bp_process_wormbase: move program to new Bio-DB-Ace distribution

[bioperl-live.git] / t / data / so.obo

format-version: 1.2
date: 13:02:2006 15:53
saved-by: kareneilbeck
auto-generated-by: OBO-Edit 1.000-beta15
subsetdef: SOFA "SO feature annotation"
default-namespace: sequence
remark: autogenerated-by\:   DAG-Edit version 1.417\nsaved-by\:       eilbeck\ndate\:         Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $

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

[Term]
id: SO:0000001
name: region
def: "Continuous sequence." [SO:ke]
subset: SOFA
synonym: "sequence" RELATED []
is_a: SO:0000110 ! located_sequence_feature

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

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

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

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

[Term]
id: SO:0000006
name: PCR_product
def: "A region amplified by a PCR reaction." [SO:ke]
subset: SOFA
synonym: "amplicon" RELATED []
is_a: SO:0000695 ! reagent

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

[Term]
id: SO:0000008
name: gene_sensu_your_favorite_organism
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000009
name: gene_class
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000010
name: protein_coding_gene
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000011
name: non_protein_coding_gene
is_a: SO:0000009 ! gene_class

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

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

[Term]
id: SO:0000014
name: INR_motif
def: "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739]
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000015
name: DPE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters; always found with the INR_motif. Positioned from +28 to +32 with respect to the TSS (+1). Consensus sequence (A|G)G(A|T)(C|T)(G|A|C). Required for TFIID binding to TATA-less promoters." [PMID:12651739]
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000016
name: BRE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739]
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000017
name: PSE_motif
def: "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]
relationship: part_of SO:0000170 ! RNApol_II_promoter

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

[Term]
id: SO:0000019
name: RNA_hairpin_loop
is_a: SO:0000715 ! RNA_motif

[Term]
id: SO:0000020
name: RNA_internal_loop
is_a: SO:0000715 ! RNA_motif

[Term]
id: SO:0000021
name: asymmetric_RNA_internal_loop
is_a: SO:0000020 ! RNA_internal_loop

[Term]
id: SO:0000022
name: A_minor_RNA_motif
is_a: SO:0000021 ! asymmetric_RNA_internal_loop

[Term]
id: SO:0000023
name: K_turn_RNA_motif
is_a: SO:0000021 ! asymmetric_RNA_internal_loop

[Term]
id: SO:0000024
name: Sarcin_like_RNA_motif
is_a: SO:0000021 ! asymmetric_RNA_internal_loop

[Term]
id: SO:0000025
name: symmetric_RNA_internal_loop
is_a: SO:0000020 ! RNA_internal_loop

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

[Term]
id: SO:0000027
name: RNA_hook_turn
is_a: SO:0000026 ! RNA_junction_loop

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

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

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

[Term]
id: SO:0000031
name: aptamer
def: "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:http://aptamer.icmb.utexas.edu]
is_a: SO:0000351 ! synthetic_sequence
is_a: SO:0000696 ! oligo

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

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

[Term]
id: SO:0000034
name: morpholino
def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http:www.gene-tools.com/Morpholinos/morpholinos.HTML]
is_a: SO:0000351 ! synthetic_sequence
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000035
name: riboswitch
def: "Riboswitches are mRNAs that can act as direct sensors of small molecules to control their own expression. A riboswitch contains a cis element within mRNA, that can act as a direct sensor of metabolites without a protein intermediate." [PMID:2820954]
is_a: SO:0000234 ! mRNA

[Term]
id: SO:0000036
name: matrix_attachment_site
def: "A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]
synonym: "MAR" RELATED []
synonym: "SMAR" RELATED []
synonym: "scaffold_attachment_site" RELATED []
is_a: SO:0000626 ! chromosomal_regulatory_element

[Term]
id: SO:0000037
name: locus_control_region
def: "A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000038
name: match_set
def: "A collection of match parts" [SO:ke]
subset: SOFA
is_a: SO:0000343 ! match

[Term]
id: SO:0000039
name: match_part
def: "A part of a match, for example an hsp from blast isa match_part." [SO:ke]
subset: SOFA
is_a: SO:0000343 ! match
relationship: part_of SO:0000038 ! match_set

[Term]
id: SO:0000040
name: genomic_clone
def: "A clone of a DNA region of a genome." [SO:ma]
is_a: SO:0000151 ! clone

[Term]
id: SO:0000041
name: variation_operation
def: "An operation that can be applied to a sequence, that results in a chnage." [SO:ke]
is_a: SO:0000000 ! Sequence_Ontology

[Term]
id: SO:0000042
name: pseudogene_attribute
def: "An attribute of a pseudogene (SO:0000336)." [SO:ma]
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000043
name: processed_pseudogene
synonym: "pseudogene_by_reverse_transcription" RELATED []
is_a: SO:0000042 ! pseudogene_attribute

[Term]
id: SO:0000044
name: pseudogene_by_unequal_crossing_over
is_a: SO:0000042 ! pseudogene_attribute

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

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

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

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

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

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

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

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

[Term]
id: SO:0000053
name: mutation_affecting_regulatory_region
is_a: SO:1000132 ! consequences_of_mutation

[Term]
id: SO:0000054
name: aneuploid
is_a: SO:1000182 ! chromosome_number_variation

[Term]
id: SO:0000055
name: hyperploid
is_a: SO:0000054 ! aneuploid

[Term]
id: SO:0000056
name: hypoploid
is_a: SO:0000054 ! aneuploid

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

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

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

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

[Term]
id: SO:0000061
name: restriction_enzyme_binding_site
is_a: SO:0000059 ! nuclease_binding_site

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

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

[Term]
id: SO:0000064
name: gene_by_transcript_attribute
comment: This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.
is_a: SO:0000401 ! gene_attribute

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

[Term]
id: SO:0000066
name: gene_by_polyadenylation_attribute
is_a: SO:0000064 ! gene_by_transcript_attribute

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

[Term]
id: SO:0000068
name: overlapping_gene
is_a: SO:0000067 ! gene_to_gene_feature

[Term]
id: SO:0000069
name: gene_included_within_intron
is_a: SO:0000068 ! overlapping_gene

[Term]
id: SO:0000070
name: gene_included_within_intron_antiparallel
is_a: SO:0000069 ! gene_included_within_intron

[Term]
id: SO:0000071
name: gene_included_within_intron_parallel
is_a: SO:0000069 ! gene_included_within_intron

[Term]
id: SO:0000072
name: end_overlapping_gene
is_a: SO:0000068 ! overlapping_gene

[Term]
id: SO:0000073
name: end_overlapping_gene_five_primethree_prime_overlap
is_a: SO:0000072 ! end_overlapping_gene

[Term]
id: SO:0000074
name: end_overlapping_gene_five_primefive_prime_overlap
is_a: SO:0000072 ! end_overlapping_gene

[Term]
id: SO:0000075
name: end_overlapping_gene_three_primethree_prime_overlap
is_a: SO:0000072 ! end_overlapping_gene

[Term]
id: SO:0000076
name: end_overlapping_gene_three_primefive_prime_overlap
is_a: SO:0000072 ! end_overlapping_gene

[Term]
id: SO:0000077
name: antisense_gene
is_a: SO:0000068 ! overlapping_gene

[Term]
id: SO:0000078
name: polycistronic_transcript
is_a: SO:0000115 ! transcript_feature

[Term]
id: SO:0000079
name: dicistronic_transcript
is_a: SO:0000078 ! polycistronic_transcript

[Term]
id: SO:0000080
name: member_of_operon
is_a: SO:0000081 ! member_gene_array

[Term]
id: SO:0000081
name: member_gene_array
is_a: SO:0000067 ! gene_to_gene_feature

[Term]
id: SO:0000082
name: processed_transcript_attribute
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000083
name: macronuclear_sequence_feature
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000084
name: micronuclear_sequence_feature
is_a: SO:0000735 ! sequence_location

[Term]
id: SO:0000085
name: gene_by_genome_location
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000086
name: gene_by_organelle_of_genome
is_a: SO:0000085 ! gene_by_genome_location

[Term]
id: SO:0000087
name: nuclear_gene
is_a: SO:0000086 ! gene_by_organelle_of_genome

[Term]
id: SO:0000088
name: mt_gene
synonym: "mitochondrial_gene" RELATED []
is_a: SO:0000086 ! gene_by_organelle_of_genome

[Term]
id: SO:0000089
name: kinetoplast_gene
is_a: SO:0000088 ! mt_gene

[Term]
id: SO:0000090
name: plastid_gene
is_a: SO:0000086 ! gene_by_organelle_of_genome

[Term]
id: SO:0000091
name: apicoplast_gene
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000092
name: ct_gene
synonym: "chloroplast_gene" RELATED []
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000093
name: chromoplast_gene
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000094
name: cyanelle_gene
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000095
name: leucoplast_gene
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000096
name: proplastid_gene
is_a: SO:0000090 ! plastid_gene

[Term]
id: SO:0000097
name: nucleomorph_gene
is_a: SO:0000086 ! gene_by_organelle_of_genome

[Term]
id: SO:0000098
name: plasmid_gene
is_a: SO:0000085 ! gene_by_genome_location

[Term]
id: SO:0000099
name: proviral_gene
is_a: SO:0000085 ! gene_by_genome_location

[Term]
id: SO:0000100
name: endogenous_retroviral_gene
is_a: SO:0000099 ! proviral_gene

[Term]
id: SO:0000101
name: transposable_element
def: "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/ ~ smaloy/Glossary/T.html]
subset: SOFA
is_a: SO:0000187 ! repeat_family
is_a: SO:1000028 ! intrachromosomal_mutation

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

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

[Term]
id: SO:0000104
name: polypeptide
def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversable denaturation." [SO:ma]
subset: SOFA
relationship: derives_from SO:0000316 ! CDS

[Term]
id: SO:0000105
name: chromosome_arm
def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.exactsciences.com/cic/glossary/_index.htm]
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000106
name: non_capped_primary_transcript
is_a: SO:0000146 ! primary_transcript_by_cap_class

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

[Term]
id: SO:0000108
name: mRNA_with_frameshift
is_a: SO:0000082 ! processed_transcript_attribute

[Term]
id: SO:0000109
name: sequence_variant
def: "A region of sequence where variation has been observed." [SO:ke]
subset: SOFA
synonym: "mutation" RELATED []
is_a: SO:0000110 ! located_sequence_feature

[Term]
id: SO:0000110
name: located_sequence_feature
def: "A biological feature that can be attributed to a region of biological sequence." [SO:ke]
subset: SOFA
is_a: SO:0000000 ! Sequence_Ontology

[Term]
id: SO:0000111
name: transposable_element_gene
def: "A gene encoded within a transposable element. For example gag, int, env and pol are the transpable element genes of the TY element in yeast." [SO:ke]
is_a: SO:0000009 ! gene_class

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

[Term]
id: SO:0000113
name: integrated_virus
def: "A viral sequence which has integrated into the host genome." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000115
name: transcript_feature
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000116
name: edited_transcript
def: "A gene whose transcript is edited." [http://www.rna.ucla.edu/]
is_a: SO:0000115 ! transcript_feature

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

[Term]
id: SO:0000118
name: transcript_with_translational_frameshift
is_a: SO:1001261 ! recoded_mRNA

[Term]
id: SO:0000119
name: gene_by_class_of_regulation
is_a: SO:0000401 ! gene_attribute

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

[Term]
id: SO:0000121
name: forward_primer
def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
is_a: SO:0000112 ! primer

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

[Term]
id: SO:0000123
name: transcriptionally_regulated
def: "." [SO:ma]
comment: by\:<protein_id>
is_a: SO:0000119 ! gene_by_class_of_regulation

[Term]
id: SO:0000124
name: transcriptionally_constitutive
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000125
name: transcriptionally_induced
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000126
name: transcriptionally_repressed
is_a: SO:0000123 ! transcriptionally_regulated

[Term]
id: SO:0000127
name: silenced_gene
is_a: SO:0000126 ! transcriptionally_repressed

[Term]
id: SO:0000128
name: gene_silenced_by_DNA_modification
is_a: SO:0000127 ! silenced_gene

[Term]
id: SO:0000129
name: gene_silenced_by_DNA_methylation
is_a: SO:0000128 ! gene_silenced_by_DNA_modification

[Term]
id: SO:0000130
name: post_translationally_regulated
synonym: "post-translationally_regulated" RELATED []
is_a: SO:0000119 ! gene_by_class_of_regulation

[Term]
id: SO:0000131
name: translationally_regulated
is_a: SO:0000119 ! gene_by_class_of_regulation

[Term]
id: SO:0000132
name: reverse_primer
def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
is_a: SO:0000112 ! primer

[Term]
id: SO:0000133
name: gene_by_epigenetic_modification
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000134
name: imprinted
is_a: SO:0000119 ! gene_by_class_of_regulation
is_a: SO:0000133 ! gene_by_epigenetic_modification

[Term]
id: SO:0000135
name: maternally_imprinted
is_a: SO:0000134 ! imprinted

[Term]
id: SO:0000136
name: paternally_imprinted
is_a: SO:0000134 ! imprinted

[Term]
id: SO:0000137
name: allelically_excluded
is_a: SO:0000133 ! gene_by_epigenetic_modification

[Term]
id: SO:0000138
name: gene_rearranged_at_DNA_level
is_a: SO:0000133 ! gene_by_epigenetic_modification

[Term]
id: SO:0000139
name: ribosome_entry_site
def: "Region in mRNA where ribosome assembles." [SO:ke]
comment: gene\:<gene_id>
subset: SOFA
relationship: part_of SO:0000203 ! UTR

[Term]
id: SO:0000140
name: attenuator
def: "A sequence segment located between the promoter and a structural gene that causes partial termination of transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0000752 ! gene_group_regulatory_region
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000141
name: terminator
def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0000752 ! gene_group_regulatory_region
is_a: SO:0005836 ! regulatory_region

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

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

[Term]
id: SO:0000144
name: primary_transcript_attribute
is_a: SO:0000237 ! transcript_attribute

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

[Term]
id: SO:0000146
name: primary_transcript_by_cap_class
is_a: SO:0000144 ! primary_transcript_attribute

[Term]
id: SO:0000147
name: exon
def: "A region of the genome that codes for portion of spliced messenger RNA (SO:0000234); may contain 5'-untranslated region (SO:0000204), all open reading frames (SO:0000236) and 3'-untranslated region (SO:0000205)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
relationship: part_of SO:0000673 ! transcript

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

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

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

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

[Term]
id: SO:0000152
name: YAC
def: "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]
is_a: SO:0000440 ! vector
relationship: part_of SO:0000760 ! YAC_clone

[Term]
id: SO:0000153
name: BAC
def: "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]
is_a: SO:0000440 ! vector
relationship: part_of SO:0000764 ! BAC_clone

[Term]
id: SO:0000154
name: PAC
def: "P1 Artificial Chromosome. These vectors can hold large inserts, typically 80-200 kb, and propagate in E. coli as a single copy episome." [https://www.ncbi.nlm.nih.gov/genome/guide/mouse/glossary.htm]
synonym: "P1" RELATED []
is_a: SO:0000440 ! vector
relationship: part_of SO:0000762 ! PAC_clone

[Term]
id: SO:0000155
name: plasmid
def: "A self-replicating circular DNA molecule that is distinct from a chromosome in the organism." [SO:ma]
is_a: SO:0000695 ! reagent

[Term]
id: SO:0000156
name: cosmid
def: "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as aplasmids or packaged as a phage,since they retain the lambda cos sites." [SO:ma]
comment: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1)\:9-20.
is_a: SO:0000440 ! vector
relationship: part_of SO:0000765 ! cosmid_clone

[Term]
id: SO:0000157
name: phagemid
def: "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]
is_a: SO:0000440 ! vector
relationship: part_of SO:0000761 ! phagemid_clone

[Term]
id: SO:0000158
name: fosmid
def: "A cloning vector that utilises the E. coli F factor." [SO:ma]
comment: Birren BW et al. A human chromosome 22 fosmid resource\: mapping and analysis of 96 clones. Genomics 1996;
is_a: SO:0000440 ! vector
relationship: part_of SO:0000763 ! fosmid_clone

[Term]
id: SO:0000159
name: deletion
def: "The sequence that is deleted." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0000109 ! sequence_variant
relationship: sequence_of SO:0000045 ! delete

[Term]
id: SO:0000160
name: lambda_clone
def: "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]
is_a: SO:0000151 ! clone

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

[Term]
id: SO:0000162
name: splice_site
def: "The position where intron is excised." [SO:ke]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000185 ! primary_transcript

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

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

[Term]
id: SO:0000165
name: enhancer
def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000166
name: enhancer_by_bound_factor
is_a: SO:0000402 ! enhancer_attribute

[Term]
id: SO:0000167
name: promoter
def: "The region on a DNA molecule involved in RNA polymerase binding to initiate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
is_a: SO:0005836 ! regulatory_region

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

[Term]
id: SO:0000169
name: RNApol_I_promoter
def: "A DNA sequence sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]
synonym: "RNA_polymerase_A_promoter" RELATED []
is_a: SO:0000167 ! promoter

[Term]
id: SO:0000170
name: RNApol_II_promoter
def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]
synonym: "RNA_polymerase_B_promoter" RELATED []
is_a: SO:0000167 ! promoter

[Term]
id: SO:0000171
name: RNApol_III_promoter
def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]
synonym: "RNA_polymerase_C_promoter" RELATED []
is_a: SO:0000167 ! promoter

[Term]
id: SO:0000172
name: CAAT_signal
def: "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
relationship: part_of SO:0000170 ! RNApol_II_promoter

[Term]
id: SO:0000173
name: GC_rich_region
def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "GC-rich_region" RELATED []
relationship: part_of SO:0000170 ! RNApol_II_promoter

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

[Term]
id: SO:0000175
name: minus_10_signal
def: "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "-10_signal" RELATED []
synonym: "Pribnow_box" RELATED []
relationship: part_of SO:0000613 ! bacterial_RNApol_promoter

[Term]
id: SO:0000176
name: minus_35_signal
def: "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
synonym: "-35_signal" RELATED []
relationship: part_of SO:0000613 ! bacterial_RNApol_promoter

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

[Term]
id: SO:0000178
name: operon
def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]
subset: SOFA
is_a: SO:0005855 ! gene_group

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

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

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

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

[Term]
id: SO:0000183
name: non_transcribed_region
def: "A region of the gene which is not transcribed." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
relationship: part_of SO:0000704 ! gene

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

[Term]
id: SO:0000185
name: primary_transcript
def: "The primary (initial, unprocessed) transcript; includes five_prime_clip (SO:0000555), five_prime_untranslated_region (SO:0000204), open reading frames (SO:0000236), introns (SO:0000188) and three_prime_ untranslated_region (three_prime_UTR), and three_prime_clip (SO:0000557)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
synonym: "precursor_RNA" RELATED []
is_a: SO:0000673 ! transcript

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

[Term]
id: SO:0000187
name: repeat_family
def: "A group of characterized repeat sequences." [SO:ke]
subset: SOFA
is_a: SO:0000657 ! repeat_region

[Term]
id: SO:0000188
name: intron
def: "A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
relationship: part_of SO:0000185 ! primary_transcript

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

[Term]
id: SO:0000190
name: five_prime_intron
is_a: SO:0000188 ! intron

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

[Term]
id: SO:0000192
name: three_prime_intron
is_a: SO:0000188 ! intron

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

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

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

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

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

[Term]
id: SO:0000198
name: noncoding_exon
def: "An exon that does not contain any codons." [SO:ke]
synonym: "noncoding_exon" RELATED []
is_a: SO:0000147 ! exon

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

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

[Term]
id: SO:0000201
name: interior_exon
is_a: SO:0000147 ! exon

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

[Term]
id: SO:0000203
name: UTR
def: "Messenger RNA sequences that are untranslated and lie five prime and three prime to sequences which are translated." [SO:ke]
subset: SOFA
synonym: "untranslated_region" RELATED []
relationship: part_of SO:0000234 ! mRNA

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

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

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

[Term]
id: SO:0000207
name: simple_sequence_length_polymorphism
is_a: SO:0000248 ! sequence_length_variation

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

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

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

[Term]
id: SO:0000211
name: alanine_tRNA_primary_transcript
is_a: SO:0000210 ! tRNA_primary_transcript

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000233
name: processed_transcript
def: "A transcript which has undergone processing to remove parts such as introns and transcribed_spacer_regions." [SO:ke]
comment: A processed transcript cannot contain introns.
subset: SOFA
is_a: SO:0000673 ! transcript
relationship: derives_from SO:0000185 ! primary_transcript

[Term]
id: SO:0000234
name: mRNA
def: "Messenger RNA is the intermediate molecule between DNA and protein. It  includes UTR and coding sequences. It does not contain introns." [SO:ma]
comment: mRNA does not contain introns as it is a processd_transcript.nThe equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns.
subset: SOFA
synonym: "messenger_RNA" RELATED []
is_a: SO:0000233 ! processed_transcript

[Term]
id: SO:0000235
name: TF_binding_site
def: "A region of a molecule that binds to a transcription factor." [SO:ke]
subset: SOFA
synonym: "transcription_factor_binding_site" RELATED []
is_a: SO:0000410 ! protein_binding_site
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000236
name: ORF
def: "The inframe interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER" [SO:ma, SO:rb]
comment: The definition was modified by Rama. This terms now basically is the same as a CDS. This must be revised.
subset: SOFA
synonym: "open_reading_frame" RELATED []
is_a: SO:0000717 ! reading_frame

[Term]
id: SO:0000237
name: transcript_attribute
is_a: SO:0000400 ! sequence_attribute

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

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

[Term]
id: SO:0000240
name: chromosome_variation
is_a: SO:0000000 ! Sequence_Ontology

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

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

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

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

[Term]
id: SO:0000245
name: mRNA_by_polyadenylation_status
is_a: SO:0000082 ! processed_transcript_attribute

[Term]
id: SO:0000246
name: mRNA_polyadenylated
is_a: SO:0000245 ! mRNA_by_polyadenylation_status

[Term]
id: SO:0000247
name: mRNA_not_polyadenylated
is_a: SO:0000245 ! mRNA_by_polyadenylation_status

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

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

[Term]
id: SO:0000250
name: modified_RNA_base_feature
def: "A post_transcriptionally modified base." [SO:ke]
relationship: part_of SO:0000673 ! transcript

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

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

[Term]
id: SO:0000253
name: tRNA
def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. tRNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). tRNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]
subset: SOFA
synonym: "transfer_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000254
name: alanyl_tRNA
is_a: SO:0000253 ! tRNA

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

[Term]
id: SO:0000256
name: asparaginyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000257
name: aspartyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000258
name: cysteinyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000259
name: glutaminyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000260
name: glutamyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000261
name: glycyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000262
name: histidyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000263
name: isoleucyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000264
name: leucyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000265
name: lysyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000266
name: methionyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000267
name: phenylalanyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000268
name: prolyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000269
name: seryl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000270
name: threonyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000271
name: tryptophanyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000272
name: tyrosyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000273
name: valyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0000274
name: snRNA
def: "Small non-coding RNA in the nucleoplasm. A small nuclear RNA molecule involved in pre-mRNA splicing and processing" [ems:WB, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types, PMID:11733745]
subset: SOFA
synonym: "small_nuclear_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000275
name: snoRNA
def: "Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus. There are two main classes of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member of the box C/D class. Indeed, the box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]
subset: SOFA
synonym: "small_nucleolar_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

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

[Term]
id: SO:0000277
name: transcript_by_bound_factor
is_a: SO:0000237 ! transcript_attribute

[Term]
id: SO:0000278
name: transcript_by_bound_nucleic_acid
is_a: SO:0000277 ! transcript_by_bound_factor

[Term]
id: SO:0000279
name: transcript_by_bound_protein
is_a: SO:0000277 ! transcript_by_bound_factor

[Term]
id: SO:0000280
name: engineered_gene
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000281
name: engineered_foreign_gene
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000285 ! foreign_gene

[Term]
id: SO:0000282
name: mRNA_with_minus_1_frameshift
is_a: SO:0000108 ! mRNA_with_frameshift

[Term]
id: SO:0000283
name: engineered_foreign_transposable_element_gene
is_a: SO:0000111 ! transposable_element_gene
is_a: SO:0000280 ! engineered_gene

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

[Term]
id: SO:0000285
name: foreign_gene
is_a: SO:0000452 ! transgene

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

[Term]
id: SO:0000287
name: fusion_gene
is_a: SO:0000009 ! gene_class

[Term]
id: SO:0000288
name: engineered_fusion_gene
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000287 ! fusion_gene

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

[Term]
id: SO:0000290
name: dinucleotide_repeat_microsatellite_feature
is_a: SO:0000289 ! microsatellite

[Term]
id: SO:0000291
name: trinucleotide_repeat_microsatellite_feature
is_a: SO:0000289 ! microsatellite

[Term]
id: SO:0000292
name: repetitive_element
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000293
name: engineered_foreign_repetitive_element
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000292 ! repetitive_element

[Term]
id: SO:0000294
name: inverted_repeat
def: "The sequence is complementarily repeated on the opposite strand. Example: GCTGA-----TCAGC." [SO:ke]
subset: SOFA
is_a: SO:0000657 ! repeat_region

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

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

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

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

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

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

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

[Term]
id: SO:0000302
name: J_gene_recombination_feature
def: "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#J-RS]
synonym: "J-RS" RELATED []
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000303
name: clip
def: "Part of the primary transcript that is clipped off during processing." [SO:ke]
subset: SOFA
relationship: part_of SO:0000185 ! primary_transcript

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

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

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

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

[Term]
id: SO:0000308
name: sequence_feature_locating_method
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000309
name: computed_feature
is_a: SO:0000308 ! sequence_feature_locating_method

[Term]
id: SO:0000310
name: predicted_ab_initio_computation
is_a: SO:0000309 ! computed_feature

[Term]
id: SO:0000311
name: computed_feature_by_similarity
def: "." [SO:ma]
comment: similar to\:<sequence_id>
is_a: SO:0000309 ! computed_feature

[Term]
id: SO:0000312
name: experimentally_determined_feature
is_a: SO:0000308 ! sequence_feature_locating_method

[Term]
id: SO:0000313
name: stem_loop
def: "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
is_a: SO:0000002 ! sequence_secondary_structure

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

[Term]
id: SO:0000315
name: transcription_start_site
def: "The site where transcription begins." [SO:ke]
subset: SOFA
synonym: "TSS" RELATED []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000185 ! primary_transcript

[Term]
id: SO:0000316
name: CDS
def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]
subset: SOFA
synonym: "coding_sequence" RELATED []
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000317
name: cDNA_clone
def: "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
is_a: SO:0000151 ! clone

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

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

[Term]
id: SO:0000320
name: intronic_splice_enhancer
def: "Sequences within the intron that modulate splice site selection for some introns." [SO:ke]
is_a: SO:0000344 ! splice_enhancer
relationship: part_of SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000321
name: mRNA_with_plus_1_frameshift
is_a: SO:0000108 ! mRNA_with_frameshift

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

[Term]
id: SO:0000323
name: coding_start
def: "The first base to be translated into protein." [SO:ke]
synonym: "translation_start" RELATED []
relationship: part_of SO:0000316 ! CDS

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

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

[Term]
id: SO:0000326
name: SAGE_tag
def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [https://www.ncbi.nlm.nih.gov/pubmed/7570003]
subset: SOFA
is_a: SO:0000324 ! tag

[Term]
id: SO:0000327
name: coding_end
def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke]
synonym: "translation_end" RELATED []
relationship: part_of SO:0000316 ! CDS

[Term]
id: SO:0000328
name: microarray_oligo
synonym: "microarray_oligonucleotide" RELATED []
is_a: SO:0000051 ! probe
is_a: SO:0000324 ! tag
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000329
name: mRNA_with_plus_2_frameshift
is_a: SO:0000108 ! mRNA_with_frameshift

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

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

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

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

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

[Term]
id: SO:0000335
name: mRNA_with_minus_2_frameshift
is_a: SO:0000108 ! mRNA_with_frameshift

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

[Term]
id: SO:0000337
name: RNAi_reagent
def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]
subset: SOFA
is_a: SO:0000695 ! reagent
is_a: SO:0000696 ! oligo

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

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

[Term]
id: SO:0000340
name: chromosome
def: "Structural unit composed of long DNA molecule." [http://biotech.icmb.utexas.edu/search/dict-search.mhtml]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000341
name: chromosome_band
def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]
synonym: "cytological_band" RELATED []
relationship: part_of SO:0000340 ! chromosome

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

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

[Term]
id: SO:0000344
name: splice_enhancer
def: "Region of a transcript that regulates splicing." [SO:ke]
subset: SOFA
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000345
name: EST
def: "Expressed Sequence Tag: The sequence of a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [http://genomics.phrma.org/lexicon/e.html]
subset: SOFA
synonym: "expressed_sequence_tag" RELATED []
is_a: SO:0000695 ! reagent
relationship: derives_from SO:0000234 ! mRNA

[Term]
id: SO:0000346
name: Cre_recombination_target_region
synonym: "lox_site" RELATED []
is_a: SO:0000342 ! site_specific_recombination_target_region

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

[Term]
id: SO:0000348
name: nucleic_acid
is_a: SO:0000443 ! polymer_type

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

[Term]
id: SO:0000350
name: FLP_recombination_target_region
synonym: "FRT_site" RELATED []
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000351
name: synthetic_sequence
def: "A sequence of nucleotides or amino acids that has been designed by an experimentor and which may, or may not, correspond with any natural sequence." [SO:ma]
is_a: SO:0000443 ! polymer_type

[Term]
id: SO:0000352
name: DNA
is_a: SO:0000348 ! nucleic_acid

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

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

[Term]
id: SO:0000355
name: haplotype_block
def: "A region of the genome which in which markers are co-inherited as the result of the lack of historic recombination between them due to their close proximity." [SO:ma]
is_a: SO:0000298 ! recombination_feature

[Term]
id: SO:0000356
name: RNA
is_a: SO:0000348 ! nucleic_acid

[Term]
id: SO:0000357
name: sequence_by_flanking_target_attribute
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000358
name: protein
def: "One or more polypeptides which may, or may not, be covalently bonded, and which assume a native secondary and tertiary structure." [SO:ma]
comment: This definition no longer matches the meaning of the concept! Term should probably be proteinacious or something... KEn
is_a: SO:0000443 ! polymer_type

[Term]
id: SO:0000359
name: floxed_sequence
is_a: SO:0000357 ! sequence_by_flanking_target_attribute
is_a: SO:0000452 ! transgene

[Term]
id: SO:0000360
name: codon
def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together signify a unique amino acid or the termination of translation." [http://genomics.phrma.org/lexicon/c.html]
subset: SOFA
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:0000361
name: FRT_flanked_sequence
is_a: SO:0000357 ! sequence_by_flanking_target_attribute

[Term]
id: SO:0000362
name: chimeric_cDNA_clone
def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]
is_a: SO:0000317 ! cDNA_clone

[Term]
id: SO:0000363
name: floxed_gene
is_a: SO:0000359 ! floxed_sequence

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

[Term]
id: SO:0000365
name: integron
def: "DNA elements capable of mobilizing individual gene cassettes into bacterial chromosomes by site- specific recombination." [http://www.genomicglossaries.com/content/DNA.asp]
is_a: SO:0000669 ! sequence_rearrangement_feature

[Term]
id: SO:0000366
name: insertion_site
def: "The junction where an insertion occurred." [SO:ke]
subset: SOFA
is_a: SO:0000109 ! sequence_variant
is_a: SO:0000699 ! junction
relationship: position_of SO:0000046 ! insert

[Term]
id: SO:0000367
name: attI_site
relationship: part_of SO:0000365 ! integron

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

[Term]
id: SO:0000369
name: integrase_coding_region
relationship: part_of SO:0000365 ! integron

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

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

[Term]
id: SO:0000372
name: enzymatic_RNA
def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]
subset: SOFA
is_a: SO:0000655 ! ncRNA

[Term]
id: SO:0000373
name: recombinationally_inverted
is_a: SO:0000456 ! recombinationally_rearranged_gene

[Term]
id: SO:0000374
name: ribozyme
def: "An RNA with catalytic activity." [SO:ma]
subset: SOFA
is_a: SO:0000372 ! enzymatic_RNA

[Term]
id: SO:0000375
name: rRNA_5.8S
def: "5.8S ribosomal RNA (5.8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5.8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]
subset: SOFA
synonym: "5.8S_rRNA" RELATED []
is_a: SO:0000252 ! rRNA

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

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

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

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

[Term]
id: SO:0000380
name: hammerhead_ribozyme
def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [http:rnaworld.bio.ukans.edu/class/RNA/RNA00/RNA_World_3.html]
subset: SOFA
is_a: SO:0000374 ! ribozyme

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

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

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

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

[Term]
id: SO:0000385
name: RNase_MRP_RNA
def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]
subset: SOFA
is_a: SO:0000372 ! enzymatic_RNA

[Term]
id: SO:0000386
name: RNase_P_RNA
def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterised activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]
subset: SOFA
is_a: SO:0000374 ! ribozyme

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

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

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

[Term]
id: SO:0000390
name: telomerase_RNA
def: "The RNA component of telomerase, a reverse transcriptase that synthesises telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]
subset: SOFA
is_a: SO:0000372 ! enzymatic_RNA

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

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

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

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

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

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

[Term]
id: SO:0000397
name: U6atac_snRNA
def: "U6atac_snRNA -An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [https://www.ncbi.nlm.nih.gov/pubmed/12409455]
subset: SOFA
is_a: SO:0000274 ! snRNA

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

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

[Term]
id: SO:0000400
name: sequence_attribute
is_a: SO:0000000 ! Sequence_Ontology

[Term]
id: SO:0000401
name: gene_attribute
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000402
name: enhancer_attribute
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000403
name: U14_snRNA
def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016]
subset: SOFA
is_a: SO:0000274 ! snRNA

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

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

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

[Term]
id: SO:0000407
name: rRNA_18S
def: "18S_rRNA -A large polynucleotide which functions as a part of the small subunit of the ribosome" [SO:ke]
subset: SOFA
synonym: "16S_rRNA" RELATED []
is_a: SO:0000252 ! rRNA

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

[Term]
id: SO:0000409
name: binding_site
def: "A region on the surface of a molecule that may interact with another molecule." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000411
name: rescue_fragment
is_a: SO:0000695 ! reagent

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

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

[Term]
id: SO:0000414
name: genomically_contaminated_cDNA_clone
is_a: SO:0000317 ! cDNA_clone

[Term]
id: SO:0000415
name: genomic_polyA_primed_cDNA_clone
is_a: SO:0000317 ! cDNA_clone

[Term]
id: SO:0000416
name: partially_unprocessed_cDNA_clone
is_a: SO:0000317 ! cDNA_clone

[Term]
id: SO:0000417
name: polypeptide_domain
def: "A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains." [http:www.molbiol.bbsrc.ac.uk/new_protein/domains.html]
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000418
name: signal_peptide
def: "The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence." [http:www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "signal peptide coding sequence" RELATED []
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000419
name: mature_peptide
def: "The coding sequence for the mature or final peptide or protein product following post-translational modification." [http:www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000420
name: five_prime_terminal_inverted_repeat
is_a: SO:0000481 ! terminal_inverted_repeat

[Term]
id: SO:0000421
name: three_prime_terminal_inverted_repeat
is_a: SO:0000481 ! terminal_inverted_repeat

[Term]
id: SO:0000422
name: U5_LTR_region
relationship: part_of SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000423
name: R_LTR_region
relationship: part_of SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000424
name: U3_LTR_region
relationship: part_of SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000425
name: five_prime_LTR
is_a: SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000426
name: three_prime_LTR
is_a: SO:0000286 ! long_terminal_repeat

[Term]
id: SO:0000427
name: R_five_prime_LTR_region
is_a: SO:0000423 ! R_LTR_region
relationship: part_of SO:0000425 ! five_prime_LTR

[Term]
id: SO:0000428
name: U5_five_prime_LTR_region
is_a: SO:0000422 ! U5_LTR_region
relationship: part_of SO:0000425 ! five_prime_LTR

[Term]
id: SO:0000429
name: U3_five_prime_LTR_region
is_a: SO:0000424 ! U3_LTR_region
relationship: part_of SO:0000425 ! five_prime_LTR

[Term]
id: SO:0000430
name: R_three_prime_LTR_region
relationship: part_of SO:0000426 ! three_prime_LTR

[Term]
id: SO:0000431
name: U3_three_prime_LTR_region
relationship: part_of SO:0000426 ! three_prime_LTR

[Term]
id: SO:0000432
name: U5_three_prime_LTR_region
relationship: part_of SO:0000426 ! three_prime_LTR

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

[Term]
id: SO:0000434
name: transposable_element_target_site_duplication
def: "A sequence of DNA that is duplicated when a transposable element inserts; usually found at each end the insertion." [http:www.koko.gov.my/CocoaBioTech/Glossaryt.html]
is_a: SO:0000657 ! repeat_region

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

[Term]
id: SO:0000436
name: ARS
def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]
subset: SOFA
synonym: "autonomously_replicating_sequence" RELATED []
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000438
name: gene_not_polyadenylated
is_a: SO:0000066 ! gene_by_polyadenylation_attribute

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

[Term]
id: SO:0000440
name: vector
def: "A DNA molecule that can be used to transfer DNA molecules between organisms." [SO:ma]
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000151 ! clone

[Term]
id: SO:0000441
name: ss_oligo
def: "A single stranded oligonucleotide." [SO:ke]
synonym: "single stranded oligonucleotide.new synonym" RELATED []
synonym: "ss_oligonucleotide" RELATED []
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000442
name: ds_oligo
def: "A double stranded oligonucleotide." [SO:ke]
synonym: "double stranded oligonucleotide" RELATED []
synonym: "ds_oligonucleotide" RELATED []
is_a: SO:0000696 ! oligo

[Term]
id: SO:0000443
name: polymer_type
is_a: SO:0000400 ! sequence_attribute

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

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

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

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

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

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

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

[Term]
id: SO:0000451
name: gene_polyadenylated
is_a: SO:0000066 ! gene_by_polyadenylation_attribute

[Term]
id: SO:0000452
name: transgene
is_a: SO:0000009 ! gene_class

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

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

[Term]
id: SO:0000455
name: gene_with_mRNA_with_frameshift
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000456
name: recombinationally_rearranged_gene
is_a: SO:0000401 ! gene_attribute

[Term]
id: SO:0000457
name: interchromosomal_duplication
is_a: SO:1000037 ! chromosomal_duplication

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

[Term]
id: SO:0000459
name: gene_with_trans_spliced_transcript
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000460
name: vertebrate_immunoglobulin_T_cell_receptor_gene
synonym: "vertebrate_immunoglobulin/T-cell_receptor_gene" RELATED []
is_a: SO:0000456 ! recombinationally_rearranged_gene

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

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

[Term]
id: SO:0000463
name: gene_with_alternately_spliced_transcript
is_a: SO:0000064 ! gene_by_transcript_attribute

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

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

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

[Term]
id: SO:0000467
name: post_translationally_regulated_by_protein_stability
synonym: "post-translationally_regulated_by_protein_stability" RELATED []
is_a: SO:0000130 ! post_translationally_regulated

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

[Term]
id: SO:0000469
name: post_translationally_regulated_by_protein_modification
synonym: "post-translationally_regulated_by_protein_modification" RELATED []
is_a: SO:0000130 ! post_translationally_regulated

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

[Term]
id: SO:0000471
name: autoregulated
is_a: SO:0000123 ! transcriptionally_regulated

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

[Term]
id: SO:0000473
name: negatively_autoregulated
is_a: SO:0000126 ! transcriptionally_repressed
is_a: SO:0000471 ! autoregulated

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

[Term]
id: SO:0000475
name: positively_autoregulated
is_a: SO:0000125 ! transcriptionally_induced
is_a: SO:0000471 ! autoregulated

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

[Term]
id: SO:0000477
name: polycistronic_gene
is_a: SO:0000081 ! member_gene_array

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

[Term]
id: SO:0000479
name: trans_spliced_transcript
synonym: "trans-spliced_transcript" RELATED []
is_a: SO:0000082 ! processed_transcript_attribute

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

[Term]
id: SO:0000481
name: terminal_inverted_repeat
def: "An inverted repeat (SO:0000294) occuring at the termini of a DNA transposon." [SO:ke]
synonym: "TIR" RELATED []
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000208 ! terminal_inverted_repeat_element

[Term]
id: SO:0000482
name: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
synonym: "vertebrate_immunoglobulin/T-cell_receptor_gene-cluster" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene

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

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

[Term]
id: SO:0000485
name: DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(DJ)-J-CLUSTER]
synonym: "(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000486
name: five_prime_exon_noncoding_region
def: "The sequence of the 5' exon preceeding the start codon." [SO:ke]
synonym: "five_prime_exon_noncoding_region" RELATED []
relationship: part_of SO:0000200 ! five_prime_coding_exon

[Term]
id: SO:0000487
name: VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VDJ)-J-C-CLUSTER]
synonym: "(VDJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000488
name: VDJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VDJ)-J-CLUSTER]
synonym: "(VDJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000489
name: VJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VJ)-C-CLUSTER]
synonym: "(VJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000490
name: VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VJ)-J-C-CLUSTER]
synonym: "(VJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000491
name: VJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VJ)-J-CLUSTER]
synonym: "(VJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000492
name: D_gene_recombination_feature
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

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

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000504
name: D_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-(DJ)-C-CLUSTER]
synonym: "D-(DJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000505
name: D_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-(DJ)-CLUSTER]
synonym: "D-(DJ)-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000506
name: D_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-(DJ)-J-C-CLUSTER]
synonym: "D-(DJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000507
name: pseudogenic_exon
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000147 ! exon
relationship: part_of SO:0000516 ! pseudogenic_transcript

[Term]
id: SO:0000508
name: D_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-(DJ)-J-CLUSTER]
synonym: "D-(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

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

[Term]
id: SO:0000510
name: VD_gene
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-GENE]
synonym: "V_D_GENE" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene

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

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

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

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

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

[Term]
id: SO:0000516
name: pseudogenic_transcript
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000673 ! transcript
relationship: part_of SO:0000336 ! pseudogene

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

[Term]
id: SO:0000518
name: V_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(DJ)-CLUSTER]
synonym: "V-(DJ)-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000519
name: V_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(DJ)-J-CLUSTER]
synonym: "V-(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000520
name: V_VDJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VDJ)-C-CLUSTER]
synonym: "V-(VDJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000521
name: V_VDJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VDJ)-CLUSTER]
synonym: "V-(VDJ)-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000522
name: V_VDJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VDJ)-J-CLUSTER]
synonym: "V-(VDJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000523
name: V_VJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VJ)-C-CLUSTER]
synonym: "V-(VJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000524
name: V_VJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VJ)-CLUSTER]
synonym: "V-(VJ)-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000525
name: V_VJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VJ)-J-CLUSTER]
synonym: "V-(VJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

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

[Term]
id: SO:0000527
name: V_D_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-(DJ)-C-CLUSTER]
synonym: "V-D-(DJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000528
name: V_D_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-(DJ)-CLUSTER]
synonym: "V-D-(DJ)-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000529
name: V_D_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-(DJ)-J-C-CLUSTER]
synonym: "V-D-(DJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000530
name: V_D_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-(DJ)-J-CLUSTER]
synonym: "V-D-(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000531
name: V_D_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-J-C-CLUSTER]
synonym: "V-D-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000532
name: V_D_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-J-CLUSTER]
synonym: "V-D-J-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

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

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

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

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

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

[Term]
id: SO:0000538
name: V_gene_recombination_feature
def: "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-RS]
synonym: "V-RS" RELATED []
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000539
name: DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(DJ)-C-CLUSTER]
synonym: "(DJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000540
name: DJ_J_C_cluster
def: "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(DJ)-J-C-CLUSTER]
synonym: "(DJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000541
name: VDJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#(VDJ)-C-CLUSTER]
synonym: "(VDJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000542
name: V_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(DJ)-C-CLUSTER]
synonym: "V-(DJ)-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

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

[Term]
id: SO:0000544
name: helitron
def: "A rolling circle transposon. Autonomous Helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]
is_a: SO:0000101 ! transposable_element

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

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

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

[Term]
id: SO:0000548
name: gene_with_edited_transcript
is_a: SO:0000064 ! gene_by_transcript_attribute

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

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

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

[Term]
id: SO:0000552
name: Shine_Dalgarno_sequence
def: "Region in 5' UTR where ribosome assembles on mRNA." [SO:ke]
synonym: "RBS" RELATED []
synonym: "Shine-Dalgarno_sequence" RELATED []
synonym: "five_prime_ribosome_binding_site" RELATED []
is_a: SO:0000139 ! ribosome_entry_site

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

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

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

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

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

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

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

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

[Term]
id: SO:0000561
name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
def: " 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin/T-cell receptor gene" [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#HEPTAMER]
synonym: "HEPTAMER" RELATED []
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000562
name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000563
name: spacer_of_recombination_feature_of_vertebrate_immune_system_gene
is_a: SO:0000301 ! recombination_feature_of_vertebrate_immune_system_gene

[Term]
id: SO:0000564
name: V_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(DJ)-J-C-CLUSTER]
synonym: "V-(DJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000565
name: V_VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VDJ)-J-C-CLUSTER]
synonym: "V-(VDJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

[Term]
id: SO:0000566
name: V_VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-(VJ)-J-C-CLUSTER]
synonym: "V-(VJ)-J-C-CLUSTER" RELATED []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

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

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

[Term]
id: SO:0000569
name: retrotransposed_protein_coding_gene
alt_id: SO:0100042
synonym: "captured_pseudogene" RELATED []
is_a: SO:0000010 ! protein_coding_gene
is_a: SO:0000042 ! pseudogene_attribute

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

[Term]
id: SO:0000571
name: miRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000572
name: DJ_gene
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#D-J-GENE]
synonym: "D_J_GENE" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene
relationship: part_of SO:0000485 ! DJ_J_cluster
relationship: part_of SO:0000504 ! D_DJ_C_cluster
relationship: part_of SO:0000505 ! D_DJ_cluster
relationship: part_of SO:0000506 ! D_DJ_J_C_cluster
relationship: part_of SO:0000508 ! D_DJ_J_cluster
relationship: part_of SO:0000518 ! V_DJ_cluster
relationship: part_of SO:0000519 ! V_DJ_J_cluster
relationship: part_of SO:0000527 ! V_D_DJ_C_cluster
relationship: part_of SO:0000528 ! V_D_DJ_cluster
relationship: part_of SO:0000529 ! V_D_DJ_J_C_cluster
relationship: part_of SO:0000530 ! V_D_DJ_J_cluster
relationship: part_of SO:0000539 ! DJ_C_cluster
relationship: part_of SO:0000540 ! DJ_J_C_cluster
relationship: part_of SO:0000542 ! V_DJ_C_cluster
relationship: part_of SO:0000564 ! V_DJ_J_C_cluster

[Term]
id: SO:0000573
name: rRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000574
name: DJ_gene
def: " Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)" [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-D-J-GENE]
synonym: "V-D-J-GENE" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene
relationship: part_of SO:0000487 ! VDJ_J_C_cluster
relationship: part_of SO:0000488 ! VDJ_J_cluster
relationship: part_of SO:0000520 ! V_VDJ_C_cluster
relationship: part_of SO:0000521 ! V_VDJ_cluster
relationship: part_of SO:0000522 ! V_VDJ_J_cluster
relationship: part_of SO:0000541 ! VDJ_C_cluster
relationship: part_of SO:0000565 ! V_VDJ_J_C_cluster

[Term]
id: SO:0000575
name: scRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000576
name: VJ_gene
def: " Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)" [http://imgt.cines.fr/ligmdb/LIGMlect?query=7#V-J-GENE]
synonym: "V-J-GENE" RELATED []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_gene
relationship: part_of SO:0000489 ! VJ_C_cluster
relationship: part_of SO:0000490 ! VJ_J_C_cluster
relationship: part_of SO:0000491 ! VJ_J_cluster
relationship: part_of SO:0000523 ! V_VJ_C_cluster
relationship: part_of SO:0000524 ! V_VJ_cluster
relationship: part_of SO:0000525 ! V_VJ_J_cluster
relationship: part_of SO:0000566 ! V_VJ_J_C_cluster

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

[Term]
id: SO:0000578
name: snoRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000579
name: edited_transcript_feature
def: "A locatable feature on a transcript that is edited." [SO:ma]
relationship: part_of SO:0000673 ! transcript

