format-version: 1.2
date: 17:01:2008 20:43
saved-by: kareneilbeck
auto-generated-by: OBO-Edit 1.101
subsetdef: biosapiens "biosapiens protein feature ontology"
subsetdef: SOFA "SO feature annotation"
default-namespace: sequence
remark: autogenerated-by\:   DAG-Edit version 1.417\nsaved-by\:       eilbeck\ndate\:         Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $

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

[Term]
id: SO:0000001
name: region
def: "A sequence_feature with an extent greater than zero." [SO:ke]
subset: SOFA
synonym: "sequence" EXACT []
is_a: SO:0000110 ! sequence_feature

[Term]
id: SO:0000002
name: sequence_secondary_structure
def: "A folded sequence." [SO:ke]
is_a: SO:0000001 ! region

[Term]
id: SO:0000003
name: G_quartet
def: "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.library.csi.cuny.edu/~davis/molbiol/lecture_notes/post-transcriptional_processes/RNACapping.pdf]
synonym: "G-quadruplex" EXACT []
synonym: "G-quartet" EXACT []
synonym: "G_quadruplex" EXACT []
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000004
name: interior_coding_exon
subset: SOFA
is_a: SO:0000195 ! coding_exon

[Term]
id: SO:0000005
name: satellite_DNA
def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000006
name: PCR_product
def: "A region amplified by a PCR reaction." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "amplicon" RELATED []
synonym: "PCR product" EXACT []
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000007
name: read_pair
def: "A pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000149 ! contig

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

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

[Term]
id: SO:0000010
name: protein_coding
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000011
name: non_protein_coding
is_a: SO:0000401 ! gene_attribute

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

[Term]
id: SO:0000013
name: scRNA
def: "Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]
subset: SOFA
synonym: " small cytoplasmic RNA" EXACT []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000012 ! scRNA_primary_transcript

[Term]
id: SO:0000014
name: INR_motif
def: "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739]
synonym: "DMp2" RELATED []
synonym: "initiator" EXACT []
synonym: "initiator motif" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0000015
name: DPE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739\:12537576]
synonym: "CRWMGCGWKCGCTTS" NARROW []
synonym: "downstream core promoter element" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0000016
name: BRE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739]
synonym: " transcription factor B-recognition element" EXACT []
synonym: "B-recognition element" EXACT []
synonym: "TFIIB recognition element" RELATED []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0000017
name: PSE_motif
def: "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]
synonym: "proximal sequence element" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0000018
name: linkage_group
def: "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046]
is_a: SO:0000001 ! region

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

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

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

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

[Term]
id: SO:0000024
name: Sarcin_like_RNA_motif
def: "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://proton.chem.yale.edu/pdf/7897662.pdf]
synonym: " sarcin/ricin RNA domain" EXACT []
synonym: "sarcin/ricin domain" EXACT []
synonym: "sarcin/ricin loop" EXACT []
is_a: SO:0000021 ! asymmetric_RNA_internal_loop

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

[Term]
id: SO:0000026
name: RNA_junction_loop
is_a: SO:0000715 ! RNA_motif

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

[Term]
id: SO:0000028
name: base_pair
is_a: SO:0000002 ! sequence_secondary_structure

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

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

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

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

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

[Term]
id: SO:0000034
name: morpholino_oligo
def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/Morpholinos/morpholinos.HTML]
synonym: "morpholino oligo" EXACT []
is_a: SO:0000696 ! implied link automatically realized ! oligo
intersection_of: SO:0000696 ! oligo
intersection_of: has_quality SO:0001183 ! morpholino
relationship: has_quality SO:0001183 ! implied link automatically realized ! morpholino

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

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

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

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

[Term]
id: SO:0000039
name: match_part
def: "A part of a match, for example an hsp from blast isa match_part." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
relationship: part_of SO:0000343 ! match

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

[Term]
id: SO:0000041
name: operation
def: "An operation that can be applied to a sequence, that results in a change." [SO:ke]
is_a: SO:0000000 ! Sequence_Ontology
disjoint_from: SO:0000110 ! sequence_feature
disjoint_from: SO:0000240 ! chromosome_variation
disjoint_from: SO:0000400 ! sequence_attribute
disjoint_from: SO:0000968 ! replication_mode
disjoint_from: SO:0001026 ! genome
disjoint_from: SO:0001060 ! sequence_variant
disjoint_from: SO:1000132 ! mutation

[Term]
id: SO:0000042
name: pseudogene_attribute
def: "An attribute of a pseudogene (SO:0000336)." [SO:ma]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000043
name: processed_pseudogene
def: "A pseudogene that is processed." [SO:xp]
synonym: "pseudogene by reverse transcription" RELATED []
is_a: SO:0000336 ! implied link automatically realized ! pseudogene
intersection_of: SO:0000336 ! pseudogene
intersection_of: has_quality SO:0000900 ! processed
relationship: has_quality SO:0000900 ! implied link automatically realized ! processed

[Term]
id: SO:0000044
name: pseudogene_by_unequal_crossing_over
def: "A pseudogene caused by unequal crossing over at recombination." [SO:ke]
is_a: SO:0000336 ! implied link automatically realized ! pseudogene
intersection_of: SO:0000336 ! pseudogene
intersection_of: has_quality SO:0000901 ! unequally_crossed_over
relationship: has_quality SO:0000901 ! implied link automatically realized ! unequally_crossed_over

[Term]
id: SO:0000045
name: delete
def: "To remove a subsection of sequence." [SO:ke]
is_a: SO:0000041 ! operation

[Term]
id: SO:0000046
name: insert
def: "To insert a subsection of sequence." [SO:ke]
is_a: SO:0000041 ! operation

[Term]
id: SO:0000047
name: invert
def: "To invert a subsection of sequence." [SO:ke]
is_a: SO:0000041 ! operation

[Term]
id: SO:0000048
name: substitute
def: "To substitute a subsection of sequence for another." [SO:ke]
is_a: SO:0000041 ! operation

[Term]
id: SO:0000049
name: translocate
def: "To translocate a subsection of sequence." [SO:ke]
is_a: SO:0000041 ! operation

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

[Term]
id: SO:0000051
name: probe
def: "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]
is_a: SO:0000695 ! reagent

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

[Term]
id: SO:0000053
name: mutation_affecting_regulatory_region
def: "A kind of mutation that affects a regulatory region of a gene." [SO:ke]
is_a: SO:1000132 ! mutation

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

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

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

[Term]
id: SO:0000057
name: operator
def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]
subset: SOFA
synonym: "operator segment" EXACT []
is_a: SO:0000752 ! gene_group_regulatory_region

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

[Term]
id: SO:0000059
name: nuclease_binding_site
is_a: SO:0000410 ! protein_binding_site

[Term]
id: SO:0000060
name: compound_chromosome_arm
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:0000061
name: restriction_enzyme_binding_site
synonym: "restriction endonuclease binding site" EXACT []
synonym: "restriction endonuclease recognition site" RELATED []
synonym: "restriction enzyme recognition site" RELATED []
is_a: SO:0000059 ! nuclease_binding_site

[Term]
id: SO:0000062
name: deficient_intrachromosomal_transposition
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:0000063
name: deficient_interchromosomal_transposition
is_a: SO:1000155 ! interchromosomal_transposition

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

[Term]
id: SO:0000065
name: free_chromosome_arm
is_a: SO:1000183 ! chromosome_structure_variation

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

[Term]
id: SO:0000067
name: gene_to_gene_feature
is_a: SO:0000401 ! gene_attribute

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000077
name: antisense
is_a: SO:0000068 ! overlapping

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

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

[Term]
id: SO:0000080
name: operon_member
is_a: SO:0000081 ! gene_array_member

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

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

[Term]
id: SO:0000083
name: macronuclear_sequence
is_a: SO:0000736 ! organelle_sequence

[Term]
id: SO:0000084
name: micronuclear_sequence
is_a: SO:0000736 ! organelle_sequence

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

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

[Term]
id: SO:0000087
name: nuclear_gene
def: "A gene from nuclear sequence." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_origin SO:0000738 ! nuclear_sequence
relationship: has_origin SO:0000738 ! implied link automatically realized ! nuclear_sequence

[Term]
id: SO:0000088
name: mt_gene
def: "A gene located in mitochondrial sequence." [SO:xp]
synonym: "mitochondrial gene" EXACT []
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_origin SO:0000737 ! mitochondrial_sequence
relationship: has_origin SO:0000737 ! implied link automatically realized ! mitochondrial_sequence

[Term]
id: SO:0000089
name: kinetoplast_gene
def: "A gene located in kinetoplast sequence." [SO:xp]
is_a: SO:0000088 ! implied link automatically realized ! mt_gene
intersection_of: SO:0000088 ! mt_gene
intersection_of: has_origin SO:0000741 ! kinetoplast_sequence
relationship: has_origin SO:0000741 ! implied link automatically realized ! kinetoplast_sequence

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

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

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

[Term]
id: SO:0000093
name: chromoplast_gene
def: "A gene from chromoplast_sequence." [SO:xp]
is_a: SO:0000090 ! implied link automatically realized ! plastid_gene
intersection_of: SO:0000090 ! plastid_gene
intersection_of: has_origin SO:0000744 ! chromoplast_sequence
relationship: has_origin SO:0000744 ! implied link automatically realized ! chromoplast_sequence

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000104
name: polypeptide
def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
is_a: SO:0000001 ! region
relationship: derives_from SO:0000316 ! CDS

[Term]
id: SO:0000105
name: chromosome_arm
def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.exactsciences.com/cic/glossary/_index.htm]
is_a: SO:0000830 ! chromosome_part

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

[Term]
id: SO:0000107
name: sequencing_primer
is_a: SO:0000112 ! primer

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

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

[Term]
id: SO:0000110
name: sequence_feature
def: "An extent of biological sequence." [SO:ke]
subset: SOFA
synonym: "located sequence feature" RELATED []
synonym: "located_sequence_feature" EXACT []
is_a: SO:0000000 ! Sequence_Ontology
disjoint_from: SO:0000041 ! operation
disjoint_from: SO:0000240 ! chromosome_variation
disjoint_from: SO:0000400 ! sequence_attribute
disjoint_from: SO:0000968 ! replication_mode
disjoint_from: SO:0001026 ! genome
disjoint_from: SO:0001060 ! sequence_variant
disjoint_from: SO:1000132 ! mutation

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

[Term]
id: SO:0000112
name: primer
def: "A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase." [http://www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/glossary.html]
subset: SOFA
synonym: "primer oligonucleotide" EXACT []
synonym: "primer polynucleotide" EXACT []
synonym: "primer sequence" EXACT []
is_a: SO:0000696 ! oligo

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

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

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

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

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

[Term]
id: SO:0000118
name: transcript_with_translational_frameshift
def: "A transcript with a translational frameshift." [SO:xp]
is_a: SO:0000673 ! implied link automatically realized ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000887 ! translational_frameshift
relationship: has_quality SO:0000887 ! implied link automatically realized ! translational_frameshift

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000134
name: imprinted
def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]
is_a: SO:0000119 ! regulated
is_a: SO:0000133 ! epigenetically_modified

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

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

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

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

[Term]
id: SO:0000139
name: ribosome_entry_site
def: "Region in mRNA where ribosome assembles." [SO:ke]
comment: Gene:<gene_id>.
subset: SOFA
is_a: SO:0000837 ! UTR_region

[Term]
id: SO:0000140
name: attenuator
def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]
subset: SOFA
synonym: "attenuator sequence" EXACT []
is_a: SO:0005836 ! regulatory_region
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000141
name: terminator
def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "terminator sequence" EXACT []
is_a: SO:0005836 ! regulatory_region

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

[Term]
id: SO:0000143
name: assembly_component
def: "A region of sequence which may be used to manufacture a longer assembled, sequence." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000145
name: recoded_codon
is_a: SO:0000360 ! codon

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

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

[Term]
id: SO:0000148
name: supercontig
def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]
subset: SOFA
synonym: "scaffold" RELATED []
is_a: SO:0000353 ! assembly
relationship: part_of SO:0000719 ! ultracontig

[Term]
id: SO:0000149
name: contig
def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unvailable bases." [SO:ls]
subset: SOFA
is_a: SO:0000143 ! assembly_component
is_a: SO:0000353 ! assembly
relationship: part_of SO:0000148 ! supercontig

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

[Term]
id: SO:0000151
name: clone
def: "A piece of DNA that has been inserted in a vector so that it can be propagated in E. coli or some other organism." [http://www.geospiza.com/community/support/glossary/]
subset: SOFA
is_a: SO:0000695 ! reagent

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

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

[Term]
id: SO:0000154
name: PAC
def: "P1 Artificial Chromosome. These vectors can hold large inserts, typically 80-200 kb, and propagate in E. coli as a single copy episome." [http://www.ncbi.nlm.nih.gov/genome/guide/mouse/glossary.htm]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "P1" EXACT []
synonym: "P1 artificial chromosome" EXACT []
is_a: SO:0000440 ! vector

[Term]
id: SO:0000155
name: plasmid
def: "A self-replicating circular DNA molecule that is distinct from a chromosome in the organism." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "plasmid sequence" EXACT []
is_a: SO:0000695 ! reagent
is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element

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

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

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

[Term]
id: SO:0000159
name: deletion
def: "The point at which a deletion occured." [SO:ke]
subset: SOFA
synonym: "deleted_sequence" EXACT []
is_a: SO:0000001 ! region
is_a: SO:0001059 ! sequence_alteration
relationship: sequence_of SO:0000045 ! delete

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

[Term]
id: SO:0000161
name: methylated_A
def: "A methylated adenine." [SO:ke]
subset: SOFA
synonym: "methylated A" EXACT []
synonym: "methylated adenine" EXACT []
synonym: "methylated adenine base" EXACT []
synonym: "methylated adenine residue" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature
is_a: SO:0000306 ! methylated_base_feature

[Term]
id: SO:0000162
name: splice_site
def: "The position where intron is excised." [SO:ke]
subset: SOFA
is_a: SO:0000835 ! primary_transcript_region

[Term]
id: SO:0000163
name: five_prime_splice_site
def: "The junction between the 3 prime end of an exon and the following intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
subset: SOFA
synonym: "5' splice site" EXACT []
synonym: "donor" RELATED []
synonym: "donor splice site" EXACT []
synonym: "splice donor site" EXACT []
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0000164
name: three_prime_splice_site
def: "The junction between the 3 prime end of an intron and the following exon." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
subset: SOFA
synonym: "3' splice site" RELATED []
synonym: "acceptor" RELATED []
synonym: "acceptor splice site" EXACT []
synonym: "splice acceptor site" EXACT []
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0000165
name: enhancer
def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
is_a: SO:0000727 ! CRM
relationship: part_of SO:0000234 ! mRNA

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

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

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

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

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

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

[Term]
id: SO:0000172
name: CAAT_signal
def: "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "CAAT box" EXACT []
synonym: "CAAT-box" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0000173
name: GC_rich_promoter_region
def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "GC-rich region" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0000174
name: TATA_box
def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "Goldstein-Hogness box" EXACT []
is_a: SO:0000832 ! promoter_region
relationship: part_of SO:0000170 ! RNApol_II_promoter
relationship: part_of SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000175
name: minus_10_signal
def: "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "-10 signal" EXACT []
synonym: "Pribnow box" EXACT []
synonym: "Pribnow Schaller box" EXACT []
synonym: "Pribnow-Schaller box" EXACT []
is_a: SO:0000843 ! bacterial_RNApol_promoter_region

[Term]
id: SO:0000176
name: minus_35_signal
def: "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "-35 signal" EXACT []
is_a: SO:0000843 ! bacterial_RNApol_promoter_region

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

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

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

[Term]
id: SO:0000180
name: retrotransposon
def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.genpromag.com/scripts/glossary.asp?LETTER=R]
synonym: "class I" RELATED []
synonym: "class I transposon" EXACT []
synonym: "retrotransposon element" EXACT []
is_a: SO:0000101 ! transposable_element

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

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

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

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

[Term]
id: SO:0000185
name: primary_transcript
def: "A transcript that in its initial state requires modification to be functional." [SO:ma]
subset: SOFA
synonym: "precursor RNA" EXACT []
is_a: SO:0000673 ! transcript

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

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

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

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

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

[Term]
id: SO:0000191
name: interior_intron
is_a: SO:0000188 ! intron

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

[Term]
id: SO:0000193
name: RFLP_fragment
def: "A polymorphism detectable by the size differences in DNA fragments generated by a restriction enzyme." [PMID:6247908]
subset: SOFA
synonym: "restriction fragment length polymorphism" EXACT []
synonym: "RFLP" EXACT []
is_a: SO:0000412 ! restriction_fragment

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

[Term]
id: SO:0000195
name: coding_exon
def: "An exon whereby at least one base is part of a codon, including the stop_codon." [SO:ke]
subset: SOFA
is_a: SO:0000147 ! exon

[Term]
id: SO:0000196
name: five_prime_exon_coding_region
def: "The sequence of the 5' exon that encodes for protein." [SO:ke]
subset: SOFA
is_a: SO:0000195 ! coding_exon
relationship: part_of SO:0000200 ! five_prime_coding_exon

[Term]
id: SO:0000197
name: three_prime_exon_coding_region
def: "The sequence of the 3' exon that encodes for protein." [SO:ke]
subset: SOFA
is_a: SO:0000195 ! coding_exon
relationship: part_of SO:0000202 ! three_prime_coding_exon

[Term]
id: SO:0000198
name: noncoding_exon
def: "An exon that does not contain any codons." [SO:ke]
subset: SOFA
synonym: "noncoding exon" EXACT []
is_a: SO:0000147 ! exon
relationship: part_of SO:0000655 ! ncRNA

[Term]
id: SO:0000199
name: translocation
def: "A region of nucleotide sequence that has translocated to a new position." [SO:ke]
synonym: "translocated sequence" EXACT []
is_a: SO:0001059 ! sequence_alteration
relationship: sequence_of SO:0000049 ! translocate

[Term]
id: SO:0000200
name: five_prime_coding_exon
def: "The 5' most coding exon." [SO:ke]
synonym: "5' coding exon" EXACT []
is_a: SO:0000147 ! exon

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

[Term]
id: SO:0000202
name: three_prime_coding_exon
def: "The exon that is most 3-prime on a given transcript." [SO:ma]
synonym: "3' coding exon" RELATED []
is_a: SO:0000147 ! exon

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000235
name: TF_binding_site
def: "A region of a molecule that binds a TF complex [GO:0005667]." [SO:ke]
subset: SOFA
synonym: "transcription factor binding site" EXACT []
is_a: SO:0000410 ! protein_binding_site
is_a: SO:0005836 ! regulatory_region

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

[Term]
id: SO:0000237
name: transcript_attribute
is_a: SO:0000733 ! feature_attribute

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

[Term]
id: SO:0000239
name: flanking_region
def: "The DNA sequences extending on either side of a specific locus." [http://biotech.icmb.utexas.edu/search/dict-search.mhtml]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000240
name: chromosome_variation
is_a: SO:0000000 ! Sequence_Ontology
disjoint_from: SO:0000041 ! operation
disjoint_from: SO:0000110 ! sequence_feature
disjoint_from: SO:0000400 ! sequence_attribute
disjoint_from: SO:0000968 ! replication_mode
disjoint_from: SO:0001026 ! genome
disjoint_from: SO:0001060 ! sequence_variant
disjoint_from: SO:1000132 ! mutation

[Term]
id: SO:0000241
name: internal_UTR
is_a: SO:0000203 ! UTR

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

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

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

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

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

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

[Term]
id: SO:0000248
name: sequence_length_variation
is_a: SO:1000002 ! substitution

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

[Term]
id: SO:0000250
name: modified_RNA_base_feature
def: "A post_transcriptionally modified base." [SO:ke]
is_a: SO:0000833 ! transcript_region

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000276
name: miRNA
def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000]
subset: SOFA
synonym: "micro RNA" EXACT []
is_a: SO:0000370 ! small_regulatory_ncRNA
relationship: derives_from SO:0000647 ! miRNA_primary_transcript

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

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

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

[Term]
id: SO:0000280
name: engineered_gene
def: "A gene that is engineered." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
is_a: SO:0000804 ! implied link automatically realized ! engineered_region
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000783 ! engineered

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

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

[Term]
id: SO:0000283
name: engineered_foreign_transposable_element_gene
def: "A transposible_element that is engineered and foreign." [SO:xp]
is_a: SO:0000111 ! implied link automatically realized ! transposable_element_gene
is_a: SO:0000281 ! implied link automatically realized ! engineered_foreign_gene
intersection_of: SO:0000111 ! transposable_element_gene
intersection_of: has_quality SO:0000783 ! engineered
intersection_of: has_quality SO:0000784 ! foreign

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

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

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

[Term]
id: SO:0000287
name: fusion_gene
def: "A gene that is a fusion." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000806 ! fusion
relationship: has_quality SO:0000806 ! implied link automatically realized ! fusion

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

[Term]
id: SO:0000289
name: microsatellite
def: "A very short unit sequence of DNA (2 to 4 bp) that is repeated multiple times in tandem." [http://www.informatics.jax.org/silver/glossary.shtml]
subset: SOFA
synonym: "microsatellite locus" EXACT []
synonym: "microsatellite marker" EXACT []
synonym: "VNTR" EXACT []
is_a: SO:0000705 ! tandem_repeat

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

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

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

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

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

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

[Term]
id: SO:0000296
name: origin_of_replication
def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: " ori" EXACT []
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000298
name: recombination_feature
is_a: SO:0000001 ! region

[Term]
id: SO:0000299
name: specific_recombination_site
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000300
name: recombination_feature_of_rearranged_gene
is_a: SO:0000299 ! specific_recombination_site

[Term]
id: SO:0000301
name: vertebrate_immune_system_gene_recombination_feature
is_a: SO:0000300 ! recombination_feature_of_rearranged_gene

[Term]
id: SO:0000302
name: J_gene_recombination_feature
def: "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "J-RS" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature

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

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

[Term]
id: SO:0000305
name: modified_base_site
def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Modified base:<modified_base>.
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000306
name: methylated_base_feature
def: "A nucleotide modified by methylation." [SO:ke]
subset: SOFA
is_a: SO:0000305 ! modified_base_site

[Term]
id: SO:0000307
name: CpG_island
def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]
subset: SOFA
synonym: "CG island" EXACT []
is_a: SO:0000001 ! region

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

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

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

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

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

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

[Term]
id: SO:0000314
name: direct_repeat
def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke]
subset: SOFA
is_a: SO:0000657 ! repeat_region

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

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

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

[Term]
id: SO:0000318
name: start_codon
def: "First codon to be translated by a ribosome." [SO:ke]
subset: SOFA
synonym: "initiation codon" EXACT []
is_a: SO:0000360 ! codon

[Term]
id: SO:0000319
name: stop_codon
def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]
subset: SOFA
is_a: SO:0000360 ! codon

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

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

[Term]
id: SO:0000322
name: nuclease_hypersensitive_site
is_a: SO:0000684 ! nuclease_sensitive_site

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

[Term]
id: SO:0000324
name: tag
def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]
subset: SOFA
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000325
name: rRNA_large_subunit_primary_transcript
def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]
is_a: SO:0000209 ! rRNA_primary_transcript

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

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

[Term]
id: SO:0000328
name: microarray_oligo
synonym: "microarray oligonucleotide" EXACT []
is_a: SO:0000051 ! probe
is_a: SO:0000324 ! tag
is_a: SO:0000696 ! oligo

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

[Term]
id: SO:0000330
name: conserved_region
def: "Region of sequence similarity by descent from a common ancestor." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

