO:0005836 ! 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 [] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000142 name: DNA_sequence_secondary_structure def: "A folded DNA sequence." [SO:ke] is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000143 name: assembly_component def: "A region of sequence which may be used to manufacture a longer assembled, sequence." [SO:ke] subset: SOFA is_a: SO:0000001 ! region [Term] id: SO:0000144 name: primary_transcript_attribute is_obsolete: true [Term] id: SO:0000145 name: recoded_codon 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 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:0000353 ! 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 unvailable bases." [SO:ls] subset: SOFA is_a: SO:0000143 ! assembly_component is_a: SO:0000353 ! 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 E. coli or some other organism." [http://www.geospiza.com/community/support/glossary/] subset: SOFA 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 [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 [Term] id: SO:0000154 name: PAC def: "P1 Artificial Chromosome. These vectors can hold large inserts, typically 80-200 kb, and propagate in E. coli as a single copy episome." [http://www.ncbi.nlm.nih.gov/genome/guide/mouse/glossary.htm] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "P1" EXACT [] synonym: "P1 artificial chromosome" EXACT [] is_a: SO:0000440 ! vector [Term] id: SO:0000155 name: plasmid def: "A self-replicating circular DNA 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:0000695 ! reagent is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element [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 [] is_a: SO:0000440 ! vector [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 [] is_a: SO:0000440 ! vector [Term] id: SO:0000158 name: fosmid def: "A cloning vector that utilises 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 [] is_a: SO:0000440 ! vector [Term] id: SO:0000159 name: deletion def: "The point at which a deletion occured." [SO:ke] subset: SOFA synonym: "deleted_sequence" EXACT [] is_a: SO:0000001 ! region is_a: SO:0001059 ! sequence_alteration relationship: sequence_of SO:0000045 ! delete [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 methylated adenine." [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:0000250 ! modified_RNA_base_feature is_a: SO:0000306 ! methylated_base_feature [Term] id: SO:0000162 name: splice_site def: "The position where intron is excised." [SO:ke] subset: SOFA is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000163 name: five_prime_splice_site def: "The junction between the 3 prime end of an exon and the following intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] subset: SOFA synonym: "5' splice site" EXACT [] synonym: "donor" RELATED [] synonym: "donor splice site" EXACT [] synonym: "splice donor site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0000164 name: three_prime_splice_site def: "The junction between the 3 prime end of an intron and the following exon." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] subset: SOFA synonym: "3' splice site" RELATED [] synonym: "acceptor" RELATED [] synonym: "acceptor splice site" EXACT [] synonym: "splice acceptor site" EXACT [] is_a: SO:0000162 ! 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] subset: SOFA is_a: SO:0000727 ! CRM relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000166 name: enhancer_bound_by_factor def: "An enhancer bound by a factor." [SO:xp] is_a: SO:0000165 ! implied link automatically realized ! enhancer intersection_of: SO:0000165 ! enhancer intersection_of: has_quality SO:0000277 ! bound_by_factor relationship: has_quality SO:0000277 ! implied link automatically realized ! 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.\nThe region on a DNA molecule involved in RNA polymerase binding to initiate transcription. subset: SOFA synonym: "promoter sequence" EXACT [] 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 [] 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 [] 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 [] 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-box" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [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 region" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [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] synonym: "Goldstein-Hogness box" EXACT [] is_a: SO:0000832 ! promoter_region relationship: part_of SO:0000170 ! RNApol_II_promoter relationship: part_of SO:0000171 ! RNApol_III_promoter [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." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "-10 signal" EXACT [] synonym: "Pribnow box" EXACT [] synonym: "Pribnow Schaller box" EXACT [] synonym: "Pribnow-Schaller box" EXACT [] is_a: SO:0000843 ! bacterial_RNApol_promoter_region [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." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "-35 signal" EXACT [] is_a: SO:0000843 ! bacterial_RNApol_promoter_region [Term] id: SO:0000177 name: cross_genome_match def: "A nucleotide match against a sequence from another organism." [SO:ma] subset: SOFA 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 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 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.genpromag.com/scripts/glossary.asp?LETTER=R] synonym: "class I" RELATED [] synonym: "class I transposon" EXACT [] synonym: "retrotransposon element" EXACT [] 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 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 [] 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 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. 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 [] 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 [] 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 segment of DNA 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 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] is_a: SO:0000180 ! retrotransposon [Term] id: SO:0000190 name: five_prime_intron synonym: "5' intron" EXACT [] synonym: "5' intron sequence" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000191 name: interior_intron is_a: SO:0000188 ! intron [Term] id: SO:0000192 name: three_prime_intron synonym: "3' intron" EXACT [] synonym: "3' intron sequence" RELATED [] is_a: SO:0000188 ! intron [Term] id: SO:0000193 name: RFLP_fragment def: "A polymorphism detectable by the size differences in DNA fragments generated by a restriction enzyme." [PMID:6247908] subset: SOFA synonym: "restriction fragment length polymorphism" EXACT [] synonym: "RFLP" EXACT [] 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: "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, including the stop_codon." [SO:ke] subset: SOFA is_a: SO:0000147 ! exon [Term] id: SO:0000196 name: five_prime_exon_coding_region def: "The sequence of the 5' exon that encodes for protein." [SO:ke] subset: SOFA is_a: SO:0000195 ! coding_exon relationship: part_of SO:0000200 ! five_prime_coding_exon [Term] id: SO:0000197 name: three_prime_exon_coding_region def: "The sequence of the 3' exon that encodes for protein." [SO:ke] subset: SOFA is_a: SO:0000195 ! coding_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 relationship: part_of SO:0000655 ! ncRNA [Term] id: SO:0000199 name: translocation def: "A region of nucleotide sequence that has translocated to a new position." [SO:ke] synonym: "translocated sequence" EXACT [] is_a: SO:0001059 ! sequence_alteration relationship: sequence_of SO:0000049 ! translocate [Term] id: SO:0000200 name: five_prime_coding_exon def: "The 5' most coding exon." [SO:ke] synonym: "5' coding exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000201 name: interior_exon def: "An exon that is bounded by 5' and 3' splice sites." [PMID:10373547] is_a: SO:0000147 ! exon [Term] id: SO:0000202 name: three_prime_coding_exon def: "The exon that is most 3-prime on a given transcript." [SO:ma] synonym: "3' coding exon" RELATED [] is_a: SO:0000147 ! exon [Term] id: SO:0000203 name: UTR def: "Messenger RNA sequences that are untranslated and lie five prime and 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_untranslated_region" EXACT [] 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 [] 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 [] 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 [] 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" 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] synonym: "ribosomal RNA 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000231 name: snRNA_primary_transcript def: "A primary transcript encoding a small nuclear mRNA (SO:0000274)." [SO:ke] 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] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000233 name: processed_transcript def: "A transcript which has undergone the necessary modifications 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 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 [] is_a: SO:0000233 ! processed_transcript [Term] id: SO:0000235 name: TF_binding_site def: "A region of a molecule that binds a TF complex [GO:0005667]." [SO:ke] subset: SOFA synonym: "transcription factor binding site" EXACT [] is_a: SO:0000410 ! protein_binding_site is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000236 name: ORF def: "The inframe 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." [SO:ma, SO:rb] comment: The definition was modified by Rama. This term is now basically the same as a CDS. This must be revised. 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 is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000238 name: foldback_element def: "A transposable element with extensive secondary structure, characterised by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] 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 DNA sequences extending on either side of a specific locus." [http://biotech.icmb.utexas.edu/search/dict-search.mhtml] subset: SOFA is_a: SO:0000001 ! region [Term] id: SO:0000240 name: chromosome_variation is_a: SO:0000000 ! Sequence_Ontology disjoint_from: SO:0000041 ! operation disjoint_from: SO:0000110 ! sequence_feature disjoint_from: SO:0000400 ! sequence_attribute disjoint_from: SO:0000968 ! replication_mode disjoint_from: SO:0001026 ! genome disjoint_from: SO:0001060 ! sequence_variant disjoint_from: SO:1000132 ! mutation [Term] id: SO:0000241 name: internal_UTR 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] 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: "IRES" EXACT [] 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 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] is_a: SO:0000833 ! transcript_region [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 [] 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 [] 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-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] 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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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: "Small non-coding RNA in the nucleoplasm. A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [ems:WB, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "small nuclear RNA" EXACT [] 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 [] 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 [] 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. 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. is_a: SO:0000673 ! implied link automatically realized ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000876 ! bound_by_nucleic_acid relationship: has_quality SO:0000876 ! implied link automatically realized ! 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. is_a: SO:0000673 ! implied link automatically realized ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000875 ! bound_by_protein relationship: has_quality SO:0000875 ! implied link automatically realized ! bound_by_protein [Term] id: SO:0000280 name: engineered_gene def: "A gene that is engineered." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene is_a: SO:0000804 ! implied link automatically realized ! engineered_region intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000783 ! engineered [Term] id: SO:0000281 name: engineered_foreign_gene def: "A gene that is engineered and foreign." [SO:xp] is_a: SO:0000280 ! implied link automatically realized ! engineered_gene is_a: SO:0000285 ! implied link automatically realized ! foreign_gene is_a: SO:0000805 ! implied link automatically realized ! engineered_foreign_region intersection_of: SO:0000280 ! engineered_gene intersection_of: has_quality SO:0000783 ! engineered intersection_of: 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] is_a: SO:0000108 ! implied link automatically realized ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000866 ! minus_1_frameshift relationship: has_quality SO:0000866 ! implied link automatically realized ! minus_1_frameshift [Term] id: SO:0000283 name: engineered_foreign_transposable_element_gene def: "A transposible_element that is engineered and foreign." [SO:xp] is_a: SO:0000111 ! implied link automatically realized ! transposable_element_gene is_a: SO:0000281 ! implied link automatically realized ! engineered_foreign_gene intersection_of: SO:0000111 ! transposable_element_gene intersection_of: has_quality SO:0000783 ! engineered intersection_of: 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] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000784 ! implied link automatically realized ! 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 [] 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] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000806 ! fusion relationship: has_quality SO:0000806 ! implied link automatically realized ! fusion [Term] id: SO:0000288 name: engineered_fusion_gene def: "A fusion gene that is engineered." [SO:xp] is_a: SO:0000280 ! implied link automatically realized ! engineered_gene is_a: SO:0000287 ! implied link automatically realized ! fusion_gene intersection_of: SO:0000287 ! fusion_gene intersection_of: has_quality SO:0000783 ! engineered [Term] id: SO:0000289 name: microsatellite def: "A very short unit sequence of DNA (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 [] is_a: SO:0000705 ! tandem_repeat [Term] id: SO:0000290 name: dinucleotide_repeat_microsatellite_feature synonym: "dinucleotide repeat microsatellite" 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 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] is_a: SO:0000657 ! implied link automatically realized ! repeat_region is_a: SO:0000805 ! implied link automatically realized ! engineered_foreign_region intersection_of: SO:0000657 ! repeat_region intersection_of: has_quality SO:0000783 ! engineered intersection_of: 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 [] 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-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 [] is_a: SO:0000001 ! region [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: "displacement loop" RELATED [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000298 name: recombination_feature is_a: SO:0000001 ! region [Term] id: SO:0000299 name: specific_recombination_site is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000300 name: recombination_feature_of_rearranged_gene is_a: SO:0000299 ! specific_recombination_site [Term] id: SO:0000301 name: vertebrate_immune_system_gene_recombination_feature 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] 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_site def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Modified base:. subset: SOFA is_a: SO:0000001 ! region [Term] id: SO:0000306 name: methylated_base_feature def: "A nucleotide modified by methylation." [SO:ke] subset: SOFA is_a: SO:0000305 ! modified_base_site [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 [] is_a: SO:0000001 ! 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 experiemntally verified." [SO:ke] 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 [] 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 is_a: SO:0000657 ! repeat_region [Term] id: SO:0000315 name: transcription_start_site def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] subset: SOFA synonym: "TSS" 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. is_a: SO:0000151 ! implied link automatically realized ! clone intersection_of: SO:0000151 ! clone intersection_of: has_quality SO:0000756 ! cDNA relationship: has_quality SO:0000756 ! implied link automatically realized ! 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 [] 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 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] 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] is_a: SO:0000108 ! implied link automatically realized ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000868 ! plus_1_frameshift relationship: has_quality SO:0000868 ! implied link automatically realized ! plus_1_frameshift [Term] id: SO:0000322 name: nuclease_hypersensitive_site 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: "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:0000695 ! reagent [Term] id: SO:0000325 name: rRNA_large_subunit_primary_transcript def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke] 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 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: "translation_end" RELATED [] is_a: SO:0000851 ! CDS_region [Term] id: SO:0000328 name: microarray_oligo synonym: "microarray oligonucleotide" EXACT [] is_a: SO:0000051 ! probe is_a: SO:0000324 ! tag is_a: SO:0000696 ! oligo [Term] id: SO:0000329 name: mRNA_with_plus_2_frameshift def: "An mRNA with a plus 2 frameshift." [SO:xp] is_a: SO:0000108 ! implied link automatically realized ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000869 ! plus_2_framshift relationship: has_quality SO:0000869 ! implied link automatically realized ! 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 is_a: SO:0000001 ! region [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 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 is_a: SO:0000699 ! junction relationship: part_of SO:0000233 ! processed_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: "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] is_a: SO:0000108 ! implied link automatically realized ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000867 ! minus_2_frameshift relationship: has_quality SO:0000867 ! implied link automatically realized ! 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 is_a: SO:0000462 ! pseudogenic_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 is_a: SO:0000696 ! 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] 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 is_a: SO:0000001 ! region [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: "cytoband" EXACT [] synonym: "cytological band" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000342 name: site_specific_recombination_target_region 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:0000001 ! region [Term] id: SO:0000344 name: splice_enhancer def: "Region of a transcript that regulates splicing." [SO:ke] subset: SOFA is_a: SO:0001056 ! splicing_regulatory_region [Term] id: SO:0000345 name: EST def: "Expressed Sequence Tag: The sequence of a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [http://genomics.phrma.org/lexicon/e.html] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "expressed sequence tag" EXACT [] is_a: SO:0000695 ! reagent relationship: derives_from SO:0000234 ! mRNA [Term] id: SO:0000346 name: loxP_site synonym: "Cre-recombination target region" RELATED [] is_a: SO:0000947 ! resolution_site [Term] id: SO:0000347 name: nucleotide_match def: "A match against a nucleotide sequence." [SO:ke] subset: SOFA 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] is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000349 name: protein_match def: "A match against a protein sequence." [SO:ke] subset: SOFA 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 [] 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] 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: assembly def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] subset: SOFA is_a: SO:0000001 ! region [Term] id: SO:0000354 name: group_1_intron_homing_endonuclease_target_region 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] 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 is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000358 name: protein def: "An attribute describing a sequence composed of amino acid residues joined by peptide bonds." [SO:ke] comment: Do not use this for feature annotation. Use polypeptide (SO:0000104) instead. is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000359 name: floxed def: "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke] 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 signify a unique amino acid or the termination of translation." [http://genomics.phrma.org/lexicon/c.html] subset: SOFA is_a: SO:0000836 ! mRNA_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] 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] is_a: SO:0000790 ! invalidated [Term] id: SO:0000363 name: floxed_gene def: "A transgene that is floxed." [SO:xp] is_a: SO:0000902 ! implied link automatically realized ! transgene intersection_of: SO:0000902 ! transgene intersection_of: has_quality SO:0000359 ! floxed relationship: has_quality SO:0000359 ! implied link automatically realized ! floxed [Term] id: SO:0000364 name: transposable_element_flanking_region def: "The region of sequence surrounding a transposible element." [SO:ke] 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] 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 is_a: SO:0000699 ! junction relationship: position_of SO:0000046 ! insert [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 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 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] 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 is_a: SO:0000673 ! implied link automatically realized ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0001185 ! enzymatic relationship: has_quality SO:0001185 ! implied link automatically realized ! enzymatic [Term] id: SO:0000373 name: recombinationally_inverted_gene def: "A recombinationally rearranged gene by inversion." [SO:xp] is_a: SO:0000456 ! implied link automatically realized ! recombinationally_rearranged_gene intersection_of: SO:0000456 ! recombinationally_rearranged_gene intersection_of: associated_with SO:0000047 ! invert relationship: associated_with SO:0000047 ! implied link automatically realized ! invert [Term] id: SO:0000374 name: ribozyme def: "An RNA with catalytic activity." [SO:ma] subset: SOFA is_a: SO:0000372 ! implied link automatically realized ! enzymatic_RNA intersection_of: SO:0000372 ! enzymatic_RNA intersection_of: has_quality SO:0001186 ! ribozymic relationship: has_quality SO:0001186 ! implied link automatically realized ! 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 [] 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 [] 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 [] 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] 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] 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." [http://rnaworld.bio.ukans.edu/class/RNA/RNA00/RNA_World_3.html] subset: SOFA is_a: SO:0000715 ! implied link automatically realized ! RNA_motif intersection_of: SO:0000715 ! RNA_motif intersection_of: has_quality SO:0001186 ! ribozymic relationship: has_quality SO:0001186 ! implied link automatically realized ! ribozymic [Term] id: SO:0000381 name: group_IIA_intron is_a: SO:0000603 ! group_II_intron [Term] id: SO:0000382 name: group_IIB_intron 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] 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] 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 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 characterised 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 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] 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] 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] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000390 name: telomerase_RNA def: "The RNA component of telomerase, a reverse transcriptase that synthesises telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025] subset: SOFA 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] 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] 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] 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] 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] 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] 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] 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] is_a: SO:0000274 ! snRNA [Term] id: SO:0000400 name: sequence_attribute def: "An attribute describes a quality of sequence." [SO:ke] is_a: SO:0000000 ! Sequence_Ontology disjoint_from: SO:0000041 ! operation disjoint_from: SO:0000110 ! sequence_feature disjoint_from: SO:0000240 ! chromosome_variation disjoint_from: SO:0000968 ! replication_mode disjoint_from: SO:0001026 ! genome disjoint_from: SO:0001060 ! sequence_variant disjoint_from: SO:1000132 ! mutation [Term] id: SO:0000401 name: gene_attribute 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 [] 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 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 is_a: SO:0000655 ! ncRNA [Term] id: SO:0000406 name: twintron def: "An intron within an intron." [PMID:1899376] 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 [] 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 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: Discrete. subset: biosapiens subset: SOFA synonym: "binding_or_interaction_site" EXACT [] synonym: "site" RELATED [] is_a: SO:0000001 ! region [Term] id: SO:0000410 name: protein_binding_site def: "A region of a molecule that binds to a protein." [SO:ke] 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 segment" RELATED [] is_a: SO:0000695 ! implied link automatically realized ! reagent intersection_of: SO:0000695 ! reagent intersection_of: has_quality SO:0000814 ! rescue relationship: has_quality SO:0000814 ! implied link automatically realized ! rescue [Term] id: SO:0000412 name: restriction_fragment def: "Any of the individual polynucleotide sequences produced by digestion of DNA with a restriction endonuclease." [http://www.agron.missouri.edu/cgi-bin/sybgw_mdb/mdb3/Term/119] subset: SOFA is_a: SO:0000695 ! reagent [Term] id: SO:0000413 name: sequence_difference def: "A region where the sequence differs from that of a specified sequence." [SO:ke] subset: SOFA 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] 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] 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] is_a: SO:0000790 ! invalidated [Term] id: SO:0000417 name: polypeptide_domain alt_id: BS:00012 def: "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. Region which has been shown to recur throughout evolution." [EBIBS:GAR, http://www.molbiol.bbsrc.ac.uk/new_protein/domains.html] 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" NARROW [] synonym: "DNA_bind" NARROW [] synonym: "domain" RELATED [] synonym: "np_bind" NARROW [] synonym: "polypeptide_domain" EXACT [] synonym: "zn_fing" NARROW [] is_a: SO:0000839 ! polypeptide_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 [] synonym: "signal peptide coding sequence" EXACT [] synonym: "signal_peptide" EXACT [] is_a: SO:0001063 ! immature_peptide_region [Term] id: SO:0000419 name: mature_protein_region alt_id: BS:00149 def: "The extent of a polypeptide chain in the mature protein." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 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" EXACT [] synonym: "mature peptide" RELATED [] synonym: "mature_protein_region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0000420 name: five_prime_terminal_inverted_repeat synonym: "5' TIR" EXACT [] is_a: SO:0000481 ! terminal_inverted_repeat [Term] id: SO:0000421 name: three_prime_terminal_inverted_repeat synonym: "3' TIR" EXACT [] is_a: SO:0000481 ! terminal_inverted_repeat [Term] id: SO:0000422 name: U5_LTR_region synonym: "U5 long terminal repeat region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000423 name: R_LTR_region synonym: "R long terminal repeat region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000424 name: U3_LTR_region synonym: "U3 long terminal repeat 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 [] 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 [] 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 [] 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 [] 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 [] 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 [] 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 [] 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 [] 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] 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] is_a: SO:0000314 ! direct_repeat [Term] id: SO:0000435 name: RR_tract def: "A polypurine tract within an LTR_retrotransposon." [SO:ke] synonym: "LTR retrotransposon poly purine tract" RELATED [] is_a: 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 is_a: SO:1000030 ! chromosomal_inversion is_a: SO:1000045 ! ring_chromosome [Term] id: SO:0000440 name: vector def: "A DNA molecule that can be used to transfer DNA molecules between organisms." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. is_a: SO:0000695 ! reagent 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. synonym: "single strand oligo" EXACT [] synonym: "single strand oligonucleotide" EXACT [] synonym: "single stranded oligonucleotide" 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. synonym: "double stranded oligonucleotide" 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] 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] 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 [] is_a: SO:0000198 ! noncoding_exon [Term] id: SO:0000446 name: UTR_intron def: "Intron located in the untranslated region." [SO:ke] is_a: SO:0000188 ! intron [Term] id: SO:0000447 name: five_prime_UTR_intron def: "An intron located in the 5' UTR." [SO:ke] 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] 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] 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] is_a: SO:0000341 ! chromosome_band [Term] id: SO:0000451 name: gene_with_polyadenylated_mRNA def: "A gene that encodes a polyadenylated mRNA." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: associated_with SO:0000871 ! polyadenylated_mRNA relationship: associated_with SO:0000871 ! implied link automatically realized ! polyadenylated_mRNA [Term] id: SO:0000452 name: transgene_attribute is_obsolete: true [Term] id: SO:0000453 name: transposition is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:0000454 name: rasiRNA def: "A small, 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 [] 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] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: associated_with SO:0000865 ! frameshift relationship: associated_with SO:0000865 ! implied link automatically realized ! frameshift [Term] id: SO:0000456 name: recombinationally_rearranged_gene def: "A gene that is recombinationally rearranged." [SO:ke] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000940 ! recombinationally_rearranged relationship: has_quality SO:0000940 ! implied link automatically realized ! recombinationally_rearranged [Term] id: SO:0000457 name: interchromosomal_duplication def: "A chromosome duplication involving an insertion from another chromosome." [SO:ke] is_a: SO:1000037 ! chromosomal_duplication [Term] id: SO:0000458 name: D_gene def: "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "D-GENE" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment relationship: part_of SO:0000504 ! D_DJ_C_cluster relationship: part_of SO:0000505 ! D_DJ_cluster relationship: part_of SO:0000506 ! D_DJ_J_C_cluster relationship: part_of SO:0000508 ! D_DJ_J_cluster relationship: part_of SO:0000509 ! D_J_C_cluster relationship: part_of SO:0000527 ! V_D_DJ_C_cluster relationship: part_of SO:0000528 ! V_D_DJ_cluster relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster relationship: part_of SO:0000530 ! V_D_DJ_J_cluster relationship: part_of SO:0000531 ! V_D_J_C_cluster relationship: part_of SO:0000532 ! V_D_J_cluster relationship: part_of SO:0000559 ! D_cluster relationship: part_of SO:0000560 ! D_J_cluster [Term] id: SO:0000459 name: gene_with_trans_spliced_transcript def: "A gene with a transcript that is trans-spliced." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: associated_with SO:0000479 ! trans_spliced_transcript relationship: associated_with SO:0000479 ! implied link automatically realized ! 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 gene" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000461 name: inversion_derived_bipartite_deficiency def: "A chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km] 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 is_a: SO:0000001 ! region [Term] id: SO:0000463 name: encodes_alternately_spliced_transcripts def: "A gene that encodes more than one transcript." [SO:ke] 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 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 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] is_a: SO:1000029 ! chromosomal_deletion is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000466 name: V_gene def: "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-GENE" EXACT [] synonym: "variable_gene" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment relationship: part_of SO:0000518 ! V_DJ_cluster relationship: part_of SO:0000519 ! V_DJ_J_cluster relationship: part_of SO:0000520 ! V_VDJ_C_cluster relationship: part_of SO:0000521 ! V_VDJ_cluster relationship: part_of SO:0000522 ! V_VDJ_J_cluster relationship: part_of SO:0000523 ! V_VJ_C_cluster relationship: part_of SO:0000524 ! V_VJ_cluster relationship: part_of SO:0000525 ! V_VJ_J_cluster relationship: part_of SO:0000526 ! V_cluster relationship: part_of SO:0000527 ! V_D_DJ_C_cluster relationship: part_of SO:0000528 ! V_D_DJ_cluster relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster relationship: part_of SO:0000530 ! V_D_DJ_J_cluster relationship: part_of SO:0000531 ! V_D_J_C_cluster relationship: part_of SO:0000532 ! V_D_J_cluster relationship: part_of SO:0000534 ! V_J_cluster relationship: part_of SO:0000535 ! V_J_C_cluster relationship: part_of SO:0000542 ! V_DJ_C_cluster relationship: part_of SO:0000564 ! V_DJ_J_C_cluster relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster relationship: part_of SO:0000566 ! V_VJ_J_C_cluster [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 [] 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 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 [] is_a: SO:0000130 ! post_translationally_regulated [Term] id: SO:0000470 name: J_gene 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "J-GENE" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment relationship: part_of SO:0000485 ! DJ_J_cluster relationship: part_of SO:0000487 ! VDJ_J_C_cluster relationship: part_of SO:0000488 ! VDJ_J_cluster relationship: part_of SO:0000490 ! VJ_J_C_cluster relationship: part_of SO:0000491 ! VJ_J_cluster relationship: part_of SO:0000506 ! D_DJ_J_C_cluster relationship: part_of SO:0000508 ! D_DJ_J_cluster relationship: part_of SO:0000509 ! D_J_C_cluster relationship: part_of SO:0000511 ! J_C_cluster relationship: part_of SO:0000513 ! J_cluster relationship: part_of SO:0000519 ! V_DJ_J_cluster relationship: part_of SO:0000522 ! V_VDJ_J_cluster relationship: part_of SO:0000525 ! V_VJ_J_cluster relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster relationship: part_of SO:0000530 ! V_D_DJ_J_cluster relationship: part_of SO:0000531 ! V_D_J_C_cluster relationship: part_of SO:0000532 ! V_D_J_cluster relationship: part_of SO:0000534 ! V_J_cluster relationship: part_of SO:0000535 ! V_J_C_cluster relationship: part_of SO:0000540 ! DJ_J_C_cluster relationship: part_of SO:0000560 ! D_J_cluster relationship: part_of SO:0000564 ! V_DJ_J_C_cluster relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster relationship: part_of SO:0000566 ! V_VJ_J_C_cluster [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." [CJM:SO] subset: SOFA is_a: SO:0000353 ! 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] 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 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] 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] 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 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "C_GENE" EXACT [] synonym: "constant gene" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment relationship: part_of SO:0000487 ! VDJ_J_C_cluster relationship: part_of SO:0000489 ! VJ_C_cluster relationship: part_of SO:0000490 ! VJ_J_C_cluster relationship: part_of SO:0000504 ! D_DJ_C_cluster relationship: part_of SO:0000506 ! D_DJ_J_C_cluster relationship: part_of SO:0000509 ! D_J_C_cluster relationship: part_of SO:0000511 ! J_C_cluster relationship: part_of SO:0000520 ! V_VDJ_C_cluster relationship: part_of SO:0000523 ! V_VJ_C_cluster relationship: part_of SO:0000527 ! V_D_DJ_C_cluster relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster relationship: part_of SO:0000531 ! V_D_J_C_cluster relationship: part_of SO:0000535 ! V_J_C_cluster relationship: part_of SO:0000539 ! DJ_C_cluster relationship: part_of SO:0000540 ! DJ_J_C_cluster relationship: part_of SO:0000541 ! VDJ_C_cluster relationship: part_of SO:0000542 ! V_DJ_C_cluster relationship: part_of SO:0000558 ! C_cluster relationship: part_of SO:0000564 ! V_DJ_J_C_cluster relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster relationship: part_of SO:0000566 ! V_VJ_J_C_cluster [Term] id: SO:0000479 name: trans_spliced_transcript def: "A transcript that is trans-spliced." [SO:xp] synonym: "trans-spliced transcript" EXACT [] is_a: SO:0000673 ! implied link automatically realized ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000870 ! trans_spliced relationship: has_quality SO:0000870 ! implied link automatically realized ! 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] 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) occuring at the termini of a DNA transposon." [SO:ke] 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 [] 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: "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] synonym: "three_prime_exon_noncoding_region" EXACT [] is_a: SO:0000852 ! exon_region 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "(DJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [Term] id: SO:0000486 name: five_prime_coding_exon_noncoding_region def: "The sequence of the 5' exon preceding the start codon." [SO:ke] synonym: "five_prime_exon_noncoding_region" EXACT [] is_a: SO:0000852 ! exon_region 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "(VDJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "(VDJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "(VJ)-C-CLUSTER" RELATED [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "(VJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "(VJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [Term] id: SO:0000492 name: D_gene_recombination_feature 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "3'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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "3'D-NOMAMER" 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "3'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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "5'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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "5'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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "5'-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 is_a: SO:0000353 ! 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] 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] 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "D-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "D-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "D-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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 mutatations. 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "D-(DJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "D-J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [Term] id: SO:0000510 name: VD_gene 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V_D_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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [Term] id: SO:0000512 name: inversion_derived_deficiency_plus_aneuploid def: "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] 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] 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 mutatations. 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(DJ)-J-CLUSTER" RELATED [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(VDJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(VDJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(VDJ)-J-CLUSTER" RELATED [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(VJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(VJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(VJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-D-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-D-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-D-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-D-(DJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-D-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-D-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "(VDJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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 [] 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] is_a: SO:0000591 ! pseudoknot relationship: part_of SO:1001268 ! recoding_stimulatory_region [Term] id: SO:0000546 name: designed_sequence 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] 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] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: associated_with SO:0000873 ! edited_transcript relationship: associated_with SO:0000873 ! implied link automatically realized ! 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] is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000550 name: aneuploid_chromosome 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 [] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000552 name: Shine_Dalgarno_sequence def: "Region in 5' UTR where ribosome assembles on mRNA." [SO:ke] synonym: "five prime ribosome binding site" EXACT [] synonym: "RBS" RELATED [] synonym: "Shine Dalgarno sequence" EXACT [] synonym: "Shine-Dalgarno sequence" EXACT [] is_a: SO:0000139 ! ribosome_entry_site [Term] id: SO:0000553 name: polyA_site def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA is_a: SO:0000699 ! junction relationship: part_of SO:0000233 ! processed_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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "5'RS" 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 [] 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://imgt.cines.fr/ligmb/LIGMlect?query=7] synonym: "C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "D-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "D-J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [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\nJ-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "HEPTAMER" RELATED [] 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 is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000563 name: vertebrate_immune_system_gene_recombination_spacer 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(VDJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-(VJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster [Term] id: SO:0000567 name: inversion_derived_aneuploid_chromosome def: "A chromosome may be generated by recombination between two inverversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km] is_a: SO:0000550 ! aneuploid_chromosome [Term] id: SO:0000568 name: bidirectional_promoter is_a: SO:0000167 ! promoter [Term] id: SO:0000569 name: retrotransposed alt_id: SO:0100042 def: "An attribute of protein-coding genes where the protein product has been retrotransposed." [SO:ke] is_a: SO:0000010 ! protein_coding is_a: SO:0000042 ! pseudogene_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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "3'D-RS" EXACT [] synonym: "three_prime_D-recombination_signal_sequence" EXACT [] is_a: SO:0000492 ! D_gene_recombination_feature [Term] id: SO:0000571 name: miRNA_encoding is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000572 name: DJ_gene 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "D-J-GENE" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment relationship: part_of SO:0000485 ! DJ_J_cluster relationship: part_of SO:0000504 ! D_DJ_C_cluster relationship: part_of SO:0000505 ! D_DJ_cluster relationship: part_of SO:0000506 ! D_DJ_J_C_cluster relationship: part_of SO:0000508 ! D_DJ_J_cluster relationship: part_of SO:0000518 ! V_DJ_cluster relationship: part_of SO:0000519 ! V_DJ_J_cluster relationship: part_of SO:0000527 ! V_D_DJ_C_cluster relationship: part_of SO:0000528 ! V_D_DJ_cluster relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster relationship: part_of SO:0000530 ! V_D_DJ_J_cluster relationship: part_of SO:0000539 ! DJ_C_cluster relationship: part_of SO:0000540 ! DJ_J_C_cluster relationship: part_of SO:0000542 ! V_DJ_C_cluster relationship: part_of SO:0000564 ! V_DJ_J_C_cluster [Term] id: SO:0000573 name: rRNA_encoding is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000574 name: VDJ_gene 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-D-J-GENE" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment relationship: part_of SO:0000487 ! VDJ_J_C_cluster relationship: part_of SO:0000488 ! VDJ_J_cluster relationship: part_of SO:0000520 ! V_VDJ_C_cluster relationship: part_of SO:0000521 ! V_VDJ_cluster relationship: part_of SO:0000522 ! V_VDJ_J_cluster relationship: part_of SO:0000541 ! VDJ_C_cluster relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster [Term] id: SO:0000575 name: scRNA_encoding is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000576 name: VJ_gene 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://imgt.cines.fr/ligmdb/LIGMlect?query=7] synonym: "V-J-GENE" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment relationship: part_of SO:0000489 ! VJ_C_cluster relationship: part_of SO:0000490 ! VJ_J_C_cluster relationship: part_of SO:0000491 ! VJ_J_cluster relationship: part_of SO:0000523 ! V_VJ_C_cluster relationship: part_of SO:0000524 ! V_VJ_cluster relationship: part_of SO:0000525 ! V_VJ_J_cluster relationship: part_of SO:0000566 ! V_VJ_J_C_cluster [Term] id: SO:0000577 name: centromere def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] subset: SOFA is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000578 name: snoRNA_encoding 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] 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] 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 is_a: SO:0000001 ! region [Term] id: SO:0000582 name: rRNA_cleavage_snoRNA_primary_transcript def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke] 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://www.rna.ucla.edu] 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 [] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000585 name: C_D_box_snoRNA_encoding 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 [] 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 catalyse 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] subset: SOFA is_a: SO:0000188 ! intron [Term] id: SO:0000588 name: autocatalytically_spliced_intron def: "A self spliced intron." [SO:ke] subset: SOFA is_a: SO:0000188 ! implied link automatically realized ! intron intersection_of: SO:0000188 ! intron intersection_of: has_quality SO:0001186 ! ribozymic relationship: has_quality SO:0001186 ! implied link automatically realized ! ribozymic [Term] id: SO:0000589 name: SRP_RNA_primary_transcript def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke] 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 [] 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] 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-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] synonym: "box C/D 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 [] 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] 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] 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 def: "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." [http://nsm1.utdallas.edu/bio/miller/physarum/overview.htm] 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 [] 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] subset: SOFA is_a: SO:0000188 ! intron [Term] id: SO:0000604 name: editing_block def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://www.rna.ucla/] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000605 name: intergenic_region def: "The region between two known genes." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA is_a: SO:0000001 ! region [Term] id: SO:0000606 name: editing_domain def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://www.rna.ucla/] 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://www.rna.ucla.edu/] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000608 name: H_ACA_box_snoRNA_encoding 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/] is_a: SO:0000001 ! 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 is_a: SO:0000001 ! region [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_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 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] 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] is_a: SO:0000752 ! gene_group_regulatory_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000615 name: terminator_of_type_2_RNApol_III_promoter def: "A terminator signal for RNA polymerase III transcription." [SO:ke] is_a: SO:0000951 ! eukaryotic_terminator [Term] id: SO:0000616 name: transcription_end_site def: "The base where transcription ends." [SO:ke] subset: SOFA is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000617 name: RNApol_III_promoter_type_1 is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000618 name: RNApol_III_promoter_type_2 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 recognised by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke] is_a: SO:0000846 ! RNApol_III_promoter_type_2_region [Term] id: SO:0000620 name: B_box def: "A variably distant linear promoter region recognised by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke] is_a: SO:0000846 ! RNApol_III_promoter_type_2_region [Term] id: SO:0000621 name: RNApol_III_promoter_type_3 is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000622 name: C_box def: "An RNA polymerase II type 1 promoter with consensus sequence CAnnCCn." [SO:ke] is_a: SO:0000845 ! RNApol_III_promoter_type_1_region [Term] id: SO:0000623 name: snRNA_encoding 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 is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000625 name: silencer def: "Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes." [http://www.brunel.ac.uk/depts/bio/project/old_hmg/gloss3.htm] subset: SOFA is_a: SO:0000727 ! CRM [Term] id: SO:0000626 name: chromosomal_regulatory_element is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000627 name: insulator def: "A trancriptional 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 [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000628 name: chromosomal_structural_element subset: SOFA is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000629 name: five_prime_open_reading_frame 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] is_a: SO:0000837 ! UTR_region [Term] id: SO:0000631 name: polycistronic_primary_transcript def: "A primary transcript encoding for more than one gene product." [SO:ke] is_a: SO:0000078 ! implied link automatically realized ! polycistronic_transcript is_a: SO:0000185 ! implied link automatically realized ! primary_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: has_quality SO:0000880 ! polycistronic [Term] id: SO:0000632 name: monocistronic_primary_transcript def: "A primary transcript encoding for more than one gene product." [SO:ke] is_a: SO:0000185 ! implied link automatically realized ! primary_transcript is_a: SO:0000665 ! implied link automatically realized ! monocistronic_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: 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 processed transcript" EXACT [] is_a: SO:0000234 ! implied link automatically realized ! mRNA is_a: SO:0000665 ! implied link automatically realized ! monocistronic_transcript intersection_of: SO:0000234 ! mRNA intersection_of: 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 processed transcript" RELATED [] is_a: SO:0000078 ! implied link automatically realized ! polycistronic_transcript is_a: SO:0000234 ! implied link automatically realized ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: 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 [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000636 name: spliced_leader_RNA synonym: "mini-exon" RELATED [] 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 gene" RELATED [] is_a: SO:0000155 ! implied link automatically realized ! plasmid is_a: SO:0000804 ! implied link automatically realized ! engineered_region intersection_of: SO:0000155 ! plasmid intersection_of: 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] 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] 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] is_a: SO:0000638 ! transcribed_spacer_region [Term] id: SO:0000641 name: tetranucleotide_repeat_microsatellite_feature is_a: SO:0000289 ! microsatellite [Term] id: SO:0000642 name: SRP_RNA_encoding is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000643 name: minisatellite def: "A repetitive sequence spanning 500 to 20,000 base pairs (a repeat unit is 5 - 30 base pairs)." [http://www.rerf.or.jp/eigo/glossary/minisate.htm] subset: SOFA is_a: SO:0000705 ! tandem_repeat [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 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 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 [] 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 [] 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 [] 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 [] 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: "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: "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 stabilises 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 [] 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 [] 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 [] is_a: SO:0000089 ! implied link automatically realized ! kinetoplast_gene intersection_of: SO:0000089 ! kinetoplast_gene intersection_of: has_origin SO:0000742 ! maxicircle_sequence relationship: has_origin SO:0000742 ! implied link automatically realized ! maxicircle_sequence [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 [] is_a: SO:0000233 ! processed_transcript [Term] id: SO:0000656 name: stRNA_encoding 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 is_a: SO:0000001 ! region [Term] id: SO:0000658 name: dispersed_repeat def: "A repeat that is located at dispersed sites in the genome." [SO:ke] subset: SOFA synonym: "interspersed repeat" EXACT [] is_a: SO:0000657 ! repeat_region [Term] id: SO:0000659 name: tmRNA_encoding 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_a: SO:0000733 ! feature_attribute [Term] id: SO:0000662 name: spliceosomal_intron def: "An intron which is spliced by the spliceosome." [SO:ke] subset: SOFA is_a: SO:0000188 ! intron [Term] id: SO:0000663 name: tRNA_encoding is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000664 name: introgressed_chromosome_region is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000665 name: monocistronic_transcript def: "A transcript that is monocistronic." [SO:xp] is_a: SO:0000673 ! implied link automatically realized ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000878 ! monocistronic relationship: has_quality SO:0000878 ! implied link automatically realized ! monocistronic [Term] id: SO:0000666 name: mobile_intron is_a: SO:0000661 ! intron_attribute [Term] id: SO:0000667 name: insertion def: "A region of sequence that has been inserted." [SO:ke] subset: SOFA is_a: SO:0000001 ! region is_a: SO:0001059 ! sequence_alteration relationship: sequence_of SO:0000046 ! insert [Term] id: SO:0000668 name: EST_match def: "A match against an EST sequence." [SO:ke] subset: SOFA is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000669 name: sequence_rearrangement_feature 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] 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] 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] 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 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 [] is_a: SO:0000162 ! splice_site [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] is_a: SO:0000162 ! splice_site [Term] id: SO:0000676 name: canonical_three_prime_splice_site def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke] is_a: SO:0000164 ! three_prime_splice_site is_a: SO:0000675 ! canonical_splice_site [Term] id: SO:0000677 name: canonical_five_prime_splice_site def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke] is_a: SO:0000163 ! five_prime_splice_site is_a: SO:0000675 ! canonical_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 three prime splice site" EXACT [] is_a: SO:0000164 ! three_prime_splice_site is_a: SO:0000674 ! non_canonical_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 five prime splice site" EXACT [] is_a: SO:0000163 ! five_prime_splice_site is_a: SO:0000674 ! non_canonical_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 [] 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] is_a: SO:0000233 ! processed_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] is_a: SO:0000344 ! splice_enhancer [Term] id: SO:0000684 name: nuclease_sensitive_site def: "A region of nucleotide sequence targeting by a nuclease enzyme." [SO:ma] subset: SOFA is_a: SO:0000001 ! region [Term] id: SO:0000685 name: DNAaseI_hypersensitive_site is_a: SO:0000322 ! nuclease_hypersensitive_site [Term] id: SO:0000686 name: translocation_element def: "For some translocations, particularly but not exclusively, reciprocal translocations, the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements." [SO:ma] 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 is_a: SO:0000699 ! junction relationship: position_of SO:0000045 ! delete [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 is_a: SO:0000353 ! assembly [Term] id: SO:0000689 name: cDNA_match def: "A match against cDNA sequence." [SO:ke] subset: SOFA 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] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: associated_with SO:0000078 ! polycistronic_transcript relationship: associated_with SO:0000078 ! implied link automatically realized ! polycistronic_transcript [Term] id: SO:0000691 name: cleaved_initiator_methionine alt_id: BS:00067 def: "Indicates when the initator methionine has been cleaved from the mature sequence." [EBIBS:GAR] subset: biosapiens synonym: "cleaved_initiator_methionine" EXACT [] synonym: "init_met" RELATED [] synonym: "initator methionine" EXACT [] is_a: SO:0001063 ! immature_peptide_region [Term] id: SO:0000692 name: gene_with_dicistronic_transcript def: "A gene that encodes a dicistronic transcript." [SO:xp] is_a: SO:0000690 ! implied link automatically realized ! gene_with_polycistronic_transcript intersection_of: SO:0000690 ! gene_with_polycistronic_transcript intersection_of: associated_with SO:0000079 ! dicistronic_transcript relationship: associated_with SO:0000079 ! implied link automatically realized ! dicistronic_transcript [Term] id: SO:0000693 name: gene_with_recoded_mRNA def: "A gene that encodes an mRNA that is recoded." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: associated_with SO:1001261 ! recoded_mRNA relationship: associated_with SO:1001261 ! implied link automatically realized ! recoded_mRNA [Term] id: SO:0000694 name: SNP def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives (alleles) exist in normal individuals in some population(s), wherein the least frequent allele has an abundance of 1% or greater." [http://www.cgr.ki.se/cgb/groups/brookes/Articles/essence_of_snps_article.pdf] subset: SOFA synonym: "single nucleotide polymorphism" EXACT [] is_a: SO:1000002 ! substitution [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:0000001 ! 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 [] 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] is_a: SO:0000693 ! implied link automatically realized ! gene_with_recoded_mRNA intersection_of: SO:0000693 ! gene_with_recoded_mRNA intersection_of: associated_with SO:0000883 ! stop_codon_read_through relationship: associated_with SO:0000883 ! implied link automatically realized ! 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] is_a: SO:0000697 ! implied link automatically realized ! gene_with_stop_codon_read_through intersection_of: SO:0000697 ! gene_with_stop_codon_read_through intersection_of: associated_with SO:0000884 ! stop_codon_redefined_as_pyrrolysine relationship: associated_with SO:0000884 ! implied link automatically realized ! 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 [] is_a: SO:0000110 ! sequence_feature disjoint_from: SO:0000001 ! region [Term] id: SO:0000700 name: remark def: "A comment about the sequence." [SO:ke] subset: SOFA is_a: SO:0000001 ! region [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 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 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 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.\nA gene may be considered as a unit of inheritance. subset: SOFA is_a: SO:0000001 ! region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000705 name: tandem_repeat def: "Two or more adjacent copies of a DNA sequence." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html] subset: SOFA is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000005 ! satellite_DNA [Term] id: SO:0000706 name: trans_splice_acceptor_site def: "The process that produces mature transcripts by combining exons of independent pre-mRNA molecules. The acceptor site lies on the 3' of these molecules." [SO:ke] subset: SOFA is_a: SO:0000164 ! three_prime_splice_site [Term] id: SO:0000707 name: trans_splice_donor_site def: "The site at which trans-splicing occurs." [SO:ke] synonym: "trans-splice donor site" EXACT [] is_a: SO:0000163 ! five_prime_splice_site [Term] id: SO:0000708 name: SL1_acceptor_site is_a: SO:0000706 ! trans_splice_acceptor_site [Term] id: SO:0000709 name: SL2_acceptor_site 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] is_a: SO:0000697 ! implied link automatically realized ! gene_with_stop_codon_read_through intersection_of: SO:0000697 ! gene_with_stop_codon_read_through intersection_of: associated_with SO:0000885 ! stop_codon_redefined_as_selenocysteine relationship: associated_with SO:0000885 ! implied link automatically realized ! 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] is_a: SO:0000693 ! implied link automatically realized ! gene_with_recoded_mRNA intersection_of: SO:0000693 ! gene_with_recoded_mRNA intersection_of: associated_with SO:0000886 ! recoded_by_translational_bypass relationship: associated_with SO:0000886 ! implied link automatically realized ! 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] is_a: SO:0000693 ! implied link automatically realized ! gene_with_recoded_mRNA intersection_of: SO:0000693 ! gene_with_recoded_mRNA intersection_of: associated_with SO:0000887 ! translational_frameshift relationship: associated_with SO:0000887 ! implied link automatically realized ! translational_frameshift [Term] id: SO:0000713 name: DNA_motif def: "A motif that is active in the DNA form of the sequence." [SO:ke] 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 is_a: SO:0000001 ! region [Term] id: SO:0000715 name: RNA_motif def: "A motif that is active in RNA sequence." [SO:ke] 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 processed transcript" RELATED [] is_a: SO:0000079 ! implied link automatically realized ! dicistronic_transcript is_a: SO:0000634 ! implied link automatically realized ! polycistronic_mRNA intersection_of: SO:0000234 ! mRNA intersection_of: 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." [SO: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 is_a: SO:0000001 ! region [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." [SO:rb] comment: Term requested by Rama from SGD. 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 is_a: SO:0000353 ! 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. is_a: SO:0000101 ! implied link automatically realized ! transposable_element intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000784 ! implied link automatically realized ! 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. is_a: SO:0000692 ! implied link automatically realized ! gene_with_dicistronic_transcript intersection_of: SO:0000692 ! gene_with_dicistronic_transcript intersection_of: associated_with SO:1001197 ! dicistronic_primary_transcript relationship: associated_with SO:1001197 ! implied link automatically realized ! 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 processed transcript" EXACT [] is_a: SO:0000692 ! implied link automatically realized ! gene_with_dicistronic_transcript intersection_of: SO:0000692 ! gene_with_dicistronic_transcript intersection_of: associated_with SO:0000716 ! dicistronic_mRNA relationship: associated_with SO:0000716 ! implied link automatically realized ! 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 [] 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 [] 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_peptide" EXACT [] is_a: SO:0001063 ! immature_peptide_region [Term] id: SO:0000726 name: repeat_unit def: "A single repeat element." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Added to comply with the feature table. is_a: SO:0000657 ! repeat_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. synonym: "cis regulatory module" EXACT [] synonym: "TF module" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [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 [] is_a: SO:0001063 ! immature_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] 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 ! assembly [Term] id: SO:0000731 name: fragment def: "An attribute to describe a feature that is incomplete." [SO:ke] comment: Term added because of request by MO people. is_a: SO:0000905 ! status [Term] id: SO:0000732 name: predicted def: "An attribute describing an unverified region." [SO:ke] is_a: SO:0000905 ! status [Term] id: SO:0000733 name: feature_attribute def: "An attribute describing a located_sequence_feature." [SO:ke] 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. is_a: SO:0000234 ! implied link automatically realized ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000864 ! exemplar relationship: has_quality SO:0000864 ! implied link automatically realized ! exemplar [Term] id: SO:0000735 name: sequence_location is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000736 name: organelle_sequence 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. is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000738 name: nuclear_sequence is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000739 name: nucleomorphic_sequence is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000740 name: plastid_sequence is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000741 name: kinetoplast_sequence is_a: SO:0000737 ! mitochondrial_sequence [Term] id: SO:0000742 name: maxicircle_sequence is_a: SO:0000741 ! kinetoplast_sequence [Term] id: SO:0000743 name: apicoplast_sequence is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000744 name: chromoplast_sequence is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000745 name: chloroplast_sequence is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000746 name: cyanelle_sequence is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000747 name: leucoplast_sequence is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000748 name: proplastid_sequence is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000749 name: plasmid_location 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] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000751 name: proviral_location is_a: SO:0000735 ! sequence_location [Term] id: SO:0000752 name: gene_group_regulatory_region subset: SOFA is_a: SO:0005836 ! regulatory_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000753 name: clone_insert is_a: SO:0000695 ! reagent [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] is_a: SO:0000440 ! vector [Term] id: SO:0000755 name: plasmid_vector is_a: SO:0000440 ! vector [Term] id: SO:0000756 name: cDNA def: "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma] is_a: SO:0000352 ! DNA [Term] id: SO:0000757 name: single_stranded_cDNA synonym: "single strand 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-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-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." [http://nar.oxfordjournals.org/cgi/content/full/32/15/4531n10, Indiana:kw] comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005. 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." [http://nar.oxfordjournals.org/cgi/content/full/32/15/4531n10, Indiana:kw] comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005. 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:0000001 ! 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 bulck of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke] comment: Genomic islands are transmissible elements characterized by large size (>10kb). 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. 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. 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. 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. 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 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 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. is_a: SO:0000637 ! implied link automatically realized ! engineered_plasmid is_a: SO:0000768 ! implied link automatically realized ! episome intersection_of: SO:0000768 ! episome intersection_of: 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 atrribute 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 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. is_a: SO:0000733 ! feature_attribute [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 segment" EXACT [] is_a: SO:0000411 ! implied link automatically realized ! rescue_region is_a: SO:0000804 ! implied link automatically realized ! engineered_region intersection_of: SO:0000411 ! rescue_region intersection_of: 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 [] is_a: SO:0000411 ! implied link automatically realized ! rescue_region is_a: SO:0000815 ! implied link automatically realized ! mini_gene intersection_of: SO:0000815 ! mini_gene intersection_of: 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." [SO:mc] comment: Modified as requested by Lynn - FB. May 2007. is_a: SO:0000101 ! implied link automatically realized ! transposable_element intersection_of: SO:0000101 ! transposable_element intersection_of: derives_from SO:0000151 ! clone intersection_of: has_quality SO:0000781 ! transgenic relationship: derives_from SO:0000151 ! implied link automatically realized ! clone relationship: has_quality SO:0000781 ! implied link automatically realized ! transgenic [Term] id: SO:0000797 name: natural_transposable_element def: "TE that exists (or existed) in nature." [SO:mc] is_a: SO:0000101 ! implied link automatically realized ! transposable_element intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000782 ! natural relationship: has_quality SO:0000782 ! implied link automatically realized ! natural [Term] id: SO:0000798 name: engineered_transposable_element def: "TE that has been modified by manipulations in vitro." [SO:mc] is_a: SO:0000101 ! implied link automatically realized ! transposable_element is_a: SO:0000804 ! implied link automatically realized ! engineered_region intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000783 ! engineered [Term] id: SO:0000799 name: engineered_foreign_transposable_element def: "A transposable_element that is engineered and foreign." [SO:mc] is_a: SO:0000720 ! implied link automatically realized ! foreign_transposable_element is_a: SO:0000798 ! implied link automatically realized ! engineered_transposable_element is_a: SO:0000805 ! implied link automatically realized ! engineered_foreign_region intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000783 ! engineered intersection_of: 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] is_a: SO:0000240 ! chromosome_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] is_a: SO:0000240 ! chromosome_variation [Term] id: SO:0000802 name: assortment_derived_deficiency def: "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm] is_a: SO:0000240 ! chromosome_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] is_a: SO:0000240 ! chromosome_variation [Term] id: SO:0000804 name: engineered_region def: "A region that is engineered." [SO:xp] synonym: "engineered sequence" EXACT [] is_a: SO:0000001 ! implied link automatically realized ! region intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! implied link automatically realized ! engineered [Term] id: SO:0000805 name: engineered_foreign_region def: "A region that is engineered and foreign." [SO:xp] is_a: SO:0000804 ! implied link automatically realized ! engineered_region intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000784 ! implied link automatically realized ! 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] is_a: SO:0000324 ! implied link automatically realized ! tag is_a: SO:0000804 ! implied link automatically realized ! engineered_region intersection_of: SO:0000324 ! tag intersection_of: has_quality SO:0000783 ! engineered [Term] id: SO:0000808 name: validated_cDNA_clone def: "A cDNA clone that has been validated." [SO:xp] is_a: SO:0000317 ! implied link automatically realized ! cDNA_clone intersection_of: SO:0000317 ! cDNA_clone intersection_of: has_quality SO:0000789 ! validated relationship: has_quality SO:0000789 ! implied link automatically realized ! validated [Term] id: SO:0000809 name: invalidated_cDNA_clone def: "A cDNA clone that is invalid." [SO:xp] is_a: SO:0000317 ! implied link automatically realized ! cDNA_clone intersection_of: SO:0000317 ! cDNA_clone intersection_of: has_quality SO:0000790 ! invalidated relationship: has_quality SO:0000790 ! implied link automatically realized ! invalidated [Term] id: SO:0000810 name: chimeric_cDNA_clone def: "A cDNA clone invalidated because it is chimeric." [SO:xp] is_a: SO:0000809 ! implied link automatically realized ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA relationship: has_quality SO:0000362 ! implied link automatically realized ! invalidated_by_chimeric_cDNA [Term] id: SO:0000811 name: genomically_contaminated_cDNA_clone def: "A cDNA clone invalidated by genomic contamination." [SO:xp] is_a: SO:0000809 ! implied link automatically realized ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000414 ! invalidated_by_genomic_contamination relationship: has_quality SO:0000414 ! implied link automatically realized ! invalidated_by_genomic_contamination [Term] id: SO:0000812 name: polyA_primed_cDNA_clone def: "A cDNA clone invalidated by polyA priming." [SO:xp] is_a: SO:0000809 ! implied link automatically realized ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA relationship: has_quality SO:0000415 ! implied link automatically realized ! 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] is_a: SO:0000809 ! implied link automatically realized ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000416 ! invalidated_by_partial_processing relationship: has_quality SO:0000416 ! implied link automatically realized ! 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))\nand 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] is_a: SO:0000695 ! reagent [Term] id: SO:0000816 name: rescue_gene def: "A gene that rescues." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000814 ! rescue relationship: has_quality SO:0000814 ! implied link automatically realized ! 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] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000818 name: wild_type_rescue_gene def: "A gene that rescues." [SO:xp] is_a: SO:0000816 ! rescue_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000817 ! wild_type relationship: has_quality SO:0000817 ! implied link automatically realized ! wild_type [Term] id: SO:0000819 name: mitochondrial_chromosome def: "A chromosome originating in a mitochondria." [SO:xp] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000737 ! mitochondrial_sequence relationship: has_origin SO:0000737 ! implied link automatically realized ! mitochondrial_sequence [Term] id: SO:0000820 name: chloroplast_chromosome def: "A chromosome originating in a chloroplast." [SO:xp] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000745 ! chloroplast_sequence relationship: has_origin SO:0000745 ! implied link automatically realized ! chloroplast_sequence [Term] id: SO:0000821 name: chromoplast_chromosome def: "A chromosome originating in a chromoplast." [SO:xp] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000744 ! chromoplast_sequence relationship: has_origin SO:0000744 ! implied link automatically realized ! chromoplast_sequence [Term] id: SO:0000822 name: cyanelle_chromosome def: "A chromosome originating in a cyanelle." [SO:xp] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000746 ! cyanelle_sequence relationship: has_origin SO:0000746 ! implied link automatically realized ! cyanelle_sequence [Term] id: SO:0000823 name: leucoplast_chromosome def: "A chromosome with origin in a leucoplast." [SO:xp] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000747 ! leucoplast_sequence relationship: has_origin SO:0000747 ! implied link automatically realized ! leucoplast_sequence [Term] id: SO:0000824 name: macronuclear_chromosome def: "A chromosome originating in a macronucleus." [SO:xp] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000083 ! macronuclear_sequence relationship: has_origin SO:0000083 ! implied link automatically realized ! macronuclear_sequence [Term] id: SO:0000825 name: micronuclear_chromosome def: "A chromosome originating in a micronucleus." [SO:xp] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000084 ! micronuclear_sequence relationship: has_origin SO:0000084 ! implied link automatically realized ! micronuclear_sequence [Term] id: SO:0000826 name: kinetoplast_chromosome def: "A chromosome with origin in the kinetoplast." [SO:xp] is_a: SO:0000819 ! implied link automatically realized ! mitochondrial_chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000741 ! kinetoplast_sequence relationship: has_origin SO:0000741 ! implied link automatically realized ! kinetoplast_sequence [Term] id: SO:0000827 name: maxicircle_chromosome def: "A chromosome originating in a maxi-circle." [SO:xp] is_a: SO:0000826 ! implied link automatically realized ! kinetoplast_chromosome intersection_of: SO:0000826 ! kinetoplast_chromosome intersection_of: has_origin SO:0000742 ! maxicircle_sequence relationship: has_origin SO:0000742 ! implied link automatically realized ! maxicircle_sequence [Term] id: SO:0000828 name: nuclear_chromosome def: "A chromosome originating in a nucleus." [SO:xp] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000738 ! nuclear_sequence relationship: has_origin SO:0000738 ! implied link automatically realized ! nuclear_sequence [Term] id: SO:0000829 name: nucleomorphic_chromosome def: "A chromosome originating in a nucleomorph." [SO:xp] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000739 ! nucleomorphic_sequence relationship: has_origin SO:0000739 ! implied link automatically realized ! 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 is_a: SO:0000001 ! 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 is_a: SO:0000001 ! 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_a: SO:0005836 ! regulatory_region relationship: part_of SO:0000167 ! promoter [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 is_a: SO:0000001 ! region relationship: part_of SO:0000673 ! transcript [Term] id: SO:0000834 name: processed_transcript_region def: "A region of a processed transcript." [SO:ke] comment: A manufactured term to collect together the parts of a processed transcript and give them an is_a path to the root. subset: SOFA is_a: SO:0000833 ! transcript_region [Term] id: SO:0000835 name: primary_transcript_region def: "A region 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 is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000185 ! primary_transcript [Term] id: SO:0000836 name: mRNA_region 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 is_a: SO:0000834 ! processed_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 is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000203 ! UTR [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. 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 protein." [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" EXACT [] synonym: "positional polypeptide feature" EXACT [] synonym: "region or site annotation" EXACT [] is_a: SO:0000001 ! 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. is_a: SO:0000001 ! region relationship: part_of SO:0000657 ! repeat_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 is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000662 ! spliceosomal_intron [Term] id: SO:0000842 name: gene_component_region subset: SOFA is_a: SO:0000001 ! 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_a: SO:0000832 ! promoter_region relationship: part_of SO:0000613 ! bacterial_RNApol_promoter [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_a: SO:0000832 ! promoter_region relationship: part_of SO:0000170 ! RNApol_II_promoter [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_a: SO:0000832 ! promoter_region relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 [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_a: SO:0000832 ! promoter_region relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 [Term] id: SO:0000847 name: tmRNA_region 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. is_a: SO:0000834 ! processed_transcript_region relationship: part_of SO:0000584 ! tmRNA [Term] id: SO:0000848 name: LTR_component synonym: "long term repeat 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 [] 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 [] is_a: SO:0000848 ! LTR_component relationship: part_of SO:0000425 ! five_prime_LTR [Term] id: SO:0000851 name: CDS_region subset: SOFA 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] 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] is_a: SO:0000330 ! implied link automatically realized ! conserved_region intersection_of: SO:0000330 ! conserved_region intersection_of: has_quality SO:0000856 ! conserved relationship: has_quality SO:0000856 ! implied link automatically realized ! conserved [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 witht he paralogous_to relationship. is_a: SO:0000853 ! implied link automatically realized ! homologous_region intersection_of: SO:0000853 ! homologous_region intersection_of: has_quality SO:0000859 ! paralogous relationship: has_quality SO:0000859 ! implied link automatically realized ! 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 conjuction with the similarity relationships defined in SO. is_a: SO:0000853 ! implied link automatically realized ! homologous_region intersection_of: SO:0000853 ! homologous_region intersection_of: has_quality SO:0000858 ! orthologous relationship: has_quality SO:0000858 ! implied link automatically realized ! 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: "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: "A kind of homology where divergence occured 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] is_a: SO:0000856 ! conserved [Term] id: SO:0000861 name: capped_primary_transcript def: "A primary transcript that is capped." [SO:xp] is_a: SO:0000185 ! implied link automatically realized ! primary_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: adjacent_to SO:0000581 ! cap intersection_of: has_quality SO:0000146 ! capped relationship: adjacent_to SO:0000581 ! implied link automatically realized ! cap relationship: has_quality SO:0000146 ! implied link automatically realized ! capped [Term] id: SO:0000862 name: capped_mRNA def: "An mRNA that is capped." [SO:xp] is_a: SO:0000234 ! implied link automatically realized ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: adjacent_to SO:0000581 ! cap intersection_of: has_quality SO:0000146 ! capped relationship: adjacent_to SO:0000581 ! implied link automatically realized ! cap relationship: has_quality SO:0000146 ! implied link automatically realized ! capped [Term] id: SO:0000863 name: mRNA_attribute def: "An attribute describing an mRNA feature." [SO:ke] 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] is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000866 name: minus_1_frameshift def: "A frameshift caused by deleting one base." [SO:ke] is_a: SO:0000865 ! frameshift [Term] id: SO:0000867 name: minus_2_frameshift def: "A frameshift caused by deleting two bases." [SO:ke] is_a: SO:0000865 ! frameshift [Term] id: SO:0000868 name: plus_1_frameshift def: "A frameshift caused by inserting one base." [SO:ke] is_a: SO:0000865 ! frameshift [Term] id: SO:0000869 name: plus_2_framshift def: "A frameshift caused by inserting two bases." [SO:ke] 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] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000871 name: polyadenylated_mRNA def: "An mRNA that is polyadenylated." [SO:xp] is_a: SO:0000234 ! implied link automatically realized ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: adjacent_to SO:0000610 ! polyA_sequence intersection_of: has_quality SO:0000246 ! polyadenylated relationship: adjacent_to SO:0000610 ! implied link automatically realized ! polyA_sequence relationship: has_quality SO:0000246 ! implied link automatically realized ! polyadenylated [Term] id: SO:0000872 name: trans_spliced_mRNA def: "An mRNA that is trans-spliced." [SO:xp] is_a: SO:0000234 ! implied link automatically realized ! mRNA is_a: SO:0000479 ! implied link automatically realized ! trans_spliced_transcript intersection_of: SO:0000234 ! mRNA intersection_of: adjacent_to SO:0000636 ! spliced_leader_RNA intersection_of: has_quality SO:0000870 ! trans_spliced relationship: adjacent_to SO:0000636 ! implied link automatically realized ! spliced_leader_RNA [Term] id: SO:0000873 name: edited_transcript def: "A transcript that is edited." [SO:ke] is_a: SO:0000673 ! implied link automatically realized ! transcript intersection_of: SO:0000673 ! transcript intersection_of: associated_with SO:0000602 ! guide_RNA intersection_of: associated_with SO:0000977 ! anchor_binding_site intersection_of: has_quality SO:0000116 ! edited relationship: associated_with SO:0000602 ! implied link automatically realized ! guide_RNA relationship: associated_with SO:0000977 ! implied link automatically realized ! anchor_binding_site relationship: has_quality SO:0000116 ! implied link automatically realized ! 