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

[Term]
id: SO:0000581
name: cap
def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
subset: SOFA
relationship: adjacent_to SO:0000234 ! mRNA

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

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

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

[Term]
id: SO:0000585
name: C_D_box_snoRNA_gene
is_a: SO:0000578 ! snoRNA_gene

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

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

[Term]
id: SO:0000588
name: autocatalytically_spliced_intron
def: "A self spliced intron." [SO:ke]
subset: SOFA
is_a: SO:0000188 ! intron
is_a: SO:0000374 ! ribozyme

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

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

[Term]
id: SO:0000591
name: pseudoknot
def: "A stem-loop RNA structure where nucleotides in the loop participate in complementary interactions with a region of RNA downstream of the stem-loop." [https://www.ncbi.nlm.nih.gov/pubmed/12519954]
is_a: SO:0000002 ! sequence_secondary_structure

[Term]
id: SO:0000592
name: H_pseudoknot
def: "A pseudoknot which contains two stems and at least two loops." [https://www.ncbi.nlm.nih.gov/pubmed/10334330]
synonym: "H-pseudoknot" RELATED []
is_a: SO:0000591 ! pseudoknot

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

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

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

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

[Term]
id: SO:0000597
name: transcript_edited_by_U_insertion/deletion
def: "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." [http://www.rna.ucla.edu/index.html]
is_a: SO:0000116 ! edited_transcript

[Term]
id: SO:0000598
name: transcript_edited_by_C_insertion_and_dinucleotide_insertion
def: "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs." [http://nsm1.utdallas.edu/bio/miller/physarum/overview.htm]
synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED []
is_a: SO:0000116 ! edited_transcript

[Term]
id: SO:0000599
name: transcript_edited_by_C_to_U_substitution
is_a: SO:0000116 ! edited_transcript

[Term]
id: SO:0000600
name: transcript_edited_by_A_to_I_substitution
is_a: SO:0000116 ! edited_transcript

[Term]
id: SO:0000601
name: transcript_edited_by_G_addition
is_a: SO:0000116 ! edited_transcript

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

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

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

[Term]
id: SO:0000605
name: intergenic_region
def: "The region between two known genes." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

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

[Term]
id: SO:0000608
name: H_ACA_box_snoRNA_gene
is_a: SO:0000578 ! snoRNA_gene

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

[Term]
id: SO:0000610
name: polyA_sequence
def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]
subset: SOFA
relationship: adjacent_to SO:0000234 ! mRNA

[Term]
id: SO:0000611
name: branch_site
def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]
subset: SOFA
synonym: "branch_point" RELATED []
relationship: part_of SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000612
name: polypyrimidine_tract
def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]
subset: SOFA
relationship: part_of SO:0000662 ! spliceosomal_intron

[Term]
id: SO:0000613
name: bacterial_RNApol_promoter
def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]
is_a: SO:0000167 ! promoter
is_a: SO:0000752 ! gene_group_regulatory_region

[Term]
id: SO:0000614
name: bacterial_terminator
def: "A terminator signal for bacterial transcription." [SO:ke]
is_a: SO:0000141 ! terminator

[Term]
id: SO:0000615
name: terminator_of_type_2_RNApol_III_promoter
def: "A terminator signal for RNA polymerase III transcription." [SO:ke]
is_a: SO:0000141 ! terminator

[Term]
id: SO:0000616
name: transcription_end_site
def: "The site where transcription ends." [SO:ke]
subset: SOFA
is_a: SO:0000699 ! junction
relationship: part_of SO:0000185 ! primary_transcript

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

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

[Term]
id: SO:0000619
name: A_box
relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2

[Term]
id: SO:0000620
name: B_box
relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2

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

[Term]
id: SO:0000622
name: C_box
relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1

[Term]
id: SO:0000623
name: snRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

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

[Term]
id: SO:0000625
name: silencer
def: "Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes." [http://www.brunel.ac.uk/depts/bio/project/old_hmg/gloss3.htm#s]
subset: SOFA
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000626
name: chromosomal_regulatory_element
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000627
name: insulator
subset: SOFA
synonym: "insulator_element" RELATED []
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000628
name: chromosomal_structural_element
subset: SOFA
relationship: part_of SO:0000340 ! chromosome

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

[Term]
id: SO:0000630
name: upstream_AUG_codon
relationship: part_of SO:0000203 ! UTR

[Term]
id: SO:0000631
name: polycistronic_primary_transcript
def: "A primary transcript encoding for more than one protein product." [SO:ke]
is_a: SO:0000078 ! polycistronic_transcript

[Term]
id: SO:0000632
name: monocistronic_primary_transcript
def: "A primary transcript encoding for more than one protein product." [SO:ke]
is_a: SO:0000665 ! monocistronic_transcript

[Term]
id: SO:0000633
name: monocistronic_mRNA
def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]
synonym: "monocistronic_processed_transcript" RELATED []
is_a: SO:0000665 ! monocistronic_transcript

[Term]
id: SO:0000634
name: polycistronic_mRNA
def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]
synonym: "polycistronic_processed_transcript" RELATED []
is_a: SO:0000078 ! polycistronic_transcript

[Term]
id: SO:0000635
name: mini_exon_donor_RNA
def: "The 3' site of a mini-exon which is trans-spliced on to the 5'end of a mature mRNA." [SO:ke]
synonym: "mini-exon_donor_RNA" RELATED []
is_a: SO:0000185 ! primary_transcript

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

[Term]
id: SO:0000637
name: engineered_plasmid
synonym: "engineered_plasmid_gene" RELATED []
is_a: SO:0000098 ! plasmid_gene
is_a: SO:0000280 ! engineered_gene

[Term]
id: SO:0000638
name: transcribed_spacer_region
def: "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]
relationship: part_of SO:0000209 ! rRNA_primary_transcript

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

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

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

[Term]
id: SO:0000642
name: SRP_RNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

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

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

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

[Term]
id: SO:0000646
name: siRNA
def: "Small RNA molecule that is the product of a longerexogenous or endogenous dsRNA, which is either a bimolecular duplexe or very longhairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulatefrom both strands of the dsRNA. sRNAs trigger the cleavage of their target molecules." [PMID:12592000]
subset: SOFA
synonym: "small_interfering_RNA" RELATED []
is_a: SO:0000655 ! ncRNA

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

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

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

[Term]
id: SO:0000650
name: small_subunit_rRNA
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000651
name: large_subunit_rRNA
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000652
name: rRNA_5S
def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilises 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]
subset: SOFA
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000653
name: rRNA_28S
def: "A component of the large ribosomal subunit." [SO:ke]
subset: SOFA
synonym: "23S_rRNA" RELATED []
synonym: "28S_rRNA" RELATED []
is_a: SO:0000252 ! rRNA

[Term]
id: SO:0000654
name: maxi_circle_gene
synonym: "maxi-circle" RELATED []
is_a: SO:0000088 ! mt_gene

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

[Term]
id: SO:0000656
name: stRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

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

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

[Term]
id: SO:0000659
name: tmRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000660
name: DNA_invertase_target_sequence
is_a: SO:0000342 ! site_specific_recombination_target_region

[Term]
id: SO:0000661
name: intron_attribute
is_a: SO:0000401 ! gene_attribute

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

[Term]
id: SO:0000663
name: tRNA_gene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:0000664
name: introgressed_chromosome_region
relationship: part_of SO:0000340 ! chromosome

[Term]
id: SO:0000665
name: monocistronic_transcript
is_a: SO:0000115 ! transcript_feature

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

[Term]
id: SO:0000667
name: insertion
def: "A region of sequence identified as having been inserted." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0000109 ! sequence_variant
relationship: sequence_of SO:0000046 ! insert

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

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

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

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

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

[Term]
id: SO:0000673
name: transcript
def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]
subset: SOFA
relationship: member_of SO:0000704 ! gene

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000683
name: exonic_splice_enhancer
def: "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [https://www.ncbi.nlm.nih.gov/pubmed/12403462]
is_a: SO:0000344 ! splice_enhancer

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

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

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

[Term]
id: SO:0000687
name: deletion_junction
def: "The space between two bases in a sequence which marks the position where a deletion has occured." [SO:ke]
subset: SOFA
is_a: SO:0000109 ! sequence_variant
is_a: SO:0000699 ! junction
relationship: position_of SO:0000045 ! delete

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

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

[Term]
id: SO:0000690
name: gene_with_polycistronic_transcript
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000691
name: translocation_site
def: "The space between two bases in a sequence which marks the position where a translocation has occurred." [SO:ke]
relationship: position_of SO:0000049 ! translocate

[Term]
id: SO:0000692
name: gene_with_dicistronic_transcript
is_a: SO:0000690 ! gene_with_polycistronic_transcript

[Term]
id: SO:0000693
name: gene_with_recoded_mRNA
is_a: SO:0000064 ! gene_by_transcript_attribute

[Term]
id: SO:0000694
name: SNP
def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives (alleles) exist in normal individuals in some population(s), wherein the least frequent allele has an abundance of 1% or greater." [http://www.cgr.ki.se/cgb/groups/brookes/Articles/essence_of_snps_article.pdf]
subset: SOFA
synonym: "single_nucleotide_polymorphism" RELATED []
is_a: SO:1000008 ! point_mutation

[Term]
id: SO:0000695
name: reagent
def: "A sequence used in experiment." [SO:ke]
subset: SOFA
is_a: SO:0000001 ! region

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

[Term]
id: SO:0000697
name: gene_with_stop_codon_read_through
is_a: SO:0000693 ! gene_with_recoded_mRNA

[Term]
id: SO:0000698
name: gene_with_stop_codon_redefined_as_pyrrolysine
is_a: SO:0000697 ! gene_with_stop_codon_read_through

[Term]
id: SO:0000699
name: junction
def: "A junction refers to an interbase location of zero in a sequence." [SO:ke]
subset: SOFA
synonym: "boundary" RELATED []
is_a: SO:0000110 ! located_sequence_feature

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

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

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

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

[Term]
id: SO:0000704
name: gene
def: "A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions" [SO:rd]
subset: SOFA
is_a: SO:0000001 ! region
relationship: member_of SO:0005855 ! gene_group

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

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

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

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

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

[Term]
id: SO:0000710
name: gene_with_stop_codon_redefined_as_selenocysteine
is_a: SO:0000697 ! gene_with_stop_codon_read_through

[Term]
id: SO:0000711
name: gene_with_mRNA_recoded_by_translational_bypass
is_a: SO:0000693 ! gene_with_recoded_mRNA

[Term]
id: SO:0000712
name: gene_with_transcript_with_translational_frameshift
is_a: SO:0000693 ! gene_with_recoded_mRNA

[Term]
id: SO:0000713
name: DNA_motif
is_a: SO:0000714 ! nucleotide_motif

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

[Term]
id: SO:0000715
name: RNA_motif
is_a: SO:0000714 ! nucleotide_motif

[Term]
id: SO:0000716
name: dicistronic_mRNA
synonym: "dicistronic_processed_transcript" RELATED []
is_a: SO:0000079 ! dicistronic_transcript

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

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

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

[Term]
id: SO:0000720
name: foreign_transposable_element
comment: requested by Michael on 19 Nov 2004
is_a: SO:0000101 ! transposable_element

[Term]
id: SO:0000721
name: gene_with_dicistronic_primary_transcript
comment: Requested by Michael, 19 nov 2004
is_a: SO:0000692 ! gene_with_dicistronic_transcript

[Term]
id: SO:0000722
name: gene_with_dicistronic_mRNA
comment: Requested by MA nov 19 2004
synonym: "gene_with_dicistronic_processed_transcript" RELATED []
is_a: SO:0000692 ! gene_with_dicistronic_transcript

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

[Term]
id: SO:0000724
name: origin_of_transfer
def: "A region of a DNA molecule whre transfer is initiated during the process of conjugation or mobilization." [http:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
subset: SOFA
synonym: "oriT" RELATED []
is_a: SO:0000001 ! region

[Term]
id: SO:0000725
name: transit_peptide
def: "The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein: this domain is involved in post translational import of the protein into the organelle." [http:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#line_types]
comment: Added to bring SO inline with the embl ddbj genbank feature table.
subset: SOFA
relationship: part_of SO:0000104 ! polypeptide