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

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

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

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

[Term]
id: SO:0000336
name: pseudogene
def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
subset: SOFA
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000704 ! gene

[Term]
id: SO:0000337
name: RNAi_reagent
def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]
subset: SOFA
is_a: SO:0000696 ! oligo

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

[Term]
id: SO:0000339
name: recombination_hotspot
def: "A region in a genome which promotes recombination." [SO:rd]
is_a: SO:0000298 ! recombination_feature

[Term]
id: SO:0000340
name: chromosome
def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000342
name: site_specific_recombination_target_region
is_a: SO:0000299 ! specific_recombination_site

[Term]
id: SO:0000343
name: match
def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000345
name: EST
def: "Expressed Sequence Tag: The sequence of a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [http://genomics.phrma.org/lexicon/e.html]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "expressed sequence tag" EXACT []
is_a: SO:0000695 ! reagent
relationship: derives_from SO:0000234 ! mRNA

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

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

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

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

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

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

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

[Term]
id: SO:0000353
name: assembly
def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000354
name: group_1_intron_homing_endonuclease_target_region
is_a: SO:0000684 ! nuclease_sensitive_site

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

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

[Term]
id: SO:0000357
name: flanked
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000358
name: protein
def: "An attribute describing a sequence composed of amino acid residues joined by peptide bonds." [SO:ke]
comment: Do not use this for feature annotation. Use polypeptide (SO:0000104) instead.
is_a: SO:0000443 ! polymer_attribute

[Term]
id: SO:0000359
name: floxed
def: "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke]
is_a: SO:0000357 ! flanked

[Term]
id: SO:0000360
name: codon
def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together signify a unique amino acid or the termination of translation." [http://genomics.phrma.org/lexicon/c.html]
subset: SOFA
is_a: SO:0000836 ! mRNA_region

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

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

[Term]
id: SO:0000363
name: floxed_gene
def: "A transgene that is floxed." [SO:xp]
is_a: SO:0000902 ! implied link automatically realized ! transgene
intersection_of: SO:0000902 ! transgene
intersection_of: has_quality SO:0000359 ! floxed
relationship: has_quality SO:0000359 ! implied link automatically realized ! floxed

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

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

[Term]
id: SO:0000366
name: insertion_site
def: "The junction where an insertion occurred." [SO:ke]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: position_of SO:0000046 ! insert

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

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

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

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

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

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

[Term]
id: SO:0000373
name: recombinationally_inverted_gene
def: "A recombinationally rearranged gene by inversion." [SO:xp]
is_a: SO:0000456 ! implied link automatically realized ! recombinationally_rearranged_gene
intersection_of: SO:0000456 ! recombinationally_rearranged_gene
intersection_of: associated_with SO:0000047 ! invert
relationship: associated_with SO:0000047 ! implied link automatically realized ! invert

[Term]
id: SO:0000374
name: ribozyme
def: "An RNA with catalytic activity." [SO:ma]
subset: SOFA
is_a: SO:0000372 ! implied link automatically realized ! enzymatic_RNA
intersection_of: SO:0000372 ! enzymatic_RNA
intersection_of: has_quality SO:0001186 ! ribozymic
relationship: has_quality SO:0001186 ! implied link automatically realized ! ribozymic

[Term]
id: SO:0000375
name: rRNA_5.8S
def: "5.8S ribosomal RNA (5.8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5.8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]
subset: SOFA
synonym: "5.8S LSU rRNA" EXACT []
synonym: "5.8S ribosomal RNA" EXACT []
synonym: "5.8S rRNA" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA

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

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

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

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

[Term]
id: SO:0000380
name: hammerhead_ribozyme
def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [http://rnaworld.bio.ukans.edu/class/RNA/RNA00/RNA_World_3.html]
subset: SOFA
is_a: SO:0000715 ! implied link automatically realized ! RNA_motif
intersection_of: SO:0000715 ! RNA_motif
intersection_of: has_quality SO:0001186 ! ribozymic
relationship: has_quality SO:0001186 ! implied link automatically realized ! ribozymic

[Term]
id: SO:0000381
name: group_IIA_intron
is_a: SO:0000603 ! group_II_intron

[Term]
id: SO:0000382
name: group_IIB_intron
is_a: SO:0000603 ! group_II_intron

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000400
name: sequence_attribute
def: "An attribute describes a quality of sequence." [SO:ke]
is_a: SO:0000000 ! Sequence_Ontology
disjoint_from: SO:0000041 ! operation
disjoint_from: SO:0000110 ! sequence_feature
disjoint_from: SO:0000240 ! chromosome_variation
disjoint_from: SO:0000968 ! replication_mode
disjoint_from: SO:0001026 ! genome
disjoint_from: SO:0001060 ! sequence_variant
disjoint_from: SO:1000132 ! mutation

[Term]
id: SO:0000401
name: gene_attribute
is_a: SO:0000733 ! feature_attribute

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

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

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

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

[Term]
id: SO:0000406
name: twintron
def: "An intron within an intron." [PMID:1899376]
is_a: SO:0000188 ! intron

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

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

[Term]
id: SO:0000409
name: binding_site
alt_id: BS:00033
def: "A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]
comment: Discrete.
subset: biosapiens
subset: SOFA
synonym: "binding_or_interaction_site" EXACT []
synonym: "site" RELATED []
is_a: SO:0000001 ! region

[Term]
id: SO:0000410
name: protein_binding_site
def: "A region of a molecule that binds to a protein." [SO:ke]
is_a: SO:0000409 ! binding_site

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

[Term]
id: SO:0000412
name: restriction_fragment
def: "Any of the individual polynucleotide sequences produced by digestion of DNA with a restriction endonuclease." [http://www.agron.missouri.edu/cgi-bin/sybgw_mdb/mdb3/Term/119]
subset: SOFA
is_a: SO:0000695 ! reagent

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

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

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

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

[Term]
id: SO:0000417
name: polypeptide_domain
alt_id: BS:00012
def: "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. Region which has been shown to recur throughout evolution." [EBIBS:GAR, http://www.molbiol.bbsrc.ac.uk/new_protein/domains.html]
comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
subset: biosapiens
synonym: "ca_bind" NARROW []
synonym: "DNA_bind" NARROW []
synonym: "domain" RELATED []
synonym: "np_bind" NARROW []
synonym: "polypeptide_domain" EXACT []
synonym: "zn_fing" NARROW []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0000418
name: signal_peptide
alt_id: BS:00159
def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
subset: biosapiens
subset: SOFA
synonym: "signal" RELATED []
synonym: "signal peptide coding sequence" EXACT []
synonym: "signal_peptide" EXACT []
is_a: SO:0001063 ! immature_peptide_region

[Term]
id: SO:0000419
name: mature_protein_region
alt_id: BS:00149
def: "The extent of a polypeptide chain in the mature protein." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
subset: biosapiens
subset: SOFA
synonym: "chain" EXACT []
synonym: "mature peptide" RELATED []
synonym: "mature_protein_region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0000420
name: five_prime_terminal_inverted_repeat
synonym: "5' TIR" EXACT []
is_a: SO:0000481 ! terminal_inverted_repeat

[Term]
id: SO:0000421
name: three_prime_terminal_inverted_repeat
synonym: "3' TIR" EXACT []
is_a: SO:0000481 ! terminal_inverted_repeat

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000439
name: inverted_ring_chromosome
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000045 ! ring_chromosome

[Term]
id: SO:0000440
name: vector
def: "A DNA molecule that can be used to transfer DNA molecules between organisms." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000151 ! clone

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000450
name: interband
def: "A light region between two darkly staining bands in a polytene chromosome." [SO:ma]
is_a: SO:0000341 ! chromosome_band

[Term]
id: SO:0000451
name: gene_with_polyadenylated_mRNA
def: "A gene that encodes a polyadenylated mRNA." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: associated_with SO:0000871 ! polyadenylated_mRNA
relationship: associated_with SO:0000871 ! implied link automatically realized ! polyadenylated_mRNA

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

[Term]
id: SO:0000453
name: transposition
is_a: SO:1000183 ! chromosome_structure_variation

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

[Term]
id: SO:0000455
name: gene_with_mRNA_with_frameshift
def: "A gene that encodes an mRNA with a frameshift." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: associated_with SO:0000865 ! frameshift
relationship: associated_with SO:0000865 ! implied link automatically realized ! frameshift

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

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

[Term]
id: SO:0000458
name: D_gene
def: "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "D-GENE" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
relationship: part_of SO:0000504 ! D_DJ_C_cluster
relationship: part_of SO:0000505 ! D_DJ_cluster
relationship: part_of SO:0000506 ! D_DJ_J_C_cluster
relationship: part_of SO:0000508 ! D_DJ_J_cluster
relationship: part_of SO:0000509 ! D_J_C_cluster
relationship: part_of SO:0000527 ! V_D_DJ_C_cluster
relationship: part_of SO:0000528 ! V_D_DJ_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000530 ! V_D_DJ_J_cluster
relationship: part_of SO:0000531 ! V_D_J_C_cluster
relationship: part_of SO:0000532 ! V_D_J_cluster
relationship: part_of SO:0000559 ! D_cluster
relationship: part_of SO:0000560 ! D_J_cluster

[Term]
id: SO:0000459
name: gene_with_trans_spliced_transcript
def: "A gene with a transcript that is trans-spliced." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: associated_with SO:0000479 ! trans_spliced_transcript
relationship: associated_with SO:0000479 ! implied link automatically realized ! trans_spliced_transcript

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

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

[Term]
id: SO:0000462
name: pseudogenic_region
def: "A non-functional descendent of a functional entity." [SO:cjm]
subset: SOFA
is_a: SO:0000001 ! region

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

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

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

[Term]
id: SO:0000466
name: V_gene
def: "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-GENE" EXACT []
synonym: "variable_gene" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
relationship: part_of SO:0000518 ! V_DJ_cluster
relationship: part_of SO:0000519 ! V_DJ_J_cluster
relationship: part_of SO:0000520 ! V_VDJ_C_cluster
relationship: part_of SO:0000521 ! V_VDJ_cluster
relationship: part_of SO:0000522 ! V_VDJ_J_cluster
relationship: part_of SO:0000523 ! V_VJ_C_cluster
relationship: part_of SO:0000524 ! V_VJ_cluster
relationship: part_of SO:0000525 ! V_VJ_J_cluster
relationship: part_of SO:0000526 ! V_cluster
relationship: part_of SO:0000527 ! V_D_DJ_C_cluster
relationship: part_of SO:0000528 ! V_D_DJ_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000530 ! V_D_DJ_J_cluster
relationship: part_of SO:0000531 ! V_D_J_C_cluster
relationship: part_of SO:0000532 ! V_D_J_cluster
relationship: part_of SO:0000534 ! V_J_cluster
relationship: part_of SO:0000535 ! V_J_C_cluster
relationship: part_of SO:0000542 ! V_DJ_C_cluster
relationship: part_of SO:0000564 ! V_DJ_J_C_cluster
relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster
relationship: part_of SO:0000566 ! V_VJ_J_C_cluster

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

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

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

[Term]
id: SO:0000470
name: J_gene
def: "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "J-GENE" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
relationship: part_of SO:0000485 ! DJ_J_cluster
relationship: part_of SO:0000487 ! VDJ_J_C_cluster
relationship: part_of SO:0000488 ! VDJ_J_cluster
relationship: part_of SO:0000490 ! VJ_J_C_cluster
relationship: part_of SO:0000491 ! VJ_J_cluster
relationship: part_of SO:0000506 ! D_DJ_J_C_cluster
relationship: part_of SO:0000508 ! D_DJ_J_cluster
relationship: part_of SO:0000509 ! D_J_C_cluster
relationship: part_of SO:0000511 ! J_C_cluster
relationship: part_of SO:0000513 ! J_cluster
relationship: part_of SO:0000519 ! V_DJ_J_cluster
relationship: part_of SO:0000522 ! V_VDJ_J_cluster
relationship: part_of SO:0000525 ! V_VJ_J_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000530 ! V_D_DJ_J_cluster
relationship: part_of SO:0000531 ! V_D_J_C_cluster
relationship: part_of SO:0000532 ! V_D_J_cluster
relationship: part_of SO:0000534 ! V_J_cluster
relationship: part_of SO:0000535 ! V_J_C_cluster
relationship: part_of SO:0000540 ! DJ_J_C_cluster
relationship: part_of SO:0000560 ! D_J_cluster
relationship: part_of SO:0000564 ! V_DJ_J_C_cluster
relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster
relationship: part_of SO:0000566 ! V_VJ_J_C_cluster

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

[Term]
id: SO:0000472
name: tiling_path
def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [CJM:SO]
subset: SOFA
is_a: SO:0000353 ! assembly

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

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

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

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

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

[Term]
id: SO:0000478
name: C_gene
def: "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "C_GENE" EXACT []
synonym: "constant gene" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
relationship: part_of SO:0000487 ! VDJ_J_C_cluster
relationship: part_of SO:0000489 ! VJ_C_cluster
relationship: part_of SO:0000490 ! VJ_J_C_cluster
relationship: part_of SO:0000504 ! D_DJ_C_cluster
relationship: part_of SO:0000506 ! D_DJ_J_C_cluster
relationship: part_of SO:0000509 ! D_J_C_cluster
relationship: part_of SO:0000511 ! J_C_cluster
relationship: part_of SO:0000520 ! V_VDJ_C_cluster
relationship: part_of SO:0000523 ! V_VJ_C_cluster
relationship: part_of SO:0000527 ! V_D_DJ_C_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000531 ! V_D_J_C_cluster
relationship: part_of SO:0000535 ! V_J_C_cluster
relationship: part_of SO:0000539 ! DJ_C_cluster
relationship: part_of SO:0000540 ! DJ_J_C_cluster
relationship: part_of SO:0000541 ! VDJ_C_cluster
relationship: part_of SO:0000542 ! V_DJ_C_cluster
relationship: part_of SO:0000558 ! C_cluster
relationship: part_of SO:0000564 ! V_DJ_J_C_cluster
relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster
relationship: part_of SO:0000566 ! V_VJ_J_C_cluster

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

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

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

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

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

[Term]
id: SO:0000484
name: three_prime_coding_exon_noncoding_region
def: "The sequence of the 3' exon that is not coding." [SO:ke]
synonym: "three_prime_exon_noncoding_region" EXACT []
is_a: SO:0000852 ! exon_region
relationship: part_of SO:0000202 ! three_prime_coding_exon

[Term]
id: SO:0000485
name: DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "(DJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000486
name: five_prime_coding_exon_noncoding_region
def: "The sequence of the 5' exon preceding the start codon." [SO:ke]
synonym: "five_prime_exon_noncoding_region" EXACT []
is_a: SO:0000852 ! exon_region
relationship: part_of SO:0000200 ! five_prime_coding_exon

[Term]
id: SO:0000487
name: VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "(VDJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000488
name: VDJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "(VDJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000489
name: VJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "(VJ)-C-CLUSTER" RELATED []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000490
name: VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "(VJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000491
name: VJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "(VJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000492
name: D_gene_recombination_feature
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature

[Term]
id: SO:0000493
name: three_prime_D_heptamer
def: "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "3'D-HEPTAMER" EXACT []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence

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

[Term]
id: SO:0000495
name: three_prime_D_spacer
def: "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "3'D-SPACER" EXACT []
is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence

[Term]
id: SO:0000496
name: five_prime_D_heptamer
def: "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "5'D-HEPTAMER" EXACT []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence

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

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

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

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

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

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

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

[Term]
id: SO:0000504
name: D_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "D-(DJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000505
name: D_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "D-(DJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000506
name: D_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "D-(DJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

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

[Term]
id: SO:0000508
name: D_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "D-(DJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000509
name: D_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "D-J-C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

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

[Term]
id: SO:0000511
name: J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "J-C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

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

[Term]
id: SO:0000513
name: J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "J-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

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

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

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

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

[Term]
id: SO:0000518
name: V_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(DJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000519
name: V_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000520
name: V_VDJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(VDJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000521
name: V_VDJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(VDJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000522
name: V_VDJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(VDJ)-J-CLUSTER" RELATED []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000523
name: V_VJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(VJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000524
name: V_VJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(VJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000525
name: V_VJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(VJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000526
name: V_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000527
name: V_D_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-D-(DJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000528
name: V_D_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-D-(DJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000529
name: V_D_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-D-(DJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000530
name: V_D_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-D-(DJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000531
name: V_D_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-D-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000532
name: V_D_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-D-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

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

[Term]
id: SO:0000534
name: V_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-J-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000535
name: V_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-J-C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

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

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

[Term]
id: SO:0000538
name: V_gene_recombination_feature
def: "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-RS" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature

[Term]
id: SO:0000539
name: DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "(DJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000540
name: DJ_J_C_cluster
def: "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "(DJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000541
name: VDJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "(VDJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000542
name: V_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(DJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

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

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

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

[Term]
id: SO:0000546
name: designed_sequence
is_a: SO:0000351 ! synthetic_sequence

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

[Term]
id: SO:0000548
name: gene_with_edited_transcript
def: "A gene that encodes a transcript that is edited." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: associated_with SO:0000873 ! edited_transcript
relationship: associated_with SO:0000873 ! implied link automatically realized ! edited_transcript

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

[Term]
id: SO:0000550
name: aneuploid_chromosome
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:0000551
name: polyA_signal_sequence
def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "poly(A) signal" EXACT []
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000552
name: Shine_Dalgarno_sequence
def: "Region in 5' UTR where ribosome assembles on mRNA." [SO:ke]
synonym: "five prime ribosome binding site" EXACT []
synonym: "RBS" RELATED []
synonym: "Shine Dalgarno sequence" EXACT []
synonym: "Shine-Dalgarno sequence" EXACT []
is_a: SO:0000139 ! ribosome_entry_site

[Term]
id: SO:0000553
name: polyA_site
def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000233 ! processed_transcript

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

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

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

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

[Term]
id: SO:0000558
name: C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://imgt.cines.fr/ligmb/LIGMlect?query=7]
synonym: "C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000559
name: D_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "D-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000560
name: D_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "D-J-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000561
name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
def: "Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or\nJ-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "HEPTAMER" RELATED []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature

[Term]
id: SO:0000562
name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature

[Term]
id: SO:0000563
name: vertebrate_immune_system_gene_recombination_spacer
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000564
name: V_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(DJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000565
name: V_VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(VDJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

[Term]
id: SO:0000566
name: V_VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-(VJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

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

[Term]
id: SO:0000568
name: bidirectional_promoter
is_a: SO:0000167 ! promoter

[Term]
id: SO:0000569
name: retrotransposed
alt_id: SO:0100042
def: "An attribute of protein-coding genes where the protein product has been retrotransposed." [SO:ke]
is_a: SO:0000010 ! protein_coding
is_a: SO:0000042 ! pseudogene_attribute

[Term]
id: SO:0000570
name: three_prime_D_recombination_signal_sequence
def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "3'D-RS" EXACT []
synonym: "three_prime_D-recombination_signal_sequence" EXACT []
is_a: SO:0000492 ! D_gene_recombination_feature

[Term]
id: SO:0000571
name: miRNA_encoding
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000572
name: DJ_gene
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "D-J-GENE" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
relationship: part_of SO:0000485 ! DJ_J_cluster
relationship: part_of SO:0000504 ! D_DJ_C_cluster
relationship: part_of SO:0000505 ! D_DJ_cluster
relationship: part_of SO:0000506 ! D_DJ_J_C_cluster
relationship: part_of SO:0000508 ! D_DJ_J_cluster
relationship: part_of SO:0000518 ! V_DJ_cluster
relationship: part_of SO:0000519 ! V_DJ_J_cluster
relationship: part_of SO:0000527 ! V_D_DJ_C_cluster
relationship: part_of SO:0000528 ! V_D_DJ_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000530 ! V_D_DJ_J_cluster
relationship: part_of SO:0000539 ! DJ_C_cluster
relationship: part_of SO:0000540 ! DJ_J_C_cluster
relationship: part_of SO:0000542 ! V_DJ_C_cluster
relationship: part_of SO:0000564 ! V_DJ_J_C_cluster

[Term]
id: SO:0000573
name: rRNA_encoding
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000574
name: VDJ_gene
def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-D-J-GENE" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
relationship: part_of SO:0000487 ! VDJ_J_C_cluster
relationship: part_of SO:0000488 ! VDJ_J_cluster
relationship: part_of SO:0000520 ! V_VDJ_C_cluster
relationship: part_of SO:0000521 ! V_VDJ_cluster
relationship: part_of SO:0000522 ! V_VDJ_J_cluster
relationship: part_of SO:0000541 ! VDJ_C_cluster
relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster

[Term]
id: SO:0000575
name: scRNA_encoding
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000576
name: VJ_gene
def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7]
synonym: "V-J-GENE" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
relationship: part_of SO:0000489 ! VJ_C_cluster
relationship: part_of SO:0000490 ! VJ_J_C_cluster
relationship: part_of SO:0000491 ! VJ_J_cluster
relationship: part_of SO:0000523 ! V_VJ_C_cluster
relationship: part_of SO:0000524 ! V_VJ_cluster
relationship: part_of SO:0000525 ! V_VJ_J_cluster
relationship: part_of SO:0000566 ! V_VJ_J_C_cluster

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

[Term]
id: SO:0000578
name: snoRNA_encoding
is_a: SO:0000011 ! non_protein_coding

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

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

[Term]
id: SO:0000581
name: cap
def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
subset: SOFA
is_a: SO:0000001 ! region

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

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

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

[Term]
id: SO:0000585
name: C_D_box_snoRNA_encoding
is_a: SO:0000578 ! snoRNA_encoding

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

[Term]
id: SO:0000587
name: group_I_intron
def: "Group I catalytic introns are large self-splicing ribozymes. They catalyse their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]
subset: SOFA
is_a: SO:0000188 ! intron

[Term]
id: SO:0000588
name: autocatalytically_spliced_intron
def: "A self spliced intron." [SO:ke]
subset: SOFA
is_a: SO:0000188 ! implied link automatically realized ! intron
intersection_of: SO:0000188 ! intron
intersection_of: has_quality SO:0001186 ! ribozymic
relationship: has_quality SO:0001186 ! implied link automatically realized ! ribozymic

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000598
name: edited_by_C_insertion_and_dinucleotide_insertion
def: "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs." [http://nsm1.utdallas.edu/bio/miller/physarum/overview.htm]
synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED []
is_obsolete: true

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

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

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

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

[Term]
id: SO:0000603
name: group_II_intron
def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]
subset: SOFA
is_a: SO:0000188 ! intron

[Term]
id: SO:0000604
name: editing_block
def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://www.rna.ucla/]
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000605
name: intergenic_region
def: "The region between two known genes." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000606
name: editing_domain
def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://www.rna.ucla/]
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000607
name: unedited_region
def: "The region of an edited transcript that will not be edited." [http://www.rna.ucla.edu/]
is_a: SO:0000579 ! edited_transcript_feature

[Term]
id: SO:0000608
name: H_ACA_box_snoRNA_encoding
is_a: SO:0000578 ! snoRNA_encoding

[Term]
id: SO:0000609
name: oligo_U_tail
def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]
is_a: SO:0000001 ! region
relationship: adjacent_to SO:0000602 ! guide_RNA

[Term]
id: SO:0000610
name: polyA_sequence
def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

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

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

[Term]
id: SO:0000614
name: bacterial_terminator
def: "A terminator signal for bacterial transcription." [SO:ke]
is_a: SO:0000752 ! gene_group_regulatory_region
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000615
name: terminator_of_type_2_RNApol_III_promoter
def: "A terminator signal for RNA polymerase III transcription." [SO:ke]
is_a: SO:0000951 ! eukaryotic_terminator

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

[Term]
id: SO:0000617
name: RNApol_III_promoter_type_1
is_a: SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000618
name: RNApol_III_promoter_type_2
synonym: "tRNA promoter" RELATED []
is_a: SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000619
name: A_box
def: "A variably distant linear promoter region recognised by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]
is_a: SO:0000846 ! RNApol_III_promoter_type_2_region

[Term]
id: SO:0000620
name: B_box
def: "A variably distant linear promoter region recognised by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]
is_a: SO:0000846 ! RNApol_III_promoter_type_2_region

[Term]
id: SO:0000621
name: RNApol_III_promoter_type_3
is_a: SO:0000171 ! RNApol_III_promoter

[Term]
id: SO:0000622
name: C_box
def: "An RNA polymerase II type 1 promoter with consensus sequence CAnnCCn." [SO:ke]
is_a: SO:0000845 ! RNApol_III_promoter_type_1_region

[Term]
id: SO:0000623
name: snRNA_encoding
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000624
name: telomere
def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]
subset: SOFA
is_a: SO:0000628 ! chromosomal_structural_element

[Term]
id: SO:0000625
name: silencer
def: "Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes." [http://www.brunel.ac.uk/depts/bio/project/old_hmg/gloss3.htm]
subset: SOFA
is_a: SO:0000727 ! CRM

[Term]
id: SO:0000626
name: chromosomal_regulatory_element
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0000627
name: insulator
def: "A trancriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]
subset: SOFA
synonym: "insulator element" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region

[Term]
id: SO:0000628
name: chromosomal_structural_element
subset: SOFA
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0000629
name: five_prime_open_reading_frame
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000204 ! five_prime_UTR

[Term]
id: SO:0000630
name: upstream_AUG_codon
def: "A start codon upstream of the ORF." [SO:ke]
is_a: SO:0000837 ! UTR_region

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

[Term]
id: SO:0000632
name: monocistronic_primary_transcript
def: "A primary transcript encoding for more than one gene product." [SO:ke]
is_a: SO:0000185 ! implied link automatically realized ! primary_transcript
is_a: SO:0000665 ! implied link automatically realized ! monocistronic_transcript
intersection_of: SO:0000185 ! primary_transcript
intersection_of: has_quality SO:0000878 ! monocistronic

[Term]
id: SO:0000633
name: monocistronic_mRNA
def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]
synonym: "monocistronic processed transcript" EXACT []
is_a: SO:0000234 ! implied link automatically realized ! mRNA
is_a: SO:0000665 ! implied link automatically realized ! monocistronic_transcript
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000878 ! monocistronic

[Term]
id: SO:0000634
name: polycistronic_mRNA
def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]
synonym: "polycistronic processed transcript" RELATED []
is_a: SO:0000078 ! implied link automatically realized ! polycistronic_transcript
is_a: SO:0000234 ! implied link automatically realized ! mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000880 ! polycistronic

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

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

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

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

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

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

[Term]
id: SO:0000641
name: tetranucleotide_repeat_microsatellite_feature
is_a: SO:0000289 ! microsatellite

[Term]
id: SO:0000642
name: SRP_RNA_encoding
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000643
name: minisatellite
def: "A repetitive sequence spanning 500 to 20,000 base pairs (a repeat unit is 5 - 30 base pairs)." [http://www.rerf.or.jp/eigo/glossary/minisate.htm]
subset: SOFA
is_a: SO:0000705 ! tandem_repeat

[Term]
id: SO:0000644
name: antisense_RNA
def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]
subset: SOFA
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000645 ! antisense_primary_transcript

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

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

[Term]
id: SO:0000647
name: miRNA_primary_transcript
def: "A primary transcript encoding a micro RNA." [SO:ke]
synonym: "micro RNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript

[Term]
id: SO:0000648
name: stRNA_primary_transcript
def: "A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke]
synonym: "small temporal RNA primary transcript" EXACT []
is_a: SO:0000647 ! miRNA_primary_transcript

[Term]
id: SO:0000649
name: stRNA
def: "Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512]
subset: SOFA
synonym: "small temporal RNA" EXACT []
is_a: SO:0000655 ! ncRNA

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

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

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

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

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

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

[Term]
id: SO:0000656
name: stRNA_encoding
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000657
name: repeat_region
def: "A region of sequence containing one or more repeat units." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000659
name: tmRNA_encoding
is_a: SO:0000011 ! non_protein_coding

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

[Term]
id: SO:0000661
name: intron_attribute
is_a: SO:0000733 ! feature_attribute

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

[Term]
id: SO:0000663
name: tRNA_encoding
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000664
name: introgressed_chromosome_region
is_a: SO:0000830 ! chromosome_part

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

[Term]
id: SO:0000666
name: mobile_intron
is_a: SO:0000661 ! intron_attribute

[Term]
id: SO:0000667
name: insertion
def: "A region of sequence that has been inserted." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0001059 ! sequence_alteration
relationship: sequence_of SO:0000046 ! insert

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

[Term]
id: SO:0000669
name: sequence_rearrangement_feature
is_a: SO:0000298 ! recombination_feature

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

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

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

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

[Term]
id: SO:0000674
name: non_canonical_splice_site
def: "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke]
synonym: "non-canonical splice site" EXACT []
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0000675
name: canonical_splice_site
def: "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke]
is_a: SO:0000162 ! splice_site

[Term]
id: SO:0000676
name: canonical_three_prime_splice_site
def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke]
is_a: SO:0000164 ! three_prime_splice_site
is_a: SO:0000675 ! canonical_splice_site

[Term]
id: SO:0000677
name: canonical_five_prime_splice_site
def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke]
is_a: SO:0000163 ! five_prime_splice_site
is_a: SO:0000675 ! canonical_splice_site

[Term]
id: SO:0000678
name: non_canonical_three_prime_splice_site
def: "A 3' splice site that does not have the sequence \"AG\"." [SO:ke]
synonym: "non-canonical three prime splice site" EXACT []
is_a: SO:0000164 ! three_prime_splice_site
is_a: SO:0000674 ! non_canonical_splice_site

[Term]
id: SO:0000679
name: non_canonical_five_prime_splice_site
def: "A 5' splice site which does not have the sequence \"GT\"." [SO:ke]
synonym: "non-canonical five prime splice site" EXACT []
is_a: SO:0000163 ! five_prime_splice_site
is_a: SO:0000674 ! non_canonical_splice_site

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

[Term]
id: SO:0000681
name: aberrant_processed_transcript
def: "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." [SO:ke]
is_a: SO:0000233 ! processed_transcript

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

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

[Term]
id: SO:0000684
name: nuclease_sensitive_site
def: "A region of nucleotide sequence targeting by a nuclease enzyme." [SO:ma]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000685
name: DNAaseI_hypersensitive_site
is_a: SO:0000322 ! nuclease_hypersensitive_site

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

[Term]
id: SO:0000687
name: deletion_junction
def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: position_of SO:0000045 ! delete

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

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

[Term]
id: SO:0000690
name: gene_with_polycistronic_transcript
def: "A gene that encodes a polycistronic transcript." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: associated_with SO:0000078 ! polycistronic_transcript
relationship: associated_with SO:0000078 ! implied link automatically realized ! polycistronic_transcript

[Term]
id: SO:0000691
name: cleaved_initiator_methionine
alt_id: BS:00067
def: "Indicates when the initator methionine has been cleaved from the mature sequence." [EBIBS:GAR]
subset: biosapiens
synonym: "cleaved_initiator_methionine" EXACT []
synonym: "init_met" RELATED []
synonym: "initator methionine" EXACT []
is_a: SO:0001063 ! immature_peptide_region

[Term]
id: SO:0000692
name: gene_with_dicistronic_transcript
def: "A gene that encodes a dicistronic transcript." [SO:xp]
is_a: SO:0000690 ! implied link automatically realized ! gene_with_polycistronic_transcript
intersection_of: SO:0000690 ! gene_with_polycistronic_transcript
intersection_of: associated_with SO:0000079 ! dicistronic_transcript
relationship: associated_with SO:0000079 ! implied link automatically realized ! dicistronic_transcript

[Term]
id: SO:0000693
name: gene_with_recoded_mRNA
def: "A gene that encodes an mRNA that is recoded." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: associated_with SO:1001261 ! recoded_mRNA
relationship: associated_with SO:1001261 ! implied link automatically realized ! recoded_mRNA

[Term]
id: SO:0000694
name: SNP
def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives (alleles) exist in normal individuals in some population(s), wherein the least frequent allele has an abundance of 1% or greater." [http://www.cgr.ki.se/cgb/groups/brookes/Articles/essence_of_snps_article.pdf]
subset: SOFA
synonym: "single nucleotide polymorphism" EXACT []
is_a: SO:1000002 ! substitution

[Term]
id: SO:0000695
name: reagent
def: "A sequence used in experiment." [SO:ke]
comment: Requested by Lynn Crosby, jan 2006.
subset: SOFA
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000697
name: gene_with_stop_codon_read_through
def: "A gene that encodes a transcript with stop codon readthrough." [SO:xp]
is_a: SO:0000693 ! implied link automatically realized ! gene_with_recoded_mRNA
intersection_of: SO:0000693 ! gene_with_recoded_mRNA
intersection_of: associated_with SO:0000883 ! stop_codon_read_through
relationship: associated_with SO:0000883 ! implied link automatically realized ! stop_codon_read_through

[Term]
id: SO:0000698
name: gene_with_stop_codon_redefined_as_pyrrolysine
def: "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]
is_a: SO:0000697 ! implied link automatically realized ! gene_with_stop_codon_read_through
intersection_of: SO:0000697 ! gene_with_stop_codon_read_through
intersection_of: associated_with SO:0000884 ! stop_codon_redefined_as_pyrrolysine
relationship: associated_with SO:0000884 ! implied link automatically realized ! stop_codon_redefined_as_pyrrolysine

[Term]
id: SO:0000699
name: junction
def: "A sequence_feature with an extent of zero." [SO:ke]
comment: A junction is a boundary between regions. A boundary has an extent of zero.
subset: SOFA
synonym: "boundary" EXACT []
is_a: SO:0000110 ! sequence_feature
disjoint_from: SO:0000001 ! region

[Term]
id: SO:0000700
name: remark
def: "A comment about the sequence." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

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

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

[Term]
id: SO:0000704
name: gene
def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.\nA gene may be considered as a unit of inheritance.
subset: SOFA
is_a: SO:0000001 ! region
relationship: member_of SO:0005855 ! gene_group

[Term]
id: SO:0000705
name: tandem_repeat
def: "Two or more adjacent copies of a DNA sequence." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]
subset: SOFA
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000005 ! satellite_DNA

[Term]
id: SO:0000706
name: trans_splice_acceptor_site
def: "The process that produces mature transcripts by combining exons of independent pre-mRNA molecules. The acceptor site lies on the 3' of these molecules." [SO:ke]
subset: SOFA
is_a: SO:0000164 ! three_prime_splice_site

[Term]
id: SO:0000707
name: trans_splice_donor_site
def: "The site at which trans-splicing occurs." [SO:ke]
synonym: "trans-splice donor site" EXACT []
is_a: SO:0000163 ! five_prime_splice_site

[Term]
id: SO:0000708
name: SL1_acceptor_site
is_a: SO:0000706 ! trans_splice_acceptor_site

[Term]
id: SO:0000709
name: SL2_acceptor_site
is_a: SO:0000706 ! trans_splice_acceptor_site

[Term]
id: SO:0000710
name: gene_with_stop_codon_redefined_as_selenocysteine
def: "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]
is_a: SO:0000697 ! implied link automatically realized ! gene_with_stop_codon_read_through
intersection_of: SO:0000697 ! gene_with_stop_codon_read_through
intersection_of: associated_with SO:0000885 ! stop_codon_redefined_as_selenocysteine
relationship: associated_with SO:0000885 ! implied link automatically realized ! stop_codon_redefined_as_selenocysteine

[Term]
id: SO:0000711
name: gene_with_mRNA_recoded_by_translational_bypass
def: "A gene with mRNA recoded by translational bypass." [SO:xp]
is_a: SO:0000693 ! implied link automatically realized ! gene_with_recoded_mRNA
intersection_of: SO:0000693 ! gene_with_recoded_mRNA
intersection_of: associated_with SO:0000886 ! recoded_by_translational_bypass
relationship: associated_with SO:0000886 ! implied link automatically realized ! recoded_by_translational_bypass

[Term]
id: SO:0000712
name: gene_with_transcript_with_translational_frameshift
def: "A gene encoding a transcript that has a translational frameshift." [SO:xp]
is_a: SO:0000693 ! implied link automatically realized ! gene_with_recoded_mRNA
intersection_of: SO:0000693 ! gene_with_recoded_mRNA
intersection_of: associated_with SO:0000887 ! translational_frameshift
relationship: associated_with SO:0000887 ! implied link automatically realized ! translational_frameshift

[Term]
id: SO:0000713
name: DNA_motif
def: "A motif that is active in the DNA form of the sequence." [SO:ke]
is_a: SO:0000714 ! nucleotide_motif

[Term]
id: SO:0000714
name: nucleotide_motif
def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

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

[Term]
id: SO:0000717
name: reading_frame
def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SO:rb]
comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
subset: SOFA
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000719
name: ultracontig
def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]
subset: SOFA
is_a: SO:0000353 ! assembly

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

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

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

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

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

[Term]
id: SO:0000725
name: transit_peptide
alt_id: BS:00055
def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Added to bring SO inline with the embl ddbj genbank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
subset: biosapiens
subset: SOFA
synonym: "signal" RELATED []
synonym: "transit_peptide" EXACT []
is_a: SO:0001063 ! immature_peptide_region

[Term]
id: SO:0000726
name: repeat_unit
def: "A single repeat element." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Added to comply with the feature table.
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000727
name: CRM
def: "A regulatory_region where more than 1 TF_binding_site together are regulatorily active." [SO:SG]
comment: Requested by Stepen Grossmann Dec 2004.
synonym: "cis regulatory module" EXACT []
synonym: "TF module" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region

[Term]
id: SO:0000728
name: intein
def: "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]
comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein.
synonym: "protein intron" RELATED []
is_a: SO:0001063 ! immature_peptide_region

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

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

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

[Term]
id: SO:0000732
name: predicted
def: "An attribute describing an unverified region." [SO:ke]
is_a: SO:0000905 ! status

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

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

[Term]
id: SO:0000735
name: sequence_location
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000736
name: organelle_sequence
is_a: SO:0000735 ! sequence_location

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

[Term]
id: SO:0000738
name: nuclear_sequence
is_a: SO:0000736 ! organelle_sequence

[Term]
id: SO:0000739
name: nucleomorphic_sequence
is_a: SO:0000736 ! organelle_sequence

[Term]
id: SO:0000740
name: plastid_sequence
is_a: SO:0000736 ! organelle_sequence

[Term]
id: SO:0000741
name: kinetoplast_sequence
is_a: SO:0000737 ! mitochondrial_sequence

[Term]
id: SO:0000742
name: maxicircle_sequence
is_a: SO:0000741 ! kinetoplast_sequence

[Term]
id: SO:0000743
name: apicoplast_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000744
name: chromoplast_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000745
name: chloroplast_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000746
name: cyanelle_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000747
name: leucoplast_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000748
name: proplastid_sequence
is_a: SO:0000740 ! plastid_sequence

[Term]
id: SO:0000749
name: plasmid_location
is_a: SO:0000735 ! sequence_location

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

[Term]
id: SO:0000751
name: proviral_location
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000752
name: gene_group_regulatory_region
subset: SOFA
is_a: SO:0005836 ! regulatory_region
relationship: member_of SO:0005855 ! gene_group

[Term]
id: SO:0000753
name: clone_insert
is_a: SO:0000695 ! reagent

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

[Term]
id: SO:0000755
name: plasmid_vector
is_a: SO:0000440 ! vector

[Term]
id: SO:0000756
name: cDNA
def: "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]
is_a: SO:0000352 ! DNA

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

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

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000769
name: tmRNA_coding_piece
def: "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [http://nar.oxfordjournals.org/cgi/content/full/32/15/4531n10, Indiana:kw]
comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005.
is_a: SO:0000847 ! tmRNA_region

[Term]
id: SO:0000770
name: tmRNA_acceptor_piece
def: "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [http://nar.oxfordjournals.org/cgi/content/full/32/15/4531n10, Indiana:kw]
comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005.
is_a: SO:0000847 ! tmRNA_region

[Term]
id: SO:0000771
name: QTL
def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/]
comment: Added in respose to request by Simon Twigger November 14th 2005.
synonym: "quantitative trait locus" EXACT []
is_a: SO:0000001 ! region

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000786
name: reagent_attribute
comment: Added jan 2006 by KE.
is_a: SO:0000733 ! feature_attribute

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

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

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

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

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

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

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

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

[Term]
id: SO:0000795
name: rescue_mini_gene
def: "A mini_gene that rescues." [SO:xp]
synonym: "rescue mini-gene" EXACT []
is_a: SO:0000411 ! implied link automatically realized ! rescue_region
is_a: SO:0000815 ! implied link automatically realized ! mini_gene
intersection_of: SO:0000815 ! mini_gene
intersection_of: has_quality SO:0000814 ! rescue

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

[Term]
id: SO:0000797
name: natural_transposable_element
def: "TE that exists (or existed) in nature." [SO:mc]
is_a: SO:0000101 ! implied link automatically realized ! transposable_element
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000782 ! natural
relationship: has_quality SO:0000782 ! implied link automatically realized ! natural

[Term]
id: SO:0000798
name: engineered_transposable_element
def: "TE that has been modified by manipulations in vitro." [SO:mc]
is_a: SO:0000101 ! implied link automatically realized ! transposable_element
is_a: SO:0000804 ! implied link automatically realized ! engineered_region
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000799
name: engineered_foreign_transposable_element
def: "A transposable_element that is engineered and foreign." [SO:mc]
is_a: SO:0000720 ! implied link automatically realized ! foreign_transposable_element
is_a: SO:0000798 ! implied link automatically realized ! engineered_transposable_element
is_a: SO:0000805 ! implied link automatically realized ! engineered_foreign_region
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000783 ! engineered
intersection_of: has_quality SO:0000784 ! foreign

[Term]
id: SO:0000800
name: assortment_derived_duplication
def: "A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:0000801
name: assortment_derived_deficiency_plus_duplication
def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:0000802
name: assortment_derived_deficiency
def: "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:0000803
name: assortment_derived_aneuploid
def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [fb:gm]
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:0000804
name: engineered_region
def: "A region that is engineered." [SO:xp]
synonym: "engineered sequence" EXACT []
is_a: SO:0000001 ! implied link automatically realized ! region
intersection_of: SO:0000001 ! region
intersection_of: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000783 ! implied link automatically realized ! engineered

[Term]
id: SO:0000805
name: engineered_foreign_region
def: "A region that is engineered and foreign." [SO:xp]
is_a: SO:0000804 ! implied link automatically realized ! engineered_region
intersection_of: SO:0000001 ! region
intersection_of: has_quality SO:0000783 ! engineered
intersection_of: has_quality SO:0000784 ! foreign
relationship: has_quality SO:0000784 ! implied link automatically realized ! foreign

[Term]
id: SO:0000806
name: fusion
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000807
name: engineered_tag
def: "A tag that is engineered." [SO:xp]
is_a: SO:0000324 ! implied link automatically realized ! tag
is_a: SO:0000804 ! implied link automatically realized ! engineered_region
intersection_of: SO:0000324 ! tag
intersection_of: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000808
name: validated_cDNA_clone
def: "A cDNA clone that has been validated." [SO:xp]
is_a: SO:0000317 ! implied link automatically realized ! cDNA_clone
intersection_of: SO:0000317 ! cDNA_clone
intersection_of: has_quality SO:0000789 ! validated
relationship: has_quality SO:0000789 ! implied link automatically realized ! validated

[Term]
id: SO:0000809
name: invalidated_cDNA_clone
def: "A cDNA clone that is invalid." [SO:xp]
is_a: SO:0000317 ! implied link automatically realized ! cDNA_clone
intersection_of: SO:0000317 ! cDNA_clone
intersection_of: has_quality SO:0000790 ! invalidated
relationship: has_quality SO:0000790 ! implied link automatically realized ! invalidated

[Term]
id: SO:0000810
name: chimeric_cDNA_clone
def: "A cDNA clone invalidated because it is chimeric." [SO:xp]
is_a: SO:0000809 ! implied link automatically realized ! invalidated_cDNA_clone
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA
relationship: has_quality SO:0000362 ! implied link automatically realized ! invalidated_by_chimeric_cDNA

[Term]
id: SO:0000811
name: genomically_contaminated_cDNA_clone
def: "A cDNA clone invalidated by genomic contamination." [SO:xp]
is_a: SO:0000809 ! implied link automatically realized ! invalidated_cDNA_clone
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000414 ! invalidated_by_genomic_contamination
relationship: has_quality SO:0000414 ! implied link automatically realized ! invalidated_by_genomic_contamination

[Term]
id: SO:0000812
name: polyA_primed_cDNA_clone
def: "A cDNA clone invalidated by polyA priming." [SO:xp]
is_a: SO:0000809 ! implied link automatically realized ! invalidated_cDNA_clone
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA
relationship: has_quality SO:0000415 ! implied link automatically realized ! invalidated_by_genomic_polyA_primed_cDNA

[Term]
id: SO:0000813
name: partially_processed_cDNA_clone
def: "A cDNA invalidated clone by partial processing." [SO:xp]
is_a: SO:0000809 ! implied link automatically realized ! invalidated_cDNA_clone
intersection_of: SO:0000809 ! invalidated_cDNA_clone
intersection_of: has_quality SO:0000416 ! invalidated_by_partial_processing
relationship: has_quality SO:0000416 ! implied link automatically realized ! invalidated_by_partial_processing

[Term]
id: SO:0000814
name: rescue
def: "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000815
name: mini_gene
def: "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL))\nand MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000816
name: rescue_gene
def: "A gene that rescues." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000814 ! rescue
relationship: has_quality SO:0000814 ! implied link automatically realized ! rescue

[Term]
id: SO:0000817
name: wild_type
def: "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000818
name: wild_type_rescue_gene
def: "A gene that rescues." [SO:xp]
is_a: SO:0000816 ! rescue_gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000817 ! wild_type
relationship: has_quality SO:0000817 ! implied link automatically realized ! wild_type

[Term]
id: SO:0000819
name: mitochondrial_chromosome
def: "A chromosome originating in a mitochondria." [SO:xp]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000737 ! mitochondrial_sequence
relationship: has_origin SO:0000737 ! implied link automatically realized ! mitochondrial_sequence

[Term]
id: SO:0000820
name: chloroplast_chromosome
def: "A chromosome originating in a chloroplast." [SO:xp]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000745 ! chloroplast_sequence
relationship: has_origin SO:0000745 ! implied link automatically realized ! chloroplast_sequence

[Term]
id: SO:0000821
name: chromoplast_chromosome
def: "A chromosome originating in a chromoplast." [SO:xp]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000744 ! chromoplast_sequence
relationship: has_origin SO:0000744 ! implied link automatically realized ! chromoplast_sequence

[Term]
id: SO:0000822
name: cyanelle_chromosome
def: "A chromosome originating in a cyanelle." [SO:xp]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000746 ! cyanelle_sequence
relationship: has_origin SO:0000746 ! implied link automatically realized ! cyanelle_sequence

[Term]
id: SO:0000823
name: leucoplast_chromosome
def: "A chromosome with origin in a leucoplast." [SO:xp]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000747 ! leucoplast_sequence
relationship: has_origin SO:0000747 ! implied link automatically realized ! leucoplast_sequence

[Term]
id: SO:0000824
name: macronuclear_chromosome
def: "A chromosome originating in a macronucleus." [SO:xp]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000083 ! macronuclear_sequence
relationship: has_origin SO:0000083 ! implied link automatically realized ! macronuclear_sequence

[Term]
id: SO:0000825
name: micronuclear_chromosome
def: "A chromosome originating in a micronucleus." [SO:xp]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000084 ! micronuclear_sequence
relationship: has_origin SO:0000084 ! implied link automatically realized ! micronuclear_sequence

[Term]
id: SO:0000826
name: kinetoplast_chromosome
def: "A chromosome with origin in the kinetoplast." [SO:xp]
is_a: SO:0000819 ! implied link automatically realized ! mitochondrial_chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000741 ! kinetoplast_sequence
relationship: has_origin SO:0000741 ! implied link automatically realized ! kinetoplast_sequence

[Term]
id: SO:0000827
name: maxicircle_chromosome
def: "A chromosome originating in a maxi-circle." [SO:xp]
is_a: SO:0000826 ! implied link automatically realized ! kinetoplast_chromosome
intersection_of: SO:0000826 ! kinetoplast_chromosome
intersection_of: has_origin SO:0000742 ! maxicircle_sequence
relationship: has_origin SO:0000742 ! implied link automatically realized ! maxicircle_sequence

[Term]
id: SO:0000828
name: nuclear_chromosome
def: "A chromosome originating in a nucleus." [SO:xp]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000738 ! nuclear_sequence
relationship: has_origin SO:0000738 ! implied link automatically realized ! nuclear_sequence

[Term]
id: SO:0000829
name: nucleomorphic_chromosome
def: "A chromosome originating in a nucleomorph." [SO:xp]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000739 ! nucleomorphic_sequence
relationship: has_origin SO:0000739 ! implied link automatically realized ! nucleomorphic_sequence

[Term]
id: SO:0000830
name: chromosome_part
def: "A region of a chromosome." [SO:ke]
comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
subset: SOFA
is_a: SO:0000001 ! region
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000831
name: gene_member_region
def: "A region of a gene." [SO:ke]
comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root.
subset: SOFA
is_a: SO:0000001 ! region
relationship: member_of SO:0000704 ! gene

[Term]
id: SO:0000832
name: promoter_region
def: "A region of sequence which is part of a promoter." [SO:ke]
comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.
is_a: SO:0005836 ! regulatory_region
relationship: part_of SO:0000167 ! promoter

[Term]
id: SO:0000833
name: transcript_region
def: "A region of a transcript." [SO:ke]
comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
subset: SOFA
is_a: SO:0000001 ! region
relationship: part_of SO:0000673 ! transcript

[Term]
id: SO:0000834
name: processed_transcript_region
def: "A region of a processed transcript." [SO:ke]
comment: A manufactured term to collect together the parts of a processed transcript and give them an is_a path to the root.
subset: SOFA
is_a: SO:0000833 ! transcript_region

[Term]
id: SO:0000835
name: primary_transcript_region
def: "A region of a primary transcript." [SO:ke]
comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
subset: SOFA
is_a: SO:0000833 ! transcript_region
relationship: part_of SO:0000185 ! primary_transcript

[Term]
id: SO:0000836
name: mRNA_region
comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
subset: SOFA
is_a: SO:0000834 ! processed_transcript_region
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000837
name: UTR_region
def: "A region of UTR." [SO:ke]
comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
subset: SOFA
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000203 ! UTR

[Term]
id: SO:0000838
name: rRNA_primary_transcript_region
def: "A region of an rRNA primary transcript." [SO:ke]
comment: To allow transcribed_spacer_region to have a path to the root.
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000209 ! rRNA_primary_transcript

[Term]
id: SO:0000839
name: polypeptide_region
alt_id: BS:00124
alt_id: BS:00331
def: "Biological sequence region that can be assigned to a specific subsequence of a protein." [SO:GAR, SO:ke]
comment: Added to allow the polypeptide regions to have is_a paths back to the root.
subset: biosapiens
subset: SOFA
synonym: "positional" EXACT []
synonym: "positional polypeptide feature" EXACT []
synonym: "region or site annotation" EXACT []
is_a: SO:0000001 ! region
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000840
name: repeat_component
def: "A region of a repeated sequence." [SO:ke]
comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root.
is_a: SO:0000001 ! region
relationship: part_of SO:0000657 ! repeat_region

[Term]
id: SO:0000841
name: spliceosomal_intron_region
def: "A region within an intron." [SO:ke]
comment: A terms added to allow the parts of introns to have is_a paths to the root.
subset: SOFA
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000842
name: gene_component_region
subset: SOFA
is_a: SO:0000001 ! region
relationship: part_of SO:0000704 ! gene

[Term]
id: SO:0000843
name: bacterial_RNApol_promoter_region
def: "A region which is part of a bacterial RNA polymerase promoter." [SO:ke]
comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.
is_a: SO:0000832 ! promoter_region
relationship: part_of SO:0000613 ! bacterial_RNApol_promoter

[Term]
id: SO:0000844
name: RNApol_II_promoter_region
def: "A region of sequence which is a promoter for RNA polymerase II." [SO:ke]
comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.
is_a: SO:0000832 ! promoter_region
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000845
name: RNApol_III_promoter_type_1_region
def: "A region of sequence which is a promoter for RNA polymerase III type 1." [SO:ke]
comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.
is_a: SO:0000832 ! promoter_region
relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1

[Term]
id: SO:0000846
name: RNApol_III_promoter_type_2_region
def: "A region of sequence which is a promoter for RNA polymerase III type 2." [SO:ke]
comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.
is_a: SO:0000832 ! promoter_region
relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2

[Term]
id: SO:0000847
name: tmRNA_region
comment: This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.
is_a: SO:0000834 ! processed_transcript_region
relationship: part_of SO:0000584 ! tmRNA

[Term]
id: SO:0000848
name: LTR_component
synonym: "long term repeat component" EXACT []
is_a: SO:0000840 ! repeat_component
relationship: part_of SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000849
name: three_prime_LTR_component
synonym: "3' long terminal repeat component" EXACT []
is_a: SO:0000848 ! LTR_component
relationship: part_of SO:0000426 ! three_prime_LTR

[Term]
id: SO:0000850
name: five_prime_LTR_component
synonym: "5' long term repeat component" EXACT []
is_a: SO:0000848 ! LTR_component
relationship: part_of SO:0000425 ! five_prime_LTR

[Term]
id: SO:0000851
name: CDS_region
subset: SOFA
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000316 ! CDS

[Term]
id: SO:0000852
name: exon_region
def: "A region of an exon." [RSC:cb]
is_a: SO:0000833 ! transcript_region
relationship: part_of SO:0000147 ! exon

[Term]
id: SO:0000853
name: homologous_region
def: "A region that is homologous to another region." [SO:ke]
is_a: SO:0000330 ! implied link automatically realized ! conserved_region
intersection_of: SO:0000330 ! conserved_region
intersection_of: has_quality SO:0000856 ! conserved
relationship: has_quality SO:0000856 ! implied link automatically realized ! conserved

[Term]
id: SO:0000854
name: paralogous_region
def: "A homologous_region that is paralogous to another region." [SO:ke]
comment: A term to be used in conjunction witht he paralogous_to relationship.
is_a: SO:0000853 ! implied link automatically realized ! homologous_region
intersection_of: SO:0000853 ! homologous_region
intersection_of: has_quality SO:0000859 ! paralogous
relationship: has_quality SO:0000859 ! implied link automatically realized ! paralogous

[Term]
id: SO:0000855
name: orthologous_region
def: "A homologous_region that is orthologous to another region." [SO:ke]
comment: This term should be used in conjuction with the similarity relationships defined in SO.
is_a: SO:0000853 ! implied link automatically realized ! homologous_region
intersection_of: SO:0000853 ! homologous_region
intersection_of: has_quality SO:0000858 ! orthologous
relationship: has_quality SO:0000858 ! implied link automatically realized ! orthologous

[Term]
id: SO:0000856
name: conserved
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000857
name: homologous
def: "Similarity due to common ancestry." [SO:ke]
is_a: SO:0000856 ! conserved

[Term]
id: SO:0000858
name: orthologous
def: "A kind of homology where divergence occured after a speciation event." [SO:ke]
is_a: SO:0000857 ! homologous

[Term]
id: SO:0000859
name: paralogous
def: "A kind of homology where divergence occured after a duplication event." [SO:ke]
is_a: SO:0000857 ! homologous

[Term]
id: SO:0000860
name: syntenic
def: "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke]
is_a: SO:0000856 ! conserved

[Term]
id: SO:0000861
name: capped_primary_transcript
def: "A primary transcript that is capped." [SO:xp]
is_a: SO:0000185 ! implied link automatically realized ! primary_transcript
intersection_of: SO:0000185 ! primary_transcript
intersection_of: adjacent_to SO:0000581 ! cap
intersection_of: has_quality SO:0000146 ! capped
relationship: adjacent_to SO:0000581 ! implied link automatically realized ! cap
relationship: has_quality SO:0000146 ! implied link automatically realized ! capped

[Term]
id: SO:0000862
name: capped_mRNA
def: "An mRNA that is capped." [SO:xp]
is_a: SO:0000234 ! implied link automatically realized ! mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: adjacent_to SO:0000581 ! cap
intersection_of: has_quality SO:0000146 ! capped
relationship: adjacent_to SO:0000581 ! implied link automatically realized ! cap
relationship: has_quality SO:0000146 ! implied link automatically realized ! capped

[Term]
id: SO:0000863
name: mRNA_attribute
def: "An attribute describing an mRNA feature." [SO:ke]
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000864
name: exemplar
def: "An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute

[Term]
id: SO:0000865
name: frameshift
def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute

[Term]
id: SO:0000866
name: minus_1_frameshift
def: "A frameshift caused by deleting one base." [SO:ke]
is_a: SO:0000865 ! frameshift

[Term]
id: SO:0000867
name: minus_2_frameshift
def: "A frameshift caused by deleting two bases." [SO:ke]
is_a: SO:0000865 ! frameshift

[Term]
id: SO:0000868
name: plus_1_frameshift
def: "A frameshift caused by inserting one base." [SO:ke]
is_a: SO:0000865 ! frameshift

[Term]
id: SO:0000869
name: plus_2_framshift
def: "A frameshift caused by inserting two bases." [SO:ke]
is_a: SO:0000865 ! frameshift

[Term]
id: SO:0000870
name: trans_spliced
def: "An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke]
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000871
name: polyadenylated_mRNA
def: "An mRNA that is polyadenylated." [SO:xp]
is_a: SO:0000234 ! implied link automatically realized ! mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: adjacent_to SO:0000610 ! polyA_sequence
intersection_of: has_quality SO:0000246 ! polyadenylated
relationship: adjacent_to SO:0000610 ! implied link automatically realized ! polyA_sequence
relationship: has_quality SO:0000246 ! implied link automatically realized ! polyadenylated

[Term]
id: SO:0000872
name: trans_spliced_mRNA
def: "An mRNA that is trans-spliced." [SO:xp]
is_a: SO:0000234 ! implied link automatically realized ! mRNA
is_a: SO:0000479 ! implied link automatically realized ! trans_spliced_transcript
intersection_of: SO:0000234 ! mRNA
intersection_of: adjacent_to SO:0000636 ! spliced_leader_RNA
intersection_of: has_quality SO:0000870 ! trans_spliced
relationship: adjacent_to SO:0000636 ! implied link automatically realized ! spliced_leader_RNA

[Term]
id: SO:0000873
name: edited_transcript
def: "A transcript that is edited." [SO:ke]
is_a: SO:0000673 ! implied link automatically realized ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: associated_with SO:0000602 ! guide_RNA
intersection_of: associated_with SO:0000977 ! anchor_binding_site
intersection_of: has_quality SO:0000116 ! edited
relationship: associated_with SO:0000602 ! implied link automatically realized ! guide_RNA
relationship: associated_with SO:0000977 ! implied link automatically realized ! anchor_binding_site
relationship: has_quality SO:0000116 ! implied link automatically realized ! edited

[Term]
id: SO:0000874
name: edited_transcript_by A_to_I_substitution
def: "A transcript that has been edited by A to I substitution." [SO:ke]
is_a: SO:0000929 ! implied link automatically realized ! edited_mRNA
intersection_of: SO:0000873 ! edited_transcript
intersection_of: associated_with SO:0000919 ! substitute_A_to_I
relationship: associated_with SO:0000919 ! implied link automatically realized ! substitute_A_to_I

[Term]
id: SO:0000875
name: bound_by_protein
def: "An attribute describing a sequence that is bound by a protein." [SO:ke]
is_a: SO:0000277 ! bound_by_factor

[Term]
id: SO:0000876
name: bound_by_nucleic_acid
def: "An attribute describing a sequence that is bound by a nucleic acid." [SO:ke]
is_a: SO:0000277 ! bound_by_factor

[Term]
id: SO:0000877
name: alternatively_spliced
def: "An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke]
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000878
name: monocistronic
def: "An attribute describing a sequence that contains the code for one gene product." [SO:ke]
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000879
name: dicistronic
def: "An attribute describing a sequence that contains the code for two gene products." [SO:ke]
is_a: SO:0000880 ! polycistronic

[Term]
id: SO:0000880
name: polycistronic
def: "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000881
name: recoded
def: "An attribute describing am mRNA sequences that has been reprogrammed at translation, causing localized alterations." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute

[Term]
id: SO:0000882
name: codon_redefined
def: "An attribute describing the alteration of codon meaning." [SO:ke]
is_a: SO:0000881 ! recoded

[Term]
id: SO:0000883
name: stop_codon_read_through
def: "A stop codon redefined to be a new amino acid." [SO:ke]
synonym: "stop codon readthrough" RELATED []
is_a: SO:0000882 ! codon_redefined

[Term]
id: SO:0000884
name: stop_codon_redefined_as_pyrrolysine
def: "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]
is_a: SO:0000883 ! stop_codon_read_through

[Term]
id: SO:0000885
name: stop_codon_redefined_as_selenocysteine
def: "A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]
is_a: SO:0000883 ! stop_codon_read_through

[Term]
id: SO:0000886
name: recoded_by_translational_bypass
def: "Recoded mRNA where a block of nucleotides is not translated." [SO:ke]
is_a: SO:0000881 ! recoded

[Term]
id: SO:0000887
name: translational_frameshift
def: "Recoding by frameshifting a particular site." [SO:ke]
is_a: SO:0000881 ! recoded

[Term]
id: SO:0000888
name: maternally_imprinted_gene
def: "A gene that is maternally_imprinted." [SO:xp]
is_a: SO:0000898 ! implied link automatically realized ! epigenetically_modified_gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000135 ! maternally_imprinted
relationship: has_quality SO:0000135 ! implied link automatically realized ! maternally_imprinted

[Term]
id: SO:0000889
name: paternally_imprinted_gene
def: "A gene that is paternally imprinted." [SO:xp]
is_a: SO:0000898 ! implied link automatically realized ! epigenetically_modified_gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000136 ! paternally_imprinted
relationship: has_quality SO:0000136 ! implied link automatically realized ! paternally_imprinted

[Term]
id: SO:0000890
name: post_translationally_regulated_gene
def: "A gene that is post translationally regulated." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000130 ! post_translationally_regulated
relationship: has_quality SO:0000130 ! implied link automatically realized ! post_translationally_regulated

[Term]
id: SO:0000891
name: negatively_autoregulated_gene
def: "A gene that is negatively autoreguated." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000473 ! negatively_autoregulated
relationship: has_quality SO:0000473 ! implied link automatically realized ! negatively_autoregulated

[Term]
id: SO:0000892
name: positively_autoregulated_gene
def: "A gene that is positively autoregulated." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000475 ! positively_autoregulated
relationship: has_quality SO:0000475 ! implied link automatically realized ! positively_autoregulated

[Term]
id: SO:0000893
name: silenced
def: "An epigenetic process where a gene is innactivated at transcriptional or translational level." [SO:ke]
is_a: SO:0000126 ! transcriptionally_repressed

[Term]
id: SO:0000894
name: silenced_by_DNA_modification
def: "An epigenetic process where a gene is innactivated by DNA modifications, resulting in repression of transcription." [SO:ke]
is_a: SO:0000893 ! silenced

[Term]
id: SO:0000895
name: silenced_by_DNA_methylation
def: "An epigenetic process where a gene is innactivated by DNA methylation, resulting in repression of transcription." [SO:ke]
is_a: SO:0000894 ! silenced_by_DNA_modification

[Term]
id: SO:0000896
name: translationally_regulated_gene
def: "A gene that is translationally regulated." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000131 ! translationally_regulated
relationship: has_quality SO:0000131 ! implied link automatically realized ! translationally_regulated

[Term]
id: SO:0000897
name: allelically_excluded_gene
def: "A gene that is allelically_excluded." [SO:xp]
is_a: SO:0000898 ! implied link automatically realized ! epigenetically_modified_gene
intersection_of: SO:0000898 ! epigenetically_modified_gene
intersection_of: has_quality SO:0000137 ! allelically_excluded
relationship: has_quality SO:0000137 ! implied link automatically realized ! allelically_excluded

[Term]
id: SO:0000898
name: epigenetically_modified_gene
def: "A gene that is epigenetically modified." [SO:ke]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000133 ! epigenetically_modified
relationship: has_quality SO:0000133 ! implied link automatically realized ! epigenetically_modified

[Term]
id: SO:0000899
name: nuclear_mitochondrial
def: "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke]
is_a: SO:0000042 ! pseudogene_attribute

[Term]
id: SO:0000900
name: processed
def: "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail." [SO:ke]
is_a: SO:0000042 ! pseudogene_attribute

[Term]
id: SO:0000901
name: unequally_crossed_over
def: "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." [SO:ke]
is_a: SO:0000042 ! pseudogene_attribute

[Term]
id: SO:0000902
name: transgene
def: "A gene that is transgenic." [SO:xp]
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000781 ! transgenic
relationship: has_quality SO:0000781 ! implied link automatically realized ! transgenic

[Term]
id: SO:0000903
name: endogenous_retroviral_sequence
is_a: SO:0000751 ! proviral_location

[Term]
id: SO:0000904
name: rearranged_at_DNA_level
def: "An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]
is_a: SO:0000133 ! epigenetically_modified

[Term]
id: SO:0000905
name: status
def: "An attribute describing the status of a feature, based on the available evidence." [SO:ke]
comment: This term is the hypernym of attributes and should not be annotated to.
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000906
name: independently_known
def: "Attribute to describe a feature that is independently known - not predicted." [SO:ke]
is_a: SO:0000905 ! status

[Term]
id: SO:0000907
name: supported_by_sequence_similarity
def: "An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]
is_a: SO:0000732 ! predicted

[Term]
id: SO:0000908
name: supported_by_domain_match
def: "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]
is_a: SO:0000907 ! supported_by_sequence_similarity

[Term]
id: SO:0000909
name: supported_by_EST_or_cDNA
def: "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]
is_a: SO:0000907 ! supported_by_sequence_similarity

[Term]
id: SO:0000910
name: orphan
is_a: SO:0000732 ! predicted

[Term]
id: SO:0000911
name: predicted_by_ab_initio_computation
def: "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]
is_a: SO:0000732 ! predicted

[Term]
id: SO:0000912
name: asx_turn
alt_id: BS:00203
def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx_turn" EXACT []
is_a: SO:0001128 ! turn

[Term]
id: SO:0000913
name: cloned_cDNA_insert
def: "A clone insert made from cDNA." [SO:xp]
is_a: SO:0000753 ! implied link automatically realized ! clone_insert
intersection_of: SO:0000753 ! clone_insert
intersection_of: has_quality SO:0000756 ! cDNA
relationship: has_quality SO:0000756 ! implied link automatically realized ! cDNA

[Term]
id: SO:0000914
name: cloned_genomic_insert
def: "A clone insert made from genomic DNA." [SO:xp]
is_a: SO:0000753 ! implied link automatically realized ! clone_insert
intersection_of: SO:0000753 ! clone_insert
intersection_of: has_quality SO:0000991 ! genomic_DNA
relationship: has_quality SO:0000991 ! implied link automatically realized ! genomic_DNA

[Term]
id: SO:0000915
name: engineered_insert
def: "A clone insert that is engineered." [SO:xp]
is_a: SO:0000753 ! implied link automatically realized ! clone_insert
is_a: SO:0000804 ! implied link automatically realized ! engineered_region
intersection_of: SO:0000753 ! clone_insert
intersection_of: has_quality SO:0000783 ! engineered

[Term]
id: SO:0000916
name: edit_operation
is_a: SO:0000041 ! operation

[Term]
id: SO:0000917
name: insert_U
def: "An edit to insert a U." [SO:ke]
comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
is_a: SO:0000916 ! edit_operation

[Term]
id: SO:0000918
name: delete_U
def: "An edit to delete a uridine." [SO:ke]
comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
is_a: SO:0000916 ! edit_operation

[Term]
id: SO:0000919
name: substitute_A_to_I
def: "An edit to substitute an I for an A." [SO:ke]
is_a: SO:0000916 ! edit_operation

[Term]
id: SO:0000920
name: insert_C
def: "An edit to insert a cytidine." [SO:ke]
is_a: SO:0000916 ! edit_operation

[Term]
id: SO:0000921
name: insert_dinucleotide
def: "An edit to insert a dinucleotide." [SO:ke]
is_a: SO:0000916 ! edit_operation

[Term]
id: SO:0000922
name: substitute_C_to_U
def: "An edit to substitute an U for a C." [SO:ke]
is_a: SO:0000916 ! edit_operation

[Term]
id: SO:0000923
name: insert_G
def: "An edit to insert a G." [SO:ke]
is_a: SO:0000916 ! edit_operation

[Term]
id: SO:0000924
name: insert_GC
def: "An edit to insert a GC dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
is_a: SO:0000921 ! insert_dinucleotide

[Term]
id: SO:0000925
name: insert_GU
def: "An edit to insert a GU dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
is_a: SO:0000921 ! insert_dinucleotide

[Term]
id: SO:0000926
name: insert_CU
def: "An edit to insert a CU dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
is_a: SO:0000921 ! insert_dinucleotide

[Term]
id: SO:0000927
name: insert_AU
def: "An edit to insert a AU dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
is_a: SO:0000921 ! insert_dinucleotide

[Term]
id: SO:0000928
name: insert_AA
def: "An edit to insert a AA dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
is_a: SO:0000921 ! insert_dinucleotide

[Term]
id: SO:0000929
name: edited_mRNA
def: "An mRNA that is edited." [SO:xp]
is_a: SO:0000873 ! implied link automatically realized ! edited_transcript
intersection_of: SO:0000873 ! edited_transcript
intersection_of: associated_with SO:0000916 ! edit_operation
intersection_of: has_quality SO:0000116 ! edited
relationship: associated_with SO:0000916 ! implied link automatically realized ! edit_operation

[Term]
id: SO:0000930
name: guide_RNA_region
def: "A region of guide RNA." [SO:ma]
is_a: SO:0000834 ! processed_transcript_region
relationship: part_of SO:0000602 ! guide_RNA

[Term]
id: SO:0000931
name: anchor_region
def: "A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]
is_a: SO:0000930 ! guide_RNA_region

[Term]
id: SO:0000932
name: pre_edited_mRNA
is_a: SO:0000120 ! protein_coding_primary_transcript

[Term]
id: SO:0000933
name: intermediate
def: "An attribute to describe a feature between stages of processing." [SO:ke]
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000934
name: miRNA_target_site
def: "A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]
is_a: SO:0000409 ! binding_site

[Term]
id: SO:0000935
name: edited_CDS
def: "A CDS that is edited." [SO:xp]
is_a: SO:0000316 ! implied link automatically realized ! CDS
intersection_of: SO:0000316 ! CDS
intersection_of: associated_with SO:0000916 ! edit_operation
intersection_of: has_quality SO:0000116 ! edited
relationship: associated_with SO:0000916 ! implied link automatically realized ! edit_operation
relationship: has_quality SO:0000116 ! implied link automatically realized ! edited

[Term]
id: SO:0000936
name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000937
name: vertebrate_immune_system_feature
is_obsolete: true

[Term]
id: SO:0000938
name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000939
name: vertebrate_immune_system_gene_recombination_signal_feature
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000940
name: recombinationally_rearranged
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000941
name: recombinationally_rearranged_vertebrate_immune_system_gene
def: "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]
is_a: SO:0000456 ! implied link automatically realized ! recombinationally_rearranged_gene
intersection_of: SO:0000456 ! recombinationally_rearranged_gene
intersection_of: associated_with SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
relationship: associated_with SO:0000301 ! implied link automatically realized ! vertebrate_immune_system_gene_recombination_feature

[Term]
id: SO:0000942
name: attP_site
def: "An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]
synonym: "attP site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0001042 ! phage_sequence

[Term]
id: SO:0000943
name: attB_site
def: "An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]
synonym: "attB site" EXACT []
is_a: SO:0000946 ! integration_excision_site

[Term]
id: SO:0000944
name: attL_site
def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]
synonym: "attBP'" RELATED []
synonym: "attL site" RELATED []
is_a: SO:0000946 ! integration_excision_site

[Term]
id: SO:0000945
name: attR_site
def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]
synonym: "attPB'" RELATED []
synonym: "attR site" EXACT []
is_a: SO:0000946 ! integration_excision_site

[Term]
id: SO:0000946
name: integration_excision_site
def: "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]
synonym: "attachment site" RELATED []
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000947
name: resolution_site
def: "A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]
synonym: "res site" EXACT []
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000948
name: inversion_site
def: "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]
comment: A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
synonym: "inversion site" EXACT []
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000949
name: dif_site
def: "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]
is_a: SO:0000947 ! resolution_site

[Term]
id: SO:0000950
name: attC_site
def: "An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]
synonym: "attC site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0000365 ! integron

[Term]
id: SO:0000951
name: eukaryotic_terminator
is_a: SO:0000141 ! terminator

[Term]
id: SO:0000952
name: oriV
def: "An origin of vegetative replication in plasmids and phages." [SO:as]
synonym: "origin of vegetative replication" EXACT []
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000953
name: oriC
def: "An origin of bacterial chromosome replication." [SO:as]
synonym: "origin of bacterial chromosome replication" EXACT []
is_a: SO:0000296 ! origin_of_replication

[Term]
id: SO:0000954
name: DNA_chromosome
def: "Structural unit composed of a self-replicating, DNA molecule." [SO:ma]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_quality SO:0000352 ! DNA
relationship: has_quality SO:0000352 ! implied link automatically realized ! DNA

[Term]
id: SO:0000955
name: double_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]
is_a: SO:0000954 ! implied link automatically realized ! DNA_chromosome
intersection_of: SO:0000954 ! DNA_chromosome
intersection_of: has_quality SO:0000985 ! double
relationship: has_quality SO:0000985 ! implied link automatically realized ! double

[Term]
id: SO:0000956
name: single_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]
is_a: SO:0000954 ! implied link automatically realized ! DNA_chromosome
intersection_of: SO:0000954 ! DNA_chromosome
intersection_of: has_quality SO:0000984 ! single
relationship: has_quality SO:0000984 ! implied link automatically realized ! single

[Term]
id: SO:0000957
name: linear_double_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]
is_a: SO:0000955 ! implied link automatically realized ! double_stranded_DNA_chromosome
intersection_of: SO:0000955 ! double_stranded_DNA_chromosome
intersection_of: has_quality SO:0000987 ! linear
relationship: has_quality SO:0000987 ! implied link automatically realized ! linear

[Term]
id: SO:0000958
name: circular_double_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]
is_a: SO:0000955 ! implied link automatically realized ! double_stranded_DNA_chromosome
intersection_of: SO:0000955 ! double_stranded_DNA_chromosome
intersection_of: has_quality SO:0000988 ! circular
relationship: has_quality SO:0000988 ! implied link automatically realized ! circular

[Term]
id: SO:0000959
name: linear_single_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]
is_a: SO:0000956 ! implied link automatically realized ! single_stranded_DNA_chromosome
intersection_of: SO:0000956 ! single_stranded_DNA_chromosome
intersection_of: has_quality SO:0000987 ! linear
relationship: has_quality SO:0000987 ! implied link automatically realized ! linear

[Term]
id: SO:0000960
name: circular_single_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]
is_a: SO:0000956 ! implied link automatically realized ! single_stranded_DNA_chromosome
intersection_of: SO:0000956 ! single_stranded_DNA_chromosome
intersection_of: has_quality SO:0000988 ! circular
relationship: has_quality SO:0000988 ! implied link automatically realized ! circular

[Term]
id: SO:0000961
name: RNA_chromosome
def: "Structural unit composed of a self-replicating, RNA molecule." [SO:ma]
is_a: SO:0000340 ! implied link automatically realized ! chromosome
intersection_of: SO:0000340 ! chromosome
intersection_of: has_quality SO:0000356 ! RNA
relationship: has_quality SO:0000356 ! implied link automatically realized ! RNA

[Term]
id: SO:0000962
name: single_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]
is_a: SO:0000961 ! implied link automatically realized ! RNA_chromosome
intersection_of: SO:0000961 ! RNA_chromosome
intersection_of: has_quality SO:0000984 ! single
relationship: has_quality SO:0000984 ! implied link automatically realized ! single

[Term]
id: SO:0000963
name: linear_single_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]
is_a: SO:0000962 ! implied link automatically realized ! single_stranded_RNA_chromosome
intersection_of: SO:0000962 ! single_stranded_RNA_chromosome
intersection_of: has_quality SO:0000987 ! linear
relationship: has_quality SO:0000987 ! implied link automatically realized ! linear

[Term]
id: SO:0000964
name: linear_double_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]
is_a: SO:0000965 ! implied link automatically realized ! double_stranded_RNA_chromosome
intersection_of: SO:0000965 ! double_stranded_RNA_chromosome
intersection_of: has_quality SO:0000987 ! linear
relationship: has_quality SO:0000987 ! implied link automatically realized ! linear

[Term]
id: SO:0000965
name: double_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]
is_a: SO:0000961 ! implied link automatically realized ! RNA_chromosome
intersection_of: SO:0000961 ! RNA_chromosome
intersection_of: has_quality SO:0000985 ! double
relationship: has_quality SO:0000985 ! implied link automatically realized ! double

[Term]
id: SO:0000966
name: circular_single_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]
is_a: SO:0000962 ! implied link automatically realized ! single_stranded_RNA_chromosome
intersection_of: SO:0000962 ! single_stranded_RNA_chromosome
intersection_of: has_quality SO:0000988 ! circular
relationship: has_quality SO:0000988 ! implied link automatically realized ! circular

[Term]
id: SO:0000967
name: circular_double_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]
is_a: SO:0000965 ! implied link automatically realized ! double_stranded_RNA_chromosome
intersection_of: SO:0000965 ! double_stranded_RNA_chromosome
intersection_of: has_quality SO:0000988 ! circular
relationship: has_quality SO:0000988 ! implied link automatically realized ! circular

[Term]
id: SO:0000968
name: replication_mode
is_a: SO:0000000 ! Sequence_Ontology
disjoint_from: SO:0001060 ! sequence_variant

[Term]
id: SO:0000969
name: rolling_circle
is_a: SO:0000971 ! DNA_replication_mode

[Term]
id: SO:0000970
name: theta_replication
is_a: SO:0000971 ! DNA_replication_mode

[Term]
id: SO:0000971
name: DNA_replication_mode
is_a: SO:0000968 ! replication_mode

[Term]
id: SO:0000972
name: RNA_replication_mode
is_a: SO:0000968 ! replication_mode

[Term]
id: SO:0000973
name: insertion_sequence
def: "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]
synonym: "IS" RELATED []
is_a: SO:0000208 ! terminal_inverted_repeat_element

[Term]
id: SO:0000974
name: minicircle_chromosome
is_a: SO:0000826 ! implied link automatically realized ! kinetoplast_chromosome
intersection_of: SO:0000826 ! kinetoplast_chromosome
intersection_of: has_origin SO:0000980 ! minicircle_sequence
relationship: has_origin SO:0000980 ! implied link automatically realized ! minicircle_sequence

[Term]
id: SO:0000975
name: minicircle_gene
is_a: SO:0000089 ! implied link automatically realized ! kinetoplast_gene
intersection_of: SO:0000089 ! kinetoplast_gene
intersection_of: has_origin SO:0000980 ! minicircle_sequence
relationship: has_origin SO:0000980 ! implied link automatically realized ! minicircle_sequence

[Term]
id: SO:0000976
name: cryptic
is_a: SO:0000116 ! edited

[Term]
id: SO:0000977
name: anchor_binding_site
comment: Part of an edited transcript only.
is_a: SO:0000833 ! transcript_region

[Term]
id: SO:0000978
name: template_region
def: "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]
synonym: "information region" EXACT []
is_a: SO:0000930 ! guide_RNA_region

[Term]
id: SO:0000979
name: gRNA_encoding
def: "A non-protein_coding gene that encodes a guide_RNA." [SO:ma]
is_a: SO:0000011 ! non_protein_coding

[Term]
id: SO:0000980
name: minicircle_sequence
is_a: SO:0000741 ! kinetoplast_sequence

[Term]
id: SO:0000981
name: rho_dependent_bacterial_terminator
is_a: SO:0000614 ! bacterial_terminator

[Term]
id: SO:0000982
name: rho_independent_bacterial_terminator
is_a: SO:0000614 ! bacterial_terminator

[Term]
id: SO:0000983
name: strand_attribute
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000984
name: single
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
is_a: SO:0000983 ! strand_attribute

[Term]
id: SO:0000985
name: double
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
is_a: SO:0000983 ! strand_attribute

[Term]
id: SO:0000986
name: topology_attribute
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
is_a: SO:0000443 ! polymer_attribute

[Term]
id: SO:0000987
name: linear
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
is_a: SO:0000986 ! topology_attribute
disjoint_from: SO:0000988 ! circular

[Term]
id: SO:0000988
name: circular
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
is_a: SO:0000986 ! topology_attribute
disjoint_from: SO:0000987 ! linear

[Term]
id: SO:0000989
name: class_II_RNA
def: "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]
synonym: "class II RNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000990
name: class_I_RNA
def: "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]
comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.
synonym: "class I RNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000991
name: genomic_DNA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is_a: SO:0000352 ! DNA

[Term]
id: SO:0000992
name: BAC_cloned_genomic_insert
comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006.
is_a: SO:0000914 ! implied link automatically realized ! cloned_genomic_insert
intersection_of: SO:0000914 ! cloned_genomic_insert
intersection_of: derives_from SO:0000153 ! BAC
relationship: derives_from SO:0000153 ! implied link automatically realized ! BAC

[Term]
id: SO:0000993
name: consensus
comment: Term added Dec 06 to comply with mapping to MGED terms.\nIt should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.
is_a: SO:0000905 ! status

[Term]
id: SO:0000994
name: consensus_region
comment: DO not obsolete without considering MGED mapping.
is_a: SO:0000001 ! implied link automatically realized ! region
intersection_of: SO:0000001 ! region
intersection_of: has_quality SO:0000993 ! consensus
relationship: has_quality SO:0000993 ! implied link automatically realized ! consensus

[Term]
id: SO:0000995
name: consensus_mRNA
comment: DO not obsolete without considering MGED mapping.
is_a: SO:0000234 ! implied link automatically realized ! mRNA
is_a: SO:0000994 ! implied link automatically realized ! consensus_region
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000993 ! consensus

[Term]
id: SO:0000996
name: predicted_gene
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is_a: SO:0000704 ! implied link automatically realized ! gene
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000732 ! predicted
relationship: has_quality SO:0000732 ! implied link automatically realized ! predicted

[Term]
id: SO:0000997
name: gene_fragment
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is_a: SO:0000842 ! implied link automatically realized ! gene_component_region
intersection_of: SO:0000842 ! gene_component_region
intersection_of: has_quality SO:0000731 ! fragment
relationship: has_quality SO:0000731 ! implied link automatically realized ! fragment

[Term]
id: SO:0000998
name: recursive_splice_site
def: "Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]
is_a: SO:0000188 ! intron

[Term]
id: SO:0000999
name: BAC_end
def: "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]
comment: Requested by Keith Boroevich December, 2006.
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000153 ! BAC

[Term]
id: SO:0001000
name: rRNA_16S
def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "16S ribosomal RNA" EXACT []
synonym: "16S rRNA" RELATED []
synonym: "16S SSU RNA" EXACT []
is_a: SO:0000650 ! small_subunit_rRNA

[Term]
id: SO:0001001
name: rRNA_23S
def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "23S LSU rRNA" EXACT []
synonym: "23S ribosomal RNA" RELATED []
synonym: "23S rRNA" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0001002
name: rRNA_25S
def: "A large polynucleotide which functions as\npart of the large subunit of the ribosome in some eukaryotes." [RSC:cb]
subset: SOFA
synonym: "25S LSU rRNA" EXACT []
synonym: "25S ribosomal RNA" EXACT []
synonym: "25S rRNA" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0001003
name: solo_LTR
def: "A recombination product between the 2 LTR of the same element." [SO:ke]
comment: Requested by Hadi Quesneville January 2007.
is_a: SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0001004
name: low_complexity
is_a: SO:0000905 ! status

[Term]
id: SO:0001005
name: low_complexity_region
is_a: SO:0000001 ! implied link automatically realized ! region
intersection_of: SO:0000001 ! region
intersection_of: has_quality SO:0001004 ! low_complexity
relationship: has_quality SO:0001004 ! implied link automatically realized ! low_complexity

[Term]
id: SO:0001006
name: prophage
def: "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\"." [GO:jl]
is_a: SO:0000113 ! proviral_region

[Term]
id: SO:0001007
name: cryptic_prophage
def: "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes." [GO:jl]
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0001008
name: tetraloop
def: "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]
is_a: SO:0000313 ! stem_loop

[Term]
id: SO:0001009
name: DNA_constraint_sequence
def: "A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\]&dispmax=50]
synonym: "DNA constraint" EXACT []
is_a: SO:0000442 ! ds_oligo

[Term]
id: SO:0001010
name: i_motif
def: "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]
synonym: "short intercalated motif" EXACT []
is_a: SO:0000142 ! DNA_sequence_secondary_structure

[Term]
id: SO:0001011
name: PNA_oligo
def: "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]
synonym: "peptide nucleic acid" EXACT []
is_a: SO:0000696 ! implied link automatically realized ! oligo
intersection_of: SO:0000696 ! oligo
intersection_of: has_quality SO:0001184 ! PNA
relationship: has_quality SO:0001184 ! implied link automatically realized ! PNA

[Term]
id: SO:0001012
name: DNAzyme
def: "A DNA sequence with catalytic activity." [SO:cb]
comment: Added by request from Colin Batchelor.
synonym: "catalytic DNA" EXACT []
synonym: "deoxyribozyme" RELATED []
synonym: "DNA enzyme" EXACT []
is_a: SO:0000695 ! reagent

[Term]
id: SO:0001013
name: MNP
def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]
synonym: "multiple nucleotide polymorphism" RELATED []
is_a: SO:1000005 ! complex_substitution

[Term]
id: SO:0001014
name: intron_domain
comment: Requested by Colin Batchelor, Feb 2007.
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000188 ! intron

[Term]
id: SO:0001015
name: wobble_base_pair
def: "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]
synonym: "wobble pair" EXACT []
is_a: SO:0000028 ! base_pair

[Term]
id: SO:0001016
name: internal_guide_sequence
def: "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]
synonym: "IGS" EXACT []
is_a: SO:0001014 ! intron_domain
relationship: part_of SO:0000587 ! group_I_intron

[Term]
id: SO:0001017
name: silent_mutation
comment: Added in March 2007 in after meeting with pharmgkb.
is_a: SO:1000132 ! mutation

[Term]
id: SO:0001018
name: epitope
def: "A region of a macromolecule that is recognized by the immune system." [http://en.wikipedia.org/wiki/Epitope]
comment: Requested by Trish Whetzel.
is_a: SO:0000409 ! binding_site

[Term]
id: SO:0001019
name: copy_number_variation
def: "A variation that increases or decreases the copy number of a given region." [SO:ke]
synonym: "CNP" EXACT []
synonym: "CNV" EXACT []
synonym: "copy number polymorphism" EXACT []
synonym: "copy number variation" EXACT []
is_a: SO:0001060 ! sequence_variant

[Term]
id: SO:0001020
name: mutation_affecting_copy_number
is_a: SO:1000132 ! mutation

[Term]
id: SO:0001021
name: chromosome_breakpoint
is_a: SO:0000830 ! chromosome_part

[Term]
id: SO:0001022
name: inversion_breakpoint
is_a: SO:0001021 ! chromosome_breakpoint

[Term]
id: SO:0001023
name: allele
def: "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop]
is_a: SO:0001060 ! sequence_variant
relationship: variant_of SO:0000704 ! gene

[Term]
id: SO:0001024
name: haplotype
def: "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop]
is_a: SO:0001060 ! sequence_variant
relationship: variant_of SO:0000355 ! haplotype_block

[Term]
id: SO:0001025
name: polymorphic_sequence_variant
def: "A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop]
is_a: SO:0001060 ! sequence_variant

[Term]
id: SO:0001026
name: genome
def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]
is_a: SO:0000000 ! Sequence_Ontology
disjoint_from: SO:0000110 ! sequence_feature
disjoint_from: SO:0000240 ! chromosome_variation
disjoint_from: SO:0000400 ! sequence_attribute
disjoint_from: SO:0000968 ! replication_mode
disjoint_from: SO:0001060 ! sequence_variant
disjoint_from: SO:1000132 ! mutation

[Term]
id: SO:0001027
name: genotype
def: "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop]
is_a: SO:0001060 ! sequence_variant
relationship: variant_of SO:0001026 ! genome

[Term]
id: SO:0001028
name: diplotype
def: "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop]
is_a: SO:0001027 ! genotype

[Term]
id: SO:0001029
name: direction_attribute
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0001030
name: forward
is_a: SO:0001029 ! direction_attribute

[Term]
id: SO:0001031
name: reverse
is_a: SO:0001029 ! direction_attribute

[Term]
id: SO:0001032
name: mitochondrial_DNA
comment: This terms is used by MO.
is_a: SO:0000737 ! implied link automatically realized ! mitochondrial_sequence
intersection_of: SO:0000737 ! mitochondrial_sequence
intersection_of: has_quality SO:0000352 ! DNA
relationship: has_quality SO:0000352 ! implied link automatically realized ! DNA

[Term]
id: SO:0001033
name: chloroplast_DNA
comment: This term is used by MO.
is_a: SO:0000745 ! implied link automatically realized ! chloroplast_sequence
intersection_of: SO:0000745 ! chloroplast_sequence
intersection_of: has_quality SO:0000352 ! DNA
relationship: has_quality SO:0000352 ! implied link automatically realized ! DNA

[Term]
id: SO:0001034
name: mitron
def: "An intron from whose debranched product an miRNA is derived." [SO:ma]
comment: Ruby et al. Nature 448:83 desribe a new class of miRNAs that are derived from debranched introns.
is_a: SO:0000276 ! implied link automatically realized ! miRNA
intersection_of: SO:0000276 ! miRNA
intersection_of: derives_from SO:0000188 ! intron
relationship: derives_from SO:0000188 ! implied link automatically realized ! intron

[Term]
id: SO:0001035
name: piRNA
def: "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]
synonym: "piwi-associated RNA" EXACT []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0001036
name: arginyl_tRNA
def: "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000212 ! arginine_tRNA_primary_transcript

[Term]
id: SO:0001037
name: mobile_genetic_element
def: "A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]
synonym: "MGE" EXACT []
is_a: SO:0000001 ! region

[Term]
id: SO:0001038
name: extrachromosomal_mobile_genetic_element
def: "An MGE that is not integrated into the host chromosome." [SO:ke]
is_a: SO:0001037 ! mobile_genetic_element

[Term]
id: SO:0001039
name: integrated_mobile_genetic_element
def: "An MGE that is integrated into the host chromosome." [SO:ke]
is_a: SO:0001037 ! mobile_genetic_element

[Term]
id: SO:0001040
name: integrated_plasmid
def: "A plasmid sequence that is integrated within the host chromosome." [SO:ke]
is_a: SO:0001039 ! integrated_mobile_genetic_element

[Term]
id: SO:0001041
name: viral_sequence
def: "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]
comment: The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.
synonym: "viral sequence" EXACT []
synonym: "virus sequence" EXACT []
is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element

[Term]
id: SO:0001042
name: phage_sequence
def: "The nucleotide sequence of a virus that infects bacteria." [SO:ke]
synonym: "bacteriophage" EXACT []
synonym: "phage" EXACT []
synonym: "phage sequence" EXACT []
is_a: SO:0001041 ! viral_sequence

[Term]
id: SO:0001043
name: attCtn_site
def: "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]
synonym: "attCtn site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0000371 ! conjugative_transposon

[Term]
id: SO:0001044
name: nuclear_mt_pseudogene
def: "A pseudogene that is nuclear/mitochondrial." [SO:xp]
synonym: "nuclear mitochondrial pseudogene" EXACT []
synonym: "NUMT" EXACT []
is_a: SO:0000336 ! implied link automatically realized ! pseudogene
intersection_of: SO:0000336 ! pseudogene
intersection_of: has_quality SO:0000899 ! nuclear_mitochondrial
relationship: has_quality SO:0000899 ! implied link automatically realized ! nuclear_mitochondrial

[Term]
id: SO:0001045
name: cointegrated_replicon
def: "A MGE region consisting of two fused replicons/plasmids resulting from a replicative transposition event." [Phigo:at]
is_a: SO:0001039 ! integrated_mobile_genetic_element

[Term]
id: SO:0001046
name: IRLinv_site
def: "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]
is_a: SO:0001048 ! inversion_site_part
relationship: part_of SO:0000948 ! inversion_site

[Term]
id: SO:0001047
name: IRRinv_site
def: "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]
is_a: SO:0001048 ! inversion_site_part
relationship: part_of SO:0000948 ! inversion_site

[Term]
id: SO:0001048
name: inversion_site_part
def: "A region located within an inversion site." [SO:ke]
comment: A term created to allow the parts of an inversion site have an is_a path back to the root.
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0001049
name: defective_conjugative_transposon
def: "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]
synonym: "defective conjugative transposon" EXACT []
is_a: SO:0000772 ! genomic_island

[Term]
id: SO:0001050
name: repeat_fragment
def: "A portion of a repeat, interrupted by the insertion of another element." [SO:ke]
comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats.
is_a: SO:0000657 ! implied link automatically realized ! repeat_region
is_a: SO:0000840 ! repeat_component
intersection_of: SO:0000657 ! repeat_region
intersection_of: has_quality SO:0000731 ! fragment
relationship: has_quality SO:0000731 ! implied link automatically realized ! fragment

