format-version: 1.2
date: 30:01:2008 17:03
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]
comment: Please not the synonym R psi M uses the spelled out form of the greek letter.
synonym: "pseudogene by reverse transcription" RELATED []
synonym: "R psi G" RELATED []
synonym: "retropseudogene" EXACT []
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 ! translationally_frameshifted
relationship: has_quality SO:0000887 ! implied link automatically realized ! translationally_frameshifted

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

[Term]
id: SO:0000120
name: protein_coding_primary_transcript
def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]
comment: May contain introns.
subset: SOFA
synonym: "pre mRNA" RELATED []
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]
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:0001215 ! coding_region_of_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:0001215 ! coding_region_of_exon
relationship: part_of SO:0000202 ! three_prime_coding_exon

[Term]
id: SO:0000198
name: noncoding_exon
def: "An exon that does not contain any codons." [SO:ke]
subset: SOFA
synonym: "noncoding exon" EXACT []
is_a: SO:0000147 ! exon
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 RNA (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: "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. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]
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: