format-version: 1.2 date: 13:02:2006 15:53 saved-by: kareneilbeck auto-generated-by: OBO-Edit 1.000-beta15 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: "Continuous sequence." [SO:ke] subset: SOFA synonym: "sequence" RELATED [] is_a: SO:0000110 ! located_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 nucelic 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-quartet" RELATED [] is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000004 name: interior_coding_exon 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#line_types] is_a: SO:0000657 ! repeat_region [Term] id: SO:0000006 name: PCR_product def: "A region amplified by a PCR reaction." [SO:ke] subset: SOFA synonym: "amplicon" RELATED [] 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_a: SO:0000009 ! gene_class [Term] id: SO:0000009 name: gene_class is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000010 name: protein_coding_gene is_a: SO:0000009 ! gene_class [Term] id: SO:0000011 name: non_protein_coding_gene is_a: SO:0000009 ! gene_class [Term] id: SO:0000012 name: scRNA_primary_transcript def: "The primary transcript of any one of several small cytoplasmic RNA moleculespresent in the cytoplasm and sometimes nucleus of a eukaryote." [http:www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html] 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 moleculespresent in the cytoplasm and sometimes nucleus of a eukaryote." [http:www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html] subset: SOFA is_a: SO:0000655 ! ncRNA [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] relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000015 name: DPE_motif def: "A sequence element characteristic of some RNA polymerase II promoters; always found with the INR_motif. Positioned from +28 to +32 with respect to the TSS (+1). Consensus sequence (A|G)G(A|T)(C|T)(G|A|C). Required for TFIID binding to TATA-less promoters." [PMID:12651739] relationship: part_of SO:0000170 ! RNApol_II_promoter [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] relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000017 name: PSE_motif def: "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739] relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000018 name: linkage_group def: "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046] is_a: SO:0000001 ! region [Term] id: SO:0000019 name: RNA_hairpin_loop is_a: SO:0000715 ! RNA_motif [Term] id: SO:0000020 name: RNA_internal_loop is_a: SO:0000715 ! RNA_motif [Term] id: SO:0000021 name: asymmetric_RNA_internal_loop is_a: SO:0000020 ! RNA_internal_loop [Term] id: SO:0000022 name: A_minor_RNA_motif is_a: SO:0000021 ! asymmetric_RNA_internal_loop [Term] id: SO:0000023 name: K_turn_RNA_motif is_a: SO:0000021 ! asymmetric_RNA_internal_loop [Term] id: SO:0000024 name: Sarcin_like_RNA_motif is_a: SO:0000021 ! asymmetric_RNA_internal_loop [Term] id: SO:0000025 name: symmetric_RNA_internal_loop 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 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: "Watson_Crick_based_pair" RELATED [] 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:http://aptamer.icmb.utexas.edu] is_a: SO:0000351 ! synthetic_sequence 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 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] is_a: SO:0000351 ! synthetic_sequence is_a: SO:0000696 ! oligo [Term] id: SO:0000035 name: riboswitch def: "Riboswitches are mRNAs that can act as direct sensors of small molecules to control their own expression. A riboswitch contains a cis element within mRNA, that can act as a direct sensor of metabolites without a protein intermediate." [PMID:2820954] is_a: 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" RELATED [] synonym: "SMAR" RELATED [] synonym: "scaffold_attachment_site" RELATED [] 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] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000038 name: match_set def: "A collection of match parts" [SO:ke] subset: SOFA is_a: SO:0000343 ! match [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:0000343 ! match relationship: part_of SO:0000038 ! match_set [Term] id: SO:0000040 name: genomic_clone def: "A clone of a DNA region of a genome." [SO:ma] is_a: SO:0000151 ! clone [Term] id: SO:0000041 name: variation_operation def: "An operation that can be applied to a sequence, that results in a chnage." [SO:ke] is_a: SO:0000000 ! Sequence_Ontology [Term] id: SO:0000042 name: pseudogene_attribute def: "An attribute of a pseudogene (SO:0000336)." [SO:ma] is_a: SO:0000009 ! gene_class [Term] id: SO:0000043 name: processed_pseudogene synonym: "pseudogene_by_reverse_transcription" RELATED [] is_a: SO:0000042 ! pseudogene_attribute [Term] id: SO:0000044 name: pseudogene_by_unequal_crossing_over is_a: SO:0000042 ! pseudogene_attribute [Term] id: SO:0000045 name: delete def: "To remove a subsection of sequence." [SO:ke] is_a: SO:0000041 ! variation_operation [Term] id: SO:0000046 name: insert def: "To insert a subsection of sequence." [SO:ke] is_a: SO:0000041 ! variation_operation [Term] id: SO:0000047 name: invert def: "To invert a subsection of sequence." [SO:ke] is_a: SO:0000041 ! variation_operation [Term] id: SO:0000048 name: substitute def: "To substitute a subsection of sequence for another." [SO:ke] is_a: SO:0000041 ! variation_operation [Term] id: SO:0000049 name: translocate def: "To translocate a subsection of sequence." [SO:ke] is_a: SO:0000041 ! variation_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 is 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 is_a: SO:1000132 ! consequences_of_mutation [Term] id: SO:0000054 name: aneuploid is_a: SO:1000182 ! chromosome_number_variation [Term] id: SO:0000055 name: hyperploid is_a: SO:0000054 ! aneuploid [Term] id: SO:0000056 name: hypoploid is_a: SO:0000054 ! aneuploid [Term] id: SO:0000057 name: operator def: "A regulatory element of an operon to which activators or repressors bind hereby effecting translation of genes in that operon." [SO:ma] subset: SOFA 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 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_a: SO:0000401 ! gene_attribute [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_a: SO:0000064 ! gene_by_transcript_attribute [Term] id: SO:0000067 name: gene_to_gene_feature is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000068 name: overlapping_gene is_a: SO:0000067 ! gene_to_gene_feature [Term] id: SO:0000069 name: gene_included_within_intron is_a: SO:0000068 ! overlapping_gene [Term] id: SO:0000070 name: gene_included_within_intron_antiparallel is_a: SO:0000069 ! gene_included_within_intron [Term] id: SO:0000071 name: gene_included_within_intron_parallel is_a: SO:0000069 ! gene_included_within_intron [Term] id: SO:0000072 name: end_overlapping_gene is_a: SO:0000068 ! overlapping_gene [Term] id: SO:0000073 name: end_overlapping_gene_five_primethree_prime_overlap is_a: SO:0000072 ! end_overlapping_gene [Term] id: SO:0000074 name: end_overlapping_gene_five_primefive_prime_overlap is_a: SO:0000072 ! end_overlapping_gene [Term] id: SO:0000075 name: end_overlapping_gene_three_primethree_prime_overlap is_a: SO:0000072 ! end_overlapping_gene [Term] id: SO:0000076 name: end_overlapping_gene_three_primefive_prime_overlap is_a: SO:0000072 ! end_overlapping_gene [Term] id: SO:0000077 name: antisense_gene is_a: SO:0000068 ! overlapping_gene [Term] id: SO:0000078 name: polycistronic_transcript is_a: SO:0000115 ! transcript_feature [Term] id: SO:0000079 name: dicistronic_transcript is_a: SO:0000078 ! polycistronic_transcript [Term] id: SO:0000080 name: member_of_operon is_a: SO:0000081 ! member_gene_array [Term] id: SO:0000081 name: member_gene_array is_a: SO:0000067 ! gene_to_gene_feature [Term] id: SO:0000082 name: processed_transcript_attribute is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000083 name: macronuclear_sequence_feature is_a: SO:0000735 ! sequence_location [Term] id: SO:0000084 name: micronuclear_sequence_feature is_a: SO:0000735 ! sequence_location [Term] id: SO:0000085 name: gene_by_genome_location is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000086 name: gene_by_organelle_of_genome is_a: SO:0000085 ! gene_by_genome_location [Term] id: SO:0000087 name: nuclear_gene is_a: SO:0000086 ! gene_by_organelle_of_genome [Term] id: SO:0000088 name: mt_gene synonym: "mitochondrial_gene" RELATED [] is_a: SO:0000086 ! gene_by_organelle_of_genome [Term] id: SO:0000089 name: kinetoplast_gene is_a: SO:0000088 ! mt_gene [Term] id: SO:0000090 name: plastid_gene is_a: SO:0000086 ! gene_by_organelle_of_genome [Term] id: SO:0000091 name: apicoplast_gene is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000092 name: ct_gene synonym: "chloroplast_gene" RELATED [] is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000093 name: chromoplast_gene is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000094 name: cyanelle_gene is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000095 name: leucoplast_gene is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000096 name: proplastid_gene is_a: SO:0000090 ! plastid_gene [Term] id: SO:0000097 name: nucleomorph_gene is_a: SO:0000086 ! gene_by_organelle_of_genome [Term] id: SO:0000098 name: plasmid_gene is_a: SO:0000085 ! gene_by_genome_location [Term] id: SO:0000099 name: proviral_gene is_a: SO:0000085 ! gene_by_genome_location [Term] id: SO:0000100 name: endogenous_retroviral_gene is_a: SO:0000099 ! proviral_gene [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 is_a: SO:0000187 ! repeat_family is_a: SO:1000028 ! intrachromosomal_mutation [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 irreversable denaturation." [SO:ma] subset: SOFA 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] relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0000106 name: non_capped_primary_transcript is_a: SO:0000146 ! primary_transcript_by_cap_class [Term] id: SO:0000107 name: sequencing_primer is_a: SO:0000112 ! primer [Term] id: SO:0000108 name: mRNA_with_frameshift is_a: SO:0000082 ! processed_transcript_attribute [Term] id: SO:0000109 name: sequence_variant def: "A region of sequence where variation has been observed." [SO:ke] subset: SOFA synonym: "mutation" RELATED [] is_a: SO:0000110 ! located_sequence_feature [Term] id: SO:0000110 name: located_sequence_feature def: "A biological feature that can be attributed to a region of biological sequence." [SO:ke] subset: SOFA is_a: SO:0000000 ! Sequence_Ontology [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 transpable element genes of the TY element in yeast." [SO:ke] is_a: SO:0000009 ! gene_class [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 is_a: SO:0000696 ! oligo [Term] id: SO:0000113 name: integrated_virus def: "A viral sequence which has integrated into the host genome." [SO:ke] subset: SOFA is_a: SO:0000001 ! region [Term] id: SO:0000114 name: methylated_C def: "A methylated deoxy-cytosine." [SO:ke] subset: SOFA is_a: SO:0000306 ! methylated_base_feature [Term] id: SO:0000115 name: transcript_feature is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000116 name: edited_transcript def: "A gene whose transcript is edited." [http://www.rna.ucla.edu/] is_a: SO:0000115 ! transcript_feature [Term] id: SO:0000117 name: transcript_with_readthrough_stop_codon is_obsolete: true [Term] id: SO:0000118 name: transcript_with_translational_frameshift is_a: SO:1001261 ! recoded_mRNA [Term] id: SO:0000119 name: gene_by_class_of_regulation 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] 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: "." [SO:ma] comment: by\: is_a: SO:0000119 ! gene_by_class_of_regulation [Term] id: SO:0000124 name: transcriptionally_constitutive is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000125 name: transcriptionally_induced is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000126 name: transcriptionally_repressed is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000127 name: silenced_gene is_a: SO:0000126 ! transcriptionally_repressed [Term] id: SO:0000128 name: gene_silenced_by_DNA_modification is_a: SO:0000127 ! silenced_gene [Term] id: SO:0000129 name: gene_silenced_by_DNA_methylation is_a: SO:0000128 ! gene_silenced_by_DNA_modification [Term] id: SO:0000130 name: post_translationally_regulated synonym: "post-translationally_regulated" RELATED [] is_a: SO:0000119 ! gene_by_class_of_regulation [Term] id: SO:0000131 name: translationally_regulated is_a: SO:0000119 ! gene_by_class_of_regulation [Term] id: SO:0000132 name: reverse_primer def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] is_a: SO:0000112 ! primer [Term] id: SO:0000133 name: gene_by_epigenetic_modification is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000134 name: imprinted is_a: SO:0000119 ! gene_by_class_of_regulation is_a: SO:0000133 ! gene_by_epigenetic_modification [Term] id: SO:0000135 name: maternally_imprinted is_a: SO:0000134 ! imprinted [Term] id: SO:0000136 name: paternally_imprinted is_a: SO:0000134 ! imprinted [Term] id: SO:0000137 name: allelically_excluded is_a: SO:0000133 ! gene_by_epigenetic_modification [Term] id: SO:0000138 name: gene_rearranged_at_DNA_level is_a: SO:0000133 ! gene_by_epigenetic_modification [Term] id: SO:0000139 name: ribosome_entry_site def: "Region in mRNA where ribosome assembles." [SO:ke] comment: gene\: subset: SOFA relationship: part_of SO:0000203 ! UTR [Term] id: SO:0000140 name: attenuator def: "A sequence segment located between the promoter and a structural gene that causes partial termination of transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types] subset: SOFA is_a: SO:0000752 ! gene_group_regulatory_region is_a: SO:0005836 ! regulatory_region [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#line_types] subset: SOFA is_a: SO:0000752 ! gene_group_regulatory_region 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_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000145 name: recoded_codon is_a: SO:0000360 ! codon [Term] id: SO:0000146 name: primary_transcript_by_cap_class is_a: SO:0000144 ! primary_transcript_attribute [Term] id: SO:0000147 name: exon def: "A region of the genome that codes for portion of spliced messenger RNA (SO:0000234); may contain 5'-untranslated region (SO:0000204), all open reading frames (SO:0000236) and 3'-untranslated region (SO:0000205)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types] subset: SOFA relationship: part_of SO:0000673 ! transcript [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] is_a: SO:0000440 ! vector relationship: part_of SO:0000760 ! YAC_clone [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] is_a: SO:0000440 ! vector relationship: part_of SO:0000764 ! BAC_clone [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." [https://www.ncbi.nlm.nih.gov/genome/guide/mouse/glossary.htm] synonym: "P1" RELATED [] is_a: SO:0000440 ! vector relationship: part_of SO:0000762 ! PAC_clone [Term] id: SO:0000155 name: plasmid def: "A self-replicating circular DNA molecule that is distinct from a chromosome in the organism." [SO:ma] is_a: SO:0000695 ! reagent [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 aplasmids or packaged as a phage,since they retain the lambda cos sites." [SO:ma] comment: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1)\:9-20. is_a: SO:0000440 ! vector relationship: part_of SO:0000765 ! cosmid_clone [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] is_a: SO:0000440 ! vector relationship: part_of SO:0000761 ! phagemid_clone [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; is_a: SO:0000440 ! vector relationship: part_of SO:0000763 ! fosmid_clone [Term] id: SO:0000159 name: deletion def: "The sequence that is deleted." [SO:ke] subset: SOFA is_a: SO:0000001 ! region is_a: SO:0000109 ! sequence_variant 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_a: SO:0000151 ! clone [Term] id: SO:0000161 name: methylated_A def: "A methylated adenine." [SO:ke] subset: SOFA 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:0000699 ! junction relationship: part_of SO:0000185 ! primary_transcript [Term] id: SO:0000163 name: splice_donor_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: "donor" RELATED [] synonym: "donor_splice_site" RELATED [] is_a: SO:0000162 ! splice_site [Term] id: SO:0000164 name: splice_acceptor_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: "acceptor" RELATED [] synonym: "acceptor_splice_site" RELATED [] 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#line_types] subset: SOFA is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000166 name: enhancer_by_bound_factor is_a: SO:0000402 ! enhancer_attribute [Term] id: SO:0000167 name: promoter def: "The region on a DNA molecule involved in RNA polymerase binding to initiate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types] subset: SOFA is_a: SO:0005836 ! 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 sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke] synonym: "RNA_polymerase_A_promoter" RELATED [] is_a: SO:0000167 ! 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: "RNA_polymerase_B_promoter" RELATED [] is_a: SO:0000167 ! 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: "RNA_polymerase_C_promoter" RELATED [] is_a: SO:0000167 ! 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#line_types] relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000173 name: GC_rich_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#line_types] synonym: "GC-rich_region" RELATED [] relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000174 name: TATA_box def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types] 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#line_types] synonym: "-10_signal" RELATED [] synonym: "Pribnow_box" RELATED [] relationship: part_of SO:0000613 ! bacterial_RNApol_promoter [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#line_types] synonym: "-35_signal" RELATED [] relationship: part_of SO:0000613 ! bacterial_RNApol_promoter [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] 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] 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] 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 is_a: SO:0000001 ! region relationship: part_of SO:0000704 ! gene [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: "The primary (initial, unprocessed) transcript; includes five_prime_clip (SO:0000555), five_prime_untranslated_region (SO:0000204), open reading frames (SO:0000236), introns (SO:0000188) and three_prime_ untranslated_region (three_prime_UTR), and three_prime_clip (SO:0000557)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types] subset: SOFA synonym: "precursor_RNA" RELATED [] is_a: SO:0000673 ! transcript [Term] id: SO:0000186 name: LTR_retrotransposon def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke] is_a: SO:0000180 ! retrotransposon [Term] id: SO:0000187 name: repeat_family def: "A group of characterized repeat sequences." [SO:ke] subset: SOFA is_a: SO:0000657 ! repeat_region [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#line_types] subset: SOFA relationship: part_of SO:0000185 ! primary_transcript [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 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 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" RELATED [] 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: "Long interspersed element" RELATED [] synonym: "Long interspersed nuclear element" RELATED [] 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] 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] 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] 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] synonym: "noncoding_exon" RELATED [] is_a: SO:0000147 ! exon [Term] id: SO:0000199 name: translocation def: "A region of nucleotide sequence that has translocated to a new position." [SO:ke] relationship: sequence_of SO:0000049 ! translocate [Term] id: SO:0000200 name: five_prime_coding_exon def: "The 5' most coding exon." [SO:ke] is_a: SO:0000147 ! exon [Term] id: SO:0000201 name: interior_exon 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] 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" RELATED [] relationship: part_of SO:0000234 ! mRNA [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#line_types] subset: SOFA synonym: "five_prime_untranslated_region" RELATED [] 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#line_types] subset: SOFA synonym: "three_prime_untranslated_region" RELATED [] 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" RELATED [] synonym: "Short interspersed nuclear element" RELATED [] is_a: SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000207 name: simple_sequence_length_polymorphism 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] 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" RELATED [] 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 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 processing to remove parts such as introns and transcribed_spacer_regions." [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: mRNA does not contain introns as it is a processd_transcript.nThe equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. subset: SOFA synonym: "messenger_RNA" RELATED [] is_a: SO:0000233 ! processed_transcript [Term] id: SO:0000235 name: TF_binding_site def: "A region of a molecule that binds to a transcription factor." [SO:ke] subset: SOFA synonym: "transcription_factor_binding_site" RELATED [] 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 terms now basically is the same as a CDS. This must be revised. subset: SOFA synonym: "open_reading_frame" RELATED [] is_a: SO:0000717 ! reading_frame [Term] id: SO:0000237 name: transcript_attribute is_a: SO:0000400 ! sequence_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: "LVR element" RELATED [] synonym: "long inverted repeat 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 [Term] id: SO:0000241 name: internal_UTR is_a: SO:0000203 ! UTR [Term] id: SO:0000242 name: untranslated_region_polyicistronic_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: "IRES" RELATED [] 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_a: SO:0000082 ! processed_transcript_attribute [Term] id: SO:0000246 name: mRNA_polyadenylated is_a: SO:0000245 ! mRNA_by_polyadenylation_status [Term] id: SO:0000247 name: mRNA_not_polyadenylated is_a: SO:0000245 ! mRNA_by_polyadenylation_status [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] relationship: part_of SO:0000673 ! transcript [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#line_types, ISBN:0198506732] subset: SOFA synonym: "ribsomal_RNA" RELATED [] is_a: SO:0000655 ! ncRNA [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. tRNAs 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). tRNAs 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] subset: SOFA synonym: "transfer_RNA" RELATED [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000254 name: alanyl_tRNA is_a: SO:0000253 ! tRNA [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 is_a: SO:0000253 ! tRNA [Term] id: SO:0000257 name: aspartyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000258 name: cysteinyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000259 name: glutaminyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000260 name: glutamyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000261 name: glycyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000262 name: histidyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000263 name: isoleucyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000264 name: leucyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000265 name: lysyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000266 name: methionyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000267 name: phenylalanyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000268 name: prolyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000269 name: seryl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000270 name: threonyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000271 name: tryptophanyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000272 name: tyrosyl_tRNA is_a: SO:0000253 ! tRNA [Term] id: SO:0000273 name: valyl_tRNA is_a: SO:0000253 ! tRNA [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#line_types, PMID:11733745] subset: SOFA synonym: "small_nuclear_RNA" RELATED [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000275 name: snoRNA def: "Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus. There are two main classes of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member of the box C/D class. Indeed, the box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. 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] subset: SOFA synonym: "small_nucleolar_RNA" RELATED [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000276 name: miRNA def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. miRNAs are produced from precursor molecules (SO:0000647) that can form local hairpin strcutures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpinprecursor molecule. miRNAs may trigger the cleavage of their target molecules oract as translational repressors." [PMID:12592000] subset: SOFA synonym: "micro_RNA" RELATED [] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000277 name: transcript_by_bound_factor is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000278 name: transcript_by_bound_nucleic_acid is_a: SO:0000277 ! transcript_by_bound_factor [Term] id: SO:0000279 name: transcript_by_bound_protein is_a: SO:0000277 ! transcript_by_bound_factor [Term] id: SO:0000280 name: engineered_gene is_a: SO:0000009 ! gene_class [Term] id: SO:0000281 name: engineered_foreign_gene is_a: SO:0000280 ! engineered_gene is_a: SO:0000285 ! foreign_gene [Term] id: SO:0000282 name: mRNA_with_minus_1_frameshift is_a: SO:0000108 ! mRNA_with_frameshift [Term] id: SO:0000283 name: engineered_foreign_transposable_element_gene is_a: SO:0000111 ! transposable_element_gene is_a: SO:0000280 ! engineered_gene [Term] id: SO:0000284 name: type_I_enzyme_restriction_site def: "The recognition site is bipartate and interupted." [http://www.promega.com] is_obsolete: true [Term] id: SO:0000285 name: foreign_gene is_a: SO:0000452 ! transgene [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#line_types] synonym: "LTR" RELATED [] synonym: "direct_terminal _repeat" RELATED [] is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000186 ! LTR_retrotransposon [Term] id: SO:0000287 name: fusion_gene is_a: SO:0000009 ! gene_class [Term] id: SO:0000288 name: engineered_fusion_gene is_a: SO:0000280 ! engineered_gene is_a: SO:0000287 ! fusion_gene [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 is_a: SO:0000705 ! tandem_repeat [Term] id: SO:0000290 name: dinucleotide_repeat_microsatellite_feature is_a: SO:0000289 ! microsatellite [Term] id: SO:0000291 name: trinucleotide_repeat_microsatellite_feature is_a: SO:0000289 ! microsatellite [Term] id: SO:0000292 name: repetitive_element is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000293 name: engineered_foreign_repetitive_element is_a: SO:0000280 ! engineered_gene is_a: SO:0000292 ! repetitive_element [Term] id: SO:0000294 name: inverted_repeat def: "The sequence is complementarily repeated on the opposite strand. Example: GCTGA-----TCAGC." [SO:ke] subset: SOFA 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. 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#line_types] subset: SOFA 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#line_types] 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: recombination_feature_of_vertebrate_immune_system_gene 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#J-RS] synonym: "J-RS" RELATED [] is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene [Term] id: SO:0000303 name: clip def: "Part of the primary transcript that is clipped off during processing." [SO:ke] subset: SOFA relationship: part_of SO:0000185 ! primary_transcript [Term] id: SO:0000304 name: type_II_enzyme_restriction_site def: "The recognition site is either palindromic, partially palindromic or an interupted palidrome. 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#line_types] 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" RELATED [] is_a: SO:0000001 ! region [Term] id: SO:0000308 name: sequence_feature_locating_method is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000309 name: computed_feature is_a: SO:0000308 ! sequence_feature_locating_method [Term] id: SO:0000310 name: predicted_ab_initio_computation is_a: SO:0000309 ! computed_feature [Term] id: SO:0000311 name: computed_feature_by_similarity def: "." [SO:ma] comment: similar to\: is_a: SO:0000309 ! computed_feature [Term] id: SO:0000312 name: experimentally_determined_feature is_a: SO:0000308 ! sequence_feature_locating_method [Term] id: SO:0000313 name: stem_loop 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#line_types] is_a: SO:0000002 ! 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 site where transcription begins." [SO:ke] subset: SOFA synonym: "TSS" RELATED [] is_a: SO:0000699 ! junction relationship: part_of SO:0000185 ! primary_transcript [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" RELATED [] relationship: part_of SO:0000234 ! mRNA [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] is_a: SO:0000151 ! clone [Term] id: SO:0000318 name: start_codon def: "First codon to be translated by a ribosome." [SO:ke] synonym: "initiation codon" RELATED [] 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] 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 relationship: part_of SO:0000662 ! spliceosomal_intron [Term] id: SO:0000321 name: mRNA_with_plus_1_frameshift is_a: SO:0000108 ! mRNA_with_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 [] relationship: part_of SO:0000316 ! CDS [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." [https://www.ncbi.nlm.nih.gov/pubmed/7570003] 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 [] relationship: part_of SO:0000316 ! CDS [Term] id: SO:0000328 name: microarray_oligo synonym: "microarray_oligonucleotide" RELATED [] 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 is_a: SO:0000108 ! mRNA_with_frameshift [Term] id: SO:0000330 name: conserved_region def: "Region of sequence similarity by descent from a common ancestor." [SO:ke] 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" RELATED [] 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] 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] synonym: "noncoding_conserved_region" RELATED [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000335 name: mRNA_with_minus_2_frameshift is_a: SO:0000108 ! mRNA_with_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:0000695 ! reagent 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] is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000339 name: recombination_hotspot def: "A region in a genome whioch promotes recombination." [SO:rd] is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000340 name: chromosome def: "Structural unit composed of long DNA molecule." [http://biotech.icmb.utexas.edu/search/dict-search.mhtml] 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] synonym: "cytological_band" RELATED [] relationship: part_of SO:0000340 ! chromosome [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:0005836 ! 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] subset: SOFA synonym: "expressed_sequence_tag" RELATED [] is_a: SO:0000695 ! reagent relationship: derives_from SO:0000234 ! mRNA [Term] id: SO:0000346 name: Cre_recombination_target_region synonym: "lox_site" RELATED [] is_a: SO:0000342 ! site_specific_recombination_target_region [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 is_a: SO:0000443 ! polymer_type [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: FLP_recombination_target_region synonym: "FRT_site" RELATED [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000351 name: synthetic_sequence def: "A sequence of nucleotides or amino acids that has been designed by an experimentor and which may, or may not, correspond with any natural sequence." [SO:ma] is_a: SO:0000443 ! polymer_type [Term] id: SO:0000352 name: DNA 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 in which markers are co-inherited as the result of the lack of historic recombination between them due to their close proximity." [SO:ma] is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000356 name: RNA is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0000357 name: sequence_by_flanking_target_attribute is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000358 name: protein def: "One or more polypeptides which may, or may not, be covalently bonded, and which assume a native secondary and tertiary structure." [SO:ma] comment: This definition no longer matches the meaning of the concept! Term should probably be proteinacious or something... KEn is_a: SO:0000443 ! polymer_type [Term] id: SO:0000359 name: floxed_sequence is_a: SO:0000357 ! sequence_by_flanking_target_attribute is_a: SO:0000452 ! transgene [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 relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000361 name: FRT_flanked_sequence is_a: SO:0000357 ! sequence_by_flanking_target_attribute [Term] id: SO:0000362 name: chimeric_cDNA_clone def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma] is_a: SO:0000317 ! cDNA_clone [Term] id: SO:0000363 name: floxed_gene is_a: SO:0000359 ! floxed_sequence [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: "DNA elements capable of mobilizing individual gene cassettes into bacterial chromosomes by site- specific recombination." [http://www.genomicglossaries.com/content/DNA.asp] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000366 name: insertion_site def: "The junction where an insertion occurred." [SO:ke] subset: SOFA is_a: SO:0000109 ! sequence_variant is_a: SO:0000699 ! junction relationship: position_of SO:0000046 ! insert [Term] id: SO:0000367 name: attI_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 relationship: part_of SO:0000365 ! integron [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: "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:0000373 name: recombinationally_inverted is_a: SO:0000456 ! recombinationally_rearranged_gene [Term] id: SO:0000374 name: ribozyme def: "An RNA with catalytic activity." [SO:ma] subset: SOFA is_a: SO:0000372 ! enzymatic_RNA [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_rRNA" RELATED [] is_a: SO:0000252 ! 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" RELATED [] 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" RELATED [] 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:0000374 ! ribozyme [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:0000372 ! enzymatic_RNA [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:0000374 ! ribozyme [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:0000372 ! enzymatic_RNA [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 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 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 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 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 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 is_a: SO:0000274 ! snRNA [Term] id: SO:0000397 name: U6atac_snRNA def: "U6atac_snRNA -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)." [https://www.ncbi.nlm.nih.gov/pubmed/12409455] subset: SOFA 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 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 is_a: SO:0000274 ! snRNA [Term] id: SO:0000400 name: sequence_attribute is_a: SO:0000000 ! Sequence_Ontology [Term] id: SO:0000401 name: gene_attribute is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000402 name: enhancer_attribute is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000403 name: U14_snRNA 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] subset: SOFA is_a: SO:0000274 ! snRNA [Term] id: SO:0000404 name: vault_RNA def: "A family of RNAs are found as part of the enigmatic vault ribonuceoprotein 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: "18S_rRNA -A large polynucleotide which functions as a part of the small subunit of the ribosome" [SO:ke] subset: SOFA synonym: "16S_rRNA" RELATED [] is_a: SO:0000252 ! 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 def: "A region on the surface of a molecule that may interact with another molecule." [SO:ke] subset: SOFA 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_fragment is_a: SO:0000695 ! reagent [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 sequences differs from that of a specified sequence." [SO:ke] subset: SOFA is_a: SO:0000700 ! remark [Term] id: SO:0000414 name: genomically_contaminated_cDNA_clone is_a: SO:0000317 ! cDNA_clone [Term] id: SO:0000415 name: genomic_polyA_primed_cDNA_clone is_a: SO:0000317 ! cDNA_clone [Term] id: SO:0000416 name: partially_unprocessed_cDNA_clone is_a: SO:0000317 ! cDNA_clone [Term] id: SO:0000417 name: polypeptide_domain def: "A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains." [http:www.molbiol.bbsrc.ac.uk/new_protein/domains.html] relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0000418 name: signal_peptide def: "The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence." [http:www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "signal peptide coding sequence" RELATED [] relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0000419 name: mature_peptide def: "The coding sequence for the mature or final peptide or protein product following post-translational modification." [http:www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0000420 name: five_prime_terminal_inverted_repeat is_a: SO:0000481 ! terminal_inverted_repeat [Term] id: SO:0000421 name: three_prime_terminal_inverted_repeat is_a: SO:0000481 ! terminal_inverted_repeat [Term] id: SO:0000422 name: U5_LTR_region relationship: part_of SO:0000286 ! long_terminal_repeat [Term] id: SO:0000423 name: R_LTR_region relationship: part_of SO:0000286 ! long_terminal_repeat [Term] id: SO:0000424 name: U3_LTR_region relationship: part_of SO:0000286 ! long_terminal_repeat [Term] id: SO:0000425 name: five_prime_LTR is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0000426 name: three_prime_LTR is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0000427 name: R_five_prime_LTR_region is_a: SO:0000423 ! R_LTR_region relationship: part_of SO:0000425 ! five_prime_LTR [Term] id: SO:0000428 name: U5_five_prime_LTR_region is_a: SO:0000422 ! U5_LTR_region relationship: part_of SO:0000425 ! five_prime_LTR [Term] id: SO:0000429 name: U3_five_prime_LTR_region is_a: SO:0000424 ! U3_LTR_region relationship: part_of SO:0000425 ! five_prime_LTR [Term] id: SO:0000430 name: R_three_prime_LTR_region relationship: part_of SO:0000426 ! three_prime_LTR [Term] id: SO:0000431 name: U3_three_prime_LTR_region relationship: part_of SO:0000426 ! three_prime_LTR [Term] id: SO:0000432 name: U5_three_prime_LTR_region relationship: part_of SO:0000426 ! three_prime_LTR [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 relationship: part_of SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000434 name: transposable_element_target_site_duplication def: "A sequence of DNA that is duplicated when a transposable element inserts; usually found at each end the insertion." [http:www.koko.gov.my/CocoaBioTech/Glossaryt.html] is_a: SO:0000657 ! repeat_region [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" RELATED [] is_a: SO:0000001 ! region [Term] id: SO:0000437 name: assortment_derived_duplication is_obsolete: true [Term] id: SO:0000438 name: gene_not_polyadenylated is_a: SO:0000066 ! gene_by_polyadenylation_attribute [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] 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] synonym: "single stranded oligonucleotide.new synonym" RELATED [] synonym: "ss_oligonucleotide" RELATED [] is_a: SO:0000696 ! oligo [Term] id: SO:0000442 name: ds_oligo def: "A double stranded oligonucleotide." [SO:ke] synonym: "double stranded oligonucleotide" RELATED [] synonym: "ds_oligonucleotide" RELATED [] is_a: SO:0000696 ! oligo [Term] id: SO:0000443 name: polymer_type 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: "five_prime_noncoding_exon" RELATED [] 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 frequencyof 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_polyadenylated is_a: SO:0000066 ! gene_by_polyadenylation_attribute [Term] id: SO:0000452 name: transgene is_a: SO:0000009 ! gene_class [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 ofrepetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284] subset: SOFA synonym: "repeat associated small interfering RNA" RELATED [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000455 name: gene_with_mRNA_with_frameshift is_a: SO:0000064 ! gene_by_transcript_attribute [Term] id: SO:0000456 name: recombinationally_rearranged_gene is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000457 name: interchromosomal_duplication 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#D-GENE] synonym: "D-GENE" RELATED [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene 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 is_a: SO:0000064 ! gene_by_transcript_attribute [Term] id: SO:0000460 name: vertebrate_immunoglobulin_T_cell_receptor_gene synonym: "vertebrate_immunoglobulin/T-cell_receptor_gene" RELATED [] is_a: SO:0000456 ! recombinationally_rearranged_gene [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 entitity." [SO:cjm] subset: SOFA is_a: SO:0000001 ! region [Term] id: SO:0000463 name: gene_with_alternately_spliced_transcript is_a: SO:0000064 ! gene_by_transcript_attribute [Term] id: SO:0000464 name: decayed_exon def: "A non-functional descendent 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#V-GENE] synonym: "V_GENE" RELATED [] synonym: "variable_gene" RELATED [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene 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 synonym: "post-translationally_regulated_by_protein_stability" RELATED [] 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 synonym: "post-translationally_regulated_by_protein_modification" RELATED [] 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#J-GENE] synonym: "J-GENE" RELATED [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene 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 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 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 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 is_a: SO:0000081 ! member_gene_array [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#C-GENE] synonym: "C_GENE" RELATED [] synonym: "constant_gene" RELATED [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene 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 synonym: "trans-spliced_transcript" RELATED [] is_a: SO:0000082 ! processed_transcript_attribute [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.A minimal_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 attempting to minimize the overlap between adjacent clones. (LS)" [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" RELATED [] is_a: SO:0000657 ! repeat_region 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" RELATED [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene [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" RELATED [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000484 name: three_prime_exon_noncoding_region