[Term]
id: SO:0001051
name: nested_region
is_a: SO:0000001 ! region

[Term]
id: SO:0001052
name: nested_repeat
is_a: SO:0001051 ! implied link automatically realized ! nested_region
intersection_of: SO:0001051 ! nested_region
intersection_of: derives_from SO:0000657 ! repeat_region
intersection_of: has_part SO:0000001 ! region
intersection_of: has_part SO:0001050 ! repeat_fragment
relationship: derives_from SO:0000657 ! implied link automatically realized ! repeat_region
relationship: has_part SO:0001050 ! implied link automatically realized ! repeat_fragment

[Term]
id: SO:0001053
name: nested_transposon
is_a: SO:0001051 ! implied link automatically realized ! nested_region
intersection_of: SO:0001051 ! nested_region
intersection_of: derives_from SO:0000101 ! transposable_element
intersection_of: has_part SO:0000001 ! region
intersection_of: has_part SO:0001054 ! transposon_fragment
relationship: derives_from SO:0000101 ! implied link automatically realized ! transposable_element
relationship: has_part SO:0001054 ! implied link automatically realized ! transposon_fragment

[Term]
id: SO:0001054
name: transposon_fragment
is_a: SO:0000101 ! implied link automatically realized ! transposable_element
intersection_of: SO:0000101 ! transposable_element
intersection_of: has_quality SO:0000731 ! fragment
relationship: has_quality SO:0000731 ! implied link automatically realized ! fragment

[Term]
id: SO:0001055
name: transcriptional_cis_regulatory_region
def: "A regulatory_region that modulates the transcription of a gene or genes." [SO:regcreative]
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0001056
name: splicing_regulatory_region
def: "A regulatory_region that modulates splicing." [SO:ke]
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0001057
name: enhanceosome
is_a: SO:0000165 ! enhancer

[Term]
id: SO:0001058
name: promoter_targeting_sequence
def: "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]
is_a: SO:0001055 ! transcriptional_cis_regulatory_region

[Term]
id: SO:0001059
name: sequence_alteration
def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]
is_a: SO:0000110 ! sequence_feature

[Term]
id: SO:0001060
name: sequence_variant
def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
is_a: SO:0000000 ! Sequence_Ontology

[Term]
id: SO:0001061
name: propeptide_cleavage_site
alt_id: BS:00063
def: "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]
comment: Discrete.
subset: biosapiens
synonym: "propeptide_cleavage_site" EXACT []
is_a: SO:0001063 ! immature_peptide_region
relationship: part_of SO:0001062 ! propeptide

[Term]
id: SO:0001062
name: propeptide
alt_id: BS:00077
def: "Describes part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "propep" RELATED []
synonym: "propeptide" EXACT []
is_a: SO:0001063 ! immature_peptide_region

[Term]
id: SO:0001063
name: immature_peptide_region
alt_id: BS:00129
def: "An immature_peptide_region is the a region of peptide sequence that is cleaved during maturation." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "immature_peptide_region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001064
name: active_peptide
alt_id: BS:00076
def: "Active peptides are proteins which are biologically active, released from a precursor molecule. Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "active_peptide" EXACT []
synonym: "peptide" EXACT []
is_a: SO:0000419 ! mature_protein_region

[Term]
id: SO:0001066
name: compositionally_biased_region
alt_id: BS:00068
def: "Extent of a compositionally biased region. Used for homopolymeric stretches of residues and also for regions which are rich in a particular amino acid. Not used for a run of less than 4 residues." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "compbias" EXACT []
synonym: "compositional bias" EXACT []
synonym: "compositionally biased" EXACT []
synonym: "compositionally_biased_region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001067
name: polypeptide_motif
alt_id: BS:00032
def: "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "motif" RELATED []
synonym: "polypeptide_motif" EXACT []
is_a: SO:0000417 ! polypeptide_domain

[Term]
id: SO:0001068
name: polypeptide_repeat
alt_id: BS:00070
def: "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "polypeptide_repeat" EXACT []
synonym: "repeat" RELATED []
is_a: SO:0000417 ! polypeptide_domain

[Term]
id: SO:0001069
name: polypeptide_structural_domain
alt_id: BS:00134
def: "A polypeptide domain is a structural domain that is self-stabilizing and folds independently of the rest of the protein chain." [EBIBS:GAR, PMID:7020376]
subset: biosapiens
synonym: "polypeptide_structural_domain" EXACT []
synonym: "structural domain" EXACT []
is_a: SO:0000417 ! polypeptide_domain
is_a: SO:0001070 ! structural_region

[Term]
id: SO:0001070
name: structural_region
alt_id: BS:00337
def: "Backbone conformation of the polypeptide." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "structural_region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001071
name: membrane_structure
alt_id: BS:00128
def: "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "membrane_structure" EXACT []
is_a: SO:0001070 ! structural_region

[Term]
id: SO:0001072
name: extramembrane_region
alt_id: BS:00154
def: "Extent of the region not transversing the lipid bilayer." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "extramembrane" EXACT []
synonym: "topo_dom" EXACT []
is_a: SO:0001070 ! structural_region
relationship: part_of SO:0001071 ! membrane_structure

[Term]
id: SO:0001073
name: cytoplasmic_region
alt_id: BS:00145
def: "Region of the peptide in the cytoplasm." [EBIBS:GAR]
subset: biosapiens
synonym: "cytoplasm_location" EXACT []
synonym: "inside" RELATED []
is_a: SO:0001072 ! extramembrane_region

[Term]
id: SO:0001074
name: non_cytoplasmic_region
alt_id: BS:00144
def: "Region of peptide not in the cytoplasm. N.B. This could be inside an organelle within the cell." [EBIBS:GAR]
subset: biosapiens
synonym: "non_cytoplasm_location" EXACT []
synonym: "outside" RELATED []
is_a: SO:0001072 ! extramembrane_region

[Term]
id: SO:0001075
name: intramembrane_region
alt_id: BS:00156
def: "Extent of the region present in the lipid bilayer." [EBIBS:GAR]
subset: biosapiens
synonym: "intramembrane" EXACT []
is_a: SO:0001070 ! structural_region
relationship: part_of SO:0001071 ! membrane_structure

[Term]
id: SO:0001076
name: membrane_loop
alt_id: BS:00155
def: "Extent of region which enters the membrane bilayer but emerges on the same side which it entered." [EBIBS:GAR]
subset: biosapiens
synonym: "membrane_loop" EXACT []
is_a: SO:0001075 ! intramembrane_region

[Term]
id: SO:0001077
name: transmembrane_region
alt_id: BS:00158
def: "Extent of region transversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]
subset: biosapiens
synonym: "transmem" RELATED []
synonym: "transmembrane" EXACT []
is_a: SO:0001075 ! intramembrane_region

[Term]
id: SO:0001078
name: polypeptide_secondary_structure
alt_id: BS:00003
def: "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]
comment: Biosapien term was secondary_structure.
subset: biosapiens
synonym: "2nary structure" EXACT []
synonym: "secondary structure" EXACT []
synonym: "secondary structure region" RELATED []
synonym: "secondary_structure" EXACT []
is_a: SO:0001070 ! structural_region

[Term]
id: SO:0001079
name: polypeptide_structural_motif
alt_id: BS:0000338
def: "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]
subset: biosapiens
synonym: "structural_motif" EXACT []
is_a: SO:0001070 ! structural_region

[Term]
id: SO:0001080
name: coiled_coil
alt_id: BS:00041
def: "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "coiled" RELATED []
synonym: "coiled_coil" EXACT []
is_a: SO:0001079 ! polypeptide_structural_motif

[Term]
id: SO:0001081
name: helix_turn_helix
alt_id: BS:00147
def: "A motif comprising two helices separated by a turn." [EBIBS:GAR]
subset: biosapiens
synonym: "DNA binding motif" RELATED []
synonym: "helix_turn_helix" EXACT []
synonym: "HTH" EXACT []
is_a: SO:0001079 ! polypeptide_structural_motif

[Term]
id: SO:0001082
name: polypeptide_sequencing_information
alt_id: BS:00125
def: "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "sequencing_information" EXACT []
is_a: SO:0000700 ! remark

[Term]
id: SO:0001083
name: non_adjacent_residues
alt_id: BS:00182
def: "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "non consecutive" EXACT []
synonym: "non_adjacent_residues" EXACT []
synonym: "non_cons" EXACT []
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001084
name: non_terminal_residue
alt_id: BS:00072
def: "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "non terminal" EXACT []
synonym: "non_ter" EXACT []
synonym: "non_terminal_residue" EXACT []
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001085
name: sequence_conflict
alt_id: BS:00069
def: "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "conflict" EXACT []
synonym: "sequence_conflict" EXACT []
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001086
name: sequence_uncertainty
alt_id: BS:00181
def: "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "sequence_uncertainty" EXACT []
synonym: "unsure" RELATED []
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001087
name: cross_link
alt_id: BS:00178
def: "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "cross_link" EXACT []
synonym: "crosslink" RELATED []
is_obsolete: true

[Term]
id: SO:0001088
name: disulfide_bond
alt_id: BS:00028
def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." [EBIBS:GAR, UniProt:curation_manual]
comment: 2 discreet & joined.
subset: biosapiens
synonym: "disulfid" RELATED []
synonym: "disulfide" RELATED []
synonym: "disulfide bond" RELATED []
synonym: "disulfide_bond" EXACT []
synonym: "disulphide" EXACT []
synonym: "disulphide bond" RELATED []
is_obsolete: true

[Term]
id: SO:0001089
name: post_translationally_modified_region
alt_id: BS:00052
def: "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAM, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "mod_res" RELATED []
synonym: "modified residue" EXACT []
synonym: "post_translational_modification" EXACT []
is_a: SO:0100001 ! biochemical_region

[Term]
id: SO:0001090
name: covalent_binding_site
alt_id: BS:00246
def: "Binding involving a covalent bond." [EBIBS:GAR]
subset: biosapiens
synonym: "covalent_binding_site" EXACT []
is_obsolete: true

[Term]
id: SO:0001091
name: non_covalent_binding_site
alt_id: BS:00029
def: "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR]
comment: Discrete.
subset: biosapiens
synonym: "binding" RELATED [uniprot:curation]
synonym: "binding site" RELATED []
synonym: "non_covalent_binding_site" EXACT []
is_obsolete: true

[Term]
id: SO:0001092
name: metal_contact
alt_id: BS:00027
def: "Residue is part of a binding site for a metal ion." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "metal" RELATED []
synonym: "metal_binding" EXACT []
is_a: SO:0000409 ! binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0001093
name: protein_protein_contact
alt_id: BS:00131
def: "Residues involved in protein-protein interactions." [EBIBS:GAR, UniProt:Curation_manual]
subset: biosapiens
synonym: "protein_protein_interaction" EXACT []
is_a: SO:0000409 ! binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0001094
name: Ca_contact_site
alt_id: BS:00186
def: "Residue involved in contact with calcium." [EBIBS:GAR]
subset: biosapiens
synonym: "ca bind" EXACT []
synonym: "Ca_contact_site" EXACT []
is_a: SO:0001092 ! metal_contact

[Term]
id: SO:0001095
name: Co_contact_site
alt_id: BS:00136
def: "Residue involved in contact with cobalt." [EBIBS:GAR]
subset: biosapiens
synonym: "Co_contact_site" EXACT []
is_a: SO:0001092 ! metal_contact

[Term]
id: SO:0001096
name: Cu_contact_site
alt_id: BS:00146
def: "Residue involved in contact with copper." [EBIBS:GAR]
subset: biosapiens
synonym: "Cu_contact_site" EXACT []
is_a: SO:0001092 ! metal_contact

[Term]
id: SO:0001097
name: Fe_contact_site
alt_id: BS:00137
def: "Residue involved in contact with iron." [EBIBS:GAR]
subset: biosapiens
synonym: "Fe_contact_site" EXACT []
is_a: SO:0001092 ! metal_contact

[Term]
id: SO:0001098
name: Mg_contact_site
alt_id: BS:00187
def: "Residue involved in contact with magnesium." [EBIBS:GAR]
subset: biosapiens
synonym: "Mg_contact_site" EXACT []
is_a: SO:0001092 ! metal_contact

[Term]
id: SO:0001099
name: Mn_contact_site
alt_id: BS:00140
def: "Residue involved in contact with manganese." [EBIBS:GAR]
subset: biosapiens
synonym: "Mn_contact_site" EXACT []
is_a: SO:0001092 ! metal_contact

[Term]
id: SO:0001100
name: Mo_contact_site
alt_id: BS:00141
def: "Residue involved in contact with molybdenum." [EBIBS:GAR]
subset: biosapiens
synonym: "Mo_contact_site" EXACT []
is_a: SO:0001092 ! metal_contact

[Term]
id: SO:0001101
name: Ni_contact_site
alt_id: BS:00142
def: "Residue involved in contact with nickel." [EBIBS:GAR]
subset: biosapiens
synonym: "Ni_contact_site" EXACT []
is_a: SO:0001092 ! metal_contact

[Term]
id: SO:0001102
name: W_contact_site
alt_id: BS:00143
def: "Residue involved in contact with tungsten." [EBIBS:GAR]
subset: biosapiens
synonym: "W_contact_site" EXACT []
is_a: SO:0001092 ! metal_contact

[Term]
id: SO:0001103
name: Zn_contact_site
alt_id: BS:00185
def: "Residue involved in contact with zinc." [EBIBS:GAR]
subset: biosapiens
synonym: "Zn_contact_site" EXACT []
is_a: SO:0001092 ! metal_contact

[Term]
id: SO:0001104
name: catalytic_residue
alt_id: BS:00026
def: "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "act_site" RELATED []
synonym: "active site residue" EXACT []
synonym: "site" BROAD []
is_a: SO:0100001 ! biochemical_region

[Term]
id: SO:0001105
name: protein_ligand_contact
alt_id: BS:00157
def: "Residues which interact with a ligand." [EBIBS:GAR]
subset: biosapiens
synonym: "protein-ligand interaction" EXACT []
is_a: SO:0000409 ! binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0001106
name: asx_motif
alt_id: BS:00202
def: "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd_srv/msdmotif/]
subset: biosapiens
synonym: "asx_motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001107
name: beta_bulge
alt_id: BS:00208
def: "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd_srv/msdmotif/]
subset: biosapiens
synonym: "beta_bulge" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001108
name: beta_bulge_loop
alt_id: BS:00209
def: "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd_srv/msdmotif/]
subset: biosapiens
synonym: "beta_bulge_loop" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001109
name: beta_bulge_loop_five
alt_id: BS:00210
def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd_srv/msdmotif/]
subset: biosapiens
synonym: "beta_bulge_loop_five" EXACT []
is_a: SO:0001108 ! beta_bulge_loop

[Term]
id: SO:0001110
name: beta_bulge_loop_six
alt_id: BS:00211
def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd_srv/msdmotif/]
subset: biosapiens
synonym: "beta_bulge_loop_six" EXACT []
is_a: SO:0001108 ! beta_bulge_loop

[Term]
id: SO:0001111
name: beta_strand
alt_id: BS:00042
def: "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "beta_strand" EXACT []
synonym: "strand" RELATED []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001112
name: antiparallel_beta_strand
alt_id: BS:0000341
def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "antiparallel_beta_strand" EXACT []
is_a: SO:0001111 ! beta_strand

[Term]
id: SO:0001113
name: parallel_beta_strand
alt_id: BS:00151
def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "parallel_beta_strand" EXACT []
is_a: SO:0001111 ! beta_strand

[Term]
id: SO:0001114
name: helix
alt_id: BS:00152
def: "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "helix" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001115
name: left_handed_helix
alt_id: BS:00222
def: "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]
subset: biosapiens
synonym: "helix-l" RELATED []
synonym: "left handed helix" EXACT []
is_a: SO:0001114 ! helix

[Term]
id: SO:0001116
name: right_handed_helix
alt_id: BS:0000339
def: "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]
subset: biosapiens
synonym: "helix" RELATED []
synonym: "right handed helix" EXACT []
is_a: SO:0001114 ! helix

[Term]
id: SO:0001117
name: alpha_helix
alt_id: BS:00040
def: "The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "a-helix" EXACT []
synonym: "alpha_helix" EXACT []
synonym: "helix" RELATED []
is_a: SO:0001116 ! right_handed_helix

[Term]
id: SO:0001118
name: pi_helix
alt_id: BS:00153
def: "The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "pi_helix" EXACT []
is_a: SO:0001116 ! right_handed_helix

[Term]
id: SO:0001119
name: three_ten_helix
alt_id: BS:0000340
def: "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "3(10) helix" EXACT []
synonym: "3-10 helix" EXACT []
synonym: "310 helix" EXACT []
synonym: "three_ten_helix" EXACT []
is_a: SO:0001116 ! right_handed_helix

[Term]
id: SO:0001120
name: nest
alt_id: BS:00223
def: "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest" EXACT []
synonym: "nest_motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001121
name: nest_left_right
alt_id: BS:00224
def: "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest_left_right" EXACT []
synonym: "nest_lr" EXACT []
is_a: SO:0001120 ! nest

[Term]
id: SO:0001122
name: nest_right_left
alt_id: BS:00225
def: "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest_right_left" EXACT []
synonym: "nest_rl" EXACT []
is_a: SO:0001120 ! nest

[Term]
id: SO:0001123
name: schellmann_loop
alt_id: BS:00226
def: "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "paperclip" RELATED []
synonym: "paperclip loop" RELATED []
synonym: "schellmann_loop" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001124
name: schellmann_loop_seven
alt_id: BS:00228
def: "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "schellmann_loop_seven" EXACT []
synonym: "seven-residue schellmann loop" EXACT []
is_a: SO:0001123 ! schellmann_loop

[Term]
id: SO:0001125
name: schellmann_loop_six
alt_id: BS:00227
def: "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "schellmann_loop_six" EXACT []
synonym: "six-residue schellmann loop" EXACT []
is_a: SO:0001123 ! schellmann_loop

[Term]
id: SO:0001126
name: st_motif
alt_id: BS:00229
def: "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st_motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001127
name: st_staple
alt_id: BS:00230
def: "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st_staple" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001128
name: turn
alt_id: BS:00148
def: "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "turn" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001129
name: asx_turn_left_handed_type_one
alt_id: BS:00206
def: "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx_turn_il" RELATED []
synonym: "asx_turn_left_handed_type_one" EXACT []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001130
name: asx_turn_left_handed_type_two
alt_id: BS:00204
def: "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx_turn_iil" EXACT []
synonym: "asx_turn_left_handed_type_two" EXACT []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001131
name: asx_turn_right_handed_type_two
alt_id: BS:00205
def: "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx_turn_iir" EXACT []
synonym: "asx_turn_right_handed_type_two" EXACT []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001132
name: asx_turn_type_right_handed_type_one
alt_id: BS:00207
def: "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAM, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx_turn_ir" EXACT []
synonym: "asx_turn_type_right_handed_type_one" EXACT []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001133
name: beta_turn
alt_id: BS:00212
def: "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta_turn" EXACT []
is_a: SO:0001128 ! turn

[Term]
id: SO:0001134
name: beta_turn_left_handed_type_one
alt_id: BS:00215
def: "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta_turn_il" EXACT []
synonym: "beta_turn_left_handed_type_one" EXACT []
synonym: "Type I' beta turn" EXACT []
synonym: "Type I' turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001135
name: beta_turn_left_handed_type_two
alt_id: BS:00213
def: "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta_turn_iil" EXACT []
synonym: "beta_turn_left_handed_type_two" EXACT []
synonym: "Type II' beta turn" EXACT []
synonym: "Type II' turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001136
name: beta_turn_right_handed_type_one
alt_id: BS:00216
def: "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta_turn_ir" EXACT []
synonym: "beta_turn_right_handed_type_one" EXACT []
synonym: "Type I beta turn" EXACT []
synonym: "Type I turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001137
name: beta_turn_right_handed_type_two
alt_id: BS:00214
def: "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta_turn_iir" EXACT []
synonym: "beta_turn_right_handed_type_two" EXACT []
synonym: "Type II beta turn" EXACT []
synonym: "Type II turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001138
name: gamma_turn
alt_id: BS:00219
def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "gamma_turn" EXACT []
is_a: SO:0001128 ! turn

[Term]
id: SO:0001139
name: gamma_turn_classic
alt_id: BS:00220
def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "classic gamma turn" EXACT []
synonym: "gamma_turn_classic" EXACT []
is_a: SO:0001138 ! gamma_turn

[Term]
id: SO:0001140
name: gamma_turn_inverse
alt_id: BS:00221
def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "gamma_turn_inverse" EXACT []
is_a: SO:0001138 ! gamma_turn

[Term]
id: SO:0001141
name: st_turn
alt_id: BS:00231
def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAM, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st_turn" EXACT []
is_a: SO:0001128 ! turn

[Term]
id: SO:0001142
name: st_turn_left_handed_type_one
alt_id: BS:00234
def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st_turn_il" EXACT []
synonym: "st_turn_left_handed_type_one" EXACT []
is_a: SO:0001141 ! st_turn

[Term]
id: SO:0001143
name: st_turn_left_handed_type_two
alt_id: BS:00232
def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st_turn_iil" EXACT []
synonym: "st_turn_left_handed_type_two" EXACT []
is_a: SO:0001141 ! st_turn

[Term]
id: SO:0001144
name: st_turn_right_handed_type_one
alt_id: BS:00235
def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st_turn_ir" EXACT []
synonym: "st_turn_right_handed_type_one" EXACT []
is_a: SO:0001141 ! st_turn

[Term]
id: SO:0001145
name: st_turn_right_handed_type_two
alt_id: BS:00233
def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st_turn_iir" EXACT []
synonym: "st_turn_right_handed_type_two" EXACT []
is_a: SO:0001141 ! st_turn

[Term]
id: SO:0001146
name: polypeptide_variation_site
alt_id: BS:00336
def: "A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]
comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
subset: biosapiens
synonym: "sequence_variations" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001147
name: natural_variant_site
alt_id: BS:00071
def: "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "natural_variant" EXACT []
synonym: "sequence variation" RELATED []
synonym: "variant" RELATED []
is_a: SO:0001146 ! polypeptide_variation_site

[Term]
id: SO:0001148
name: mutated_variant_site
alt_id: BS:00036
def: "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "mutagen" RELATED []
synonym: "mutagenesis" RELATED []
synonym: "mutated_site" EXACT []
is_a: SO:0001146 ! polypeptide_variation_site

[Term]
id: SO:0001149
name: alternate_sequence_site
alt_id: BS:00073
alt_id: SO:0001065
def: "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "alternative_sequence" EXACT []
synonym: "isoform" NARROW []
synonym: "sequence variation" RELATED []
synonym: "var_seq" RELATED []
synonym: "varsplic" NARROW []
is_a: SO:0001146 ! polypeptide_variation_site

[Term]
id: SO:0001150
name: beta_turn_type_six
subset: biosapiens
synonym: "Type VI beta turn" EXACT []
synonym: "Type VI turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001151
name: beta_turn_type_six_a
subset: biosapiens
synonym: "Type VI a beta turn" EXACT []
synonym: "Type VI a turn" EXACT []
is_a: SO:0001150 ! beta_turn_type_six

[Term]
id: SO:0001152
name: beta_turn_type_six_a_one
subset: biosapiens
synonym: "Type VI a1 beta turn" EXACT []
synonym: "Type VI a1 turn" EXACT []
is_a: SO:0001151 ! beta_turn_type_six_a