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

[Term]
id: SO:0000727
name: TF_module
def: "A regulatory_region where more than 1 TF_binding_site together are regulatorily active" [SO:SG]
comment: Requested by Stepen Grossmann Dec 2004.
synonym: "CRM" RELATED []
synonym: "cis_regulatory_module" RELATED []
is_a: SO:0005836 ! regulatory_region

[Term]
id: SO:0000728
name: intein
relationship: part_of SO:0000104 ! polypeptide

[Term]
id: SO:0000729
name: intein_containing_protein_coding_gene
is_a: SO:0000010 ! protein_coding_gene

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

[Term]
id: SO:0000731
name: fragment
comment: added because of request by MO people.
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000732
name: predicted
is_a: SO:0000733 ! feature_attribute

[Term]
id: SO:0000733
name: feature_attribute
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:0000734
name: exemplar_mRNA
def: "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http:mged.sourceforge.net/ontologies/MGEDontology.php#exemplar_mRNA]
comment: Added for the MO people.
is_a: SO:0000082 ! processed_transcript_attribute

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

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

[Term]
id: SO:0000737
name: mitochondrial_sequence
is_a: SO:0000736 ! organelle_location

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

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

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

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

[Term]
id: SO:0000742
name: maxicircle_sequence
is_a: SO:0000737 ! mitochondrial_sequence

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

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

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

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

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

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

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

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

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

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

[Term]
id: SO:0000753
name: clone_insert
relationship: part_of SO:0000151 ! clone

[Term]
id: SO:0000754
name: lambda_vector
is_a: SO:0000440 ! vector
relationship: part_of SO:0000160 ! lambda_clone

[Term]
id: SO:0000755
name: plasmid_vector
is_a: SO:0000440 ! vector
relationship: part_of SO:0000759 ! plasmid_clone

[Term]
id: SO:0000756
name: cDNA
def: "DNA synthesized by reverse transcriptase using RNA as a template" [SO:ma]
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000317 ! cDNA_clone

[Term]
id: SO:0000757
name: single_stranded_cDNA
is_a: SO:0000756 ! cDNA

[Term]
id: SO:0000758
name: double_stranded_cDNA
is_a: SO:0000756 ! cDNA

[Term]
id: SO:0000759
name: plasmid_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000760
name: YAC_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000761
name: phagemid_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000762
name: PAC_clone
synonym: "P1_clone" RELATED []
is_a: SO:0000151 ! clone

[Term]
id: SO:0000763
name: fosmid_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000764
name: BAC_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000765
name: cosmid_clone
is_a: SO:0000151 ! clone

[Term]
id: SO:0000766
name: pyrrolysyl_tRNA
is_a: SO:0000253 ! tRNA

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

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

[Term]
id: SO:0000769
name: tmRNA_coding_piece
def: "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [Indiana:kw]
comment: Added in response to comment from Kelly Williams from Indiana.nhttp://nar.oxfordjournals.org/cgi/content/full/32/15/4531n10 Nov, 2005
relationship: part_of SO:0000584 ! tmRNA

[Term]
id: SO:0000770
name: tmRNA_acceptor_piece
def: "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [Indiana:kw]
comment: Added in response to Kelly Williams from Indiananhttp://nar.oxfordjournals.org/cgi/content/full/32/15/4531n10 nov 2005
relationship: part_of SO:0000584 ! tmRNA

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

[Term]
id: SO:0000772
name: genomic_island
comment: Genomic islands are transmissible elements characterized by large size (>10kb).
is_a: SO:0000001 ! region

[Term]
id: SO:0000773
name: pathogenic_island
def: "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]
comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038/nrmicro884 nGENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMSnUlrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker
is_a: SO:0000772 ! genomic_island

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

[Term]
id: SO:0000775
name: adaptive_island
comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands.nNature Reviews Microbiology 2, 414-424 (2004); doi:10.1038/nrmicro884 nGENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMSnUlrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker
is_a: SO:0000772 ! genomic_island

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

[Term]
id: SO:0000777
name: pseudogenic_rRNA
comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase.
subset: SOFA
is_a: SO:0000462 ! pseudogenic_region

[Term]
id: SO:0000778
name: pseudogenic_tRNA
comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase.
subset: SOFA
is_a: SO:0000462 ! pseudogenic_region

[Term]
id: SO:0001044
name: nuclear_mt_pseudogene
synonym: "NUMT" RELATED []
synonym: "nuclear_mitochondrial_pseudogene" RELATED []
is_a: SO:0000042 ! pseudogene_attribute

[Term]
id: SO:0005836
name: regulatory_region
def: "A DNA sequence that controls the expression of a gene." [http://www.genpromag.com/scripts/glossary.asp?LETTER=R]
subset: SOFA
is_a: SO:0000001 ! region
relationship: member_of SO:0000704 ! gene

[Term]
id: SO:0005837
name: snRNA_4.5S_primary_transcript
def: "A primary transcript encoding a 4.5S snRNA." [SO:ke]
synonym: "4.5S_snRNA_primary_transcript" RELATED []
is_a: SO:0000231 ! snRNA_primary_transcript

[Term]
id: SO:0005839
name: snRNA_4.5S
synonym: "4.5S_snRNA" RELATED []
is_a: SO:0000274 ! snRNA

[Term]
id: SO:0005841
name: methylation_guide_snoRNA
is_a: SO:0000275 ! snoRNA

[Term]
id: SO:0005843
name: rRNA_cleavage_snoRNA
is_a: SO:0000275 ! snoRNA

[Term]
id: SO:0005845
name: single_exon
is_a: SO:0000147 ! exon

[Term]
id: SO:0005847
name: member_of_gene_cassette_array
is_a: SO:0005848 ! member_of_gene_cassette

[Term]
id: SO:0005848
name: member_of_gene_cassette
is_a: SO:0000081 ! member_gene_array

[Term]
id: SO:0005849
name: member_of_gene_subarray
is_a: SO:0000081 ! member_gene_array

[Term]
id: SO:0005850
name: primer_binding_site
def: "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http:www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
relationship: part_of SO:0000186 ! LTR_retrotransposon

[Term]
id: SO:0005851
name: gene_array
def: "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]
comment: This would include\, for example\, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0005852
name: gene_subarray
def: "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]
comment: This would include\, for example\, a cluster of genes encoding different histones.
is_a: SO:0005851 ! gene_array

[Term]
id: SO:0005853
name: gene_cassette
def: "A non-functional gene that, when captured by recombination forms a functional gene." [SO:ma]
comment: This would include\, for example\, the mating type gene cassettes of S. cerevisiae.
is_a: SO:0005855 ! gene_group

[Term]
id: SO:0005854
name: gene_cassette_array
def: "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]
comment: This would include\, for example\, the arrays of non-functional VSG genes of Trypanosomes.
is_a: SO:0005853 ! gene_cassette

[Term]
id: SO:0005855
name: gene_group
def: "A collection of related genes." [SO:ma]
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0005856
name: selenocysteine_tRNA_primary_transcript
def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
is_a: SO:0000210 ! tRNA_primary_transcript

[Term]
id: SO:0005857
name: selenocysteinyl_tRNA
is_a: SO:0000253 ! tRNA

[Term]
id: SO:0005858
name: syntenic_region
def: "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://tbase.jax.org/docs/glossary.html]
is_a: SO:0000330 ! conserved_region

[Term]
id: SO:1000002
name: substitution
def: "Any change in genomic DNA caused by a single event." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0000109 ! sequence_variant
relationship: sequence_of SO:0000048 ! substitute

[Term]
id: SO:1000004
name: partially_characterised_change_in_DNA_sequence
def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000007 ! uncharacterised_change_in_nucleotide_sequence

[Term]
id: SO:1000005
name: complex_substitution
def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000007
name: uncharacterised_change_in_nucleotide_sequence
def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000008
name: point_mutation
def: "A mutation event where a single DNA nucleotide changes into another nucleotide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:1000002 ! substitution

[Term]
id: SO:1000009
name: transition
def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000008 ! point_mutation

[Term]
id: SO:1000010
name: pyrimidine_transition
def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]
is_a: SO:1000009 ! transition

[Term]
id: SO:1000011
name: C_to_T_transition
def: "A transition of a cytidine to a thymine." [SO:ke]
is_a: SO:1000010 ! pyrimidine_transition

[Term]
id: SO:1000012
name: C_to_T_transition_at_pCpG_site
def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000011 ! C_to_T_transition

[Term]
id: SO:1000013
name: T_to_C_transition
is_a: SO:1000010 ! pyrimidine_transition

[Term]
id: SO:1000014
name: purine_transition
def: "A substitution of a purine, A or G, for another purine." [SO:ke]
is_a: SO:1000009 ! transition

[Term]
id: SO:1000015
name: A_to_G_transition
def: "A transition of an adenine to a guanine." [SO:ke]
is_a: SO:1000014 ! purine_transition

[Term]
id: SO:1000016
name: G_to_A_transition
def: "A transition of a guanine to an adenine." [SO:ke]
is_a: SO:1000014 ! purine_transition

[Term]
id: SO:1000017
name: transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000008 ! point_mutation

[Term]
id: SO:1000018
name: pyrimidine_to_purine_transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]
is_a: SO:1000017 ! transversion

[Term]
id: SO:1000019
name: C_to_A_transversion
def: "A transversion from cytidine to adenine." [SO:ke]
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000020
name: C_to_G_transversion
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000021
name: T_to_A_transversion
def: "A transversion from T to A." [SO:ke]
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000022
name: T_to_G_transversion
def: "A transversion from T to G." [SO:ke]
is_a: SO:1000018 ! pyrimidine_to_purine_transversion

[Term]
id: SO:1000023
name: purine_to_pyrimidine_transversion
def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]
is_a: SO:1000017 ! transversion

[Term]
id: SO:1000024
name: A_to_C_transversion
def: "A transversion from adenine to cytidine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000025
name: A_to_T_transversion
def: "A transversion from adenine to thymine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000026
name: G_to_C_transversion
def: "A transversion from guanine to cytidine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000027
name: G_to_T_transversion
def: "A transversion from guanine to thymine." [SO:ke]
is_a: SO:1000023 ! purine_to_pyrimidine_transversion

[Term]
id: SO:1000028
name: intrachromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000029
name: chromosomal_deletion
synonym: "(Drosophila)Df" RELATED []
synonym: "(bacteria)&ampDgr;" RELATED []
synonym: "(fungi)D" RELATED []
is_a: SO:0000550 ! aneuploid_chromosome
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000030
name: chromosomal_inversion
synonym: "(Drosophila)In" RELATED []
synonym: "(bacteria)IN" RELATED []
synonym: "(fungi)In" RELATED []
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000031
name: interchromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000032
name: indel
def: "A hybrid term (insertion/deletion) to describe sequence length change when the direction of the change is unspecified." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:0000109 ! sequence_variant

[Term]
id: SO:1000033
name: nucleotide_deletion
def: "One or more continuous nucleotides are excised from the sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000032 ! indel

[Term]
id: SO:1000034
name: nucleotide_insertion
def: "One or more nucleotides are added between two adjacent nucleotides in the sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000032 ! indel

[Term]
id: SO:1000035
name: nucleotide_duplication
def: "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000034 ! nucleotide_insertion

[Term]
id: SO:1000036
name: inversion
def: "A continuous nucleotide sequence is inverted in the same position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
is_a: SO:0000001 ! region
is_a: SO:0000109 ! sequence_variant
relationship: sequence_of SO:0000047 ! invert

[Term]
id: SO:1000037
name: chromosomal_duplication
synonym: "(Drosophila)Dp" RELATED []
synonym: "(fungi)Dp" RELATED []
is_a: SO:0000550 ! aneuploid_chromosome
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000038
name: intrachromosomal_duplication
is_a: SO:1000028 ! intrachromosomal_mutation
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000039
name: direct_tandem_duplication
is_a: SO:1000173 ! tandem_duplication

[Term]
id: SO:1000040
name: inverted_tandem_duplication
is_a: SO:1000173 ! tandem_duplication