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] is_a: SO:0000929 ! implied link automatically realized ! edited_mRNA intersection_of: SO:0000873 ! edited_transcript intersection_of: associated_with SO:0000919 ! substitute_A_to_I relationship: associated_with SO:0000919 ! implied link automatically realized ! substitute_A_to_I [Term] id: SO:0000875 name: bound_by_protein def: "An attribute describing a sequence that is bound by a protein." [SO:ke] 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] 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] 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 am mRNA sequences 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] 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 readthrough" RELATED [] is_a: SO:0000882 ! codon_redefined [Term] id: SO:0000884 name: stop_codon_redefined_as_pyrrolysine def: "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke] 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] 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] is_a: SO:0000881 ! recoded [Term] id: SO:0000887 name: translational_frameshift def: "Recoding by frameshifting a particular site." [SO:ke] is_a: SO:0000881 ! recoded [Term] id: SO:0000888 name: maternally_imprinted_gene def: "A gene that is maternally_imprinted." [SO:xp] is_a: SO:0000898 ! implied link automatically realized ! epigenetically_modified_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000135 ! maternally_imprinted relationship: has_quality SO:0000135 ! implied link automatically realized ! maternally_imprinted [Term] id: SO:0000889 name: paternally_imprinted_gene def: "A gene that is paternally imprinted." [SO:xp] is_a: SO:0000898 ! implied link automatically realized ! epigenetically_modified_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000136 ! paternally_imprinted relationship: has_quality SO:0000136 ! implied link automatically realized ! paternally_imprinted [Term] id: SO:0000890 name: post_translationally_regulated_gene def: "A gene that is post translationally regulated." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000130 ! post_translationally_regulated relationship: has_quality SO:0000130 ! implied link automatically realized ! post_translationally_regulated [Term] id: SO:0000891 name: negatively_autoregulated_gene def: "A gene that is negatively autoreguated." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000473 ! negatively_autoregulated relationship: has_quality SO:0000473 ! implied link automatically realized ! negatively_autoregulated [Term] id: SO:0000892 name: positively_autoregulated_gene def: "A gene that is positively autoregulated." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000475 ! positively_autoregulated relationship: has_quality SO:0000475 ! implied link automatically realized ! positively_autoregulated [Term] id: SO:0000893 name: silenced def: "An epigenetic process where a gene is innactivated at transcriptional or translational level." [SO:ke] is_a: SO:0000126 ! transcriptionally_repressed [Term] id: SO:0000894 name: silenced_by_DNA_modification def: "An epigenetic process where a gene is innactivated by DNA modifications, resulting in repression of transcription." [SO:ke] is_a: SO:0000893 ! silenced [Term] id: SO:0000895 name: silenced_by_DNA_methylation def: "An epigenetic process where a gene is innactivated by DNA methylation, resulting in repression of transcription." [SO:ke] 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] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000131 ! translationally_regulated relationship: has_quality SO:0000131 ! implied link automatically realized ! translationally_regulated [Term] id: SO:0000897 name: allelically_excluded_gene def: "A gene that is allelically_excluded." [SO:xp] is_a: SO:0000898 ! implied link automatically realized ! epigenetically_modified_gene intersection_of: SO:0000898 ! epigenetically_modified_gene intersection_of: has_quality SO:0000137 ! allelically_excluded relationship: has_quality SO:0000137 ! implied link automatically realized ! allelically_excluded [Term] id: SO:0000898 name: epigenetically_modified_gene def: "A gene that is epigenetically modified." [SO:ke] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000133 ! epigenetically_modified relationship: has_quality SO:0000133 ! implied link automatically realized ! epigenetically_modified [Term] id: SO:0000899 name: nuclear_mitochondrial def: "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke] is_a: SO:0000042 ! pseudogene_attribute [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_a: SO:0000042 ! pseudogene_attribute [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] is_a: SO:0000042 ! pseudogene_attribute [Term] id: SO:0000902 name: transgene def: "A gene that is transgenic." [SO:xp] is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000781 ! transgenic relationship: has_quality SO:0000781 ! implied link automatically realized ! transgenic [Term] id: SO:0000903 name: endogenous_retroviral_sequence 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] 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] 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] 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] 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] 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] 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 ! turn [Term] id: SO:0000913 name: cloned_cDNA_insert def: "A clone insert made from cDNA." [SO:xp] is_a: SO:0000753 ! implied link automatically realized ! clone_insert intersection_of: SO:0000753 ! clone_insert intersection_of: has_quality SO:0000756 ! cDNA relationship: has_quality SO:0000756 ! implied link automatically realized ! cDNA [Term] id: SO:0000914 name: cloned_genomic_insert def: "A clone insert made from genomic DNA." [SO:xp] is_a: SO:0000753 ! implied link automatically realized ! clone_insert intersection_of: SO:0000753 ! clone_insert intersection_of: has_quality SO:0000991 ! genomic_DNA relationship: has_quality SO:0000991 ! implied link automatically realized ! genomic_DNA [Term] id: SO:0000915 name: engineered_insert def: "A clone insert that is engineered." [SO:xp] is_a: SO:0000753 ! implied link automatically realized ! clone_insert is_a: SO:0000804 ! implied link automatically realized ! engineered_region intersection_of: SO:0000753 ! clone_insert intersection_of: has_quality SO:0000783 ! engineered [Term] id: SO:0000916 name: edit_operation is_a: SO:0000041 ! operation [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. is_a: SO:0000916 ! edit_operation [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. is_a: SO:0000916 ! edit_operation [Term] id: SO:0000919 name: substitute_A_to_I def: "An edit to substitute an I for an A." [SO:ke] is_a: SO:0000916 ! edit_operation [Term] id: SO:0000920 name: insert_C def: "An edit to insert a cytidine." [SO:ke] is_a: SO:0000916 ! edit_operation [Term] id: SO:0000921 name: insert_dinucleotide def: "An edit to insert a dinucleotide." [SO:ke] is_a: SO:0000916 ! edit_operation [Term] id: SO:0000922 name: substitute_C_to_U def: "An edit to substitute an U for a C." [SO:ke] is_a: SO:0000916 ! edit_operation [Term] id: SO:0000923 name: insert_G def: "An edit to insert a G." [SO:ke] is_a: SO:0000916 ! edit_operation [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. is_a: SO:0000921 ! insert_dinucleotide [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. is_a: SO:0000921 ! insert_dinucleotide [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. is_a: SO:0000921 ! insert_dinucleotide [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. is_a: SO:0000921 ! insert_dinucleotide [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. is_a: SO:0000921 ! insert_dinucleotide [Term] id: SO:0000929 name: edited_mRNA def: "An mRNA that is edited." [SO:xp] is_a: SO:0000873 ! implied link automatically realized ! edited_transcript intersection_of: SO:0000873 ! edited_transcript intersection_of: associated_with SO:0000916 ! edit_operation intersection_of: has_quality SO:0000116 ! edited relationship: associated_with SO:0000916 ! implied link automatically realized ! edit_operation [Term] id: SO:0000930 name: guide_RNA_region def: "A region of guide RNA." [SO:ma] is_a: SO:0000834 ! processed_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] is_a: SO:0000930 ! guide_RNA_region [Term] id: SO:0000932 name: pre_edited_mRNA 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] is_a: SO:0000409 ! binding_site [Term] id: SO:0000935 name: edited_CDS def: "A CDS that is edited." [SO:xp] is_a: SO:0000316 ! implied link automatically realized ! CDS intersection_of: SO:0000316 ! CDS intersection_of: associated_with SO:0000916 ! edit_operation intersection_of: has_quality SO:0000116 ! edited relationship: associated_with SO:0000916 ! implied link automatically realized ! edit_operation relationship: has_quality SO:0000116 ! implied link automatically realized ! edited [Term] id: SO:0000936 name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment 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 is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000939 name: vertebrate_immune_system_gene_recombination_signal_feature is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000940 name: recombinationally_rearranged 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] is_a: SO:0000456 ! implied link automatically realized ! recombinationally_rearranged_gene intersection_of: SO:0000456 ! recombinationally_rearranged_gene intersection_of: associated_with SO:0000301 ! vertebrate_immune_system_gene_recombination_feature relationship: associated_with SO:0000301 ! implied link automatically realized ! vertebrate_immune_system_gene_recombination_feature [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 [] 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 [] 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] 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 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] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_quality SO:0000352 ! DNA relationship: has_quality SO:0000352 ! implied link automatically realized ! DNA [Term] id: SO:0000955 name: double_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma] is_a: SO:0000954 ! implied link automatically realized ! DNA_chromosome intersection_of: SO:0000954 ! DNA_chromosome intersection_of: has_quality SO:0000985 ! double relationship: has_quality SO:0000985 ! implied link automatically realized ! double [Term] id: SO:0000956 name: single_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma] is_a: SO:0000954 ! implied link automatically realized ! DNA_chromosome intersection_of: SO:0000954 ! DNA_chromosome intersection_of: has_quality SO:0000984 ! single relationship: has_quality SO:0000984 ! implied link automatically realized ! 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] is_a: SO:0000955 ! implied link automatically realized ! double_stranded_DNA_chromosome intersection_of: SO:0000955 ! double_stranded_DNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! implied link automatically realized ! 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] is_a: SO:0000955 ! implied link automatically realized ! double_stranded_DNA_chromosome intersection_of: SO:0000955 ! double_stranded_DNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! implied link automatically realized ! 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] is_a: SO:0000956 ! implied link automatically realized ! single_stranded_DNA_chromosome intersection_of: SO:0000956 ! single_stranded_DNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! implied link automatically realized ! 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] is_a: SO:0000956 ! implied link automatically realized ! single_stranded_DNA_chromosome intersection_of: SO:0000956 ! single_stranded_DNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! implied link automatically realized ! circular [Term] id: SO:0000961 name: RNA_chromosome def: "Structural unit composed of a self-replicating, RNA molecule." [SO:ma] is_a: SO:0000340 ! implied link automatically realized ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_quality SO:0000356 ! RNA relationship: has_quality SO:0000356 ! implied link automatically realized ! RNA [Term] id: SO:0000962 name: single_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma] is_a: SO:0000961 ! implied link automatically realized ! RNA_chromosome intersection_of: SO:0000961 ! RNA_chromosome intersection_of: has_quality SO:0000984 ! single relationship: has_quality SO:0000984 ! implied link automatically realized ! 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] is_a: SO:0000962 ! implied link automatically realized ! single_stranded_RNA_chromosome intersection_of: SO:0000962 ! single_stranded_RNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! implied link automatically realized ! 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] is_a: SO:0000965 ! implied link automatically realized ! double_stranded_RNA_chromosome intersection_of: SO:0000965 ! double_stranded_RNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! implied link automatically realized ! linear [Term] id: SO:0000965 name: double_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma] is_a: SO:0000961 ! implied link automatically realized ! RNA_chromosome intersection_of: SO:0000961 ! RNA_chromosome intersection_of: has_quality SO:0000985 ! double relationship: has_quality SO:0000985 ! implied link automatically realized ! 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] is_a: SO:0000962 ! implied link automatically realized ! single_stranded_RNA_chromosome intersection_of: SO:0000962 ! single_stranded_RNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! implied link automatically realized ! 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] is_a: SO:0000965 ! implied link automatically realized ! double_stranded_RNA_chromosome intersection_of: SO:0000965 ! double_stranded_RNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! implied link automatically realized ! circular [Term] id: SO:0000968 name: replication_mode is_a: SO:0000000 ! Sequence_Ontology disjoint_from: SO:0001060 ! sequence_variant [Term] id: SO:0000969 name: rolling_circle is_a: SO:0000971 ! DNA_replication_mode [Term] id: SO:0000970 name: theta_replication is_a: SO:0000971 ! DNA_replication_mode [Term] id: SO:0000971 name: DNA_replication_mode is_a: SO:0000968 ! replication_mode [Term] id: SO:0000972 name: RNA_replication_mode is_a: SO:0000968 ! replication_mode [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: "IS" RELATED [] is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000974 name: minicircle_chromosome is_a: SO:0000826 ! implied link automatically realized ! kinetoplast_chromosome intersection_of: SO:0000826 ! kinetoplast_chromosome intersection_of: has_origin SO:0000980 ! minicircle_sequence relationship: has_origin SO:0000980 ! implied link automatically realized ! minicircle_sequence [Term] id: SO:0000975 name: minicircle_gene is_a: SO:0000089 ! implied link automatically realized ! kinetoplast_gene intersection_of: SO:0000089 ! kinetoplast_gene intersection_of: has_origin SO:0000980 ! minicircle_sequence relationship: has_origin SO:0000980 ! implied link automatically realized ! minicircle_sequence [Term] id: SO:0000976 name: cryptic is_a: SO:0000116 ! edited [Term] id: SO:0000977 name: anchor_binding_site comment: Part of an edited transcript only. 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 [] 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] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000980 name: minicircle_sequence is_a: SO:0000741 ! kinetoplast_sequence [Term] id: SO:0000981 name: rho_dependent_bacterial_terminator is_a: SO:0000614 ! bacterial_terminator [Term] id: SO:0000982 name: rho_independent_bacterial_terminator 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. 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. is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000987 name: linear comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. is_a: SO:0000986 ! topology_attribute disjoint_from: SO:0000988 ! circular [Term] id: SO:0000988 name: circular comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. is_a: SO:0000986 ! topology_attribute disjoint_from: SO:0000987 ! linear [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. is_a: SO:0000352 ! DNA [Term] id: SO:0000992 name: BAC_cloned_genomic_insert comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006. is_a: SO:0000914 ! implied link automatically realized ! cloned_genomic_insert intersection_of: SO:0000914 ! cloned_genomic_insert intersection_of: derives_from SO:0000153 ! BAC relationship: derives_from SO:0000153 ! implied link automatically realized ! BAC [Term] id: SO:0000993 name: consensus comment: Term added Dec 06 to comply with mapping to MGED terms.\nIt 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. is_a: SO:0000001 ! implied link automatically realized ! region intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000993 ! consensus relationship: has_quality SO:0000993 ! implied link automatically realized ! consensus [Term] id: SO:0000995 name: consensus_mRNA comment: DO not obsolete without considering MGED mapping. is_a: SO:0000234 ! implied link automatically realized ! mRNA is_a: SO:0000994 ! implied link automatically realized ! consensus_region intersection_of: SO:0000234 ! mRNA intersection_of: 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. is_a: SO:0000704 ! implied link automatically realized ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000732 ! predicted relationship: has_quality SO:0000732 ! implied link automatically realized ! predicted [Term] id: SO:0000997 name: gene_fragment comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. is_a: SO:0000842 ! implied link automatically realized ! gene_component_region intersection_of: SO:0000842 ! gene_component_region intersection_of: has_quality SO:0000731 ! fragment relationship: has_quality SO:0000731 ! implied link automatically realized ! fragment [Term] id: SO:0000998 name: recursive_splice_site def: "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] is_a: SO:0000188 ! intron [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. is_a: SO:0000695 ! reagent 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 [] 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 [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001002 name: rRNA_25S def: "A large polynucleotide which functions as\npart 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 [] 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. is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0001004 name: low_complexity is_a: SO:0000905 ! status [Term] id: SO:0001005 name: low_complexity_region is_a: SO:0000001 ! implied link automatically realized ! region intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0001004 ! low_complexity relationship: has_quality SO:0001004 ! implied link automatically realized ! 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\"." [GO:jl] 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." [GO:jl] 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] 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 [] 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: "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 [] is_a: SO:0000696 ! implied link automatically realized ! oligo intersection_of: SO:0000696 ! oligo intersection_of: has_quality SO:0001184 ! PNA relationship: has_quality SO:0001184 ! implied link automatically realized ! 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:0000695 ! reagent [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:1000005 ! complex_substitution [Term] id: SO:0001014 name: intron_domain comment: Requested by Colin Batchelor, Feb 2007. 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 pair" EXACT [] 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 [] is_a: SO:0001014 ! intron_domain relationship: part_of SO:0000587 ! group_I_intron [Term] id: SO:0001017 name: silent_mutation comment: Added in March 2007 in after meeting with pharmgkb. is_a: SO:1000132 ! mutation [Term] id: SO:0001018 name: epitope def: "A region of a macromolecule that is recognized by the immune system." [http://en.wikipedia.org/wiki/Epitope] comment: Requested by Trish Whetzel. 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] synonym: "CNP" EXACT [] synonym: "CNV" EXACT [] synonym: "copy number polymorphism" EXACT [] synonym: "copy number variation" EXACT [] is_a: SO:0001060 ! sequence_variant [Term] id: SO:0001020 name: mutation_affecting_copy_number is_a: SO:1000132 ! mutation [Term] id: SO:0001021 name: chromosome_breakpoint is_a: SO:0000830 ! chromosome_part [Term] id: SO:0001022 name: inversion_breakpoint 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] is_a: SO:0001060 ! sequence_variant 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] is_a: SO:0001060 ! sequence_variant 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] is_a: SO:0001060 ! sequence_variant [Term] id: SO:0001026 name: genome def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop] is_a: SO:0000000 ! Sequence_Ontology disjoint_from: SO:0000110 ! sequence_feature disjoint_from: SO:0000240 ! chromosome_variation disjoint_from: SO:0000400 ! sequence_attribute disjoint_from: SO:0000968 ! replication_mode disjoint_from: SO:0001060 ! sequence_variant disjoint_from: SO:1000132 ! mutation [Term] id: SO:0001027 name: genotype def: "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop] is_a: SO:0001060 ! sequence_variant 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:0001027 ! genotype [Term] id: SO:0001029 name: direction_attribute is_a: SO:0000733 ! feature_attribute [Term] id: SO:0001030 name: forward is_a: SO:0001029 ! direction_attribute [Term] id: SO:0001031 name: reverse is_a: SO:0001029 ! direction_attribute [Term] id: SO:0001032 name: mitochondrial_DNA comment: This terms is used by MO. is_a: SO:0000737 ! implied link automatically realized ! mitochondrial_sequence intersection_of: SO:0000737 ! mitochondrial_sequence intersection_of: has_quality SO:0000352 ! DNA relationship: has_quality SO:0000352 ! implied link automatically realized ! DNA [Term] id: SO:0001033 name: chloroplast_DNA comment: This term is used by MO. is_a: SO:0000745 ! implied link automatically realized ! chloroplast_sequence intersection_of: SO:0000745 ! chloroplast_sequence intersection_of: has_quality SO:0000352 ! DNA relationship: has_quality SO:0000352 ! implied link automatically realized ! DNA [Term] id: SO:0001034 name: mitron def: "An intron from whose debranched product an miRNA is derived." [SO:ma] comment: Ruby et al. Nature 448:83 desribe a new class of miRNAs that are derived from debranched introns. is_a: SO:0000276 ! implied link automatically realized ! miRNA intersection_of: SO:0000276 ! miRNA intersection_of: derives_from SO:0000188 ! intron relationship: derives_from SO:0000188 ! implied link automatically realized ! intron [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 [] 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] 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] synonym: "MGE" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001038 name: extrachromosomal_mobile_genetic_element def: "An MGE that is not integrated into the host chromosome." [SO:ke] 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] 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] is_a: SO:0001039 ! integrated_mobile_genetic_element [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 [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 [] 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 pseudogene that is nuclear/mitochondrial." [SO:xp] synonym: "nuclear mitochondrial pseudogene" EXACT [] synonym: "NUMT" EXACT [] is_a: SO:0000336 ! implied link automatically realized ! pseudogene intersection_of: SO:0000336 ! pseudogene intersection_of: has_quality SO:0000899 ! nuclear_mitochondrial relationship: has_quality SO:0000899 ! implied link automatically realized ! nuclear_mitochondrial [Term] id: SO:0001045 name: cointegrated_replicon def: "A MGE region consisting of two fused replicons/plasmids resulting from a replicative transposition event." [Phigo:at] 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] 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] 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. 