[Term]
id: SO:0001153
name: beta_turn_type_six_a_two
subset: biosapiens
synonym: "Type VI a2 beta turn" EXACT []
synonym: "Type VI a2 turn" EXACT []
is_a: SO:0001151 ! beta_turn_type_six_a

[Term]
id: SO:0001154
name: beta_turn_type_six_b
subset: biosapiens
synonym: "Type VI b beta turn" EXACT []
synonym: "Type VI b turn" EXACT []
is_a: SO:0001150 ! beta_turn_type_six

[Term]
id: SO:0001155
name: beta_turn_type_eight
subset: biosapiens
synonym: "Type VIII beta turn" EXACT []
synonym: "Type VIII turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001156
name: DRE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]
comment: This consensus sequence was identified computationally using the MEME\nalgorithm within core promoter sequences from -60 to +40, with an E value\nof 1.7e-183.  Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.
synonym: "NDM4" EXACT []
synonym: "WATCGATW_motif" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001157
name: DMv4_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941\:12537576]
synonym: "directional motif v4" EXACT []
synonym: "DMv4" EXACT []
synonym: "motif 1 element" EXACT []
synonym: "promoter motif 1" EXACT []
synonym: "YGGTCACATR" NARROW []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001158
name: E_box_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576\:16827941]
synonym: "AWCAGCTGWT" NARROW []
synonym: "E box motif" EXACT []
synonym: "generic E box motif" EXACT []
synonym: "NDM5" RELATED []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001159
name: DMv5_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576\:16827941]
synonym: "directional motif v5" EXACT []
synonym: "DMv5" EXACT []
synonym: "KTYRGTATWTTT" NARROW []
synonym: "promoter motif 6" RELATED []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001160
name: DMv3_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576\:16827941]
synonym: "directional motif v3" EXACT []
synonym: "DMv3" EXACT []
synonym: "KNNCAKCNCTRNY" NARROW []
synonym: "promoter motif 7" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001161
name: DMv2_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576\:16827941]
synonym: "directional motif v2" EXACT []
synonym: "DMv2" EXACT []
synonym: "MKSYGGCARCGSYSS" NARROW []
synonym: "promoter motif 8" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001162
name: MTE
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576\:15231738]
synonym: "CSARCSSAACGS" NARROW []
synonym: "motif ten element" EXACT []
synonym: "motif_ten_element" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001163
name: INR1_motif
def: "A promoter motif with consensus sequence TCATTCG." [PMID:16827941]
synonym: "directional motif p3" EXACT []
synonym: "directional promoter motif 3" EXACT []
synonym: "DMp3" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001164
name: DPE1_motif
def: "A promoter motif with consensus sequence CGGACGT." [PMID:16827941]
synonym: "directional motif 5" EXACT []
synonym: "directional promoter motif 5" RELATED []
synonym: "DMp5" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001165
name: DMv1_motif
def: "A promoter motif with consensus sequence CARCCCT." [PMID:16827941]
synonym: "directional promoter motif v1" RELATED []
synonym: "DMv1" RELATED []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001166
name: GAGA_motif
def: "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]
synonym: "GAGA" EXACT []
synonym: "NDM1" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001167
name: NDM2_motif
def: "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]
synonym: "NDM2" EXACT []
synonym: "non directional promoter motif 2" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001168
name: NDM3_motif
def: "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]
synonym: "NDM3" EXACT []
synonym: "non directional motif 3" EXACT []
is_a: SO:0000844 ! RNApol_II_promoter_region

[Term]
id: SO:0001169
name: ds_RNA_viral_sequence
def: "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]
synonym: "double stranded RNA virus sequence" EXACT []
is_a: SO:0001041 ! viral_sequence

[Term]
id: SO:0001170
name: polinton
def: "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]
synonym: "maverick element" RELATED []
is_a: SO:0000208 ! terminal_inverted_repeat_element

[Term]
id: SO:0001171
name: rRNA_21S
def: "A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]
synonym: "21S LSU rRNA" EXACT []
synonym: "21S ribosomal RNA" EXACT []
synonym: "21S rRNA" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA

[Term]
id: SO:0001172
name: tRNA_region
def: "A region of a tRNA." [RSC:cb]
is_a: SO:0000834 ! processed_transcript_region
relationship: part_of SO:0000253 ! tRNA

[Term]
id: SO:0001173
name: anticodon_loop
def: "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]
synonym: "anti-codon loop" EXACT []
is_a: SO:0001172 ! tRNA_region

[Term]
id: SO:0001174
name: anticodon
def: "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]
synonym: "anti-codon" EXACT []
is_a: SO:0001172 ! tRNA_region
relationship: part_of SO:0001173 ! anticodon_loop

[Term]
id: SO:0001175
name: CCA_tail
def: "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]
synonym: "CCA sequence" EXACT []
is_a: SO:0001172 ! tRNA_region

[Term]
id: SO:0001176
name: DHU_loop
def: "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]
synonym: "D loop" RELATED []
is_a: SO:0001172 ! tRNA_region

[Term]
id: SO:0001177
name: T_loop
def: "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]
synonym: "TpsiC loop" EXACT []
is_a: SO:0001172 ! tRNA_region

[Term]
id: SO:0001178
name: pyrrolysine_tRNA_primary_transcript
def: "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0001179
name: U3_snoRNA
def: "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]
comment: The definition is most of the old definition for snoRNA (SO:0000275).
synonym: "small nucleolar RNA U3" EXACT []
synonym: "snoRNA U3" EXACT []
synonym: "U3 small nucleolar RNA" EXACT []
is_a: SO:0000593 ! C_D_box_snoRNA

[Term]
id: SO:0001180
name: AU_rich_element
def: "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]
synonym: "ARE" RELATED []
synonym: "AU-rich element" EXACT []
is_a: SO:0000837 ! UTR_region
relationship: part_of SO:0000205 ! three_prime_UTR

[Term]
id: SO:0001181
name: Bruno_response_element
def: "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]
comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.
synonym: "BRE" RELATED []
is_a: SO:0000837 ! UTR_region
relationship: part_of SO:0000205 ! three_prime_UTR

[Term]
id: SO:0001182
name: iron_responsive_element
def: "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]
synonym: "IRE" EXACT []
is_a: SO:0000837 ! UTR_region

[Term]
id: SO:0001183
name: morpholino
def: "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb]
comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0001184
name: PNA
def: "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb]
comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0001185
name: enzymatic
def: "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]
comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0001186
name: ribozymic
def: "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb]
comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.
is_a: SO:0001185 ! enzymatic

[Term]
id: SO:0001187
name: pseudouridylation_guide_snoRNA
def: "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]
comment: Has RNA pseudouridylation guide activity (GO:0030558).
is_a: SO:0000594 ! H_ACA_box_snoRNA

[Term]
id: SO:0001188
name: LNA
def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010]
comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0001189
name: LNA_oligo
def: "An oligo composed of LNA residues." [RSC:cb]
synonym: "locked nucleic acid" EXACT []
is_a: SO:0000696 ! implied link automatically realized ! oligo
intersection_of: SO:0000696 ! oligo
intersection_of: has_quality SO:0001188 ! LNA
relationship: has_quality SO:0001188 ! implied link automatically realized ! LNA

[Term]
id: SO:0001190
name: TNA
def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019]
comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0001191
name: TNA_oligo
def: "An oligo composed of TNA residues." [RSC:cb]
synonym: "threose nucleic acid" EXACT []
is_a: SO:0000696 ! implied link automatically realized ! oligo
intersection_of: SO:0000696 ! oligo
intersection_of: has_quality SO:0001190 ! TNA
relationship: has_quality SO:0001190 ! implied link automatically realized ! TNA

[Term]
id: SO:0001192
name: GNA
def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]
comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0001193
name: GNA_oligo
def: "An oligo composed of GNA residues." [RSC:cb]
synonym: "glycerol nucleic acid" EXACT []
synonym: "glycol nucleic acid" EXACT []
is_a: SO:0000696 ! implied link automatically realized ! oligo
intersection_of: SO:0000696 ! oligo
intersection_of: has_quality SO:0001192 ! GNA
relationship: has_quality SO:0001192 ! implied link automatically realized ! GNA

[Term]
id: SO:0001194
name: R_GNA
def: "An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]
comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.
is_a: SO:0001192 ! GNA

[Term]
id: SO:0001195
name: R_GNA_oligo
def: "An oligo composed of (R)-GNA residues." [RSC:cb]
synonym: "(R)-glycerol nucleic acid" EXACT []
synonym: "(R)-glycol nucleic acid" EXACT []
is_a: SO:0001193 ! implied link automatically realized ! GNA_oligo
intersection_of: SO:0001193 ! GNA_oligo
intersection_of: has_quality SO:0001194 ! R_GNA
relationship: has_quality SO:0001194 ! implied link automatically realized ! R_GNA

[Term]
id: SO:0001196
name: S_GNA
def: "An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]
comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.
is_a: SO:0001192 ! GNA

[Term]
id: SO:0001197
name: S_GNA_oligo
def: "An oligo composed of (S)-GNA residues." [RSC:cb]
synonym: "(S)-glycerol nucleic acid" EXACT []
synonym: "(S)-glycol nucleic acid" EXACT []
is_a: SO:0001193 ! implied link automatically realized ! GNA_oligo
intersection_of: SO:0001193 ! GNA_oligo
intersection_of: has_quality SO:0001196 ! S_GNA
relationship: has_quality SO:0001196 ! implied link automatically realized ! S_GNA

[Term]
id: SO:0001198
name: ds_DNA_viral_sequence
def: "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]
synonym: "double stranded DNA virus" EXACT []
is_a: SO:0001041 ! viral_sequence

[Term]
id: SO:0001199
name: ss_RNA_viral_sequence
def: "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]
synonym: "single strand RNA virus" EXACT []
is_a: SO:0001041 ! viral_sequence

[Term]
id: SO:0001200
name: negative_sense_ssRNA_viral_sequence
def: "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]
synonym: "negative sense single stranded RNA virus" RELATED []
is_a: SO:0001199 ! ss_RNA_viral_sequence

[Term]
id: SO:0001201
name: positive_sense_ssRNA_viral_sequence
def: "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]
synonym: "positive sense single stranded RNA virus" RELATED []
is_a: SO:0001199 ! ss_RNA_viral_sequence

[Term]
id: SO:0001202
name: ambisense_ssRNA_viral_sequence
def: "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]
synonym: "ambisense single stranded RNA virus" EXACT []
is_a: SO:0001199 ! ss_RNA_viral_sequence

[Term]
id: SO:0001203
name: RNA_polymerase_promoter
def: "A region (DNA) to which RNA polymerase binds, to begin\ntranscription." [xenbase:jb]
is_a: SO:0000167 ! promoter

[Term]
id: SO:0001204
name: Phage_RNA_Polymerase_Promoter
def: "Aregion (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]
is_a: SO:0001203 ! RNA_polymerase_promoter

[Term]
id: SO:0001205
name: SP6_RNA_Polymerase_Promoter
def: "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]
is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter

[Term]
id: SO:0001206
name: T3_RNA_Polymerase_Promoter
def: "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]
is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter

[Term]
id: SO:0001207
name: T7_RNA_Polymerase_Promoter
def: "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]
is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter

[Term]
id: SO:0001208
name: five_prime_EST
def: "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]
synonym: "5' EST" EXACT []
is_a: SO:0000345 ! EST

[Term]
id: SO:0001209
name: three_prime_EST
def: "An EST read from the 3' end of a transcript. They are more\nlikely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]
synonym: "3' EST" EXACT []
is_a: SO:0000345 ! EST

[Term]
id: SO:0005836
name: regulatory_region
def: "A DNA sequence that controls the expression of a gene." [http://www.genpromag.com/scripts/glossary.asp?LETTER=R]
subset: SOFA
is_a: SO:0000831 ! gene_member_region

[Term]
id: SO:0005837
name: U14_snoRNA_primary_transcript
def: "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]
synonym: "4.5S snRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript

[Term]
id: SO:0005841
name: methylation_guide_snoRNA
def: "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]
comment: Has RNA 2'-O-ribose methylation guide activity (GO:0030561).
is_a: SO:0000593 ! C_D_box_snoRNA
relationship: derives_from SO:0000580 ! methylation_guide_snoRNA_primary_transcript

[Term]
id: SO:0005843
name: rRNA_cleavage_RNA
def: "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000582 ! rRNA_cleavage_snoRNA_primary_transcript

[Term]
id: SO:0005845
name: exon_of_single_exon_gene
def: "An exon that is the only exon in a gene." [RSC:cb]
synonym: "single_exon" RELATED []
synonym: "singleton exon" EXACT []
is_a: SO:0000147 ! exon

[Term]
id: SO:0005847
name: cassette_array_member
is_a: SO:0005848 ! gene_cassette_member

[Term]
id: SO:0005848
name: gene_cassette_member
is_a: SO:0000081 ! gene_array_member

[Term]
id: SO:0005849
name: gene_subarray_member
is_a: SO:0000081 ! gene_array_member

[Term]
id: SO:0005850
name: primer_binding_site
def: "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http:www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
is_a: SO:0000409 ! binding_site
relationship: part_of SO:0000186 ! LTR_retrotransposon

[Term]
id: SO:0005851
name: gene_array
def: "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]
comment: This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0005852
name: gene_subarray
def: "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]
comment: This would include, for example, a cluster of genes encoding different histones.
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0005853
name: gene_cassette
def: "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]
comment: This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid.
is_a: SO:0000704 ! gene

[Term]
id: SO:0005854
name: gene_cassette_array
def: "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]
comment: This would include, for example, the arrays of non-functional VSG genes of Trypanosomes.
is_a: SO:0005855 ! gene_group
relationship: has_part SO:0005853 ! gene_cassette

[Term]
id: SO:0005855
name: gene_group
def: "A collection of related genes." [SO:ma]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0005856
name: selenocysteine_tRNA_primary_transcript
def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0005857
name: selenocysteinyl_tRNA
def: "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]
synonym: "selenocysteinyl-transfer ribonucleic acid" EXACT []
synonym: "selenocysteinyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0005856 ! selenocysteine_tRNA_primary_transcript

[Term]
id: SO:0005858
name: syntenic_region
def: "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://tbase.jax.org/docs/glossary.html]
is_a: SO:0000853 ! implied link automatically realized ! homologous_region
intersection_of: SO:0000330 ! conserved_region
intersection_of: has_quality SO:0000860 ! syntenic
relationship: has_quality SO:0000860 ! implied link automatically realized ! syntenic

[Term]
id: SO:0100001
name: biochemical_region
def: "A region that is involved in a biochemical function." [EBIBS:GAR]
comment: Range.
subset: biosapiens
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0100002
name: molecular_contact_region
def: "A region that is involved a contact with another molecule." [EBIBS:GAR]
comment: Range.
subset: biosapiens
is_a: SO:0100001 ! biochemical_region

[Term]
id: SO:1000002
name: substitution
def: "Any change in genomic DNA caused by a single event." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0001059 ! sequence_alteration
relationship: sequence_of SO:0000048 ! substitute

[Term]
id: SO:1000004
name: partially_characterised_change_in_DNA_sequence
def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000007 ! uncharacterised_change_in_nucleotide_sequence

[Term]
id: SO:1000005
name: complex_substitution
def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000007
name: uncharacterised_change_in_nucleotide_sequence
def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000008
name: point_mutation
def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]
subset: SOFA
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000009
name: transition
def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000008 ! point_mutation

[Term]
id: SO:1000010
name: pyrimidine_transition
def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]
is_a: SO:1000009 ! transition

[Term]
id: SO:1000011
name: C_to_T_transition
def: "A transition of a cytidine to a thymine." [SO:ke]
is_a: SO:1000010 ! pyrimidine_transition

[Term]
id: SO:1000012
name: C_to_T_transition_at_pCpG_site
def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000011 ! C_to_T_transition

[Term]
id: SO:1000013
name: T_to_C_transition
is_a: SO:1000010 ! pyrimidine_transition

[Term]
id: SO:1000014
name: purine_transition
def: "A substitution of a purine, A or G, for another purine." [SO:ke]
is_a: SO:1000009 ! transition

[Term]
id: SO:1000015
name: A_to_G_transition
def: "A transition of an adenine to a guanine." [SO:ke]
is_a: SO:1000014 ! purine_transition

[Term]
id: SO:1000016
name: G_to_A_transition
def: "A transition of a guanine to an adenine." [SO:ke]
is_a: SO:1000014 ! purine_transition

[Term]
id: SO:1000017
name: transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000008 ! point_mutation

[Term]
id: SO:1000018
name: pyrimidine_to_purine_transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]
is_a: SO:1000017 ! transversion

[Term]
id: SO:1000019
name: C_to_A_transversion
def: "A transversion from cytidine to adenine." [SO:ke]
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000020
name: C_to_G_transversion
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000021
name: T_to_A_transversion
def: "A transversion from T to A." [SO:ke]
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000022
name: T_to_G_transversion
def: "A transversion from T to G." [SO:ke]
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000023
name: purine_to_pyrimidine_transversion
def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]
is_a: SO:1000017 ! transversion

[Term]
id: SO:1000024
name: A_to_C_transversion
def: "A transversion from adenine to cytidine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000025
name: A_to_T_transversion
def: "A transversion from adenine to thymine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000026
name: G_to_C_transversion
def: "A transversion from guanine to cytidine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000027
name: G_to_T_transversion
def: "A transversion from guanine to thymine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000028
name: intrachromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000029
name: chromosomal_deletion
def: "An incomplete chromosome." [SO:ke]
synonym: "(bacteria)&ampDgr;" RELATED []
synonym: "(Drosophila)Df" RELATED []
synonym: "(fungi)D" RELATED []
is_a: SO:0000550 ! aneuploid_chromosome
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000030
name: chromosomal_inversion
synonym: "(bacteria)IN" RELATED []
synonym: "(Drosophila)In" RELATED []
synonym: "(fungi)In" RELATED []
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000031
name: interchromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000032
name: indel
def: "A hybrid term (insertion/deletion) to describe sequence length change when the direction of the change is unspecified." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:0001059 ! sequence_alteration

[Term]
id: SO:1000033
name: nucleotide_deletion
def: "One or more continuous nucleotides are excised from the sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000032 ! indel

[Term]
id: SO:1000034
name: nucleotide_insertion
def: "One or more nucleotides are added between two adjacent nucleotides in the sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000032 ! indel

[Term]
id: SO:1000035
name: nucleotide_duplication
def: "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000034 ! nucleotide_insertion

[Term]
id: SO:1000036
name: inversion
def: "A continuous nucleotide sequence is inverted in the same position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0001059 ! sequence_alteration
relationship: sequence_of SO:0000047 ! invert

[Term]
id: SO:1000037
name: chromosomal_duplication
def: "An extra chromosome." [SO:ke]
synonym: "(Drosophila)Dp" RELATED []
synonym: "(fungi)Dp" RELATED []
is_a: SO:0000550 ! aneuploid_chromosome

[Term]
id: SO:1000038
name: intrachromosomal_duplication
is_a: SO:1000028 ! intrachromosomal_mutation
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000039
name: direct_tandem_duplication
is_a: SO:1000173 ! tandem_duplication

[Term]
id: SO:1000040
name: inverted_tandem_duplication
is_a: SO:1000173 ! tandem_duplication

[Term]
id: SO:1000041
name: intrachromosomal_transposition
synonym: "(Drosophila)Tp" RELATED []
is_a: SO:0000453 ! transposition
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:1000042
name: compound_chromosome
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000043
name: Robertsonian_fusion
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000044
name: chromosomal_translocation
synonym: "(Drosophila)T" RELATED []
synonym: "(fungi)T" RELATED []
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000045
name: ring_chromosome
synonym: "(Drosophila)R" RELATED []
synonym: "(fungi)C" RELATED []
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000046
name: pericentric_inversion
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000047
name: paracentric_inversion
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000048
name: reciprocal_chromosomal_translocation
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000049
name: mutation_affecting_transcript
def: "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000132 ! mutation

[Term]
id: SO:1000050
name: mutation_causing_no_change_in_transcript
def: "No effect on the state of the RNA." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000052
name: mutation_affecting_complex_change_in_transcript
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000054
name: mutation_affecting_coding_sequence
def: "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000055
name: mutation_causing_initiator_codon_change_in_transcript
def: "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000056 ! mutation_causing_amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000056
name: mutation_causing_amino_acid_coding_codon_change_in_transcript
def: "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000054 ! mutation_affecting_coding_sequence

[Term]
id: SO:1000057
name: mutation_causing_synonymous_codon_change_in_transcript
def: "The changed codon has the same translation product as the original codon." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000056 ! mutation_causing_amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000058
name: mutation_causing_non_synonymous_codon_change_in_transcript
def: "A DNA point mutation that causes a substitution of an amino acid by an other." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "non-synonymous codon change in transcript" EXACT []
is_a: SO:1000056 ! mutation_causing_amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000059
name: mutation_causing_missense_codon_change_in_transcript
def: "The nucleotide change in the codon leads to a new codon coding for a new amino acid." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000058 ! mutation_causing_non_synonymous_codon_change_in_transcript

[Term]
id: SO:1000060
name: mutation_causing_conservative_missense_codon_change_in_transcript
def: "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
is_a: SO:1000059 ! mutation_causing_missense_codon_change_in_transcript

[Term]
id: SO:1000061
name: mutation_causing_nonconservative_missense_codon_change_in_transcript
def: "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
is_a: SO:1000059 ! mutation_causing_missense_codon_change_in_transcript

[Term]
id: SO:1000062
name: mutation_causing_nonsense_codon_change_in_transcript
def: "The nucleotide change in the codon triplet creates a terminator codon." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000056 ! mutation_causing_amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000063
name: mutation_causing_terminator_codon_change_in_transcript
def: "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence." [SO:ke]
is_a: SO:1000054 ! mutation_affecting_coding_sequence

[Term]
id: SO:1000064
name: mutation_affecting_reading_frame
def: "An umbrella term for terms describing an effect of a mutation on the frame of translation." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000054 ! mutation_affecting_coding_sequence

[Term]
id: SO:1000065
name: frameshift_mutation
def: "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]
synonym: "out of frame mutation" RELATED []
is_a: SO:1000064 ! mutation_affecting_reading_frame

[Term]
id: SO:1000066
name: plus_1_frameshift_mutation
def: "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide." [SO:ke]
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000067
name: minus_1_frameshift_mutation
def: "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide." [SO:ke]
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000068
name: plus_2_frameshift_mutation
def: "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides." [SO:ke]
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000069
name: minus_2_frameshift_mutation
def: "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides." [SO:ke]
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000070
name: mutation_affecting_transcript_processing
def: "Mutation affects the way in which the primary transcriptional product is processed to form the mature transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000071
name: mutation_affecting_splicing
def: "A mutation that affects the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000132 ! mutation

[Term]
id: SO:1000072
name: splice_donor_mutation
def: "A mutation that affects the splice donor sequence." [SO:ke]
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000073
name: splice_acceptor_mutation
def: "A mutation that affects the splice acceptor sequence." [SO:ke]
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000074
name: cryptic_splice_activator_mutation
def: "A kind of mutation that creates a new (functional) splice site." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000075
name: mutation_affecting_editing
def: "Mutation affects the editing of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000070 ! mutation_affecting_transcript_processing

[Term]
id: SO:1000076
name: mutation_affecting_transcription
def: "Mutation affects the process of transcription, its initiation, progression or termination." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000078
name: mutation_decreasing_rate_of_transcription
def: "A mutation that decreases the rate a which transcription of the sequence occurs." [SO:ke]
is_a: SO:1000081 ! mutation_affecting_rate_of_transcription

[Term]
id: SO:1000079
name: mutation_affecting_transcript_sequence
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000080
name: mutation_increasing_rate_of_transcription
is_a: SO:1000081 ! mutation_affecting_rate_of_transcription

[Term]
id: SO:1000081
name: mutation_affecting_rate_of_transcription
def: "A mutation that alters the rate a which transcription of the sequence occurs." [SO:ke]
is_a: SO:1000076 ! mutation_affecting_transcription

[Term]
id: SO:1000082
name: mutation_affecting_transcript_stability
def: "Mutation affects the stability of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000083
name: mutation_increasing_transcript_stability
def: "Mutation increases the stability (half-life) of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000082 ! mutation_affecting_transcript_stability

[Term]
id: SO:1000084
name: mutation_decreasing_transcript_stability
def: "Mutation decreases the stability (half-life) of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000082 ! mutation_affecting_transcript_stability

[Term]
id: SO:1000085
name: mutation_affecting_level_of_transcript
def: "A mutation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000086
name: mutation_decreasing_level_of_transcript
def: "A mutation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
is_a: SO:1000085 ! mutation_affecting_level_of_transcript

[Term]
id: SO:1000087
name: mutation_increasing_level_of_transcript
def: "A mutation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
is_a: SO:1000085 ! mutation_affecting_level_of_transcript

[Term]
id: SO:1000088
name: mutation_affecting_translational_product
def: "Mutation causes a change in primary translation product of a transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000132 ! mutation

[Term]
id: SO:1000089
name: mutation_causing_no_change_of_translational_product
def: "The change at RNA level does not lead to any change in polypeptide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000090
name: mutation_causing_uncharacterised_change_of_translational_product
def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000091
name: mutation_causing_partially_characterised_change_of_translational_product
def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000090 ! mutation_causing_uncharacterised_change_of_translational_product

[Term]
id: SO:1000092
name: mutation_causing_complex_change_of_translational_product
def: "Any mutation effect that is known at nucleotide level but cannot be explained by using other key terms." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000093
name: mutation_causing_amino_acid_substitution
def: "The replacement of a single amino acid by another." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000094
name: mutation_causing_conservative_amino_acid_substitution
is_a: SO:1000093 ! mutation_causing_amino_acid_substitution

[Term]
id: SO:1000095
name: mutation_causing_nonconservative_amino_acid_substitution
is_a: SO:1000093 ! mutation_causing_amino_acid_substitution

[Term]
id: SO:1000096
name: mutation_causing_amino_acid_insertion
def: "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000097
name: mutation_causing_amino_acid_deletion
def: "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000098
name: mutation_causing_polypeptide_truncation
def: "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000099
name: mutation_causing_polypeptide_elongation
def: "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000100
name: mutation_causing_polypeptide_N_terminal_elongation
def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "polypeptide N-terminal elongation" EXACT []
is_a: SO:1000099 ! mutation_causing_polypeptide_elongation

[Term]
id: SO:1000101
name: mutation_causing_polypeptide_C_terminal_elongation
def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "polypeptide C-terminal elongation" EXACT []
is_a: SO:1000099 ! mutation_causing_polypeptide_elongation

[Term]
id: SO:1000102
name: mutation_affecting_level_of_translational_product
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000103
name: mutation_decreasing_level_of_translation_product
is_a: SO:1000102 ! mutation_affecting_level_of_translational_product

[Term]
id: SO:1000104
name: mutation_increasing_level_of_translation_product
is_a: SO:1000102 ! mutation_affecting_level_of_translational_product

[Term]
id: SO:1000105
name: mutation_affecting_polypeptide_amino_acid_sequence
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000106
name: mutation_causing_inframe_polypeptide_N_terminal_elongation
synonym: "inframe polypeptide N-terminal elongation" EXACT []
is_a: SO:1000100 ! mutation_causing_polypeptide_N_terminal_elongation

[Term]
id: SO:1000107
name: mutation_causing_out_of_frame_polypeptide_N_terminal_elongation
synonym: "out of frame polypeptide N-terminal elongation" EXACT []
is_a: SO:1000100 ! mutation_causing_polypeptide_N_terminal_elongation

[Term]
id: SO:1000108
name: mutaton_causing_inframe_polypeptide_C_terminal_elongation
synonym: "inframe_polypeptide C-terminal elongation" EXACT []
is_a: SO:1000101 ! mutation_causing_polypeptide_C_terminal_elongation

[Term]
id: SO:1000109
name: mutation_causing_out_of_frame_polypeptide_C_terminal_elongation
synonym: "out of frame polypeptide C-terminal elongation" EXACT []
is_a: SO:1000101 ! mutation_causing_polypeptide_C_terminal_elongation

[Term]
id: SO:1000110
name: frame_restoring_mutation
def: "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000111
name: mutation_affecting_3D_structure_of_polypeptide
def: "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule." [SO:ke]
synonym: "mutation affecting 3D-structure of polypeptide" EXACT []
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000112
name: mutation_causing_no_3D_structural_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000113
name: mutation_causing_uncharacterised_3D_structural_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000114
name: mutation_causing_partially_characterised_3D_structural_change
is_a: SO:1000113 ! mutation_causing_uncharacterised_3D_structural_change

[Term]
id: SO:1000115
name: mutation_causing_complex_3D_structural_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000116
name: mutation_causing_conformational_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000117
name: mutation_affecting_polypeptide_function
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000118
name: mutation_causing_loss_of_function_of_polypeptide
synonym: "loss of function of polypeptide" RELATED []
is_a: SO:1000117 ! mutation_affecting_polypeptide_function

[Term]
id: SO:1000119
name: mutation_causing_inactive_ligand_binding_site
is_a: SO:1000118 ! mutation_causing_loss_of_function_of_polypeptide

[Term]
id: SO:1000120
name: mutation_causing_inactive_catalytic_site
is_a: SO:1000119 ! mutation_causing_inactive_ligand_binding_site

[Term]
id: SO:1000121
name: mutation_causing_polypeptide_localization_change
is_a: SO:1000117 ! mutation_affecting_polypeptide_function

[Term]
id: SO:1000122
name: mutation_causing_polypeptide_post_translational_processing_change
synonym: "polypeptide post-translational processing affected" EXACT []
is_a: SO:1000117 ! mutation_affecting_polypeptide_function
is_a: SO:1000118 ! mutation_causing_loss_of_function_of_polypeptide

[Term]
id: SO:1000123
name: polypeptide_post_translational_processing_affected
synonym: "polypeptide_post-translational_processing_affected" RELATED []
is_obsolete: true

[Term]
id: SO:1000124
name: mutation_causing_partial_loss_of_function_of_polypeptide
synonym: "partial loss of function of polypeptide" EXACT []
is_a: SO:1000118 ! mutation_causing_loss_of_function_of_polypeptide

[Term]
id: SO:1000125
name: mutation_causing_gain_of_function_of_polypeptide
synonym: "gain of function of polypeptide" EXACT []
is_a: SO:1000117 ! mutation_affecting_polypeptide_function

[Term]
id: SO:1000126
name: mutation_affecting_transcript_secondary_structure
def: "A mutation that affects the secondary structure (folding) of the RNA transcript molecule." [SO:ke]
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000127
name: mutation_causing_compensatory_transcript_secondary_structure_mutation
is_a: SO:1000126 ! mutation_affecting_transcript_secondary_structure

[Term]
id: SO:1000132
name: mutation
def: "An event that changes nucleotide sequence." [SO:ke]
is_a: SO:0000000 ! Sequence_Ontology
disjoint_from: SO:0000041 ! operation
disjoint_from: SO:0000110 ! sequence_feature
disjoint_from: SO:0000240 ! chromosome_variation
disjoint_from: SO:0000400 ! sequence_attribute
disjoint_from: SO:0000968 ! replication_mode
disjoint_from: SO:0001060 ! sequence_variant

[Term]
id: SO:1000134
name: mutation_causing_polypeptide_fusion
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000136
name: autosynaptic_chromosome
synonym: "(Drosophila)A" RELATED []
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000138
name: homo_compound_chromosome
synonym: "homo-compound chromosome" EXACT []
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:1000140
name: hetero_compound_chromosome
synonym: "hetero-compound chromosome" EXACT []
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:1000141
name: chromosome_fission
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000142
name: dexstrosynaptic_chromosome
is_a: SO:1000136 ! autosynaptic_chromosome

[Term]
id: SO:1000143
name: laevosynaptic_chromosome
is_a: SO:1000136 ! autosynaptic_chromosome

[Term]
id: SO:1000144
name: free_duplication
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000145
name: free_ring_duplication
synonym: "(Drosophila)R" RELATED []
is_a: SO:1000045 ! ring_chromosome
is_a: SO:1000144 ! free_duplication

[Term]
id: SO:1000146
name: complex_chromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000147
name: deficient_translocation
def: "A translocation in which one of the four broken ends loses a segment before re-joining." [fb:reference_manual]
synonym: "(Drosophila)Df" RELATED []
synonym: "(Drosophila)DfT" RELATED []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000148
name: inversion_cum_translocation
def: "The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [fb:reference_manual]
synonym: "(Drosophila)InT" RELATED []
synonym: "(Drosophila)T" RELATED []
synonym: "inversion cum translocation" EXACT []
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000149
name: bipartite_duplication
def: "The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [fb:reference_manual]
synonym: "(Drosophila)bDp" RELATED []
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000150
name: cyclic_translocation
def: "Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [fb:reference_manual]
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000151
name: bipartite_inversion
def: "Three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [fb:reference_manual]
synonym: "(Drosophila)bIn" RELATED []
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000152
name: uninverted_insertional_duplication
def: "A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)eDp" RELATED []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000153
name: inverted_insertional_duplication
def: "A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)iDp" RELATED []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000154
name: insertional_duplication
def: "A chromosome duplication involving the insertion of a duplicated region." [SO:ke]
synonym: "(Drosophila)Dpp" RELATED []
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000155
name: interchromosomal_transposition
synonym: "(Drosophila)Tp" RELATED []
is_a: SO:0000453 ! transposition
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000156
name: inverted_interchromosomal_transposition
synonym: "(Drosophila)iTp" RELATED []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000157
name: uninverted_interchromosomal_transposition
synonym: "(Drosophila)eTp" RELATED []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000158
name: inverted_intrachromosomal_transposition
def: "The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)iTp" RELATED []
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:1000159
name: uninverted_intrachromosomal_transposition
def: "The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)eTp" RELATED []
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:1000160
name: unoriented_insertional_duplication
def: "A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [fb:reference_manual]
synonym: "(Drosophila)uDp" RELATED []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000161
name: unorientated_interchromosomal_transposition
synonym: "(Drosophila)uTp" RELATED []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000162
name: unorientated_intrachromosomal_transposition
def: "The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [fb:reference_manual]
synonym: "(Drosophila)uTp" RELATED []
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:1000170
name: uncharacterised_chromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000171
name: deficient_inversion
def: "Three breaks in the same chromosome; one central region lost, the other inverted." [fb:reference_manual]
synonym: "(Drosophila)Df" RELATED []
synonym: "(Drosophila)DfIn" RELATED []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000173
name: tandem_duplication
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:1000175
name: partially_characterised_chromosomal_mutation
is_a: SO:1000170 ! uncharacterised_chromosomal_mutation

[Term]
id: SO:1000177
name: mutation_causing_uncharacterised_change_in_transcript
def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000179
name: mutation_causing_partially_characterised_change_in_transcript
def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000177 ! mutation_causing_uncharacterised_change_in_transcript

[Term]
id: SO:1000180
name: mutation_affecting_gene_structure
def: "A kind of mutation that affects the structure of a gene." [SO:ke]
is_a: SO:1000132 ! mutation

[Term]
id: SO:1000181
name: mutation_causing_gene_fusion
def: "A kind of mutation that affects the structure of a gene by causing a fusion to another gene." [SO:ke]
is_a: SO:1000180 ! mutation_affecting_gene_structure

[Term]
id: SO:1000182
name: chromosome_number_variation
def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:1000183
name: chromosome_structure_variation
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:1000184
name: mutation_causes_exon_loss
def: "A mutation that affects splicing and causes an exon loss." [SO:ke]
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000185
name: mutation_causes_intron_gain
def: "Mutation causes an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000186
name: cryptic_splice_donor_activation
is_a: SO:1000074 ! cryptic_splice_activator_mutation

[Term]
id: SO:1001186
name: cryptic_splice_acceptor_activation
is_a: SO:1000074 ! cryptic_splice_activator_mutation

[Term]
id: SO:1001187
name: alternatively_spliced_transcript
def: "A transcript that is alternatively spliced." [SO:xp]
is_a: SO:0000673 ! implied link automatically realized ! transcript
intersection_of: SO:0000673 ! transcript
intersection_of: has_quality SO:0000877 ! alternatively_spliced
relationship: has_quality SO:0000877 ! implied link automatically realized ! alternatively_spliced

[Term]
id: SO:1001188
name: encodes_1_polypeptide
def: "A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]
is_a: SO:0000463 ! encodes_alternately_spliced_transcripts

[Term]
id: SO:1001189
name: encodes_greater_than_1_polypeptide
def: "A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]
is_a: SO:0000463 ! encodes_alternately_spliced_transcripts

[Term]
id: SO:1001190
name: encodes_different_polypeptides_different_stop
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]
is_a: SO:1001195 ! encodes_overlapping_peptides

[Term]
id: SO:1001191
name: encodes_overlapping_peptides_different_start
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]
is_a: SO:1001195 ! encodes_overlapping_peptides

[Term]
id: SO:1001192
name: encodes_disjoint_polypeptides
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]
is_a: SO:1001189 ! encodes_greater_than_1_polypeptide

[Term]
id: SO:1001193
name: encodes_overlapping_polypeptides_different_start_and_stop
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]
is_a: SO:1001195 ! encodes_overlapping_peptides

[Term]
id: SO:1001194
name: alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping
is_obsolete: true

[Term]
id: SO:1001195
name: encodes_overlapping_peptides
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]
is_a: SO:1001189 ! encodes_greater_than_1_polypeptide

[Term]
id: SO:1001196
name: cryptogene
def: "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]
is_a: SO:0000654 ! implied link automatically realized ! maxicircle_gene
intersection_of: SO:0000654 ! maxicircle_gene
intersection_of: has_quality SO:0000976 ! cryptic
relationship: has_quality SO:0000976 ! implied link automatically realized ! cryptic

[Term]
id: SO:1001197
name: dicistronic_primary_transcript
def: "A primary transcript that has the quality dicistronic." [SO:xp]
is_a: SO:0000079 ! implied link automatically realized ! dicistronic_transcript
is_a: SO:0000631 ! implied link automatically realized ! polycistronic_primary_transcript
intersection_of: SO:0000185 ! primary_transcript
intersection_of: has_quality SO:0000879 ! dicistronic

[Term]
id: SO:1001217
name: member_of_regulon
is_a: SO:0000081 ! gene_array_member

[Term]
id: SO:1001244
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
synonym: "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping" RELATED []
is_obsolete: true

[Term]
id: SO:1001246
name: CDS_independently_known
def: "A CDS with the evidence status of being independently known." [SO:xp]
is_a: SO:0000316 ! implied link automatically realized ! CDS
intersection_of: SO:0000316 ! CDS
intersection_of: has_quality SO:0000906 ! independently_known
relationship: has_quality SO:0000906 ! implied link automatically realized ! independently_known

[Term]
id: SO:1001247
name: orphan_CDS
def: "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]
is_a: SO:1001254 ! implied link automatically realized ! CDS_predicted
intersection_of: SO:1001254 ! CDS_predicted
intersection_of: has_origin SO:0000910 ! orphan
relationship: has_origin SO:0000910 ! implied link automatically realized ! orphan

[Term]
id: SO:1001249
name: CDS_supported_by_domain_match_data
def: "A CDS that is supported by domain similarity." [SO:xp]
is_a: SO:1001251 ! implied link automatically realized ! CDS_supported_by_sequence_similarity_data
intersection_of: SO:1001251 ! CDS_supported_by_sequence_similarity_data
intersection_of: has_quality SO:0000908 ! supported_by_domain_match
relationship: has_quality SO:0000908 ! implied link automatically realized ! supported_by_domain_match

[Term]
id: SO:1001251
name: CDS_supported_by_sequence_similarity_data
def: "A CDS that is supported by sequence similarity data." [SO:xp]
is_a: SO:1001254 ! implied link automatically realized ! CDS_predicted
intersection_of: SO:0000316 ! CDS
intersection_of: has_quality SO:0000907 ! supported_by_sequence_similarity
relationship: has_quality SO:0000907 ! implied link automatically realized ! supported_by_sequence_similarity

[Term]
id: SO:1001254
name: CDS_predicted
def: "A CDS that is predicted." [SO:ke]
is_a: SO:0000316 ! implied link automatically realized ! CDS
intersection_of: SO:0000316 ! CDS
intersection_of: has_quality SO:0000732 ! predicted
relationship: has_quality SO:0000732 ! implied link automatically realized ! predicted

[Term]
id: SO:1001255
name: status_of_coding_sequence
is_obsolete: true

[Term]
id: SO:1001259
name: CDS_supported_by_EST_or_cDNA_data
def: "A CDS that is supported by similarity to EST or cDNA data." [SO:xp]
is_a: SO:1001251 ! implied link automatically realized ! CDS_supported_by_sequence_similarity_data
intersection_of: SO:1001251 ! CDS_supported_by_sequence_similarity_data
intersection_of: has_quality SO:0000909 ! supported_by_EST_or_cDNA
relationship: has_quality SO:0000909 ! implied link automatically realized ! supported_by_EST_or_cDNA

[Term]
id: SO:1001260
name: internal_Shine_Dalgarno_sequence
def: "A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]
synonym: "internal Shine-Dalgarno sequence" EXACT []
is_a: SO:0000243 ! internal_ribosome_entry_site
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001261
name: recoded_mRNA
def: "A gene coding an mRNA which is recoded before translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]
is_a: SO:0000234 ! implied link automatically realized ! mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000881 ! recoded
relationship: has_quality SO:0000881 ! implied link automatically realized ! recoded

[Term]
id: SO:1001262
name: minus_1_translational_frameshift
def: "An attribute describing a translational frameshift of -1." [SO:ke]
is_a: SO:0000887 ! translational_frameshift

[Term]
id: SO:1001263
name: plus_1_translational_frameshift
def: "An attribute describing a translational frameshift of +1." [SO:ke]
is_a: SO:0000887 ! translational_frameshift

[Term]
id: SO:1001264
name: mRNA_recoded_by_translational_bypass
def: "A mRNA is translated by ribosomes that suspend translation at a particular codon and resume translation at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]
is_a: SO:1001261 ! implied link automatically realized ! recoded_mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000886 ! recoded_by_translational_bypass
relationship: has_quality SO:0000886 ! implied link automatically realized ! recoded_by_translational_bypass

[Term]
id: SO:1001265
name: mRNA_recoded_by_codon_redefinition
def: "A gene whose mRNA is recoded by an alteration of codon meaning." [SO:ma]
is_a: SO:1001261 ! implied link automatically realized ! recoded_mRNA
intersection_of: SO:0000234 ! mRNA
intersection_of: has_quality SO:0000882 ! codon_redefined
relationship: has_quality SO:0000882 ! implied link automatically realized ! codon_redefined

[Term]
id: SO:1001266
name: stop_codon_redefinition_as_selenocysteine
is_obsolete: true

[Term]
id: SO:1001267
name: stop_codon_readthrough
is_obsolete: true

[Term]
id: SO:1001268
name: recoding_stimulatory_region
def: "A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]
synonym: "recoding stimulatory signal" EXACT []
is_a: SO:0000836 ! mRNA_region

[Term]
id: SO:1001269
name: four_bp_start_codon
def: "A non-canonical start codon with 4 base pairs." [SO:ke]
synonym: "4bp start codon" EXACT []
is_a: SO:0000680 ! non_canonical_start_codon

[Term]
id: SO:1001270
name: stop_codon_redefinition_as_pyrrolysine
is_obsolete: true

[Term]
id: SO:1001271
name: archeal_intron
def: "Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism." [SO:ma]
is_a: SO:0000661 ! intron_attribute

[Term]
id: SO:1001272
name: tRNA_intron
is_a: SO:0000661 ! intron_attribute

[Term]
id: SO:1001273
name: CTG_start_codon
def: "A non-canonical start codon of sequence CTG." [SO:ke]
is_a: SO:0000680 ! non_canonical_start_codon

[Term]
id: SO:1001274
name: SECIS_element
def: "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001275
name: retron
def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]
is_a: SO:0000001 ! region

[Term]
id: SO:1001277
name: three_prime_recoding_site
def: "The recoding stimulatory signal located downstream of the recoding site." [SO:ke]
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001279
name: three_prime_stem_loop_structure
def: "A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001280
name: five_prime_recoding_site
def: "The recoding stimulatory signal located upstream of the recoding site." [SO:ke]
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001281
name: flanking_three_prime_quadruplet_recoding_signal
def: "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001282
name: UAG_stop_codon_signal
def: "A stop codon signal for a UAG stop codon redefinition." [SO:ke]
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001283
name: UAA_stop_codon_signal
def: "A stop codon signal for a UAA stop codon redefinition." [SO:ke]
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001284
name: regulon
def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]
subset: SOFA
is_a: SO:0005855 ! gene_group

[Term]
id: SO:1001285
name: UGA_stop_codon_signal
def: "A stop codon signal for a UGA stop codon redefinition." [SO:ke]
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001286
name: three_prime_repeat_recoding_signal
def: "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001287
name: distant_three_prime_recoding_signal
def: "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001288
name: stop_codon_signal
def: "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]
comment: This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal.
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:2000061
name: databank_entry
def: "The sequence referred to by an entry in a databank such as Genbank or SwissProt." [SO:ke]
subset: SOFA
synonym: "accession" RELATED []
is_a: SO:0000695 ! reagent

[Typedef]
id: adjacent_to
name: adjacent_to
def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence." [SO:ke]
subset: SOFA

[Typedef]
id: associated_with
name: associated_with
comment: This relationship is vague and up for discussion.
is_symmetric: true

[Typedef]
id: derives_from
name: derives_from
subset: SOFA
is_transitive: true

[Typedef]
id: genome_of
name: genome_of

[Typedef]
id: has_genome_location
name: has_genome_location
is_obsolete: true

[Typedef]
id: has_origin
name: has_origin

[Typedef]
id: has_part
name: has_part

[Typedef]
id: has_quality
name: has_quality
comment: The relationship between a feature and an atrribute.

[Typedef]
id: homologous_to
name: homologous_to
subset: SOFA
is_symmetric: true
is_a: similar_to ! similar_to

[Typedef]
id: member_of
name: member_of
comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
subset: SOFA
is_transitive: true

[Typedef]
id: non_functional_homolog_of
name: non_functional_homolog_of
def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]
subset: SOFA
is_a: homologous_to ! homologous_to

[Typedef]
id: orthologous_to
name: orthologous_to
subset: SOFA
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: paralogous_to
name: paralogous_to
subset: SOFA
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: part_of
name: part_of
subset: SOFA
is_transitive: true

[Typedef]
id: position_of
name: position_of

[Typedef]
id: regulated_by
name: regulated_by
is_obsolete: true

[Typedef]
id: sequence_of
name: sequence_of

[Typedef]
id: similar_to
name: similar_to
subset: SOFA
is_symmetric: true

[Typedef]
id: variant_of
name: variant_of
def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of s=ome instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop]
comment: Added to SO during the immunology workshop, June 2007.  This relationship was approved by Barry Smith.