def: "The sequence of the 3' exon that is not coding." [SO:ke] synonym: "three_prime_exon_noncoding_region" RELATED [] 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#(DJ)-J-CLUSTER] synonym: "(DJ)-J-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [Term] id: SO:0000486 name: five_prime_exon_noncoding_region def: "The sequence of the 5' exon preceeding the start codon." [SO:ke] synonym: "five_prime_exon_noncoding_region" RELATED [] 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#(VDJ)-J-C-CLUSTER] synonym: "(VDJ)-J-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#(VDJ)-J-CLUSTER] synonym: "(VDJ)-J-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#(VJ)-C-CLUSTER] synonym: "(VJ)-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#(VJ)-J-C-CLUSTER] synonym: "(VJ)-J-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#(VJ)-J-CLUSTER] synonym: "(VJ)-J-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [Term] id: SO:0000492 name: D_gene_recombination_feature is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene [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#3'D-HEPTAMER] synonym: "3'D-HEPTAMER" RELATED [] 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#3'D-NONAMER] synonym: "3'D-NOMAMER" RELATED [] 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#3'D-SPACER] synonym: "3'D-SPACER" RELATED [] is_a: SO:0000563 ! spacer_of_recombination_feature_of_vertebrate_immune_system_gene 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#5'D-HEPTAMER] synonym: "5'D-HEPTAMER" RELATED [] 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#5'D-NONAMER] synonym: "5'D-NONAMER" RELATED [] 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#5'D-SPACER] synonym: "5'-SPACER" RELATED [] synonym: "five_prime_D-spacer" RELATED [] is_a: SO:0000563 ! spacer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence [Term] id: SO:0000499 name: virtual_sequence def: "A continous piece of sequence similar to the 'virtual contig' concept of ensembl." [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#D-(DJ)-C-CLUSTER] synonym: "D-(DJ)-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#D-(DJ)-CLUSTER] synonym: "D-(DJ)-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#D-(DJ)-J-C-CLUSTER] synonym: "D-(DJ)-J-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster [Term] id: SO:0000507 name: pseudogenic_exon 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#D-(DJ)-J-CLUSTER] synonym: "D-(DJ)-J-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#D-J-C-CLUSTER] synonym: "D-J-C-CLUSTER" RELATED [] 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#V-D-GENE] synonym: "V_D_GENE" RELATED [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene [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#J-C-CLUSTER] synonym: "J-C-CLUSTER" RELATED [] 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#J-CLUSTER] synonym: "J-CLUSTER" RELATED [] 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#J-NONAMER] synonym: "J-NONAMER" RELATED [] 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#J-HEPTAMER] synonym: "J-HEPTAMER" RELATED [] 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 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#J-SPACER] synonym: "J-SPACER" RELATED [] is_a: SO:0000563 ! spacer_of_recombination_feature_of_vertebrate_immune_system_gene 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#V-(DJ)-CLUSTER] synonym: "V-(DJ)-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-(DJ)-J-CLUSTER] synonym: "V-(DJ)-J-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-(VDJ)-C-CLUSTER] synonym: "V-(VDJ)-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-(VDJ)-CLUSTER] synonym: "V-(VDJ)-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-(VDJ)-J-CLUSTER] synonym: "V-(VDJ)-J-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-(VJ)-C-CLUSTER] synonym: "V-(VJ)-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-(VJ)-CLUSTER] synonym: "V-(VJ)-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-(VJ)-J-CLUSTER] synonym: "V-(VJ)-J-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-CLUSTER] synonym: "V-CLUSTER" RELATED [] 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#V-D-(DJ)-C-CLUSTER] synonym: "V-D-(DJ)-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-D-(DJ)-CLUSTER] synonym: "V-D-(DJ)-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-D-(DJ)-J-C-CLUSTER] synonym: "V-D-(DJ)-J-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-D-(DJ)-J-CLUSTER] synonym: "V-D-(DJ)-J-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-D-J-C-CLUSTER] synonym: "V-D-J-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-D-J-CLUSTER] synonym: "V-D-J-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-HEPTAMER] synonym: "V-HEPTAMER" RELATED [] 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#V-J-CLUSTER] synonym: "V-J-CLUSTER" RELATED [] 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#V-J-C-CLUSTER] synonym: "V-J-C-CLUSTER" RELATED [] 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#V-NONAMER] synonym: "V-NONAMER" RELATED [] 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#V-SPACER] synonym: "V-SPACER" RELATED [] is_a: SO:0000563 ! spacer_of_recombination_feature_of_vertebrate_immune_system_gene 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#V-RS] synonym: "V-RS" RELATED [] is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene [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#(DJ)-C-CLUSTER] synonym: "(DJ)-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#(DJ)-J-C-CLUSTER] synonym: "(DJ)-J-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#(VDJ)-C-CLUSTER] synonym: "(VDJ)-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-(DJ)-C-CLUSTER] synonym: "V-(DJ)-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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] is_a: SO:0000101 ! transposable_element [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 is_a: SO:0000064 ! gene_by_transcript_attribute [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#line_types] subset: SOFA 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: "RBS" RELATED [] synonym: "Shine-Dalgarno_sequence" RELATED [] synonym: "five_prime_ribosome_binding_site" RELATED [] 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#line_types] 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#line_types] synonym: "five_prime_-clip" RELATED [] 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#5'D-RS] synonym: "5'RS" RELATED [] synonym: "five_prime_D-recombination_signal_sequence" RELATED [] 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#line_types] synonym: "3'-clip" RELATED [] 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/ligmdb/LIGMlect?query=7#C-CLUSTER] synonym: "C-CLUSTER" RELATED [] 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#D-CLUSTER] synonym: "D-CLUSTER" RELATED [] 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#D-J-CLUSTER] synonym: "D-J-CLUSTER" RELATED [] 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: " 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin/T-cell receptor gene" [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#HEPTAMER] synonym: "HEPTAMER" RELATED [] is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene [Term] id: SO:0000562 name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene [Term] id: SO:0000563 name: spacer_of_recombination_feature_of_vertebrate_immune_system_gene is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene [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#V-(DJ)-J-C-CLUSTER] synonym: "V-(DJ)-J-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-(VDJ)-J-C-CLUSTER] synonym: "V-(VDJ)-J-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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#V-(VJ)-J-C-CLUSTER] synonym: "V-(VJ)-J-C-CLUSTER" RELATED [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_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_promotor is_a: SO:0000167 ! promoter [Term] id: SO:0000569 name: retrotransposed_protein_coding_gene alt_id: SO:0100042 synonym: "captured_pseudogene" RELATED [] is_a: SO:0000010 ! protein_coding_gene 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#3'D-RS] synonym: "3'D-RS" RELATED [] synonym: "three_prime_D-recombination_signal_sequence" RELATED [] is_a: SO:0000492 ! D_gene_recombination_feature [Term] id: SO:0000571 name: miRNA_gene is_a: SO:0000011 ! non_protein_coding_gene [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#D-J-GENE] synonym: "D_J_GENE" RELATED [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene 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_gene is_a: SO:0000011 ! non_protein_coding_gene [Term] id: SO:0000574 name: DJ_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#V-D-J-GENE] synonym: "V-D-J-GENE" RELATED [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene 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_gene is_a: SO:0000011 ! non_protein_coding_gene [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#V-J-GENE] synonym: "V-J-GENE" RELATED [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene 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_gene is_a: SO:0000011 ! non_protein_coding_gene [Term] id: SO:0000579 name: edited_transcript_feature def: "A locatable feature on a transcript that is edited." [SO:ma] relationship: part_of SO:0000673 ! transcript [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 relationship: adjacent_to SO:0000234 ! mRNA [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" RELATED [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000584 name: tmRNA def: "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_gene is_a: SO:0000578 ! snoRNA_gene [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 ! intron is_a: SO:0000374 ! ribozyme [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 [Term] id: SO:0000591 name: pseudoknot def: "A stem-loop RNA structure where nucleotides in the loop participate in complementary interactions with a region of RNA downstream of the stem-loop." [https://www.ncbi.nlm.nih.gov/pubmed/12519954] 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." [https://www.ncbi.nlm.nih.gov/pubmed/10334330] synonym: "H-pseudoknot" RELATED [] 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: "C/D_box_snoRNA" RELATED [] is_a: SO:0000275 ! snoRNA [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: "H/ACA_box_snoRNA" RELATED [] is_a: SO:0000275 ! snoRNA [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_a: SO:0000116 ! edited_transcript [Term] id: SO:0000598 name: transcript_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_a: SO:0000116 ! edited_transcript [Term] id: SO:0000599 name: transcript_edited_by_C_to_U_substitution is_a: SO:0000116 ! edited_transcript [Term] id: SO:0000600 name: transcript_edited_by_A_to_I_substitution is_a: SO:0000116 ! edited_transcript [Term] id: SO:0000601 