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. is_a: SO:0000657 ! implied link automatically realized ! repeat_region is_a: SO:0000840 ! repeat_component intersection_of: SO:0000657 ! repeat_region intersection_of: has_quality SO:0000731 ! fragment relationship: has_quality SO:0000731 ! implied link automatically realized ! fragment [Term] id: SO:0001051 name: nested_region is_a: SO:0000001 ! region [Term] id: SO:0001052 name: nested_repeat is_a: SO:0001051 ! implied link automatically realized ! nested_region intersection_of: SO:0001051 ! nested_region intersection_of: derives_from SO:0000657 ! repeat_region intersection_of: has_part SO:0000001 ! region intersection_of: has_part SO:0001050 ! repeat_fragment relationship: derives_from SO:0000657 ! implied link automatically realized ! repeat_region relationship: has_part SO:0001050 ! implied link automatically realized ! repeat_fragment [Term] id: SO:0001053 name: nested_transposon is_a: SO:0001051 ! implied link automatically realized ! nested_region intersection_of: SO:0001051 ! nested_region intersection_of: derives_from SO:0000101 ! transposable_element intersection_of: has_part SO:0000001 ! region intersection_of: has_part SO:0001054 ! transposon_fragment relationship: derives_from SO:0000101 ! implied link automatically realized ! transposable_element relationship: has_part SO:0001054 ! implied link automatically realized ! transposon_fragment [Term] id: SO:0001054 name: transposon_fragment is_a: SO:0000101 ! implied link automatically realized ! transposable_element intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000731 ! fragment relationship: has_quality SO:0000731 ! implied link automatically realized ! fragment [Term] id: SO:0001055 name: transcriptional_cis_regulatory_region def: "A regulatory_region that modulates the transcription of a gene or genes." [SO:regcreative] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0001056 name: splicing_regulatory_region def: "A regulatory_region that modulates splicing." [SO:ke] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0001057 name: enhanceosome is_a: SO:0000165 ! enhancer [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] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0001059 name: sequence_alteration def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] 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] is_a: SO:0000000 ! Sequence_Ontology [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:0001063 ! immature_peptide_region relationship: part_of SO:0001062 ! propeptide [Term] id: SO:0001062 name: propeptide alt_id: BS:00077 def: "Describes 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 [] synonym: "propeptide" EXACT [] is_a: SO:0001063 ! immature_peptide_region [Term] id: SO:0001063 name: immature_peptide_region alt_id: BS:00129 def: "An immature_peptide_region is the a region of peptide sequence that is cleaved during maturation." [EBIBS:GAR] comment: Range. subset: biosapiens 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. Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "active_peptide" EXACT [] synonym: "peptide" EXACT [] is_a: SO:0000419 ! mature_protein_region [Term] id: SO:0001066 name: compositionally_biased_region alt_id: BS:00068 def: "Extent of a compositionally biased region. Used for homopolymeric stretches of residues and also for regions which are rich in a particular amino acid. Not used for a run of less than 4 residues." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "compbias" EXACT [] synonym: "compositional bias" EXACT [] synonym: "compositionally biased" EXACT [] 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" RELATED [] synonym: "polypeptide_motif" EXACT [] is_a: SO:0000417 ! polypeptide_domain [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 [] is_a: SO:0000417 ! polypeptide_domain [Term] id: SO:0001069 name: polypeptide_structural_domain alt_id: BS:00134 def: "A polypeptide domain is a structural domain that is self-stabilizing and folds independently of the rest of the protein chain." [EBIBS:GAR, PMID:7020376] subset: biosapiens synonym: "polypeptide_structural_domain" EXACT [] synonym: "structural domain" EXACT [] is_a: SO:0000417 ! polypeptide_domain is_a: SO:0001070 ! structural_region [Term] id: SO:0001070 name: structural_region alt_id: BS:00337 def: "Backbone conformation of the polypeptide." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "structural_region" EXACT [] 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 ! structural_region [Term] id: SO:0001072 name: extramembrane_region alt_id: BS:00154 def: "Extent of the region not transversing the lipid bilayer." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "extramembrane" EXACT [] synonym: "topo_dom" EXACT [] is_a: SO:0001070 ! structural_region relationship: part_of SO:0001071 ! membrane_structure [Term] id: SO:0001073 name: cytoplasmic_region alt_id: BS:00145 def: "Region of the peptide in the cytoplasm." [EBIBS:GAR] subset: biosapiens synonym: "cytoplasm_location" EXACT [] synonym: "inside" RELATED [] is_a: SO:0001072 ! extramembrane_region [Term] id: SO:0001074 name: non_cytoplasmic_region alt_id: BS:00144 def: "Region of peptide not in the cytoplasm. N.B. This could be inside an organelle within the cell." [EBIBS:GAR] subset: biosapiens synonym: "non_cytoplasm_location" EXACT [] synonym: "outside" RELATED [] is_a: SO:0001072 ! extramembrane_region [Term] id: SO:0001075 name: intramembrane_region alt_id: BS:00156 def: "Extent of the region present in the lipid bilayer." [EBIBS:GAR] subset: biosapiens synonym: "intramembrane" EXACT [] is_a: SO:0001070 ! structural_region relationship: part_of SO:0001071 ! membrane_structure [Term] id: SO:0001076 name: membrane_loop alt_id: BS:00155 def: "Extent of region which enters the membrane bilayer but emerges on the same side which it entered." [EBIBS:GAR] subset: biosapiens synonym: "membrane_loop" EXACT [] is_a: SO:0001075 ! intramembrane_region [Term] id: SO:0001077 name: transmembrane_region alt_id: BS:00158 def: "Extent of region transversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual] subset: biosapiens synonym: "transmem" RELATED [] synonym: "transmembrane" EXACT [] is_a: SO:0001075 ! intramembrane_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" EXACT [] synonym: "secondary structure" EXACT [] synonym: "secondary structure region" RELATED [] synonym: "secondary_structure" EXACT [] is_a: SO:0001070 ! 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: "structural_motif" EXACT [] is_a: SO:0001070 ! 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 [] synonym: "coiled_coil" EXACT [] 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: "DNA binding motif" RELATED [] synonym: "helix_turn_helix" EXACT [] synonym: "HTH" EXACT [] is_a: SO:0001079 ! polypeptide_structural_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_adjacent_residues" EXACT [] synonym: "non_cons" EXACT [] 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 [] synonym: "non_terminal_residue" EXACT [] 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 [] synonym: "sequence_conflict" EXACT [] 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: "sequence_uncertainty" EXACT [] synonym: "unsure" RELATED [] 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: "disulfide_bond" EXACT [] 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:GAM, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "mod_res" RELATED [] synonym: "modified residue" EXACT [] synonym: "post_translational_modification" EXACT [] is_a: SO:0100001 ! biochemical_region [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: metal_contact alt_id: BS:00027 def: "Residue is part of a binding site for a metal ion." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "metal" RELATED [] synonym: "metal_binding" EXACT [] is_a: SO:0000409 ! binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001093 name: protein_protein_contact alt_id: BS:00131 def: "Residues involved in protein-protein interactions." [EBIBS:GAR, UniProt:Curation_manual] subset: biosapiens synonym: "protein_protein_interaction" EXACT [] is_a: SO:0000409 ! binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001094 name: Ca_contact_site alt_id: BS:00186 def: "Residue involved in contact with calcium." [EBIBS:GAR] subset: biosapiens synonym: "ca bind" EXACT [] synonym: "Ca_contact_site" EXACT [] is_a: SO:0001092 ! metal_contact [Term] id: SO:0001095 name: Co_contact_site alt_id: BS:00136 def: "Residue involved in contact with cobalt." [EBIBS:GAR] subset: biosapiens synonym: "Co_contact_site" EXACT [] is_a: SO:0001092 ! metal_contact [Term] id: SO:0001096 name: Cu_contact_site alt_id: BS:00146 def: "Residue involved in contact with copper." [EBIBS:GAR] subset: biosapiens synonym: "Cu_contact_site" EXACT [] is_a: SO:0001092 ! metal_contact [Term] id: SO:0001097 name: Fe_contact_site alt_id: BS:00137 def: "Residue involved in contact with iron." [EBIBS:GAR] subset: biosapiens synonym: "Fe_contact_site" EXACT [] is_a: SO:0001092 ! metal_contact [Term] id: SO:0001098 name: Mg_contact_site alt_id: BS:00187 def: "Residue involved in contact with magnesium." [EBIBS:GAR] subset: biosapiens synonym: "Mg_contact_site" EXACT [] is_a: SO:0001092 ! metal_contact [Term] id: SO:0001099 name: Mn_contact_site alt_id: BS:00140 def: "Residue involved in contact with manganese." [EBIBS:GAR] subset: biosapiens synonym: "Mn_contact_site" EXACT [] is_a: SO:0001092 ! metal_contact [Term] id: SO:0001100 name: Mo_contact_site alt_id: BS:00141 def: "Residue involved in contact with molybdenum." [EBIBS:GAR] subset: biosapiens synonym: "Mo_contact_site" EXACT [] is_a: SO:0001092 ! metal_contact [Term] id: SO:0001101 name: Ni_contact_site alt_id: BS:00142 def: "Residue involved in contact with nickel." [EBIBS:GAR] subset: biosapiens synonym: "Ni_contact_site" EXACT [] is_a: SO:0001092 ! metal_contact [Term] id: SO:0001102 name: W_contact_site alt_id: BS:00143 def: "Residue involved in contact with tungsten." [EBIBS:GAR] subset: biosapiens synonym: "W_contact_site" EXACT [] is_a: SO:0001092 ! metal_contact [Term] id: SO:0001103 name: Zn_contact_site alt_id: BS:00185 def: "Residue involved in contact with zinc." [EBIBS:GAR] subset: biosapiens synonym: "Zn_contact_site" EXACT [] is_a: SO:0001092 ! 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 [] synonym: "active site residue" EXACT [] synonym: "site" BROAD [] is_a: SO:0100001 ! biochemical_region [Term] id: SO:0001105 name: protein_ligand_contact alt_id: BS:00157 def: "Residues which interact with a ligand." [EBIBS:GAR] subset: biosapiens synonym: "protein-ligand interaction" EXACT [] is_a: SO:0000409 ! 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 [] 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: "beta_strand" EXACT [] synonym: "strand" RELATED [] 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: 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" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001115 name: left_handed_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 ! helix [Term] id: SO:0001116 name: right_handed_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 [] synonym: "right handed helix" EXACT [] is_a: SO:0001114 ! 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" EXACT [] synonym: "alpha_helix" EXACT [] synonym: "helix" RELATED [] is_a: SO:0001116 ! right_handed_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 [] is_a: SO:0001116 ! right_handed_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 [] is_a: SO:0001116 ! right_handed_helix [Term] id: SO:0001120 name: nest 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" EXACT [] synonym: "nest_motif" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001121 name: nest_left_right 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 [] is_a: SO:0001120 ! nest [Term] id: SO:0001122 name: nest_right_left 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 [] is_a: SO:0001120 ! nest [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 [] 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: st_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: "st_motif" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001127 name: st_staple 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: "st_staple" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001128 name: turn 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] comment: Range. subset: biosapiens synonym: "turn" EXACT [] 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_il" RELATED [] synonym: "asx_turn_left_handed_type_one" EXACT [] 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_iil" EXACT [] synonym: "asx_turn_left_handed_type_two" 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_iir" EXACT [] synonym: "asx_turn_right_handed_type_two" EXACT [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001132 name: asx_turn_type_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:GAM, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx_turn_ir" EXACT [] synonym: "asx_turn_type_right_handed_type_one" 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 ! turn [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_il" EXACT [] synonym: "beta_turn_left_handed_type_one" 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_iil" EXACT [] synonym: "beta_turn_left_handed_type_two" 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_ir" EXACT [] synonym: "beta_turn_right_handed_type_one" 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_iir" EXACT [] synonym: "beta_turn_right_handed_type_two" 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 ! turn [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: st_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:GAM, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st_turn" EXACT [] is_a: SO:0001128 ! turn [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_il" EXACT [] synonym: "st_turn_left_handed_type_one" EXACT [] is_a: SO:0001141 ! st_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_iil" EXACT [] synonym: "st_turn_left_handed_type_two" EXACT [] is_a: SO:0001141 ! st_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_ir" EXACT [] synonym: "st_turn_right_handed_type_one" EXACT [] is_a: SO:0001141 ! st_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_iir" EXACT [] synonym: "st_turn_right_handed_type_two" EXACT [] is_a: SO:0001141 ! st_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" EXACT [] synonym: "sequence variation" RELATED [] synonym: "variant" RELATED [] 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" RELATED [] synonym: "mutagenesis" RELATED [] 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" RELATED [] synonym: "var_seq" RELATED [] synonym: "varsplic" NARROW [] is_a: SO:0001146 ! polypeptide_variation_site [Term] id: SO:0001150 name: beta_turn_type_six subset: biosapiens 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 subset: biosapiens synonym: "Type VI a beta turn" EXACT [] synonym: "Type VI a turn" EXACT [] is_a: SO:0001150 ! beta_turn_type_six [Term] id: SO:0001152 name: beta_turn_type_six_a_one subset: biosapiens synonym: "Type VI a1 beta turn" EXACT [] synonym: "Type VI a1 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: "Type VI a2 beta turn" EXACT [] synonym: "Type VI a2 turn" EXACT [] is_a: SO:0001151 ! beta_turn_type_six_a [Term] id: SO:0001154 name: beta_turn_type_six_b subset: biosapiens synonym: "Type VI b beta turn" EXACT [] synonym: "Type VI b turn" EXACT [] is_a: SO:0001150 ! beta_turn_type_six [Term] id: SO:0001155 name: beta_turn_type_eight subset: biosapiens 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\nalgorithm within core promoter sequences from -60 to +40, with an E value\nof 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10. synonym: "NDM4" EXACT [] synonym: "WATCGATW_motif" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [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: "motif 1 element" EXACT [] synonym: "promoter motif 1" EXACT [] synonym: "YGGTCACATR" NARROW [] is_a: SO:0000844 ! RNApol_II_promoter_region [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:0000844 ! RNApol_II_promoter_region [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: "KTYRGTATWTTT" NARROW [] synonym: "promoter motif 6" RELATED [] is_a: SO:0000844 ! RNApol_II_promoter_region [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: "KNNCAKCNCTRNY" NARROW [] synonym: "promoter motif 7" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [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: "MKSYGGCARCGSYSS" NARROW [] synonym: "promoter motif 8" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [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] synonym: "CSARCSSAACGS" NARROW [] synonym: "motif ten element" EXACT [] synonym: "motif_ten_element" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [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 [] is_a: SO:0000844 ! RNApol_II_promoter_region [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 [] is_a: SO:0000844 ! RNApol_II_promoter_region [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 [] is_a: SO:0000844 ! RNApol_II_promoter_region [Term] id: SO:0001166 name: GAGA_motif def: "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941] synonym: "GAGA" EXACT [] synonym: "NDM1" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [Term] id: SO:0001167 name: NDM2_motif def: "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941] synonym: "NDM2" EXACT [] synonym: "non directional promoter motif 2" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [Term] id: SO:0001168 name: NDM3_motif def: "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941] synonym: "NDM3" EXACT [] synonym: "non directional motif 3" EXACT [] is_a: SO:0000844 ! RNApol_II_promoter_region [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 [] 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 [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001172 name: tRNA_region def: "A region of a tRNA." [RSC:cb] is_a: SO:0000834 ! processed_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 [] 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 [] 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 [] 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 [] 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: "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] 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 [] 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 [] 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 [] 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 [] is_a: SO:0000837 ! UTR_region [Term] id: SO:0001183 name: morpholino 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. 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. 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:0000237 ! transcript_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). 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: "locked nucleic acid" EXACT [] is_a: SO:0000696 ! implied link automatically realized ! oligo intersection_of: SO:0000696 ! oligo intersection_of: has_quality SO:0001188 ! LNA relationship: has_quality SO:0001188 ! implied link automatically realized ! 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 [] is_a: SO:0000696 ! implied link automatically realized ! oligo intersection_of: SO:0000696 ! oligo intersection_of: has_quality SO:0001190 ! TNA relationship: has_quality SO:0001190 ! implied link automatically realized ! 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 [] is_a: SO:0000696 ! implied link automatically realized ! oligo intersection_of: SO:0000696 ! oligo intersection_of: has_quality SO:0001192 ! GNA relationship: has_quality SO:0001192 ! implied link automatically realized ! 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. 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 [] is_a: SO:0001193 ! implied link automatically realized ! GNA_oligo intersection_of: SO:0001193 ! GNA_oligo intersection_of: has_quality SO:0001194 ! R_GNA relationship: has_quality SO:0001194 ! implied link automatically realized ! 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. 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 [] is_a: SO:0001193 ! implied link automatically realized ! GNA_oligo intersection_of: SO:0001193 ! GNA_oligo intersection_of: has_quality SO:0001196 ! S_GNA relationship: has_quality SO:0001196 ! implied link automatically realized ! 