[Term]
id: SO:1000041
name: intrachromosomal_transposition
synonym: "(Drosophila)Tp" RELATED []
is_a: SO:0000453 ! transposition
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:1000042
name: compound_chromosome
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000043
name: Robertsonian_fusion
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000044
name: chromosomal_translocation
synonym: "(Drosophila)T" RELATED []
synonym: "(fungi)T" RELATED []
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000045
name: ring_chromosome
synonym: "(Drosophila)R" RELATED []
synonym: "(fungi)C" RELATED []
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000046
name: pericentric_inversion
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000047
name: paracentric_inversion
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000048
name: reciprocal_chromosomal_translocation
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000049
name: mutation_affecting_transcript
def: "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000132 ! consequences_of_mutation

[Term]
id: SO:1000050
name: no_change_in_transcript
def: "No effect on the state of the RNA." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000052
name: complex_change_in_transcript
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000054
name: mutation_affecting_coding_sequence
def: "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000055
name: initiator_codon_change_in_transcript
def: "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000056 ! amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000056
name: amino_acid_coding_codon_change_in_transcript
def: "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000054 ! mutation_affecting_coding_sequence

[Term]
id: SO:1000057
name: synonymous_codon_change_in_transcript
def: "The changed codon has the same translation product as the original codon." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000056 ! amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000058
name: non_synonymous_codon_change_in_transcript
def: "A DNA point mutation that causes a substitution of an amino acid by an other." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "non-synonymous_codon_change_in_transcript" RELATED []
is_a: SO:1000056 ! amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000059
name: missense_codon_change_in_transcript
def: "The nucleotide change in the codon leads to a new codon coding for a new amino acid." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000058 ! non_synonymous_codon_change_in_transcript

[Term]
id: SO:1000060
name: conservative_missense_codon_change_in_transcript
def: "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: The exact rules need to be stated\, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
is_a: SO:1000059 ! missense_codon_change_in_transcript

[Term]
id: SO:1000061
name: nonconservative_missense_codon_change_in_transcript
def: "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: The exact rules need to be stated\, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
is_a: SO:1000059 ! missense_codon_change_in_transcript

[Term]
id: SO:1000062
name: nonsense_codon_change_in_transcript
def: "The nucleotide change in the codon triplet creates a terminator codon." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000056 ! amino_acid_coding_codon_change_in_transcript

[Term]
id: SO:1000063
name: terminator_codon_change_in_transcript
is_a: SO:1000054 ! mutation_affecting_coding_sequence

[Term]
id: SO:1000064
name: mutation_affecting_reading_frame
def: "An umbrella term for terms describing an effect of a mutation on the frame of translation." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000054 ! mutation_affecting_coding_sequence

[Term]
id: SO:1000065
name: frameshift_mutation
def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000064 ! mutation_affecting_reading_frame

[Term]
id: SO:1000066
name: plus_1_frameshift_mutation
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000067
name: minus_1_frameshift_mutation
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000068
name: plus_2_frameshift_mutation
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000069
name: minus_2_frameshift_mutation
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000070
name: mutation_affecting_transcript_processing
def: "Mutation affects the way in which the primary transcriptional product is processed to form the mature transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000071
name: mutation_affecting_splicing
def: "Mutation affects the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000132 ! consequences_of_mutation

[Term]
id: SO:1000072
name: splice_donor_mutation
is_a: SO:1000071 ! mutation_affecting_splicing
is_a: SO:1000074 ! cryptic_splice_activator_mutation

[Term]
id: SO:1000073
name: splice_acceptor_mutation
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000074
name: cryptic_splice_activator_mutation
def: "Mutation creates a new (functional) splice site." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000075
name: mutation_affecting_editing
def: "Mutation affects the editing of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000070 ! mutation_affecting_transcript_processing

[Term]
id: SO:1000076
name: mutation_affecting_transcription
def: "Mutation affects the process of transcription, its initiation, progression or termination." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000078
name: mutation_decreasing_rate_of_transcription
is_a: SO:1000081 ! mutation_affecting_rate_of_transcription

[Term]
id: SO:1000079
name: mutation_affecting_transcript_sequence
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000080
name: mutation_increasing_rate_of_transcription
is_a: SO:1000081 ! mutation_affecting_rate_of_transcription

[Term]
id: SO:1000081
name: mutation_affecting_rate_of_transcription
is_a: SO:1000076 ! mutation_affecting_transcription

[Term]
id: SO:1000082
name: mutation_affecting_transcript_stability
def: "Mutation affects the stability of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000083
name: mutation_increasing_transcript_stability
def: "Mutation increases the stability (half-life) of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000082 ! mutation_affecting_transcript_stability

[Term]
id: SO:1000084
name: mutation_decreasing_transcript_stability
def: "Mutation decreases the stability (half-life) of the transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000082 ! mutation_affecting_transcript_stability

[Term]
id: SO:1000085
name: mutation_affecting_level_of_transcript
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000086
name: mutation_decreasing_level_of_transcript
is_a: SO:1000085 ! mutation_affecting_level_of_transcript

[Term]
id: SO:1000087
name: mutation_increasing_level_of_transcript
is_a: SO:1000085 ! mutation_affecting_level_of_transcript

[Term]
id: SO:1000088
name: mutation_affecting_translational_product
def: "Mutation causes a change in primary translation product of a transcript." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000132 ! consequences_of_mutation

[Term]
id: SO:1000089
name: no_change_of_translational_product
def: "The change at RNA level does not lead to any change in polypeptide." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000090
name: uncharacterised_change_of_translational_product
def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000091
name: partially_characterised_change_of_translational_product
def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000090 ! uncharacterised_change_of_translational_product

[Term]
id: SO:1000092
name: complex_change_of_translational_product
def: "Any mutation effect that is known at nucleotide level but can not be explained by using other key terms." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000093
name: amino_acid_substitution
def: "The replacement of a single amino acid by an other." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000094
name: conservative_amino_acid_substitution
is_a: SO:1000093 ! amino_acid_substitution

[Term]
id: SO:1000095
name: nonconservative_amino_acid_substitution
is_a: SO:1000093 ! amino_acid_substitution

[Term]
id: SO:1000096
name: amino_acid_insertion
def: "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000097
name: amino_acid_deletion
def: "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000098
name: polypeptide_truncation
def: "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000099
name: polypeptide_elongation
def: "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000100
name: polypeptide_N_terminal_elongation
def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "polypeptide_N-terminal_elongation" RELATED []
is_a: SO:1000099 ! polypeptide_elongation

[Term]
id: SO:1000101
name: polypeptide_C_terminal_elongation
def: "." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "polypeptide_C-terminal_elongation" RELATED []
is_a: SO:1000099 ! polypeptide_elongation

[Term]
id: SO:1000102
name: mutation_affecting_level_of_translational_product
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000103
name: mutation_decreasing_level_of_translation_product
is_a: SO:1000102 ! mutation_affecting_level_of_translational_product

[Term]
id: SO:1000104
name: mutation_increasing_level_of_translation_product
is_a: SO:1000102 ! mutation_affecting_level_of_translational_product

[Term]
id: SO:1000105
name: mutation_affecting_polypeptide_amino_acid_sequence
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000106
name: inframe_polypeptide_N_terminal_elongation
synonym: "inframe_polypeptide_N-terminal_elongation" RELATED []
is_a: SO:1000100 ! polypeptide_N_terminal_elongation

[Term]
id: SO:1000107
name: out_of_frame_polypeptide_N_terminal_elongation
synonym: "out_of_frame_polypeptide_N-terminal_elongation" RELATED []
is_a: SO:1000100 ! polypeptide_N_terminal_elongation

[Term]
id: SO:1000108
name: inframe_polypeptide_C_terminal_elongation
synonym: "inframe_polypeptide_C-terminal_elongation" RELATED []
is_a: SO:1000101 ! polypeptide_C_terminal_elongation

[Term]
id: SO:1000109
name: out_of_frame_polypeptide_C_terminal_elongation
synonym: "out_of_frame_polypeptide_C-terminal_elongation" RELATED []
is_a: SO:1000101 ! polypeptide_C_terminal_elongation

[Term]
id: SO:1000110
name: frame_restoring_mutation
is_a: SO:1000065 ! frameshift_mutation

[Term]
id: SO:1000111
name: mutation_affecting_3D_structure_of_polypeptide
synonym: "mutation_affecting_3D-structure_of_polypeptide" RELATED []
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000112
name: no_3D_structural_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000113
name: uncharacterised_3D_structural_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000114
name: partially_characterised_3D_structural_change
is_a: SO:1000113 ! uncharacterised_3D_structural_change

[Term]
id: SO:1000115
name: complex_3D_structural_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000116
name: conformational_change
is_a: SO:1000111 ! mutation_affecting_3D_structure_of_polypeptide

[Term]
id: SO:1000117
name: mutation_affecting_polypeptide_function
is_a: SO:1000088 ! mutation_affecting_translational_product

[Term]
id: SO:1000118
name: loss_of_function_of_polypeptide
synonym: "loss-of-function_of_polypeptide" RELATED []
is_a: SO:1000117 ! mutation_affecting_polypeptide_function

[Term]
id: SO:1000119
name: inactive_ligand_binding_site
is_a: SO:1000118 ! loss_of_function_of_polypeptide

[Term]
id: SO:1000120
name: inactive_catalytic_site
is_a: SO:1000119 ! inactive_ligand_binding_site

[Term]
id: SO:1000121
name: polypeptide_localization_affected
is_a: SO:1000117 ! mutation_affecting_polypeptide_function

[Term]
id: SO:1000122
name: polypeptide_post_translational_processing_affected
synonym: "polypeptide_post-translational_processing_affected" RELATED []
is_a: SO:1000117 ! mutation_affecting_polypeptide_function
is_a: SO:1000118 ! loss_of_function_of_polypeptide

[Term]
id: SO:1000123
name: polypeptide_post_translational_processing_affected
synonym: "polypeptide_post-translational_processing_affected" RELATED []
is_obsolete: true

[Term]
id: SO:1000124
name: partial_loss_of_function_of_polypeptide
synonym: "partial_loss-of-function_of_polypeptide" RELATED []
is_a: SO:1000118 ! loss_of_function_of_polypeptide

[Term]
id: SO:1000125
name: gain_of_function_of_polypeptide
synonym: "gain-of-function_of_polypeptide" RELATED []
is_a: SO:1000117 ! mutation_affecting_polypeptide_function

[Term]
id: SO:1000126
name: mutation_affecting_transcript_secondary_structure
is_a: SO:1000079 ! mutation_affecting_transcript_sequence

[Term]
id: SO:1000127
name: compensatory_transcript_secondary_structure_mutation
is_a: SO:1000126 ! mutation_affecting_transcript_secondary_structure

[Term]
id: SO:1000132
name: consequences_of_mutation
is_a: SO:0000000 ! Sequence_Ontology

[Term]
id: SO:1000134
name: polypeptide_fusion
is_a: SO:1000105 ! mutation_affecting_polypeptide_amino_acid_sequence

[Term]
id: SO:1000136
name: autosynaptic_chromosome
synonym: "(Drosophila)A" RELATED []
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000138
name: homo_compound_chromosome
synonym: "homo-compound_chromosome" RELATED []
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:1000140
name: hetero_compound_chromosome
synonym: "hetero-compound_chromosome" RELATED []
is_a: SO:1000042 ! compound_chromosome

[Term]
id: SO:1000141
name: chromosome_fission
is_a: SO:1000028 ! intrachromosomal_mutation

[Term]
id: SO:1000142
name: dexstrosynaptic_chromosome
is_a: SO:1000136 ! autosynaptic_chromosome

[Term]
id: SO:1000143
name: laevosynaptic_chromosome
is_a: SO:1000136 ! autosynaptic_chromosome

[Term]
id: SO:1000144
name: free_duplication
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000145
name: free_ring_duplication
synonym: "(Drosophila)R" RELATED []
is_a: SO:1000045 ! ring_chromosome
is_a: SO:1000144 ! free_duplication

[Term]
id: SO:1000146
name: complex_chromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000147
name: deficient_translocation
def: "A translocation in which one of the four broken ends loses a segment before re-joining." [fb:reference_manual]
synonym: "(Drosophila)Df" RELATED []
synonym: "(Drosophila)DfT" RELATED []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000148
name: inversion_cum_translocation
def: "The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [fb:reference_manual]
synonym: "(Drosophila)InT" RELATED []
synonym: "(Drosophila)T" RELATED []
synonym: "inversion-cum-translocation" RELATED []
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000149
name: bipartite_duplication
def: "The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [fb:reference_manual]
synonym: "(Drosophila)bDp" RELATED []
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000150
name: cyclic_translocation
def: "Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [fb:reference_manual]
is_a: SO:1000044 ! chromosomal_translocation

[Term]
id: SO:1000151
name: bipartite_inversion
def: "Three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [fb:reference_manual]
synonym: "(Drosophila)bIn" RELATED []
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000152
name: uninverted_insertional_duplication
def: "A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)eDp" RELATED []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000153
name: inverted_insertional_duplication
def: "A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)iDp" RELATED []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000154
name: insertional_duplication
synonym: "(Drosophila)Dpp" RELATED []
is_a: SO:1000037 ! chromosomal_duplication

[Term]
id: SO:1000155
name: interchromosomal_transposition
synonym: "(Drosophila)Tp" RELATED []
is_a: SO:0000453 ! transposition
is_a: SO:1000031 ! interchromosomal_mutation

[Term]
id: SO:1000156
name: inverted_interchromosomal_transposition
synonym: "(Drosophila)iTp" RELATED []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000157
name: uninverted_interchromosomal_transposition
synonym: "(Drosophila)eTp" RELATED []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000158
name: inverted_intrachromosomal_transposition
def: "The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)iTp" RELATED []
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:1000159
name: uninverted_intrachromosomal_transposition
def: "The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [fb:reference_manual]
synonym: "(Drosophila)eTp" RELATED []
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:1000160
name: unoriented_insertional_duplication
def: "A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [fb:reference_manual]
synonym: "(Drosophila)uDp" RELATED []
is_a: SO:1000154 ! insertional_duplication

[Term]
id: SO:1000161
name: unorientated_interchromosomal_transposition
synonym: "(Drosophila)uTp" RELATED []
is_a: SO:1000155 ! interchromosomal_transposition

[Term]
id: SO:1000162
name: unorientated_intrachromosomal_transposition
def: "The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [fb:reference_manual]
synonym: "(Drosophila)uTp" RELATED []
is_a: SO:1000041 ! intrachromosomal_transposition

[Term]
id: SO:1000170
name: uncharacterised_chromosomal_mutation
is_a: SO:1000183 ! chromosome_structure_variation

[Term]
id: SO:1000171
name: deficient_inversion
def: "Three breaks in the same chromosome; one central region lost, the other inverted." [fb:reference_manual]
synonym: "(Drosophila)Df" RELATED []
synonym: "(Drosophila)DfIn" RELATED []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000030 ! chromosomal_inversion

[Term]
id: SO:1000173
name: tandem_duplication
is_a: SO:1000038 ! intrachromosomal_duplication

[Term]
id: SO:1000175
name: partially_characterised_chromosomal_mutation
is_a: SO:1000170 ! uncharacterised_chromosomal_mutation

[Term]
id: SO:1000177
name: uncharacterised_change_in_transcript
def: "The nature of the mutation event is either uncharacterised or only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000049 ! mutation_affecting_transcript

[Term]
id: SO:1000179
name: partially_characterised_change_in_transcript
def: "The nature of the mutation event is only partially characterised." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000177 ! uncharacterised_change_in_transcript

[Term]
id: SO:1000180
name: mutation_affecting_gene_structure
is_a: SO:1000132 ! consequences_of_mutation

[Term]
id: SO:1000181
name: gene_fusion
is_a: SO:1000180 ! mutation_affecting_gene_structure

[Term]
id: SO:1000182
name: chromosome_number_variation
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:1000183
name: chromosome_structure_variation
is_a: SO:0000240 ! chromosome_variation

[Term]
id: SO:1000184
name: mutation_causes_exon_loss
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000185
name: mutation_causes_intron_gain
def: "Mutation causes an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." [http://www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:1000071 ! mutation_affecting_splicing

[Term]
id: SO:1000186
name: cryptic_splice_donor_activation
is_a: SO:1000074 ! cryptic_splice_activator_mutation

[Term]
id: SO:1001186
name: cryptic_splice_acceptor_activation
is_a: SO:1000074 ! cryptic_splice_activator_mutation

[Term]
id: SO:1001187
name: alternatively_spliced_transcript
is_a: SO:0000115 ! transcript_feature

[Term]
id: SO:1001188
name: alternatively_spliced_transcript_encoding_1_polypeptide
is_a: SO:1001187 ! alternatively_spliced_transcript

[Term]
id: SO:1001189
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide
is_a: SO:1001187 ! alternatively_spliced_transcript

[Term]
id: SO:1001190
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_same_start_codon_different_stop_codon
is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide
is_a: SO:1001194 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping

[Term]
id: SO:1001191
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_same_stop_codon
is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide
is_a: SO:1001194 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping

[Term]
id: SO:1001192
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon
is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide

[Term]
id: SO:1001193
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_overlapping
is_a: SO:1001192 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon
is_a: SO:1001194 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping

[Term]
id: SO:1001194
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_overlapping
is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide

[Term]
id: SO:1001195
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_not_overlapping
is_a: SO:1001189 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide

[Term]
id: SO:1001196
name: cryptogene
is_a: SO:0000011 ! non_protein_coding_gene

[Term]
id: SO:1001197
name: dicistronic_primary_transcript
is_a: SO:0000079 ! dicistronic_transcript

[Term]
id: SO:1001217
name: member_of_regulon
is_a: SO:0000081 ! member_gene_array

[Term]
id: SO:1001244
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
synonym: "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping" RELATED []
is_a: SO:1001192 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon
is_a: SO:1001195 ! alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_coding_regions_not_overlapping

[Term]
id: SO:1001246
name: CDS_independently_known
is_a: SO:1001255 ! status_of_coding_sequence

[Term]
id: SO:1001247
name: orphan_CDS
def: "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [MA:SO]
is_a: SO:1001254 ! CDS_predicted

[Term]
id: SO:1001249
name: CDS_supported_by_domain_match_data
is_a: SO:1001254 ! CDS_predicted

[Term]
id: SO:1001251
name: CDS_supported_by_sequence_similarity_data
is_a: SO:1001254 ! CDS_predicted

[Term]
id: SO:1001254
name: CDS_predicted
is_a: SO:1001255 ! status_of_coding_sequence

[Term]
id: SO:1001255
name: status_of_coding_sequence
is_a: SO:0000400 ! sequence_attribute

[Term]
id: SO:1001259
name: CDS_supported_by_EST_or_cDNA_data
is_a: SO:1001254 ! CDS_predicted

[Term]
id: SO:1001260
name: internal_Shine_Dalgarno_sequence
def: "A Shine Delgarno sequence that is upstream of a non-5' CDS in a polycistronic mRNA." [SO:ke]
is_a: SO:0000243 ! internal_ribosome_entry_site
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001261
name: recoded_mRNA
def: "A gene coding an mRNA which is recoded before translation, usually by special cis-acting signals." [https://www.ncbi.nlm.nih.gov/pubmed/8811194]
is_a: SO:0000115 ! transcript_feature

[Term]
id: SO:1001262
name: minus_1_translational_frameshift
is_a: SO:0000118 ! transcript_with_translational_frameshift

[Term]
id: SO:1001263
name: plus_1_translational_frameshift
is_a: SO:0000118 ! transcript_with_translational_frameshift

[Term]
id: SO:1001264
name: mRNA_recoded_by_translational_bypass
def: "A gene whose mRNA is translated by ribosomes that suspend translation at a particular codon and resume translation at a particular non-overlapping downstream codon." [https://www.ncbi.nlm.nih.gov/pubmed/8811194]
is_a: SO:1001261 ! recoded_mRNA

[Term]
id: SO:1001265
name: mRNA_recoded_by_codon_redefinition
def: "A gene whose mRNA is recoded by an alteration of codon meaning." [SO:ma]
is_a: SO:1001261 ! recoded_mRNA

[Term]
id: SO:1001266
name: stop_codon_redefinition_as_selenocysteine
is_a: SO:1001267 ! stop_codon_readthrough

[Term]
id: SO:1001267
name: stop_codon_readthrough
is_a: SO:1001265 ! mRNA_recoded_by_codon_redefinition

[Term]
id: SO:1001268
name: recoding_stimulatory_region
def: "A site in an mRNA sequence that stimulates the recoding of the same mRNA." [https://www.ncbi.nlm.nih.gov/pubmed/12519954]
synonym: "recoding_stimulatory_signal" RELATED []
relationship: part_of SO:0000234 ! mRNA

[Term]
id: SO:1001269
name: four_bp_start_codon
def: "A non-canonical start codon with 4 pase pairs." [SO:ke]
synonym: "4bp_start_codon" RELATED []
is_a: SO:0000680 ! non_canonical_start_codon

[Term]
id: SO:1001270
name: stop_codon_redefinition_as_pyrrolysine
is_a: SO:1001267 ! stop_codon_readthrough

[Term]
id: SO:1001271
name: archeal_intron
def: "Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism." [SO:ma]
is_a: SO:0000661 ! intron_attribute

[Term]
id: SO:1001272
name: tRNA_intron
is_a: SO:0000661 ! intron_attribute

[Term]
id: SO:1001273
name: CTG_start_codon
def: "A non-canonical start codon of sequence CTG." [SO:ke]
is_a: SO:0000680 ! non_canonical_start_codon

[Term]
id: SO:1001274
name: SECIS_element
def: "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001275
name: retron
def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]
is_a: SO:0000009 ! gene_class

[Term]
id: SO:1001277
name: three_prime_recoding_site
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001279
name: three_prime_stem_loop_structure
def: "The stem-loop secondary structural element downstream of the redefined region." [SO:ke]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001280
name: five_prime_recoding_site
def: "The recoding signal found 5' of the redefined codon." [SO:ke]
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:1001281
name: flanking_three_prime_quadruplet_recoding_signal
def: "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [SO:ke]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001282
name: UAG_stop_codon_signal
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001283
name: UAA_stop_codon_signal
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001284
name: regulon
def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]
subset: SOFA
is_a: SO:0005855 ! gene_group

[Term]
id: SO:1001285
name: UGA_stop_codon_signal
is_a: SO:1001288 ! stop_codon_signal

[Term]
id: SO:1001286
name: three_prime_repeat_recoding_signal
def: "It is a downstream sequence important for recoding that contains repetitive elements." [SO:ke]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001287
name: distant_three_prime_recoding_signal
def: "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [https://www.ncbi.nlm.nih.gov/pubmed/8709208]
is_a: SO:1001277 ! three_prime_recoding_site

[Term]
id: SO:1001288
name: stop_codon_signal
is_a: SO:1001268 ! recoding_stimulatory_region

[Term]
id: SO:2000061
name: databank_entry
def: "The sequence referred to by an entry in a databank such as Genbank or SwissProt." [SO:ke]
subset: SOFA
synonym: "accession" RELATED []
is_a: SO:0000695 ! reagent

[Typedef]
id: adjacent_to
name: adjacent_to
def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence." [SO:ke]
subset: SOFA
domain: SO:0000110 ! located_sequence_feature
range: SO:0000110 ! located_sequence_feature
is_symmetric: true

[Typedef]
id: associated_with
name: associated_with
comment: This relationship is vague and up for discussion.
is_symmetric: true

[Typedef]
id: derives_from
name: derives_from
subset: SOFA
is_transitive: true

[Typedef]
id: genome_of
name: genome_of

[Typedef]
id: has_genome_location
name: has_genome_location
domain: SO:0000085 ! gene_by_genome_location
range: SO:0000704 ! gene
is_obsolete: true

[Typedef]
id: homologous_to
name: homologous_to
is_symmetric: true
is_a: similar_to ! similar_to

[Typedef]
id: member_of
name: member_of
comment: A subtype of part_of.ninverse is collection_of.nWinston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
subset: SOFA
is_a: part_of ! part_of

[Typedef]
id: non_functional_homolog_of
name: non_functional_homolog_of
def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]
is_a: homologous_to ! homologous_to

[Typedef]
id: orthologous_to
name: orthologous_to
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: paralogous_to
name: paralogous_to
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: part_of
name: part_of
subset: SOFA
is_transitive: true

[Typedef]
id: position_of
name: position_of

[Typedef]
id: regulated_by
name: regulated_by
is_obsolete: true

[Typedef]
id: sequence_of
name: sequence_of

[Typedef]
id: similar_to
name: similar_to
is_symmetric: true