name: transcript_edited_by_G_addition is_a: SO:0000116 ! edited_transcript [Term] id: SO:0000602 name: guide_RNA def: "A short 3'-uridylated RNA that can form a perfect duplex (except for the oligoU tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html] subset: SOFA synonym: "gRNA" RELATED [] 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] 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_gene is_a: SO:0000578 ! snoRNA_gene [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/] 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 relationship: adjacent_to SO:0000234 ! mRNA [Term] id: SO:0000611 name: branch_site def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke] subset: SOFA synonym: "branch_point" RELATED [] relationship: part_of SO:0000662 ! spliceosomal_intron [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 relationship: part_of SO:0000662 ! spliceosomal_intron [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:0000167 ! promoter is_a: SO:0000752 ! gene_group_regulatory_region [Term] id: SO:0000614 name: bacterial_terminator def: "A terminator signal for bacterial transcription." [SO:ke] is_a: SO:0000141 ! terminator [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:0000141 ! terminator [Term] id: SO:0000616 name: transcription_end_site def: "The site where transcription ends." [SO:ke] subset: SOFA is_a: SO:0000699 ! junction relationship: part_of SO:0000185 ! primary_transcript [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 relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 [Term] id: SO:0000620 name: B_box relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 [Term] id: SO:0000621 name: RNApol_III_promoter_type_3 is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000622 name: C_box relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 [Term] id: SO:0000623 name: snRNA_gene is_a: SO:0000011 ! non_protein_coding_gene [Term] id: SO:0000624 name: telomere def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenence 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#s] subset: SOFA is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000626 name: chromosomal_regulatory_element relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0000627 name: insulator subset: SOFA synonym: "insulator_element" RELATED [] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000628 name: chromosomal_structural_element subset: SOFA relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0000629 name: five_prime_open_reading_frame relationship: part_of SO:0000204 ! five_prime_UTR [Term] id: SO:0000630 name: upstream_AUG_codon relationship: part_of SO:0000203 ! UTR [Term] id: SO:0000631 name: polycistronic_primary_transcript def: "A primary transcript encoding for more than one protein product." [SO:ke] is_a: SO:0000078 ! polycistronic_transcript [Term] id: SO:0000632 name: monocistronic_primary_transcript def: "A primary transcript encoding for more than one protein product." [SO:ke] is_a: SO:0000665 ! monocistronic_transcript [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" RELATED [] is_a: SO:0000665 ! monocistronic_transcript [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 ! polycistronic_transcript [Term] id: SO:0000635 name: mini_exon_donor_RNA def: "The 3' site of a mini-exon which is trans-spliced on to the 5'end of a mature mRNA." [SO:ke] synonym: "mini-exon_donor_RNA" RELATED [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000636 name: spliced_leader_RNA synonym: "mini-exon" RELATED [] relationship: part_of SO:0000635 ! mini_exon_donor_RNA [Term] id: SO:0000637 name: engineered_plasmid synonym: "engineered_plasmid_gene" RELATED [] is_a: SO:0000098 ! plasmid_gene is_a: SO:0000280 ! engineered_gene [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] relationship: part_of SO:0000209 ! rRNA_primary_transcript [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_gene is_a: SO:0000011 ! non_protein_coding_gene [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 [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: "Small RNA molecule that is the product of a longerexogenous or endogenous dsRNA, which is either a bimolecular duplexe or very longhairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulatefrom both strands of the dsRNA. sRNAs trigger the cleavage of their target molecules." [PMID:12592000] subset: SOFA synonym: "small_interfering_RNA" RELATED [] 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" RELATED [] 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" RELATED [] 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" RELATED [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000650 name: small_subunit_rRNA is_a: SO:0000252 ! rRNA [Term] id: SO:0000651 name: large_subunit_rRNA is_a: SO:0000252 ! rRNA [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 is_a: SO:0000252 ! rRNA [Term] id: SO:0000653 name: rRNA_28S def: "A component of the large ribosomal subunit." [SO:ke] subset: SOFA synonym: "23S_rRNA" RELATED [] synonym: "28S_rRNA" RELATED [] is_a: SO:0000252 ! rRNA [Term] id: SO:0000654 name: maxi_circle_gene synonym: "maxi-circle" RELATED [] is_a: SO:0000088 ! mt_gene [Term] id: SO:0000655 name: ncRNA def: "An mRNA sequence that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] comment: 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" RELATED [] is_a: SO:0000233 ! processed_transcript [Term] id: SO:0000656 name: stRNA_gene is_a: SO:0000011 ! non_protein_coding_gene [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" RELATED [] is_a: SO:0000657 ! repeat_region [Term] id: SO:0000659 name: tmRNA_gene is_a: SO:0000011 ! non_protein_coding_gene [Term] id: SO:0000660 name: DNA_invertase_target_sequence is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000661 name: intron_attribute is_a: SO:0000401 ! gene_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_gene is_a: SO:0000011 ! non_protein_coding_gene [Term] id: SO:0000664 name: introgressed_chromosome_region relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0000665 name: monocistronic_transcript is_a: SO:0000115 ! transcript_feature [Term] id: SO:0000666 name: mobile_intron is_a: SO:0000661 ! intron_attribute [Term] id: SO:0000667 name: insertion def: "A region of sequence identified as having been inserted." [SO:ke] subset: SOFA is_a: SO:0000001 ! region is_a: SO:0000109 ! sequence_variant 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 relationship: member_of SO:0000704 ! gene [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" RELATED [] 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 ! splice_acceptor_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 ! splice_donor_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" RELATED [] is_a: SO:0000164 ! splice_acceptor_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" RELATED [] is_a: SO:0000163 ! splice_donor_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-canonical_start_codon" RELATED [] synonym: "non_ATG_start_codon" RELATED [] 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." [https://www.ncbi.nlm.nih.gov/pubmed/12403462] 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] relationship: part_of 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 occured." [SO:ke] subset: SOFA is_a: SO:0000109 ! sequence_variant 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 is_a: SO:0000064 ! gene_by_transcript_attribute [Term] id: SO:0000691 name: translocation_site def: "The space between two bases in a sequence which marks the position where a translocation has occurred." [SO:ke] relationship: position_of SO:0000049 ! translocate [Term] id: SO:0000692 name: gene_with_dicistronic_transcript is_a: SO:0000690 ! gene_with_polycistronic_transcript [Term] id: SO:0000693 name: gene_with_recoded_mRNA is_a: SO:0000064 ! gene_by_transcript_attribute [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" RELATED [] is_a: SO:1000008 ! point_mutation [Term] id: SO:0000695 name: reagent def: "A sequence used in experiment." [SO:ke] 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" RELATED [] is_a: SO:0000695 ! reagent [Term] id: SO:0000697 name: gene_with_stop_codon_read_through is_a: SO:0000693 ! gene_with_recoded_mRNA [Term] id: SO:0000698 name: gene_with_stop_codon_redefined_as_pyrrolysine is_a: SO:0000697 ! gene_with_stop_codon_read_through [Term] id: SO:0000699 name: junction def: "A junction refers to an interbase location of zero in a sequence." [SO:ke] subset: SOFA synonym: "boundary" RELATED [] is_a: SO:0000110 ! located_sequence_feature [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 locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions" [SO:rd] 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 ! splice_acceptor_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" RELATED [] is_a: SO:0000163 ! splice_donor_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 is_a: SO:0000697 ! gene_with_stop_codon_read_through [Term] id: SO:0000711 name: gene_with_mRNA_recoded_by_translational_bypass is_a: SO:0000693 ! gene_with_recoded_mRNA [Term] id: SO:0000712 name: gene_with_transcript_with_translational_frameshift is_a: SO:0000693 ! gene_with_recoded_mRNA [Term] id: SO:0000713 name: DNA_motif 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 is_a: SO:0000714 ! nucleotide_motif [Term] id: SO:0000716 name: dicistronic_mRNA synonym: "dicistronic_processed_transcript" RELATED [] is_a: SO:0000079 ! dicistronic_transcript [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 does not contain the start or stop codon." [SO:rb] comment: This term was added after a request by SGD.nAgust 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 interupted 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 comment: requested by Michael on 19 Nov 2004 is_a: SO:0000101 ! transposable_element [Term] id: SO:0000721 name: gene_with_dicistronic_primary_transcript comment: Requested by Michael, 19 nov 2004 is_a: SO:0000692 ! gene_with_dicistronic_transcript [Term] id: SO:0000722 name: gene_with_dicistronic_mRNA comment: Requested by MA nov 19 2004 synonym: "gene_with_dicistronic_processed_transcript" RELATED [] is_a: SO:0000692 ! gene_with_dicistronic_transcript [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" RELATED [] is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000724 name: origin_of_transfer def: "A region of a DNA molecule whre transfer is initiated during the process of conjugation or mobilization." [http:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types] subset: SOFA synonym: "oriT" RELATED [] is_a: SO:0000001 ! region [Term] id: SO:0000725 name: transit_peptide def: "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." [http:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types] comment: Added to bring SO inline with the embl ddbj genbank feature table. subset: SOFA relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0000726 name: repeat_unit def: "A single repeat element." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types] comment: Added to comply with the feature table. is_a: SO:0000657 ! repeat_region [Term] id: SO:0000727 name: TF_module 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: "CRM" RELATED [] synonym: "cis_regulatory_module" RELATED [] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000728 name: intein relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0000729 name: intein_containing_protein_coding_gene is_a: SO:0000010 ! protein_coding_gene [Term] id: SO:0000730 name: gap def: "A gap in the sequence of known length. The unkown 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 comment: added because of request by MO people. is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000732 name: predicted is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000733 name: feature_attribute 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#exemplar_mRNA] comment: Added for the MO people. is_a: SO:0000082 ! processed_transcript_attribute [Term] id: SO:0000735 name: sequence_location is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000736 name: organelle_location is_a: SO:0000735 ! sequence_location [Term] id: SO:0000737 name: mitochondrial_sequence is_a: SO:0000736 ! organelle_location [Term] id: SO:0000738 name: nuclear_sequence is_a: SO:0000736 ! organelle_location [Term] id: SO:0000739 name: nucleomorphic_sequence is_a: SO:0000736 ! organelle_location [Term] id: SO:0000740 name: plastid_sequence is_a: SO:0000736 ! organelle_location [Term] id: SO:0000741 name: kinetoplast_sequence is_a: SO:0000737 ! mitochondrial_sequence [Term] id: SO:0000742 name: maxicircle_sequence is_a: SO:0000737 ! mitochondrial_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_sequence 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_sequence is_a: SO:0000735 ! sequence_location [Term] id: SO:0000752 name: gene_group_regulatory_region is_a: SO:0005836 ! regulatory_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000753 name: clone_insert relationship: part_of SO:0000151 ! clone [Term] id: SO:0000754 name: lambda_vector is_a: SO:0000440 ! vector relationship: part_of SO:0000160 ! lambda_clone [Term] id: SO:0000755 name: plasmid_vector is_a: SO:0000440 ! vector relationship: part_of SO:0000759 ! plasmid_clone [Term] id: SO:0000756 name: cDNA def: "DNA synthesized by reverse transcriptase using RNA as a template" [SO:ma] is_a: SO:0000695 ! reagent relationship: part_of SO:0000317 ! cDNA_clone [Term] id: SO:0000757 name: single_stranded_cDNA is_a: SO:0000756 ! cDNA [Term] id: SO:0000758 name: double_stranded_cDNA is_a: SO:0000756 ! cDNA [Term] id: SO:0000759 name: plasmid_clone is_a: SO:0000151 ! clone [Term] id: SO:0000760 name: YAC_clone is_a: SO:0000151 ! clone [Term] id: SO:0000761 name: phagemid_clone is_a: SO:0000151 ! clone [Term] id: SO:0000762 name: PAC_clone synonym: "P1_clone" RELATED [] is_a: SO:0000151 ! clone [Term] id: SO:0000763 name: fosmid_clone is_a: SO:0000151 ! clone [Term] id: SO:0000764 name: BAC_clone is_a: SO:0000151 ! clone [Term] id: SO:0000765 name: cosmid_clone is_a: SO:0000151 ! clone [Term] id: SO:0000766 name: pyrrolysyl_tRNA is_a: SO:0000253 ! tRNA [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." [Indiana:kw] comment: Added in response to comment from Kelly Williams from Indiana.nhttp://nar.oxfordjournals.org/cgi/content/full/32/15/4531n10 Nov, 2005 relationship: part_of SO:0000584 ! tmRNA [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." [Indiana:kw] comment: Added in response to Kelly Williams from Indiananhttp://nar.oxfordjournals.org/cgi/content/full/32/15/4531n10 nov 2005 relationship: part_of SO:0000584 ! tmRNA [Term] id: SO:0000771 name: QTL def: "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.cbi.pku.edu.cn/tu/qtls/] comment: Added in respose to request by Simon Twigger November 14th 2005 is_a: SO:0000001 ! region [Term] id: SO:0000772 name: genomic_island comment: Genomic islands are transmissible elements characterized by large size (>10kb). is_a: SO:0000001 ! region [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/nrmicro884 nGENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMSnUlrich 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 comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands.nNature Reviews Microbiology 2, 414-424 (2004); doi:10.1038/nrmicro884 nGENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMSnUlrich 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.nnEvolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA genenJohn T. Sullivan and Clive W. RonsonnPNAS 1998 Apr 28 95 (9) 5145-5149n is_a: SO:0000772 ! genomic_island [Term] id: SO:0000777 name: pseudogenic_rRNA comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. subset: SOFA is_a: SO:0000462 ! pseudogenic_region [Term] id: SO:0000778 name: pseudogenic_tRNA comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. subset: SOFA is_a: SO:0000462 ! pseudogenic_region [Term] id: SO:0001044 name: nuclear_mt_pseudogene synonym: "NUMT" RELATED [] synonym: "nuclear_mitochondrial_pseudogene" RELATED [] is_a: SO:0000042 ! pseudogene_attribute [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:0000001 ! region relationship: member_of SO:0000704 ! gene [Term] id: SO:0005837 name: snRNA_4.5S_primary_transcript def: "A primary transcript encoding a 4.5S snRNA." [SO:ke] synonym: "4.5S_snRNA_primary_transcript" RELATED [] is_a: SO:0000231 ! snRNA_primary_transcript [Term] id: SO:0005839 name: snRNA_4.5S synonym: "4.5S_snRNA" RELATED [] is_a: SO:0000274 ! snRNA [Term] id: SO:0005841 name: methylation_guide_snoRNA is_a: SO:0000275 ! snoRNA [Term] id: SO:0005843 name: rRNA_cleavage_snoRNA is_a: SO:0000275 ! snoRNA [Term] id: SO:0005845 name: single_exon is_a: SO:0000147 ! exon [Term] id: SO:0005847 name: member_of_gene_cassette_array is_a: SO:0005848 ! member_of_gene_cassette [Term] id: SO:0005848 name: member_of_gene_cassette is_a: SO:0000081 ! member_gene_array [Term] id: SO:0005849 name: member_of_gene_subarray is_a: SO:0000081 ! member_gene_array [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] 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:0005851 ! gene_array [Term] id: SO:0005853 name: gene_cassette def: "A non-functional gene that, when captured by recombination forms a functional gene." [SO:ma] comment: This would include\, for example\, the mating type gene cassettes of S. cerevisiae. is_a: SO:0005855 ! gene_group [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: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 is_a: SO:0000253 ! tRNA [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:0000330 ! conserved_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:0000109 ! sequence_variant 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 mutation event where a single DNA nucleotide changes into another nucleotide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] 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 synonym: "(Drosophila)Df" RELATED [] synonym: "(bacteria)&Dgr;" 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: "(Drosophila)In" RELATED [] synonym: "(bacteria)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:0000109 ! sequence_variant [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:0000109 ! sequence_variant relationship: sequence_of SO:0000047 ! invert [Term] id: SO:1000037 name: chromosomal_duplication synonym: "(Drosophila)Dp" RELATED [] synonym: "(fungi)Dp" RELATED [] is_a: SO:0000550 ! aneuploid_chromosome is_a: SO:1000183 ! chromosome_structure_variation [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 ! consequences_of_mutation [Term] id: SO:1000050 name: 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: 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: 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 ! amino_acid_coding_codon_change_in_transcript [Term] id: SO:1000056 name: 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: 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 ! amino_acid_coding_codon_change_in_transcript [Term] id: SO:1000058 name: 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" RELATED [] is_a: SO:1000056 ! amino_acid_coding_codon_change_in_transcript [Term] id: SO:1000059 name: 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 ! non_synonymous_codon_change_in_transcript [Term] id: SO:1000060 name: 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 ! missense_codon_change_in_transcript [Term] id: SO:1000061 name: 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 ! missense_codon_change_in_transcript [Term] id: SO:1000062 name: 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 ! amino_acid_coding_codon_change_in_transcript [Term] id: SO:1000063 name: terminator_codon_change_in_transcript 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: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000064 ! mutation_affecting_reading_frame [Term] id: SO:1000066 name: plus_1_frameshift_mutation is_a: SO:1000065 ! frameshift_mutation [Term] id: SO:1000067 name: minus_1_frameshift_mutation is_a: SO:1000065 ! frameshift_mutation [Term] id: SO:1000068 name: plus_2_frameshift_mutation is_a: SO:1000065 ! frameshift_mutation [Term] id: SO:1000069 name: minus_2_frameshift_mutation 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: "Mutation 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 ! consequences_of_mutation [Term] id: SO:1000072 name: splice_donor_mutation is_a: SO:1000071 ! mutation_affecting_splicing is_a: SO:1000074 ! cryptic_splice_activator_mutation [Term] id: SO:1000073 name: splice_acceptor_mutation is_a: SO:1000071 ! mutation_affecting_splicing [Term] id: SO:1000074 name: cryptic_splice_activator_mutation def: "Mutation 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 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 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 is_a: SO:1000049 ! mutation_affecting_transcript [Term] id: SO:1000086 name: mutation_decreasing_level_of_transcript is_a: SO:1000085 ! mutation_affecting_level_of_transcript [Term] id: SO:1000087 name: mutation_increasing_level_of_transcript 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 ! consequences_of_mutation [Term] id: SO:1000089 name: 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: 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: 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 ! uncharacterised_change_of_translational_product [Term] id: SO:1000092 name: complex_change_of_translational_product def: "Any mutation effect that is known at nucleotide level but can not 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: amino_acid_substitution def: "The replacement of a single amino acid by an other." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence [Term] id: SO:1000094 name: conservative_amino_acid_substitution is_a: SO:1000093 ! amino_acid_substitution [Term] id: SO:1000095 name: nonconservative_amino_acid_substitution is_a: SO:1000093 ! amino_acid_substitution [Term] id: SO:1000096 name: 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: 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: 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: 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: polypeptide_N_terminal_elongation def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "polypeptide_N-terminal_elongation" RELATED [] is_a: SO:1000099 ! polypeptide_elongation [Term] id: SO:1000101 name: polypeptide_C_terminal_elongation def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "polypeptide_C-terminal_elongation" RELATED [] is_a: SO:1000099 ! 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: inframe_polypeptide_N_terminal_elongation synonym: "inframe_polypeptide_N-terminal_elongation" RELATED [] is_a: SO:1000100 ! polypeptide_N_terminal_elongation [Term] id: SO:1000107 name: out_of_frame_polypeptide_N_terminal_elongation synonym: "out_of_frame_polypeptide_N-terminal_elongation" RELATED [] is_a: SO:1000100 ! polypeptide_N_terminal_elongation [Term] id: SO:1000108 name: inframe_polypeptide_C_terminal_elongation synonym: "inframe_polypeptide_C-terminal_elongation" RELATED [] is_a: SO:1000101 ! polypeptide_C_terminal_elongation [Term] id: SO:1000109 name: out_of_frame_polypeptide_C_terminal_elongation synonym: "out_of_frame_polypeptide_C-terminal_elongation" RELATED [] is_a: SO:1000101 ! polypeptide_C_terminal_elongation [Term] id: SO:1000110 name: frame_restoring_mutation is_a: SO:1000065 ! frameshift_mutation [Term] id: SO:1000111 name: mutation_affecting_3D_structure_of_polypeptide synonym: "mutation_affecting_3D-structure_of_polypeptide" RELATED [] is_a: SO:1000088 ! mutation_affecting_translational_product [Term] id: SO:1000112 name: no_3D_structural_change is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide [Term] id: SO:1000113 name: uncharacterised_3D_structural_change is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide [Term] id: SO:1000114 name: partially_characterised_3D_structural_change is_a: SO:1000113 ! uncharacterised_3D_structural_change [Term] id: SO:1000115 name: complex_3D_structural_change is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide [Term] id: SO:1000116 name: 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: 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: inactive_ligand_binding_site is_a: SO:1000118 ! loss_of_function_of_polypeptide [Term] id: SO:1000120 name: inactive_catalytic_site is_a: SO:1000119 ! inactive_ligand_binding_site [Term] id: SO:1000121 name: polypeptide_localization_affected is_a: SO:1000117 ! mutation_affecting_polypeptide_function [Term] id: SO:1000122 name: polypeptide_post_translational_processing_affected synonym: "polypeptide_post-translational_processing_affected" RELATED [] is_a: SO:1000117 ! mutation_affecting_polypeptide_function is_a: SO:1000118 ! 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: partial_loss_of_function_of_polypeptide synonym: "partial_loss-of-function_of_polypeptide" RELATED [] is_a: SO:1000118 ! loss_of_function_of_polypeptide [Term] id: SO:1000125 name: gain_of_function_of_polypeptide synonym: "gain-of-function_of_polypeptide" RELATED [] is_a: SO:1000117 ! mutation_affecting_polypeptide_function [Term] id: SO:1000126 name: mutation_affecting_transcript_secondary_structure is_a: SO:1000079 ! mutation_affecting_transcript_sequence [Term] id: SO:1000127 name: compensatory_transcript_secondary_structure_mutation is_a: SO:1000126 ! mutation_affecting_transcript_secondary_structure [Term] id: SO:1000132 name: consequences_of_mutation is_a: SO:0000000 ! Sequence_Ontology [Term] id: SO:1000134 name: 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" RELATED [] is_a: SO:1000042 ! compound_chromosome [Term] id: SO:1000140 name: hetero_compound_chromosome synonym: "hetero-compound_chromosome" RELATED [] 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" RELATED [] 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 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: 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: 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 ! uncharacterised_change_in_transcript [Term] id: SO:1000180 name: mutation_affecting_gene_structure is_a: SO:1000132 ! consequences_of_mutation [Term] id: SO:1000181 name: gene_fusion is_a: SO:1000180 ! mutation_affecting_gene_structure [Term] id: SO:1000182 name: chromosome_number_variation 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 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 is_a: SO:0000115 ! transcript_feature [Term] id: SO:1001188 name: alternatively_spliced_transcript_encoding_1_polypeptide is_a: SO:1001187 ! alternatively_spliced_transcript [Term] id: SO:1001189 name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide is_a: SO:1001187 ! alternatively_spliced_transcript [Term] id: SO:1001190 name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_same_start_codon_different_stop_codon is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide is_a: SO:1001194 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping [Term] id: SO:1001191 name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_same_stop_codon is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide is_a: SO:1001194 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping [Term] id: SO:1001192 name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide [Term] id: SO:1001193 name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_overlapping is_a: SO:1001192 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon is_a: SO:1001194 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping [Term] id: SO:1001194 name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide [Term] id: SO:1001195 name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_not_overlapping is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide [Term] id: SO:1001196 name: cryptogene is_a: SO:0000011 ! non_protein_coding_gene [Term] id: SO:1001197 name: dicistronic_primary_transcript is_a: SO:0000079 ! dicistronic_transcript [Term] id: SO:1001217 name: member_of_regulon is_a: SO:0000081 ! member_gene_array [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_a: SO:1001192 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon is_a: SO:1001195 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_not_overlapping [Term] id: SO:1001246 name: CDS_independently_known is_a: SO:1001255 ! status_of_coding_sequence [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." [MA:SO] is_a: SO:1001254 ! CDS_predicted [Term] id: SO:1001249 name: CDS_supported_by_domain_match_data is_a: SO:1001254 ! CDS_predicted [Term] id: SO:1001251 name: CDS_supported_by_sequence_similarity_data is_a: SO:1001254 ! CDS_predicted [Term] id: SO:1001254 name: CDS_predicted is_a: SO:1001255 ! status_of_coding_sequence [Term] id: SO:1001255 name: status_of_coding_sequence is_a: SO:0000400 ! sequence_attribute [Term] id: SO:1001259 name: CDS_supported_by_EST_or_cDNA_data is_a: SO:1001254 ! CDS_predicted [Term] id: SO:1001260 name: internal_Shine_Dalgarno_sequence def: "A Shine Delgarno sequence that is upstream of a non-5' CDS in a polycistronic mRNA." [SO:ke] 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." [https://www.ncbi.nlm.nih.gov/pubmed/8811194] is_a: SO:0000115 ! transcript_feature [Term] id: SO:1001262 name: minus_1_translational_frameshift is_a: SO:0000118 ! transcript_with_translational_frameshift [Term] id: SO:1001263 name: plus_1_translational_frameshift is_a: SO:0000118 ! transcript_with_translational_frameshift [Term] id: SO:1001264 name: mRNA_recoded_by_translational_bypass def: "A gene whose mRNA is translated by ribosomes that suspend translation at a particular codon and resume translation at a particular non-overlapping downstream codon." [https://www.ncbi.nlm.nih.gov/pubmed/8811194] is_a: SO:1001261 ! recoded_mRNA [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 ! recoded_mRNA [Term] id: SO:1001266 name: stop_codon_redefinition_as_selenocysteine is_a: SO:1001267 ! stop_codon_readthrough [Term] id: SO:1001267 name: stop_codon_readthrough is_a: SO:1001265 ! mRNA_recoded_by_codon_redefinition [Term] id: SO:1001268 name: recoding_stimulatory_region def: "A site in an mRNA sequence that stimulates the recoding of the same mRNA." [https://www.ncbi.nlm.nih.gov/pubmed/12519954] synonym: "recoding_stimulatory_signal" RELATED [] relationship: part_of SO:0000234 ! mRNA [Term] id: SO:1001269 name: four_bp_start_codon def: "A non-canonical start codon with 4 pase pairs." [SO:ke] synonym: "4bp_start_codon" RELATED [] is_a: SO:0000680 ! non_canonical_start_codon [Term] id: SO:1001270 name: stop_codon_redefinition_as_pyrrolysine is_a: SO:1001267 ! stop_codon_readthrough [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:0000009 ! gene_class [Term] id: SO:1001277 name: three_prime_recoding_site is_a: SO:1001268 ! recoding_stimulatory_region [Term] id: SO:1001279 name: three_prime_stem_loop_structure def: "The stem-loop secondary structural element downstream of the redefined region." [SO:ke] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001280 name: five_prime_recoding_site def: "The recoding signal found 5' of the redefined codon." [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." [SO:ke] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001282 name: UAG_stop_codon_signal is_a: SO:1001288 ! stop_codon_signal [Term] id: SO:1001283 name: UAA_stop_codon_signal 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 is_a: SO:1001288 ! stop_codon_signal [Term] id: SO:1001286 name: three_prime_repeat_recoding_signal def: "It is a downstream sequence important for recoding that contains repetitive elements." [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." [https://www.ncbi.nlm.nih.gov/pubmed/8709208] is_a: SO:1001277 ! three_prime_recoding_site [Term] id: SO:1001288 name: stop_codon_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 domain: SO:0000110 ! located_sequence_feature range: SO:0000110 ! located_sequence_feature is_symmetric: true [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 domain: SO:0000085 ! gene_by_genome_location range: SO:0000704 ! gene is_obsolete: true [Typedef] id: homologous_to name: homologous_to is_symmetric: true is_a: similar_to ! similar_to [Typedef] id: member_of name: member_of comment: A subtype of part_of.ninverse is collection_of.nWinston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. subset: SOFA is_a: part_of ! part_of [Typedef] id: non_functional_homolog_of name: non_functional_homolog_of def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke] is_a: homologous_to ! homologous_to [Typedef] id: orthologous_to name: orthologous_to is_symmetric: true is_a: homologous_to ! homologous_to [Typedef] id: paralogous_to name: paralogous_to 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 is_symmetric: true