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 [] 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 [] 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 [] 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 [] 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 [] 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\ntranscription." [xenbase:jb] is_a: SO:0000167 ! promoter [Term] id: SO:0001204 name: Phage_RNA_Polymerase_Promoter def: "Aregion (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb] 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] 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] 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] 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 [] 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\nlikely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] synonym: "3' EST" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0005836 name: regulatory_region def: "A DNA sequence that controls the expression of a gene." [http://www.genpromag.com/scripts/glossary.asp?LETTER=R] subset: SOFA is_a: SO:0000831 ! gene_member_region [Term] id: SO:0005837 name: U14_snoRNA_primary_transcript def: "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119] synonym: "4.5S snRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0005841 name: methylation_guide_snoRNA def: "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565] comment: Has RNA 2'-O-ribose methylation guide activity (GO:0030561). is_a: SO:0000593 ! C_D_box_snoRNA relationship: derives_from SO:0000580 ! methylation_guide_snoRNA_primary_transcript [Term] id: SO:0005843 name: rRNA_cleavage_RNA def: "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc] is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000582 ! rRNA_cleavage_snoRNA_primary_transcript [Term] id: SO:0005845 name: exon_of_single_exon_gene def: "An exon that is the only exon in a gene." [RSC:cb] synonym: "single_exon" RELATED [] synonym: "singleton exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0005847 name: cassette_array_member is_a: SO:0005848 ! gene_cassette_member [Term] id: SO:0005848 name: gene_cassette_member is_a: SO:0000081 ! gene_array_member [Term] id: SO:0005849 name: gene_subarray_member is_a: SO:0000081 ! gene_array_member [Term] id: SO:0005850 name: primer_binding_site def: "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http:www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] is_a: SO:0000409 ! binding_site relationship: part_of SO:0000186 ! LTR_retrotransposon [Term] id: SO:0005851 name: gene_array def: "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma] comment: This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays. is_a: SO:0005855 ! gene_group [Term] id: SO:0005852 name: gene_subarray def: "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma] comment: This would include, for example, a cluster of genes encoding different histones. is_a: SO:0005855 ! gene_group [Term] id: SO:0005853 name: gene_cassette def: "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se] comment: This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid. is_a: SO:0000704 ! gene [Term] id: SO:0005854 name: gene_cassette_array def: "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma] comment: This would include, for example, the arrays of non-functional VSG genes of Trypanosomes. is_a: SO:0005855 ! gene_group relationship: has_part SO:0005853 ! gene_cassette [Term] id: SO:0005855 name: gene_group def: "A collection of related genes." [SO:ma] subset: SOFA is_a: SO:0000001 ! region [Term] id: SO:0005856 name: selenocysteine_tRNA_primary_transcript def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0005857 name: selenocysteinyl_tRNA def: "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke] synonym: "selenocysteinyl-transfer ribonucleic acid" EXACT [] synonym: "selenocysteinyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0005856 ! selenocysteine_tRNA_primary_transcript [Term] id: SO:0005858 name: syntenic_region def: "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://tbase.jax.org/docs/glossary.html] is_a: SO:0000853 ! implied link automatically realized ! homologous_region intersection_of: SO:0000330 ! conserved_region intersection_of: has_quality SO:0000860 ! syntenic relationship: has_quality SO:0000860 ! implied link automatically realized ! syntenic [Term] id: SO:0100001 name: biochemical_region def: "A region that is involved in a biochemical function." [EBIBS:GAR] comment: Range. subset: biosapiens is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0100002 name: molecular_contact_region def: "A region that is involved a contact with another molecule." [EBIBS:GAR] comment: Range. subset: biosapiens is_a: SO:0100001 ! biochemical_region [Term] id: SO:1000002 name: substitution def: "Any change in genomic DNA caused by a single event." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] subset: SOFA is_a: SO:0000001 ! region is_a: SO:0001059 ! sequence_alteration relationship: sequence_of SO:0000048 ! substitute [Term] id: SO:1000004 name: partially_characterised_change_in_DNA_sequence def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000007 ! uncharacterised_change_in_nucleotide_sequence [Term] id: SO:1000005 name: complex_substitution def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] subset: SOFA is_a: SO:1000002 ! substitution [Term] id: SO:1000007 name: uncharacterised_change_in_nucleotide_sequence def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000002 ! substitution [Term] id: SO:1000008 name: point_mutation def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop] subset: SOFA is_a: SO:1000002 ! substitution [Term] id: SO:1000009 name: transition def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000008 ! point_mutation [Term] id: SO:1000010 name: pyrimidine_transition def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke] is_a: SO:1000009 ! transition [Term] id: SO:1000011 name: C_to_T_transition def: "A transition of a cytidine to a thymine." [SO:ke] is_a: SO:1000010 ! pyrimidine_transition [Term] id: SO:1000012 name: C_to_T_transition_at_pCpG_site def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000011 ! C_to_T_transition [Term] id: SO:1000013 name: T_to_C_transition is_a: SO:1000010 ! pyrimidine_transition [Term] id: SO:1000014 name: purine_transition def: "A substitution of a purine, A or G, for another purine." [SO:ke] is_a: SO:1000009 ! transition [Term] id: SO:1000015 name: A_to_G_transition def: "A transition of an adenine to a guanine." [SO:ke] is_a: SO:1000014 ! purine_transition [Term] id: SO:1000016 name: G_to_A_transition def: "A transition of a guanine to an adenine." [SO:ke] is_a: SO:1000014 ! purine_transition [Term] id: SO:1000017 name: transversion def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000008 ! point_mutation [Term] id: SO:1000018 name: pyrimidine_to_purine_transversion def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke] is_a: SO:1000017 ! transversion [Term] id: SO:1000019 name: C_to_A_transversion def: "A transversion from cytidine to adenine." [SO:ke] is_a: SO:1000018 ! pyrimidine_to_purine_transversion [Term] id: SO:1000020 name: C_to_G_transversion is_a: SO:1000018 ! pyrimidine_to_purine_transversion [Term] id: SO:1000021 name: T_to_A_transversion def: "A transversion from T to A." [SO:ke] is_a: SO:1000018 ! pyrimidine_to_purine_transversion [Term] id: SO:1000022 name: T_to_G_transversion def: "A transversion from T to G." [SO:ke] is_a: SO:1000018 ! pyrimidine_to_purine_transversion [Term] id: SO:1000023 name: purine_to_pyrimidine_transversion def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke] is_a: SO:1000017 ! transversion [Term] id: SO:1000024 name: A_to_C_transversion def: "A transversion from adenine to cytidine." [SO:ke] is_a: SO:1000023 ! purine_to_pyrimidine_transversion [Term] id: SO:1000025 name: A_to_T_transversion def: "A transversion from adenine to thymine." [SO:ke] is_a: SO:1000023 ! purine_to_pyrimidine_transversion [Term] id: SO:1000026 name: G_to_C_transversion def: "A transversion from guanine to cytidine." [SO:ke] is_a: SO:1000023 ! purine_to_pyrimidine_transversion [Term] id: SO:1000027 name: G_to_T_transversion def: "A transversion from guanine to thymine." [SO:ke] is_a: SO:1000023 ! purine_to_pyrimidine_transversion [Term] id: SO:1000028 name: intrachromosomal_mutation is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:1000029 name: chromosomal_deletion def: "An incomplete chromosome." [SO:ke] synonym: "(bacteria)&Dgr;" RELATED [] synonym: "(Drosophila)Df" RELATED [] synonym: "(fungi)D" RELATED [] is_a: SO:0000550 ! aneuploid_chromosome is_a: SO:1000028 ! intrachromosomal_mutation [Term] id: SO:1000030 name: chromosomal_inversion synonym: "(bacteria)IN" RELATED [] synonym: "(Drosophila)In" RELATED [] synonym: "(fungi)In" RELATED [] is_a: SO:1000028 ! intrachromosomal_mutation [Term] id: SO:1000031 name: interchromosomal_mutation is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:1000032 name: indel def: "A hybrid term (insertion/deletion) to describe sequence length change when the direction of the change is unspecified." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:0001059 ! sequence_alteration [Term] id: SO:1000033 name: nucleotide_deletion def: "One or more continuous nucleotides are excised from the sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000032 ! indel [Term] id: SO:1000034 name: nucleotide_insertion def: "One or more nucleotides are added between two adjacent nucleotides in the sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000032 ! indel [Term] id: SO:1000035 name: nucleotide_duplication def: "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000034 ! nucleotide_insertion [Term] id: SO:1000036 name: inversion def: "A continuous nucleotide sequence is inverted in the same position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] subset: SOFA is_a: SO:0000001 ! region is_a: SO:0001059 ! sequence_alteration relationship: sequence_of SO:0000047 ! invert [Term] id: SO:1000037 name: chromosomal_duplication def: "An extra chromosome." [SO:ke] synonym: "(Drosophila)Dp" RELATED [] synonym: "(fungi)Dp" RELATED [] is_a: SO:0000550 ! aneuploid_chromosome [Term] id: SO:1000038 name: intrachromosomal_duplication is_a: SO:1000028 ! intrachromosomal_mutation is_a: SO:1000037 ! chromosomal_duplication [Term] id: SO:1000039 name: direct_tandem_duplication is_a: SO:1000173 ! tandem_duplication [Term] id: SO:1000040 name: inverted_tandem_duplication is_a: SO:1000173 ! tandem_duplication [Term] id: SO:1000041 name: intrachromosomal_transposition synonym: "(Drosophila)Tp" RELATED [] is_a: SO:0000453 ! transposition is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:1000042 name: compound_chromosome is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:1000043 name: Robertsonian_fusion is_a: SO:1000044 ! chromosomal_translocation [Term] id: SO:1000044 name: chromosomal_translocation synonym: "(Drosophila)T" RELATED [] synonym: "(fungi)T" RELATED [] is_a: SO:1000031 ! interchromosomal_mutation [Term] id: SO:1000045 name: ring_chromosome synonym: "(Drosophila)R" RELATED [] synonym: "(fungi)C" RELATED [] is_a: SO:1000028 ! intrachromosomal_mutation [Term] id: SO:1000046 name: pericentric_inversion is_a: SO:1000030 ! chromosomal_inversion [Term] id: SO:1000047 name: paracentric_inversion is_a: SO:1000030 ! chromosomal_inversion [Term] id: SO:1000048 name: reciprocal_chromosomal_translocation is_a: SO:1000044 ! chromosomal_translocation [Term] id: SO:1000049 name: mutation_affecting_transcript def: "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000132 ! mutation [Term] id: SO:1000050 name: mutation_causing_no_change_in_transcript def: "No effect on the state of the RNA." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000049 ! mutation_affecting_transcript [Term] id: SO:1000052 name: mutation_affecting_complex_change_in_transcript is_a: SO:1000049 ! mutation_affecting_transcript [Term] id: SO:1000054 name: mutation_affecting_coding_sequence def: "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000079 ! mutation_affecting_transcript_sequence [Term] id: SO:1000055 name: mutation_causing_initiator_codon_change_in_transcript def: "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000056 ! mutation_causing_amino_acid_coding_codon_change_in_transcript [Term] id: SO:1000056 name: mutation_causing_amino_acid_coding_codon_change_in_transcript def: "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000054 ! mutation_affecting_coding_sequence [Term] id: SO:1000057 name: mutation_causing_synonymous_codon_change_in_transcript def: "The changed codon has the same translation product as the original codon." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000056 ! mutation_causing_amino_acid_coding_codon_change_in_transcript [Term] id: SO:1000058 name: mutation_causing_non_synonymous_codon_change_in_transcript def: "A DNA point mutation that causes a substitution of an amino acid by an other." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "non-synonymous codon change in transcript" EXACT [] is_a: SO:1000056 ! mutation_causing_amino_acid_coding_codon_change_in_transcript [Term] id: SO:1000059 name: mutation_causing_missense_codon_change_in_transcript def: "The nucleotide change in the codon leads to a new codon coding for a new amino acid." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000058 ! mutation_causing_non_synonymous_codon_change_in_transcript [Term] id: SO:1000060 name: mutation_causing_conservative_missense_codon_change_in_transcript def: "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix. is_a: SO:1000059 ! mutation_causing_missense_codon_change_in_transcript [Term] id: SO:1000061 name: mutation_causing_nonconservative_missense_codon_change_in_transcript def: "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix. is_a: SO:1000059 ! mutation_causing_missense_codon_change_in_transcript [Term] id: SO:1000062 name: mutation_causing_nonsense_codon_change_in_transcript def: "The nucleotide change in the codon triplet creates a terminator codon." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000056 ! mutation_causing_amino_acid_coding_codon_change_in_transcript [Term] id: SO:1000063 name: mutation_causing_terminator_codon_change_in_transcript def: "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence." [SO:ke] is_a: SO:1000054 ! mutation_affecting_coding_sequence [Term] id: SO:1000064 name: mutation_affecting_reading_frame def: "An umbrella term for terms describing an effect of a mutation on the frame of translation." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000054 ! mutation_affecting_coding_sequence [Term] id: SO:1000065 name: frameshift_mutation def: "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke] synonym: "out of frame mutation" RELATED [] is_a: SO:1000064 ! mutation_affecting_reading_frame [Term] id: SO:1000066 name: plus_1_frameshift_mutation def: "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide." [SO:ke] is_a: SO:1000065 ! frameshift_mutation [Term] id: SO:1000067 name: minus_1_frameshift_mutation def: "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide." [SO:ke] is_a: SO:1000065 ! frameshift_mutation [Term] id: SO:1000068 name: plus_2_frameshift_mutation def: "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides." [SO:ke] is_a: SO:1000065 ! frameshift_mutation [Term] id: SO:1000069 name: minus_2_frameshift_mutation def: "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides." [SO:ke] is_a: SO:1000065 ! frameshift_mutation [Term] id: SO:1000070 name: mutation_affecting_transcript_processing def: "Mutation affects the way in which the primary transcriptional product is processed to form the mature transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000079 ! mutation_affecting_transcript_sequence [Term] id: SO:1000071 name: mutation_affecting_splicing def: "A mutation that affects the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000132 ! mutation [Term] id: SO:1000072 name: splice_donor_mutation def: "A mutation that affects the splice donor sequence." [SO:ke] is_a: SO:1000071 ! mutation_affecting_splicing [Term] id: SO:1000073 name: splice_acceptor_mutation def: "A mutation that affects the splice acceptor sequence." [SO:ke] is_a: SO:1000071 ! mutation_affecting_splicing [Term] id: SO:1000074 name: cryptic_splice_activator_mutation def: "A kind of mutation that creates a new (functional) splice site." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000071 ! mutation_affecting_splicing [Term] id: SO:1000075 name: mutation_affecting_editing def: "Mutation affects the editing of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000070 ! mutation_affecting_transcript_processing [Term] id: SO:1000076 name: mutation_affecting_transcription def: "Mutation affects the process of transcription, its initiation, progression or termination." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000049 ! mutation_affecting_transcript [Term] id: SO:1000078 name: mutation_decreasing_rate_of_transcription def: "A mutation that decreases the rate a which transcription of the sequence occurs." [SO:ke] is_a: SO:1000081 ! mutation_affecting_rate_of_transcription [Term] id: SO:1000079 name: mutation_affecting_transcript_sequence is_a: SO:1000049 ! mutation_affecting_transcript [Term] id: SO:1000080 name: mutation_increasing_rate_of_transcription is_a: SO:1000081 ! mutation_affecting_rate_of_transcription [Term] id: SO:1000081 name: mutation_affecting_rate_of_transcription def: "A mutation that alters the rate a which transcription of the sequence occurs." [SO:ke] is_a: SO:1000076 ! mutation_affecting_transcription [Term] id: SO:1000082 name: mutation_affecting_transcript_stability def: "Mutation affects the stability of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000079 ! mutation_affecting_transcript_sequence [Term] id: SO:1000083 name: mutation_increasing_transcript_stability def: "Mutation increases the stability (half-life) of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000082 ! mutation_affecting_transcript_stability [Term] id: SO:1000084 name: mutation_decreasing_transcript_stability def: "Mutation decreases the stability (half-life) of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000082 ! mutation_affecting_transcript_stability [Term] id: SO:1000085 name: mutation_affecting_level_of_transcript def: "A mutation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] is_a: SO:1000049 ! mutation_affecting_transcript [Term] id: SO:1000086 name: mutation_decreasing_level_of_transcript def: "A mutation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] is_a: SO:1000085 ! mutation_affecting_level_of_transcript [Term] id: SO:1000087 name: mutation_increasing_level_of_transcript def: "A mutation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] is_a: SO:1000085 ! mutation_affecting_level_of_transcript [Term] id: SO:1000088 name: mutation_affecting_translational_product def: "Mutation causes a change in primary translation product of a transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000132 ! mutation [Term] id: SO:1000089 name: mutation_causing_no_change_of_translational_product def: "The change at RNA level does not lead to any change in polypeptide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000088 ! mutation_affecting_translational_product [Term] id: SO:1000090 name: mutation_causing_uncharacterised_change_of_translational_product def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000088 ! mutation_affecting_translational_product [Term] id: SO:1000091 name: mutation_causing_partially_characterised_change_of_translational_product def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000090 ! mutation_causing_uncharacterised_change_of_translational_product [Term] id: SO:1000092 name: mutation_causing_complex_change_of_translational_product def: "Any mutation effect that is known at nucleotide level but cannot be explained by using other key terms." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000088 ! mutation_affecting_translational_product [Term] id: SO:1000093 name: mutation_causing_amino_acid_substitution def: "The replacement of a single amino acid by another." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence [Term] id: SO:1000094 name: mutation_causing_conservative_amino_acid_substitution is_a: SO:1000093 ! mutation_causing_amino_acid_substitution [Term] id: SO:1000095 name: mutation_causing_nonconservative_amino_acid_substitution is_a: SO:1000093 ! mutation_causing_amino_acid_substitution [Term] id: SO:1000096 name: mutation_causing_amino_acid_insertion def: "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence [Term] id: SO:1000097 name: mutation_causing_amino_acid_deletion def: "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence [Term] id: SO:1000098 name: mutation_causing_polypeptide_truncation def: "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence [Term] id: SO:1000099 name: mutation_causing_polypeptide_elongation def: "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence [Term] id: SO:1000100 name: mutation_causing_polypeptide_N_terminal_elongation def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "polypeptide N-terminal elongation" EXACT [] is_a: SO:1000099 ! mutation_causing_polypeptide_elongation [Term] id: SO:1000101 name: mutation_causing_polypeptide_C_terminal_elongation def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "polypeptide C-terminal elongation" EXACT [] is_a: SO:1000099 ! mutation_causing_polypeptide_elongation [Term] id: SO:1000102 name: mutation_affecting_level_of_translational_product is_a: SO:1000088 ! mutation_affecting_translational_product [Term] id: SO:1000103 name: mutation_decreasing_level_of_translation_product is_a: SO:1000102 ! mutation_affecting_level_of_translational_product [Term] id: SO:1000104 name: mutation_increasing_level_of_translation_product is_a: SO:1000102 ! mutation_affecting_level_of_translational_product [Term] id: SO:1000105 name: mutation_affecting_polypeptide_amino_acid_sequence is_a: SO:1000088 ! mutation_affecting_translational_product [Term] id: SO:1000106 name: mutation_causing_inframe_polypeptide_N_terminal_elongation synonym: "inframe polypeptide N-terminal elongation" EXACT [] is_a: SO:1000100 ! mutation_causing_polypeptide_N_terminal_elongation [Term] id: SO:1000107 name: mutation_causing_out_of_frame_polypeptide_N_terminal_elongation synonym: "out of frame polypeptide N-terminal elongation" EXACT [] is_a: SO:1000100 ! mutation_causing_polypeptide_N_terminal_elongation [Term] id: SO:1000108 name: mutaton_causing_inframe_polypeptide_C_terminal_elongation synonym: "inframe_polypeptide C-terminal elongation" EXACT [] is_a: SO:1000101 ! mutation_causing_polypeptide_C_terminal_elongation [Term] id: SO:1000109 name: mutation_causing_out_of_frame_polypeptide_C_terminal_elongation synonym: "out of frame polypeptide C-terminal elongation" EXACT [] is_a: SO:1000101 ! mutation_causing_polypeptide_C_terminal_elongation [Term] id: SO:1000110 name: frame_restoring_mutation def: "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke] is_a: SO:1000065 ! frameshift_mutation [Term] id: SO:1000111 name: mutation_affecting_3D_structure_of_polypeptide def: "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule." [SO:ke] synonym: "mutation affecting 3D-structure of polypeptide" EXACT [] is_a: SO:1000088 ! mutation_affecting_translational_product [Term] id: SO:1000112 name: mutation_causing_no_3D_structural_change is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide [Term] id: SO:1000113 name: mutation_causing_uncharacterised_3D_structural_change is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide [Term] id: SO:1000114 name: mutation_causing_partially_characterised_3D_structural_change is_a: SO:1000113 ! mutation_causing_uncharacterised_3D_structural_change [Term] id: SO:1000115 name: mutation_causing_complex_3D_structural_change is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide [Term] id: SO:1000116 name: mutation_causing_conformational_change is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide [Term] id: SO:1000117 name: mutation_affecting_polypeptide_function is_a: SO:1000088 ! mutation_affecting_translational_product [Term] id: SO:1000118 name: mutation_causing_loss_of_function_of_polypeptide synonym: "loss of function of polypeptide" RELATED [] is_a: SO:1000117 ! mutation_affecting_polypeptide_function [Term] id: SO:1000119 name: mutation_causing_inactive_ligand_binding_site is_a: SO:1000118 ! mutation_causing_loss_of_function_of_polypeptide [Term] id: SO:1000120 name: mutation_causing_inactive_catalytic_site is_a: SO:1000119 ! mutation_causing_inactive_ligand_binding_site [Term] id: SO:1000121 name: mutation_causing_polypeptide_localization_change is_a: SO:1000117 ! mutation_affecting_polypeptide_function [Term] id: SO:1000122 name: mutation_causing_polypeptide_post_translational_processing_change synonym: "polypeptide post-translational processing affected" EXACT [] is_a: SO:1000117 ! mutation_affecting_polypeptide_function is_a: SO:1000118 ! mutation_causing_loss_of_function_of_polypeptide [Term] id: SO:1000123 name: polypeptide_post_translational_processing_affected synonym: "polypeptide_post-translational_processing_affected" RELATED [] is_obsolete: true [Term] id: SO:1000124 name: mutation_causing_partial_loss_of_function_of_polypeptide synonym: "partial loss of function of polypeptide" EXACT [] is_a: SO:1000118 ! mutation_causing_loss_of_function_of_polypeptide [Term] id: SO:1000125 name: mutation_causing_gain_of_function_of_polypeptide synonym: "gain of function of polypeptide" EXACT [] is_a: SO:1000117 ! mutation_affecting_polypeptide_function [Term] id: SO:1000126 name: mutation_affecting_transcript_secondary_structure def: "A mutation that affects the secondary structure (folding) of the RNA transcript molecule." [SO:ke] is_a: SO:1000079 ! mutation_affecting_transcript_sequence [Term] id: SO:1000127 name: mutation_causing_compensatory_transcript_secondary_structure_mutation is_a: SO:1000126 ! mutation_affecting_transcript_secondary_structure [Term] id: SO:1000132 name: mutation def: "An event that changes nucleotide sequence." [SO:ke] is_a: SO:0000000 ! Sequence_Ontology disjoint_from: SO:0000041 ! operation disjoint_from: SO:0000110 ! sequence_feature disjoint_from: SO:0000240 ! chromosome_variation disjoint_from: SO:0000400 ! sequence_attribute disjoint_from: SO:0000968 ! replication_mode disjoint_from: SO:0001060 ! sequence_variant [Term] id: SO:1000134 name: mutation_causing_polypeptide_fusion is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence [Term] id: SO:1000136 name: autosynaptic_chromosome synonym: "(Drosophila)A" RELATED [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:1000138 name: homo_compound_chromosome synonym: "homo-compound chromosome" EXACT [] is_a: SO:1000042 ! compound_chromosome [Term] id: SO:1000140 name: hetero_compound_chromosome synonym: "hetero-compound chromosome" EXACT [] is_a: SO:1000042 ! compound_chromosome [Term] id: SO:1000141 name: chromosome_fission is_a: SO:1000028 ! intrachromosomal_mutation [Term] id: SO:1000142 name: dexstrosynaptic_chromosome is_a: SO:1000136 ! autosynaptic_chromosome [Term] id: SO:1000143 name: laevosynaptic_chromosome is_a: SO:1000136 ! autosynaptic_chromosome [Term] id: SO:1000144 name: free_duplication is_a: SO:1000037 ! chromosomal_duplication [Term] id: SO:1000145 name: free_ring_duplication synonym: "(Drosophila)R" RELATED [] is_a: SO:1000045 ! ring_chromosome is_a: SO:1000144 ! free_duplication [Term] id: SO:1000146 name: complex_chromosomal_mutation is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:1000147 name: deficient_translocation def: "A translocation in which one of the four broken ends loses a segment before re-joining." [fb:reference_manual] synonym: "(Drosophila)Df" RELATED [] synonym: "(Drosophila)DfT" RELATED [] is_a: SO:1000029 ! chromosomal_deletion is_a: SO:1000044 ! chromosomal_translocation [Term] id: SO:1000148 name: inversion_cum_translocation def: "The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [fb:reference_manual] synonym: "(Drosophila)InT" RELATED [] synonym: "(Drosophila)T" RELATED [] synonym: "inversion cum translocation" EXACT [] is_a: SO:1000030 ! chromosomal_inversion is_a: SO:1000044 ! chromosomal_translocation [Term] id: SO:1000149 name: bipartite_duplication def: "The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [fb:reference_manual] synonym: "(Drosophila)bDp" RELATED [] is_a: SO:1000031 ! interchromosomal_mutation [Term] id: SO:1000150 name: cyclic_translocation def: "Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [fb:reference_manual] is_a: SO:1000044 ! chromosomal_translocation [Term] id: SO:1000151 name: bipartite_inversion def: "Three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [fb:reference_manual] synonym: "(Drosophila)bIn" RELATED [] is_a: SO:1000030 ! chromosomal_inversion [Term] id: SO:1000152 name: uninverted_insertional_duplication def: "A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [fb:reference_manual] synonym: "(Drosophila)eDp" RELATED [] is_a: SO:1000154 ! insertional_duplication [Term] id: SO:1000153 name: inverted_insertional_duplication def: "A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [fb:reference_manual] synonym: "(Drosophila)iDp" RELATED [] is_a: SO:1000154 ! insertional_duplication [Term] id: SO:1000154 name: insertional_duplication def: "A chromosome duplication involving the insertion of a duplicated region." [SO:ke] synonym: "(Drosophila)Dpp" RELATED [] is_a: SO:1000037 ! chromosomal_duplication [Term] id: SO:1000155 name: interchromosomal_transposition synonym: "(Drosophila)Tp" RELATED [] is_a: SO:0000453 ! transposition is_a: SO:1000031 ! interchromosomal_mutation [Term] id: SO:1000156 name: inverted_interchromosomal_transposition synonym: "(Drosophila)iTp" RELATED [] is_a: SO:1000155 ! interchromosomal_transposition [Term] id: SO:1000157 name: uninverted_interchromosomal_transposition synonym: "(Drosophila)eTp" RELATED [] is_a: SO:1000155 ! interchromosomal_transposition [Term] id: SO:1000158 name: inverted_intrachromosomal_transposition def: "The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [fb:reference_manual] synonym: "(Drosophila)iTp" RELATED [] is_a: SO:1000030 ! chromosomal_inversion is_a: SO:1000041 ! intrachromosomal_transposition [Term] id: SO:1000159 name: uninverted_intrachromosomal_transposition def: "The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [fb:reference_manual] synonym: "(Drosophila)eTp" RELATED [] is_a: SO:1000041 ! intrachromosomal_transposition [Term] id: SO:1000160 name: unoriented_insertional_duplication def: "A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [fb:reference_manual] synonym: "(Drosophila)uDp" RELATED [] is_a: SO:1000154 ! insertional_duplication [Term] id: SO:1000161 name: unorientated_interchromosomal_transposition synonym: "(Drosophila)uTp" RELATED [] is_a: SO:1000155 ! interchromosomal_transposition [Term] id: SO:1000162 name: unorientated_intrachromosomal_transposition def: "The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [fb:reference_manual] synonym: "(Drosophila)uTp" RELATED [] is_a: SO:1000041 ! intrachromosomal_transposition [Term] id: SO:1000170 name: uncharacterised_chromosomal_mutation is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:1000171 name: deficient_inversion def: "Three breaks in the same chromosome; one central region lost, the other inverted." [fb:reference_manual] synonym: "(Drosophila)Df" RELATED [] synonym: "(Drosophila)DfIn" RELATED [] is_a: SO:1000029 ! chromosomal_deletion is_a: SO:1000030 ! chromosomal_inversion [Term] id: SO:1000173 name: tandem_duplication is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:1000175 name: partially_characterised_chromosomal_mutation is_a: SO:1000170 ! uncharacterised_chromosomal_mutation [Term] id: SO:1000177 name: mutation_causing_uncharacterised_change_in_transcript def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000049 ! mutation_affecting_transcript [Term] id: SO:1000179 name: mutation_causing_partially_characterised_change_in_transcript def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000177 ! mutation_causing_uncharacterised_change_in_transcript [Term] id: SO:1000180 name: mutation_affecting_gene_structure def: "A kind of mutation that affects the structure of a gene." [SO:ke] is_a: SO:1000132 ! mutation [Term] id: SO:1000181 name: mutation_causing_gene_fusion def: "A kind of mutation that affects the structure of a gene by causing a fusion to another gene." [SO:ke] is_a: SO:1000180 ! mutation_affecting_gene_structure [Term] id: SO:1000182 name: chromosome_number_variation def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke] is_a: SO:0000240 ! chromosome_variation [Term] id: SO:1000183 name: chromosome_structure_variation is_a: SO:0000240 ! chromosome_variation [Term] id: SO:1000184 name: mutation_causes_exon_loss def: "A mutation that affects splicing and causes an exon loss." [SO:ke] is_a: SO:1000071 ! mutation_affecting_splicing [Term] id: SO:1000185 name: mutation_causes_intron_gain def: "Mutation causes an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000071 ! mutation_affecting_splicing [Term] id: SO:1000186 name: cryptic_splice_donor_activation is_a: SO:1000074 ! cryptic_splice_activator_mutation [Term] id: SO:1001186 name: cryptic_splice_acceptor_activation is_a: SO:1000074 ! cryptic_splice_activator_mutation [Term] id: SO:1001187 name: alternatively_spliced_transcript def: "A transcript that is alternatively spliced." [SO:xp] is_a: SO:0000673 ! implied link automatically realized ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000877 ! alternatively_spliced relationship: has_quality SO:0000877 ! implied link automatically realized ! alternatively_spliced [Term] id: SO:1001188 name: encodes_1_polypeptide def: "A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke] is_a: SO:0000463 ! encodes_alternately_spliced_transcripts [Term] id: SO:1001189 name: encodes_greater_than_1_polypeptide def: "A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke] is_a: SO:0000463 ! encodes_alternately_spliced_transcripts [Term] id: SO:1001190 name: encodes_different_polypeptides_different_stop def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke] is_a: SO:1001195 ! encodes_overlapping_peptides [Term] id: SO:1001191 name: encodes_overlapping_peptides_different_start def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke] is_a: SO:1001195 ! encodes_overlapping_peptides [Term] id: SO:1001192 name: encodes_disjoint_polypeptides def: "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke] is_a: SO:1001189 ! encodes_greater_than_1_polypeptide [Term] id: SO:1001193 name: encodes_overlapping_polypeptides_different_start_and_stop def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke] is_a: SO:1001195 ! encodes_overlapping_peptides [Term] id: SO:1001194 name: alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping is_obsolete: true [Term] id: SO:1001195 name: encodes_overlapping_peptides def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke] is_a: SO:1001189 ! encodes_greater_than_1_polypeptide [Term] id: SO:1001196 name: cryptogene def: "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma] is_a: SO:0000654 ! implied link automatically realized ! maxicircle_gene intersection_of: SO:0000654 ! maxicircle_gene intersection_of: has_quality SO:0000976 ! cryptic relationship: has_quality SO:0000976 ! implied link automatically realized ! cryptic [Term] id: SO:1001197 name: dicistronic_primary_transcript def: "A primary transcript that has the quality dicistronic." [SO:xp] is_a: SO:0000079 ! implied link automatically realized ! dicistronic_transcript is_a: SO:0000631 ! implied link automatically realized ! polycistronic_primary_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: has_quality SO:0000879 ! dicistronic [Term] id: SO:1001217 name: member_of_regulon is_a: SO:0000081 ! gene_array_member [Term] id: SO:1001244 name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping synonym: "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping" RELATED [] is_obsolete: true [Term] id: SO:1001246 name: CDS_independently_known def: "A CDS with the evidence status of being independently known." [SO:xp] is_a: SO:0000316 ! implied link automatically realized ! CDS intersection_of: SO:0000316 ! CDS intersection_of: has_quality SO:0000906 ! independently_known relationship: has_quality SO:0000906 ! implied link automatically realized ! independently_known [Term] id: SO:1001247 name: orphan_CDS def: "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma] is_a: SO:1001254 ! implied link automatically realized ! CDS_predicted intersection_of: SO:1001254 ! CDS_predicted intersection_of: has_origin SO:0000910 ! orphan relationship: has_origin SO:0000910 ! implied link automatically realized ! orphan [Term] id: SO:1001249 name: CDS_supported_by_domain_match_data def: "A CDS that is supported by domain similarity." [SO:xp] is_a: SO:1001251 ! implied link automatically realized ! CDS_supported_by_sequence_similarity_data intersection_of: SO:1001251 ! CDS_supported_by_sequence_similarity_data intersection_of: has_quality SO:0000908 ! supported_by_domain_match relationship: has_quality SO:0000908 ! implied link automatically realized ! supported_by_domain_match [Term] id: SO:1001251 name: CDS_supported_by_sequence_similarity_data def: "A CDS that is supported by sequence similarity data." [SO:xp] is_a: SO:1001254 ! implied link automatically realized ! CDS_predicted intersection_of: SO:0000316 ! CDS intersection_of: has_quality SO:0000907 ! supported_by_sequence_similarity relationship: has_quality SO:0000907 ! implied link automatically realized ! supported_by_sequence_similarity [Term] id: SO:1001254 name: CDS_predicted def: "A CDS that is predicted." [SO:ke] is_a: SO:0000316 ! implied link automatically realized ! CDS intersection_of: SO:0000316 ! CDS intersection_of: has_quality SO:0000732 ! predicted relationship: has_quality SO:0000732 ! implied link automatically realized ! predicted [Term] id: SO:1001255 name: status_of_coding_sequence is_obsolete: true [Term] id: SO:1001259 name: CDS_supported_by_EST_or_cDNA_data def: "A CDS that is supported by similarity to EST or cDNA data." [SO:xp] is_a: SO:1001251 ! implied link automatically realized ! CDS_supported_by_sequence_similarity_data intersection_of: SO:1001251 ! CDS_supported_by_sequence_similarity_data intersection_of: has_quality SO:0000909 ! supported_by_EST_or_cDNA relationship: has_quality SO:0000909 ! implied link automatically realized ! supported_by_EST_or_cDNA [Term] id: SO:1001260 name: internal_Shine_Dalgarno_sequence def: "A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke] synonym: "internal Shine-Dalgarno sequence" EXACT [] is_a: SO:0000243 ! internal_ribosome_entry_site is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:1001261 name: recoded_mRNA def: "A gene coding an mRNA which is recoded before translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract] is_a: SO:0000234 ! implied link automatically realized ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000881 ! recoded relationship: has_quality SO:0000881 ! implied link automatically realized ! recoded [Term] id: SO:1001262 name: minus_1_translational_frameshift def: "An attribute describing a translational frameshift of -1." [SO:ke] is_a: SO:0000887 ! translational_frameshift [Term] id: SO:1001263 name: plus_1_translational_frameshift def: "An attribute describing a translational frameshift of +1." [SO:ke] is_a: SO:0000887 ! translational_frameshift [Term] id: SO:1001264 name: mRNA_recoded_by_translational_bypass def: "A mRNA is translated by ribosomes that suspend translation at a particular codon and resume translation at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract] is_a: SO:1001261 ! implied link automatically realized ! recoded_mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000886 ! recoded_by_translational_bypass relationship: has_quality SO:0000886 ! implied link automatically realized ! recoded_by_translational_bypass [Term] id: SO:1001265 name: mRNA_recoded_by_codon_redefinition def: "A gene whose mRNA is recoded by an alteration of codon meaning." [SO:ma] is_a: SO:1001261 ! implied link automatically realized ! recoded_mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000882 ! codon_redefined relationship: has_quality SO:0000882 ! implied link automatically realized ! codon_redefined [Term] id: SO:1001266 name: stop_codon_redefinition_as_selenocysteine is_obsolete: true [Term] id: SO:1001267 name: stop_codon_readthrough is_obsolete: true [Term] id: SO:1001268 name: recoding_stimulatory_region def: "A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract] synonym: "recoding stimulatory signal" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:1001269 name: four_bp_start_codon def: "A non-canonical start codon with 4 base pairs." [SO:ke] synonym: "4bp start codon" EXACT [] is_a: SO:0000680 ! non_canonical_start_codon [Term] id: SO:1001270 name: stop_codon_redefinition_as_pyrrolysine is_obsolete: true [Term] id: SO:1001271 name: archeal_intron def: "Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism." [SO:ma] is_a: SO:0000661 ! intron_attribute [Term] id: SO:1001272 name: tRNA_intron is_a: SO:0000661 ! intron_attribute [Term] id: SO:1001273 name: CTG_start_codon def: "A non-canonical start codon of sequence CTG." [SO:ke] is_a: SO:0000680 ! non_canonical_start_codon [Term] id: SO:1001274 name: SECIS_element def: "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031] is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:1001275 name: retron def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma] is_a: SO:0000001 ! region [Term] id: SO:1001277 name: three_prime_recoding_site def: "The recoding stimulatory signal located downstream of the recoding site." [SO:ke] is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:1001279 name: three_prime_stem_loop_structure def: "A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001280 name: five_prime_recoding_site def: "The recoding stimulatory signal located upstream of the recoding site." [SO:ke] is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:1001281 name: flanking_three_prime_quadruplet_recoding_signal def: "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001282 name: UAG_stop_codon_signal def: "A stop codon signal for a UAG stop codon redefinition." [SO:ke] is_a: SO:1001288 ! stop_codon_signal [Term] id: SO:1001283 name: UAA_stop_codon_signal def: "A stop codon signal for a UAA stop codon redefinition." [SO:ke] is_a: SO:1001288 ! stop_codon_signal [Term] id: SO:1001284 name: regulon def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732] subset: SOFA is_a: SO:0005855 ! gene_group [Term] id: SO:1001285 name: UGA_stop_codon_signal def: "A stop codon signal for a UGA stop codon redefinition." [SO:ke] is_a: SO:1001288 ! stop_codon_signal [Term] id: SO:1001286 name: three_prime_repeat_recoding_signal def: "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001287 name: distant_three_prime_recoding_signal def: "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001288 name: stop_codon_signal def: "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke] comment: This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal. is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:2000061 name: databank_entry def: "The sequence referred to by an entry in a databank such as Genbank or SwissProt." [SO:ke] subset: SOFA synonym: "accession" RELATED [] is_a: SO:0000695 ! reagent [Typedef] id: adjacent_to name: adjacent_to def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence." [SO:ke] subset: SOFA [Typedef] id: associated_with name: associated_with comment: This relationship is vague and up for discussion. is_symmetric: true [Typedef] id: derives_from name: derives_from subset: SOFA is_transitive: true [Typedef] id: genome_of name: genome_of [Typedef] id: has_genome_location name: has_genome_location is_obsolete: true [Typedef] id: has_origin name: has_origin [Typedef] id: has_part name: has_part [Typedef] id: has_quality name: has_quality comment: The relationship between a feature and an atrribute. [Typedef] id: homologous_to name: homologous_to subset: SOFA is_symmetric: true is_a: similar_to ! similar_to [Typedef] id: member_of name: member_of comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. subset: SOFA is_transitive: true [Typedef] id: non_functional_homolog_of name: non_functional_homolog_of def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke] subset: SOFA is_a: homologous_to ! homologous_to [Typedef] id: orthologous_to name: orthologous_to subset: SOFA is_symmetric: true is_a: homologous_to ! homologous_to [Typedef] id: paralogous_to name: paralogous_to subset: SOFA is_symmetric: true is_a: homologous_to ! homologous_to [Typedef] id: part_of name: part_of subset: SOFA is_transitive: true [Typedef] id: position_of name: position_of [Typedef] id: regulated_by name: regulated_by is_obsolete: true [Typedef] id: sequence_of name: sequence_of [Typedef] id: similar_to name: similar_to subset: SOFA is_symmetric: true [Typedef] id: variant_of name: variant_of def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of s=ome instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop] comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.