List of all SO terms

File created on Wed Aug 16 13:55:14 2006

created from: /Users/kareneilbeck/cvs/SO/ontology/so-xp.obo

format-version: 1.2

date: 14:08:2006 16:22

saved-by: kareneilbeck

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 $

sequence_attribute terms

C_D_box_snoRNA_encoding	SO:0000585
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: C_D_box_snoRNA_encoding is_a snoRNA_encoding	Child relationships:

DNA	SO:0000352
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: DNA is_a nucleic_acid	Child relationships:

FRT_flanked	SO:0000361
Definition: An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: FRT_flanked is_a flanked	Child relationships:

H_ACA_box_snoRNA_encoding	SO:0000608
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: H_ACA_box_snoRNA_encoding is_a snoRNA_encoding	Child relationships:

RNA	SO:0000356
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: RNA is_a nucleic_acid	Child relationships:

SRP_RNA_encoding	SO:0000642
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: SRP_RNA_encoding is_a non_protein_coding	Child relationships:

allelically_excluded	SO:0000137
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: allelically_excluded is_a epigenetically_modified	Child relationships:

alternatively_spliced	SO:0000877
Definition: An attribute describing a situation where a gene may encode for more than 1 transcript.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: alternatively_spliced is_a transcript_attribute	Child relationships:

antisense	SO:0000077
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: antisense is_a overlapping	Child relationships:

apicoplast_sequence	SO:0000743
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: apicoplast_sequence is_a plastid_sequence	Child relationships:

archeal_intron	SO:1001271
Definition: Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism.
DBxref:SO:ma
Synonyms:
Aspect: sequence_attribute
Parent relationships: archeal_intron is_a intron_attribute	Child relationships:

autoregulated	SO:0000471
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: autoregulated is_a transcriptionally_regulated	Child relationships: negatively_autoregulated is_a autoregulated positively_autoregulated is_a autoregulated

bound_by_factor	SO:0000277
Definition: An attribute describing a sequence that is bound by another molecule.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: bound_by_factor is_a feature_attribute	Child relationships: bound_by_protein is_a bound_by_factor bound_by_nucleic_acid is_a bound_by_factor

bound_by_nucleic_acid	SO:0000876
Definition: An attribute describing a sequence that is bound by a nucleic acid.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: bound_by_nucleic_acid is_a bound_by_factor	Child relationships:

bound_by_protein	SO:0000875
Definition: An attribute describing a sequence that is bound by a protein.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: bound_by_protein is_a bound_by_factor	Child relationships:

cDNA	SO:0000756
Definition: DNA synthesized by reverse transcriptase using RNA as a template
DBxref:SO:ma
Synonyms:
Aspect: sequence_attribute
Parent relationships: cDNA is_a nucleic_acid	Child relationships: double_stranded_cDNA is_a cDNA single_stranded_cDNA is_a cDNA

capped	SO:0000146
Definition: An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: capped is_a transcript_attribute	Child relationships:

cassette_array_member	SO:0005847
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: cassette_array_member is_a gene_cassette_member	Child relationships:

chloroplast_sequence	SO:0000745
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: chloroplast_sequence is_a plastid_sequence	Child relationships:

chromoplast_sequence	SO:0000744
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: chromoplast_sequence is_a plastid_sequence	Child relationships:

cloned	SO:0000788
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: cloned is_a reagent_attribute	Child relationships: cloned_cDNA is_a cloned cloned_genomic is_a cloned

cloned_cDNA	SO:0000792
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: cloned_cDNA is_a cloned	Child relationships:

cloned_genomic	SO:0000791
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: cloned_genomic is_a cloned	Child relationships:

codon_redefined	SO:0000882
Definition: An attribute describing the alteration of codon meaning.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: codon_redefined is_a recoded	Child relationships: stop_codon_read_through is_a codon_redefined

conserved	SO:0000856
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: conserved is_a feature_attribute	Child relationships: homologous is_a conserved syntenic is_a conserved

cryptogene	SO:1001196
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: cryptogene is_a non_protein_coding	Child relationships:

cyanelle_sequence	SO:0000746
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: cyanelle_sequence is_a plastid_sequence	Child relationships:

designed_sequence	SO:0000546
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: designed_sequence is_a synthetic_sequence	Child relationships:

dicistronic	SO:0000879
Definition: An attribute describing a sequence that contains the code for two gene products.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: dicistronic is_a polycistronic	Child relationships:

double_stranded_cDNA	SO:0000758
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: double_stranded_cDNA is_a cDNA	Child relationships:

edited	SO:0000116
Definition: An attribute describing a sequence that is modified by editing
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: edited is_a transcript_attribute	Child relationships:

encodes_1_polypeptide	SO:1001188
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: encodes_1_polypeptide is_a encodes_alternately_spliced_transcripts	Child relationships:

encodes_alternately_spliced_transcripts	SO:0000463
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: encodes_alternately_spliced_transcripts is_a gene_attribute	Child relationships: encodes_1_polypeptide is_a encodes_alternately_spliced_transcripts encodes_greater_than_1_polypeptide is_a encodes_alternately_spliced_transcripts

encodes_different_polypeptides_different_stop	SO:1001190
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: encodes_different_polypeptides_different_stop is_a encodes_overlapping_peptides	Child relationships:

encodes_disjoint_polypeptides	SO:1001192
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: encodes_disjoint_polypeptides is_a encodes_greater_than_1_polypeptide	Child relationships:

encodes_greater_than_1_polypeptide	SO:1001189
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: encodes_greater_than_1_polypeptide is_a encodes_alternately_spliced_transcripts	Child relationships: encodes_disjoint_polypeptides is_a encodes_greater_than_1_polypeptide encodes_overlapping_peptides is_a encodes_greater_than_1_polypeptide

encodes_overlapping_peptides	SO:1001195
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: encodes_overlapping_peptides is_a encodes_greater_than_1_polypeptide	Child relationships: encodes_overlapping_polypeptides_different_start_and_stop is_a encodes_overlapping_peptides encodes_overlapping_peptides_different_start is_a encodes_overlapping_peptides encodes_different_polypeptides_different_stop is_a encodes_overlapping_peptides

encodes_overlapping_peptides_different_start	SO:1001191
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: encodes_overlapping_peptides_different_start is_a encodes_overlapping_peptides	Child relationships:

encodes_overlapping_polypeptides_different_start_and_stop	SO:1001193
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: encodes_overlapping_polypeptides_different_start_and_stop is_a encodes_overlapping_peptides	Child relationships:

endogenous_retroviral_sequence	SO:0000903
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: endogenous_retroviral_sequence is_a proviral_sequence	Child relationships:

engineered	SO:0000783
Definition: An attribute to describe a region that was modified in vitro.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: engineered is_a feature_attribute	Child relationships:

epigenetically_modified	SO:0000133
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: epigenetically_modified is_a gene_attribute	Child relationships: allelically_excluded is_a epigenetically_modified rearranged_at_DNA_level is_a epigenetically_modified imprinted is_a epigenetically_modified

exemplar	SO:0000864
Definition: An attribute describing a sequence is reprsentative of a class of similar sequences.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: exemplar is_a mRNA_attribute	Child relationships:

experimentally_determined	SO:0000312
Definition: Attribute to describe a feature that has been experiemntally verified.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: experimentally_determined is_a validated	Child relationships:

feature_attribute	SO:0000733
Definition: An attribute describing a located_sequence_feature.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: feature_attribute is_a sequence_attribute	Child relationships: gene_attribute is_a feature_attribute transcript_attribute is_a feature_attribute pseudogene_attribute is_a feature_attribute foreign is_a feature_attribute intermediate is_a feature_attribute wild_type is_a feature_attribute flanked is_a feature_attribute transgenic is_a feature_attribute engineered is_a feature_attribute conserved is_a feature_attribute intron_attribute is_a feature_attribute reagent_attribute is_a feature_attribute recombinationally_rearranged is_a feature_attribute bound_by_factor is_a feature_attribute fusion is_a feature_attribute status is_a feature_attribute natural is_a feature_attribute rescue is_a feature_attribute

five_prime_five_prime_overlap	SO:0000074
Definition: An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: five_prime_five_prime_overlap is_a overlapping	Child relationships:

five_prime_three_prime_overlap	SO:0000073
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: five_prime_three_prime_overlap is_a overlapping	Child relationships:

flanked	SO:0000357
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: flanked is_a feature_attribute	Child relationships: FRT_flanked is_a flanked floxed is_a flanked

floxed	SO:0000359
Definition: An attribute describing sequence that is flanked by Lox-P sites.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: floxed is_a flanked	Child relationships:

foreign	SO:0000784
Definition: An atrribute to describe a region from another species.
DBxref:SO:ke
Synonyms: [foreign_transposable_element]
Aspect: sequence_attribute
Parent relationships: foreign is_a feature_attribute	Child relationships:

fragment	SO:0000731
Definition: An attribute to describe a feature that is incomplete.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: fragment is_a status	Child relationships:

frameshift	SO:0000865
Definition: An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3..
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: frameshift is_a mRNA_attribute	Child relationships: minus_1_frameshift is_a frameshift plus_1_frameshift is_a frameshift minus_2_frameshift is_a frameshift plus_2_framshift is_a frameshift

fusion	SO:0000806
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: fusion is_a feature_attribute	Child relationships:

gene_array_member	SO:0000081
Definition: undefined
DBxref:
Synonyms: [gene_array_member]
Aspect: sequence_attribute
Parent relationships: gene_array_member is_a gene_attribute	Child relationships: gene_subarray_member is_a gene_array_member gene_cassette_member is_a gene_array_member operon_member is_a gene_array_member member_of_regulon is_a gene_array_member

gene_attribute	SO:0000401
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: gene_attribute is_a feature_attribute	Child relationships: gene_to_gene_feature is_a gene_attribute gene_array_member is_a gene_attribute regulated is_a gene_attribute non_protein_coding is_a gene_attribute protein_coding is_a gene_attribute epigenetically_modified is_a gene_attribute encodes_alternately_spliced_transcripts is_a gene_attribute

gene_cassette_member	SO:0005848
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: gene_cassette_member is_a gene_array_member	Child relationships: cassette_array_member is_a gene_cassette_member

gene_subarray_member	SO:0005849
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: gene_subarray_member is_a gene_array_member	Child relationships:

gene_to_gene_feature	SO:0000067
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: gene_to_gene_feature is_a gene_attribute	Child relationships: overlapping is_a gene_to_gene_feature

homologous	SO:0000857
Definition: Similarity due to common ancestry.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: homologous is_a conserved	Child relationships: paralogous is_a homologous orthologous is_a homologous

imprinted	SO:0000134
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: imprinted is_a regulated imprinted is_a epigenetically_modified	Child relationships: paternally_imprinted is_a imprinted maternally_imprinted is_a imprinted

independently_known	SO:0000906
Definition: Attribute to describe a feature that is independently_known - not predicted.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: independently_known is_a status	Child relationships:

inside_intron	SO:0000069
Definition: An attribute to describe a gene when it is located within the intron of another gene.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: inside_intron is_a overlapping	Child relationships: inside_intron_antiparallel is_a inside_intron inside_intron_parallel is_a inside_intron

inside_intron_antiparallel	SO:0000070
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: inside_intron_antiparallel is_a inside_intron	Child relationships:

inside_intron_parallel	SO:0000071
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: inside_intron_parallel is_a inside_intron	Child relationships:

intein_containing	SO:0000729
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: intein_containing is_a protein_coding	Child relationships:

intermediate	SO:0000933
Definition: An attribute to describe a feature between stages of processing.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: intermediate is_a feature_attribute	Child relationships:

intron_attribute	SO:0000661
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: intron_attribute is_a feature_attribute	Child relationships: archeal_intron is_a intron_attribute mobile_intron is_a intron_attribute tRNA_intron is_a intron_attribute

invalidated	SO:0000790
Definition: An attribute describing a feature that is invalidated.
DBxref:SO:ke
Synonyms: [invalidated_clone]
Aspect: sequence_attribute
Parent relationships: invalidated is_a status	Child relationships: invalidated_by_genomic_polyA_primed_cDNA is_a invalidated invalidated_by_chimeric_cDNA is_a invalidated invalidated_by_partial_processing is_a invalidated invalidated_by_genomic_contamination is_a invalidated

invalidated_by_chimeric_cDNA	SO:0000362
Definition: A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.
DBxref:SO:ma
Synonyms:
Aspect: sequence_attribute
Parent relationships: invalidated_by_chimeric_cDNA is_a invalidated	Child relationships:

invalidated_by_genomic_contamination	SO:0000414
Definition: An attribue to describe a feature that is invalidated due to genomic contamination.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: invalidated_by_genomic_contamination is_a invalidated	Child relationships:

invalidated_by_genomic_polyA_primed_cDNA	SO:0000415
Definition: An attribue to describe a feature that is invalidated due to polyA priming.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: invalidated_by_genomic_polyA_primed_cDNA is_a invalidated	Child relationships:

invalidated_by_partial_processing	SO:0000416
Definition: An attribue to describe a feature that is invalidated due to partial processing.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: invalidated_by_partial_processing is_a invalidated	Child relationships:

kinetoplast_sequence	SO:0000741
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: kinetoplast_sequence is_a mitochondrial_sequence	Child relationships:

leucoplast_sequence	SO:0000747
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: leucoplast_sequence is_a plastid_sequence	Child relationships:

mRNA_attribute	SO:0000863
Definition: An attribute describing an mRNA feature.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: mRNA_attribute is_a transcript_attribute	Child relationships: exemplar is_a mRNA_attribute frameshift is_a mRNA_attribute recoded is_a mRNA_attribute polyadenylated is_a mRNA_attribute

macronuclear_sequence	SO:0000083
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: macronuclear_sequence is_a organelle_location	Child relationships:

maternally_imprinted	SO:0000135
Definition: An attribute to describe genes that are regulated by maternal imprinting.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: maternally_imprinted is_a imprinted	Child relationships:

maxicircle_sequence	SO:0000742
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: maxicircle_sequence is_a mitochondrial_sequence	Child relationships:

member_of_regulon	SO:1001217
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: member_of_regulon is_a gene_array_member	Child relationships:

miRNA_encoding	SO:0000571
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: miRNA_encoding is_a non_protein_coding	Child relationships:

micronuclear_sequence	SO:0000084
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: micronuclear_sequence is_a organelle_location	Child relationships:

minus_1_frameshift	SO:0000866
Definition: A frameshift caused by deleting one base
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: minus_1_frameshift is_a frameshift	Child relationships:

minus_1_translational_frameshift	SO:1001262
Definition: An attribute describing a translational frameshift of -1.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: minus_1_translational_frameshift is_a translational_frameshift	Child relationships:

minus_2_frameshift	SO:0000867
Definition: A frameshift caused by deleting two bases
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: minus_2_frameshift is_a frameshift	Child relationships:

mitochondrial_sequence	SO:0000737
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: mitochondrial_sequence is_a organelle_location	Child relationships: maxicircle_sequence is_a mitochondrial_sequence kinetoplast_sequence is_a mitochondrial_sequence

mobile_intron	SO:0000666
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: mobile_intron is_a intron_attribute	Child relationships:

monocistronic	SO:0000878
Definition: An attribute describing a sequence that contains the code for one gene product.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: monocistronic is_a transcript_attribute	Child relationships:

natural	SO:0000782
Definition: An attribute describing a feature that occurs in nature.
DBxref:SO:ke
Synonyms: [natural_transposable_element]
Aspect: sequence_attribute
Parent relationships: natural is_a feature_attribute	Child relationships:

negatively_autoregulated	SO:0000473
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: negatively_autoregulated is_a transcriptionally_repressed negatively_autoregulated is_a autoregulated	Child relationships:

non_protein_coding	SO:0000011
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: non_protein_coding is_a gene_attribute	Child relationships: miRNA_encoding is_a non_protein_coding cryptogene is_a non_protein_coding tmRNA_encoding is_a non_protein_coding snRNA_encoding is_a non_protein_coding snoRNA_encoding is_a non_protein_coding scRNA_encoding is_a non_protein_coding stRNA_encoding is_a non_protein_coding SRP_RNA_encoding is_a non_protein_coding tRNA_encoding is_a non_protein_coding rRNA_encoding is_a non_protein_coding

nuclear_mitochondrial	SO:0000899
Definition: An attribute describing a nuclear pseudogene of a mitochndrial gene.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: nuclear_mitochondrial is_a pseudogene_attribute	Child relationships:

nuclear_sequence	SO:0000738
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: nuclear_sequence is_a organelle_location	Child relationships:

nucleic_acid	SO:0000348
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: nucleic_acid is_a polymer_type	Child relationships: cDNA is_a nucleic_acid RNA is_a nucleic_acid DNA is_a nucleic_acid

nucleomorphic_sequence	SO:0000739
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: nucleomorphic_sequence is_a organelle_location	Child relationships:

operon_member	SO:0000080
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: operon_member is_a gene_array_member	Child relationships:

organelle_location	SO:0000736
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: organelle_location is_a sequence_location	Child relationships: nucleomorphic_sequence is_a organelle_location nuclear_sequence is_a organelle_location micronuclear_sequence is_a organelle_location macronuclear_sequence is_a organelle_location plastid_sequence is_a organelle_location mitochondrial_sequence is_a organelle_location

orphan	SO:0000910
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: orphan is_a predicted	Child relationships:

orthologous	SO:0000858
Definition: A kind of homology where divergence occured after a speciation event.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: orthologous is_a homologous	Child relationships:

overlapping	SO:0000068
Definition: An attribute describing a gene that has sequence that overlaps the sequence of another gene.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: overlapping is_a gene_to_gene_feature	Child relationships: three_prime_three_prime_overlap is_a overlapping inside_intron is_a overlapping five_prime_three_prime_overlap is_a overlapping three_prime_five_prime_overlap is_a overlapping antisense is_a overlapping five_prime_five_prime_overlap is_a overlapping

paralogous	SO:0000859
Definition: A kind of homology where divergence occured after a duplication event.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: paralogous is_a homologous	Child relationships:

paternally_imprinted	SO:0000136
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: paternally_imprinted is_a imprinted	Child relationships:

plasmid_sequence	SO:0000749
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: plasmid_sequence is_a sequence_location	Child relationships:

plastid_sequence	SO:0000740
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: plastid_sequence is_a organelle_location	Child relationships: apicoplast_sequence is_a plastid_sequence leucoplast_sequence is_a plastid_sequence cyanelle_sequence is_a plastid_sequence chromoplast_sequence is_a plastid_sequence proplastid_sequence is_a plastid_sequence chloroplast_sequence is_a plastid_sequence

plus_1_frameshift	SO:0000868
Definition: A frameshift caused by inserting one base
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: plus_1_frameshift is_a frameshift	Child relationships:

plus_1_translational_frameshift	SO:1001263
Definition: An attribute describing a translational frameshift of +1.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: plus_1_translational_frameshift is_a translational_frameshift	Child relationships:

plus_2_framshift	SO:0000869
Definition: A frameshift caused by inserting two bases
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: plus_2_framshift is_a frameshift	Child relationships:

polyadenylated	SO:0000246
Definition: A attribute describing the additon of a poly A tail to the 3' end of a mRNA molecule.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: polyadenylated is_a mRNA_attribute	Child relationships:

polycistronic	SO:0000880
Definition: An attribute describing a sequence that contains the code for more than one gene product.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: polycistronic is_a transcript_attribute	Child relationships: dicistronic is_a polycistronic

polymer_type	SO:0000443
Definition: An attribute to describe the kind of biological sequence.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: polymer_type is_a sequence_attribute	Child relationships: nucleic_acid is_a polymer_type protein is_a polymer_type synthetic_sequence is_a polymer_type

positively_autoregulated	SO:0000475
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: positively_autoregulated is_a transcriptionally_induced positively_autoregulated is_a autoregulated	Child relationships:

post_translationally_regulated	SO:0000130
Definition: An attribute describing a gene that is regulated after it has been translated.
DBxref:SO:ke
Synonyms: [post-translationally_regulated]
Aspect: sequence_attribute
Parent relationships: post_translationally_regulated is_a regulated	Child relationships: post_translationally_regulated_by_protein_modification is_a post_translationally_regulated post_translationally_regulated_by_protein_stability is_a post_translationally_regulated

post_translationally_regulated_by_protein_modification	SO:0000469
Definition: An attribute describing a gene sequence where the resulting protein is modified to regulate it.
DBxref:SO:ke
Synonyms: [post-translationally_regulated_by_protein_modification]
Aspect: sequence_attribute
Parent relationships: post_translationally_regulated_by_protein_modification is_a post_translationally_regulated	Child relationships:

post_translationally_regulated_by_protein_stability	SO:0000467
Definition: undefined
DBxref:
Synonyms: [post-translationally_regulated_by_protein_stability]
Aspect: sequence_attribute
Parent relationships: post_translationally_regulated_by_protein_stability is_a post_translationally_regulated	Child relationships:

predicted	SO:0000732
Definition: An attribute describing an unverified region
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: predicted is_a status	Child relationships: supported_by_sequence_similarity is_a predicted orphan is_a predicted predicted_by_ab_initio_computation is_a predicted

predicted_by_ab_initio_computation	SO:0000911
Definition: An attribute describng a feaure that is predticted by a computer program that did not rely on sequence similarity.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: predicted_by_ab_initio_computation is_a predicted	Child relationships:

processed	SO:0000900
Definition: An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed bak inot the genome, lacking introns and promotors, but often including a polyA tail.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: processed is_a pseudogene_attribute	Child relationships:

proplastid_sequence	SO:0000748
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: proplastid_sequence is_a plastid_sequence	Child relationships:

protein	SO:0000358
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: protein is_a polymer_type	Child relationships:

protein_coding	SO:0000010
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: protein_coding is_a gene_attribute	Child relationships: retrotransposed is_a protein_coding intein_containing is_a protein_coding

proviral_sequence	SO:0000751
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: proviral_sequence is_a sequence_location	Child relationships: endogenous_retroviral_sequence is_a proviral_sequence

pseudogene_attribute	SO:0000042
Definition: An attribute of a pseudogene (SO:0000336).
DBxref:SO:ma
Synonyms:
Aspect: sequence_attribute
Parent relationships: pseudogene_attribute is_a feature_attribute	Child relationships: processed is_a pseudogene_attribute retrotransposed is_a pseudogene_attribute nuclear_mitochondrial is_a pseudogene_attribute unequally_crossed_over is_a pseudogene_attribute

rRNA_encoding	SO:0000573
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: rRNA_encoding is_a non_protein_coding	Child relationships:

random_sequence	SO:0000449
Definition: A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequencyof these components.
DBxref:SO:ma
Synonyms:
Aspect: sequence_attribute
Parent relationships: random_sequence is_a synthetic_sequence	Child relationships:

reagent_attribute	SO:0000786
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: reagent_attribute is_a feature_attribute	Child relationships: cloned is_a reagent_attribute

rearranged_at_DNA_level	SO:0000904
Definition: An attribute to describe the sequence of a feature, where the DNA is rearranged.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: rearranged_at_DNA_level is_a epigenetically_modified	Child relationships:

recoded	SO:0000881
Definition: An atribute describing am mRNA sequences that has been reprogrammed at translation, causing localized alterations.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: recoded is_a mRNA_attribute	Child relationships: codon_redefined is_a recoded recoded_by_translational_bypass is_a recoded translational_frameshift is_a recoded

recoded_by_translational_bypass	SO:0000886
Definition: Rcoding mRNA where a block of nucleotides is not translated.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: recoded_by_translational_bypass is_a recoded	Child relationships:

recombinationally_rearranged	SO:0000940
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: recombinationally_rearranged is_a feature_attribute	Child relationships:

regulated	SO:0000119
Definition: An attribute to describe a sequence that is regulated.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: regulated is_a gene_attribute	Child relationships: translationally_regulated is_a regulated transcriptionally_regulated is_a regulated imprinted is_a regulated post_translationally_regulated is_a regulated

rescue	SO:0000814
Definition: An attribute describing a regions ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: rescue is_a feature_attribute	Child relationships:

retrotransposed	SO:0000569
Definition: undefined
DBxref:
Synonyms: [captured_pseudogene] [SO:0100042]
Aspect: sequence_attribute
Parent relationships: retrotransposed is_a protein_coding retrotransposed is_a pseudogene_attribute	Child relationships:

scRNA_encoding	SO:0000575
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: scRNA_encoding is_a non_protein_coding	Child relationships:

sequence_location	SO:0000735
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: sequence_location is_a sequence_attribute	Child relationships: plasmid_sequence is_a sequence_location proviral_sequence is_a sequence_location organelle_location is_a sequence_location

silenced	SO:0000893
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: silenced is_a transcriptionally_repressed	Child relationships: silenced_by_DNA_modification is_a silenced

silenced_by_DNA_methylation	SO:0000895
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: silenced_by_DNA_methylation is_a silenced_by_DNA_modification	Child relationships:

silenced_by_DNA_modification	SO:0000894
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: silenced_by_DNA_modification is_a silenced	Child relationships: silenced_by_DNA_methylation is_a silenced_by_DNA_modification

single_stranded_cDNA	SO:0000757
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: single_stranded_cDNA is_a cDNA	Child relationships:

snRNA_encoding	SO:0000623
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: snRNA_encoding is_a non_protein_coding	Child relationships:

snoRNA_encoding	SO:0000578
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: snoRNA_encoding is_a non_protein_coding	Child relationships: H_ACA_box_snoRNA_encoding is_a snoRNA_encoding C_D_box_snoRNA_encoding is_a snoRNA_encoding

stRNA_encoding	SO:0000656
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: stRNA_encoding is_a non_protein_coding	Child relationships:

status	SO:0000905
Definition: An attribute describing the status of a feature, based on the available evidence.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: status is_a feature_attribute	Child relationships: validated is_a status fragment is_a status invalidated is_a status independently_known is_a status predicted is_a status

stop_codon_read_through	SO:0000883
Definition: A stop codon redefined to be a new amino acid
DBxref:SO:ke
Synonyms: [stop codon readthrough]
Aspect: sequence_attribute
Parent relationships: stop_codon_read_through is_a codon_redefined	Child relationships: stop_codon_redefined_as_pyrrolysine is_a stop_codon_read_through stop_codon_redefined_as_selenocysteine is_a stop_codon_read_through

stop_codon_redefined_as_pyrrolysine	SO:0000884
Definition: A stop codon redefined to be the new amino acid, pyrrolysine.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: stop_codon_redefined_as_pyrrolysine is_a stop_codon_read_through	Child relationships:

stop_codon_redefined_as_selenocysteine	SO:0000885
Definition: A stop codon redefined to be the new amino acid, selenocysteine.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: stop_codon_redefined_as_selenocysteine is_a stop_codon_read_through	Child relationships:

supported_by_EST_or_cDNA	SO:0000909
Definition: An attribute to describe a feature that has been predicted using sequence smilarity to EST or cDNA data.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: supported_by_EST_or_cDNA is_a supported_by_sequence_similarity	Child relationships:

supported_by_domain_match	SO:0000908
Definition: An attribute to describe a feature that has been predicted using sequence smilarity of a known domain.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: supported_by_domain_match is_a supported_by_sequence_similarity	Child relationships:

supported_by_sequence_similarity	SO:0000907
Definition: An attribute to describe a feature that has been predicted using sequence smilarity techniques.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: supported_by_sequence_similarity is_a predicted	Child relationships: supported_by_domain_match is_a supported_by_sequence_similarity supported_by_EST_or_cDNA is_a supported_by_sequence_similarity

syntenic	SO:0000860
Definition: Attribute describing sequence regions occurring in same order on chromosome of different species.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: syntenic is_a conserved	Child relationships:

synthetic_sequence	SO:0000351
Definition: 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.
DBxref:SO:ma
Synonyms:
Aspect: sequence_attribute
Parent relationships: synthetic_sequence is_a polymer_type	Child relationships: random_sequence is_a synthetic_sequence designed_sequence is_a synthetic_sequence

tRNA_encoding	SO:0000663
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: tRNA_encoding is_a non_protein_coding	Child relationships:

tRNA_intron	SO:1001272
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: tRNA_intron is_a intron_attribute	Child relationships:

three_prime_five_prime_overlap	SO:0000076
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: three_prime_five_prime_overlap is_a overlapping	Child relationships:

three_prime_three_prime_overlap	SO:0000075
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: three_prime_three_prime_overlap is_a overlapping	Child relationships:

tmRNA_encoding	SO:0000659
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: tmRNA_encoding is_a non_protein_coding	Child relationships:

trans_spliced	SO:0000870
Definition: An attribute describing transcript sequence that is created by splicing exons from diferent genes.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: trans_spliced is_a transcript_attribute	Child relationships:

transcript_attribute	SO:0000237
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: transcript_attribute is_a feature_attribute	Child relationships: alternatively_spliced is_a transcript_attribute capped is_a transcript_attribute edited is_a transcript_attribute monocistronic is_a transcript_attribute trans_spliced is_a transcript_attribute polycistronic is_a transcript_attribute mRNA_attribute is_a transcript_attribute

transcriptionally_constitutive	SO:0000124
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: transcriptionally_constitutive is_a transcriptionally_regulated	Child relationships:

transcriptionally_induced	SO:0000125
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: transcriptionally_induced is_a transcriptionally_regulated	Child relationships: positively_autoregulated is_a transcriptionally_induced

transcriptionally_regulated	SO:0000123
Definition: .
DBxref:SO:ma
Synonyms:
Aspect: sequence_attribute
Parent relationships: transcriptionally_regulated is_a regulated	Child relationships: transcriptionally_induced is_a transcriptionally_regulated transcriptionally_repressed is_a transcriptionally_regulated autoregulated is_a transcriptionally_regulated transcriptionally_constitutive is_a transcriptionally_regulated

transcriptionally_repressed	SO:0000126
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: transcriptionally_repressed is_a transcriptionally_regulated	Child relationships: negatively_autoregulated is_a transcriptionally_repressed silenced is_a transcriptionally_repressed

transgenic	SO:0000781
Definition: Attribute describing sequence that has been integrated with foreign sequence.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: transgenic is_a feature_attribute	Child relationships:

translational_frameshift	SO:0000887
Definition: Recoding by frameshifting a particular site.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: translational_frameshift is_a recoded	Child relationships: minus_1_translational_frameshift is_a translational_frameshift plus_1_translational_frameshift is_a translational_frameshift

translationally_regulated	SO:0000131
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: translationally_regulated is_a regulated	Child relationships:

unequally_crossed_over	SO:0000901
Definition: An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: unequally_crossed_over is_a pseudogene_attribute	Child relationships:

validated	SO:0000789
Definition: An attribute to describe a feature that has been proven.
DBxref:SO:ke
Synonyms: [validated_clone]
Aspect: sequence_attribute
Parent relationships: validated is_a status	Child relationships: experimentally_determined is_a validated

wild_type	SO:0000817
Definition: An attribute describing sequence with the genotype found in nature/or standard laboratory stock
DBxref:SO:ke
Synonyms:
Aspect: sequence_attribute
Parent relationships: wild_type is_a feature_attribute	Child relationships:

located_sequence_feature terms

ARS	SO:0000436
Definition: A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
DBxref:SO:ma
Synonyms: [autonomously_replicating_sequence]
Aspect: located_sequence_feature
Parent relationships: ARS is_a region	Child relationships:

A_box	SO:0000619
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: A_box is_a RNApol_III_promotor_type_2_region	Child relationships:

A_minor_RNA_motif	SO:0000022
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: A_minor_RNA_motif is_a asymmetric_RNA_internal_loop	Child relationships:

A_to_C_transversion	SO:1000024
Definition: A transversion from adenine to cytidine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: A_to_C_transversion is_a purine_to_pyrimidine_transversion	Child relationships:

A_to_G_transition	SO:1000015
Definition: A transition of an adenine to a guanine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: A_to_G_transition is_a purine_transition	Child relationships:

A_to_T_transversion	SO:1000025
Definition: A transversion from adenine to thymine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: A_to_T_transversion is_a purine_to_pyrimidine_transversion	Child relationships:

BAC	SO:0000153
Definition: Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: BAC is_a vector	Child relationships:

BRE_motif	SO:0000016
Definition: 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.
DBxref:PMID:12651739
Synonyms:
Aspect: located_sequence_feature
Parent relationships: BRE_motif is_a RNA_II_promotor_region	Child relationships:

B_box	SO:0000620
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: B_box is_a RNApol_III_promotor_type_2_region	Child relationships:

CAAT_signal	SO:0000172
Definition: 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.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: CAAT_signal is_a RNA_II_promotor_region	Child relationships:

CDS	SO:0000316
Definition: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
DBxref:SO:ma
Synonyms: [coding_sequence]
Aspect: located_sequence_feature
Parent relationships: CDS is_a mRNA_region	Child relationships: polypeptide derives_from CDS CDS_region part_of CDS

CDS_region	SO:0000851
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: CDS_region is_a mRNA_region CDS_region part_of CDS	Child relationships: coding_end is_a CDS_region coding_start is_a CDS_region

CTG_start_codon	SO:1001273
Definition: A non-canonical start codon of sequence CTG.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: CTG_start_codon is_a non_canonical_start_codon	Child relationships:

C_D_box_snoRNA	SO:0000593
Definition: 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'.
DBxref:external reference [http:////www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
Synonyms: [C/D_box_snoRNA]
Aspect: located_sequence_feature
Parent relationships: C_D_box_snoRNA is_a snoRNA	Child relationships:

C_D_box_snoRNA_primary_transcript	SO:0000595
Definition: A primary transcript encoding a small nucleolar RNA of the box C/D family.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: C_D_box_snoRNA_primary_transcript is_a snoRNA_primary_transcript	Child relationships:

C_box	SO:0000622
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: C_box is_a RNApol_III_promotor_type_1_region	Child relationships:

C_cluster	SO:0000558
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.
DBxref:
Synonyms: [C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: C_gene part_of C_cluster

C_gene	SO:0000478
Definition: 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).
DBxref:
Synonyms: [C_GENE] [constant_gene]
Aspect: located_sequence_feature
Parent relationships: C_gene part_of VJ_J_C_cluster C_gene part_of V_D_DJ_C_cluster C_gene part_of V_VJ_J_C_cluster C_gene part_of VDJ_C_cluster C_gene part_of V_D_J_C_cluster C_gene part_of V_D_DJ_J_C_cluster C_gene part_of D_DJ_C_cluster C_gene part_of V_J_C_cluster C_gene part_of V_DJ_C_cluster C_gene part_of V_VDJ_C_cluster C_gene part_of V_VJ_C_cluster C_gene part_of V_VDJ_J_C_cluster C_gene is_a vertebrate_immunoglobulin_T_cell_receptor_segment C_gene part_of D_DJ_J_C_cluster C_gene part_of VJ_C_cluster C_gene part_of DJ_J_C_cluster C_gene part_of D_J_C_cluster C_gene part_of J_C_cluster C_gene part_of DJ_C_cluster C_gene part_of V_DJ_J_C_cluster C_gene part_of VDJ_J_C_cluster C_gene part_of C_cluster	Child relationships:

C_to_A_transversion	SO:1000019
Definition: A transversion from cytidine to adenine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: C_to_A_transversion is_a pyrimidine_to_purine_transversion	Child relationships:

C_to_G_transversion	SO:1000020
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: C_to_G_transversion is_a pyrimidine_to_purine_transversion	Child relationships:

C_to_T_transition	SO:1000011
Definition: A transition of a cytidine to a thymine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: C_to_T_transition is_a pyrimidine_transition	Child relationships: C_to_T_transition_at_pCpG_site is_a C_to_T_transition

C_to_T_transition_at_pCpG_site	SO:1000012
Definition: The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: C_to_T_transition_at_pCpG_site is_a C_to_T_transition	Child relationships:

CpG_island	SO:0000307
Definition: 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.
DBxref:SO:rd
Synonyms: [CG_island]
Aspect: located_sequence_feature
Parent relationships: CpG_island is_a region	Child relationships:

Cre_recombination_target_region	SO:0000346
Definition: undefined
DBxref:
Synonyms: [lox_site]
Aspect: located_sequence_feature
Parent relationships: Cre_recombination_target_region is_a site_specific_recombination_target_region	Child relationships:

CsrB_RsmB_RNA	SO:0000377
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]
Synonyms: [CsrB-RsmB_RNA]
Aspect: located_sequence_feature
Parent relationships: CsrB_RsmB_RNA is_a small_regulatory_ncRNA	Child relationships:

DJ_C_cluster	SO:0000539
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene.
DBxref:
Synonyms: [(DJ)-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of DJ_C_cluster DJ_gene part_of DJ_C_cluster

DJ_J_C_cluster	SO:0000540
Definition: Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE.
DBxref:
Synonyms: [(DJ)-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of DJ_J_C_cluster J_gene part_of DJ_J_C_cluster DJ_gene part_of DJ_J_C_cluster

DJ_J_cluster	SO:0000485
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.
DBxref:
Synonyms: [(DJ)-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: J_gene part_of DJ_J_cluster DJ_gene part_of DJ_J_cluster

DJ_gene	SO:0000572
Definition: 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.
DBxref:
Synonyms: [D_J_GENE]
Aspect: located_sequence_feature
Parent relationships: DJ_gene part_of V_D_DJ_cluster DJ_gene part_of D_DJ_cluster DJ_gene part_of D_DJ_J_C_cluster DJ_gene part_of V_D_DJ_C_cluster DJ_gene part_of DJ_J_C_cluster DJ_gene part_of V_D_DJ_J_C_cluster DJ_gene part_of V_DJ_J_cluster DJ_gene part_of D_DJ_C_cluster DJ_gene part_of D_DJ_J_cluster DJ_gene is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment DJ_gene part_of V_DJ_C_cluster DJ_gene part_of DJ_C_cluster DJ_gene part_of V_D_DJ_J_cluster DJ_gene part_of DJ_J_cluster DJ_gene part_of V_DJ_J_C_cluster DJ_gene part_of V_DJ_cluster	Child relationships:

DNA_aptamer	SO:0000032
Definition: DNA molecules that have been selected from random pools based on their ability to bind other molecules.
DBxref:external reference [http://aptamer.icmb.utexas.edu]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: DNA_aptamer is_a aptamer	Child relationships:

DNA_invertase_target_sequence	SO:0000660
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: DNA_invertase_target_sequence is_a site_specific_recombination_target_region	Child relationships:

DNA_motif	SO:0000713
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: DNA_motif is_a nucleotide_motif	Child relationships:

DNA_sequence_secondary_structure	SO:0000142
Definition: A folded DNA sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: DNA_sequence_secondary_structure is_a sequence_secondary_structure	Child relationships:

DNA_transposon	SO:0000182
Definition: A transposon where the mechanism of transposition is via a DNA intermediate.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: DNA_transposon is_a transposable_element	Child relationships: terminal_inverted_repeat_element is_a DNA_transposon conjugative_transposon is_a DNA_transposon foldback_element is_a DNA_transposon

DNAaseI_hypersensitive_site	SO:0000685
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: DNAaseI_hypersensitive_site is_a nuclease_hypersensitive_site	Child relationships:

DPE_motif	SO:0000015
Definition: 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.
DBxref:PMID:12651739
Synonyms:
Aspect: located_sequence_feature
Parent relationships: DPE_motif is_a RNA_II_promotor_region	Child relationships:

D_DJ_C_cluster	SO:0000504
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.
DBxref:
Synonyms: [D-(DJ)-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: D_DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of D_DJ_C_cluster D_gene part_of D_DJ_C_cluster DJ_gene part_of D_DJ_C_cluster

D_DJ_J_C_cluster	SO:0000506
Definition: 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.
DBxref:
Synonyms: [D-(DJ)-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: D_DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of D_DJ_J_C_cluster D_gene part_of D_DJ_J_C_cluster J_gene part_of D_DJ_J_C_cluster DJ_gene part_of D_DJ_J_C_cluster

D_DJ_J_cluster	SO:0000508
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.
DBxref:
Synonyms: [D-(DJ)-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: D_DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: D_gene part_of D_DJ_J_cluster J_gene part_of D_DJ_J_cluster DJ_gene part_of D_DJ_J_cluster

D_DJ_cluster	SO:0000505
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.
DBxref:
Synonyms: [D-(DJ)-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: D_DJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: D_gene part_of D_DJ_cluster DJ_gene part_of D_DJ_cluster

D_J_C_cluster	SO:0000509
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.
DBxref:
Synonyms: [D-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: D_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: C_gene part_of D_J_C_cluster D_gene part_of D_J_C_cluster J_gene part_of D_J_C_cluster

D_J_cluster	SO:0000560
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.
DBxref:
Synonyms: [D-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: D_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: D_gene part_of D_J_cluster J_gene part_of D_J_cluster

D_cluster	SO:0000559
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene.
DBxref:
Synonyms: [D-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: D_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: D_gene part_of D_cluster

D_gene	SO:0000458
Definition: Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
DBxref:
Synonyms: [D-GENE]
Aspect: located_sequence_feature
Parent relationships: D_gene part_of V_D_DJ_cluster D_gene part_of D_DJ_cluster D_gene part_of D_DJ_J_C_cluster D_gene is_a vertebrate_immunoglobulin_T_cell_receptor_segment D_gene part_of D_J_cluster D_gene part_of V_D_J_cluster D_gene part_of V_D_DJ_C_cluster D_gene part_of D_cluster D_gene part_of D_J_C_cluster D_gene part_of V_D_J_C_cluster D_gene part_of V_D_DJ_J_C_cluster D_gene part_of D_DJ_C_cluster D_gene part_of D_DJ_J_cluster D_gene part_of V_D_DJ_J_cluster	Child relationships:

D_gene_recombination_feature	SO:0000492
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: D_gene_recombination_feature is_a vertebrate_immune_system_gene_recombination_signal_feature	Child relationships: five_prime_D_recombination_signal_sequence is_a D_gene_recombination_feature three_prime_D_recombination_signal_sequence is_a D_gene_recombination_feature

D_loop	SO:0000297
Definition: 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.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: D_loop is_a origin_of_replication	Child relationships:

DsrA_RNA	SO:0000378
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: DsrA_RNA is_a small_regulatory_ncRNA	Child relationships: GcvB_RNA is_a DsrA_RNA

EST	SO:0000345
Definition: Expressed Sequence Tag: The sequence of a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
DBxref:external reference [http:////genomics.phrma.org/lexicon/e.html]
Synonyms: [expressed_sequence_tag]
Aspect: located_sequence_feature
Parent relationships: EST is_a reagent EST derives_from mRNA	Child relationships:

EST_match	SO:0000668
Definition: A match against an EST sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: EST_match is_a expressed_sequence_match	Child relationships:

FLP_recombination_target_region	SO:0000350
Definition: undefined
DBxref:
Synonyms: [FRT_site]
Aspect: located_sequence_feature
Parent relationships: FLP_recombination_target_region is_a site_specific_recombination_target_region	Child relationships:

GC_rich_region	SO:0000173
Definition: 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.
DBxref:
Synonyms: [GC-rich_region]
Aspect: located_sequence_feature
Parent relationships: GC_rich_region is_a RNA_II_promotor_region	Child relationships:

G_quartet	SO:0000003
Definition: 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.
DBxref:external reference [http:////www.library.csi.cuny.edu/ ~ davis/molbiol/lecture_notes/post-transcriptional_processes/RNACapping.pdf]
Synonyms: [G-quartet]
Aspect: located_sequence_feature
Parent relationships: G_quartet is_a sequence_secondary_structure	Child relationships:

G_to_A_transition	SO:1000016
Definition: A transition of a guanine to an adenine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: G_to_A_transition is_a purine_transition	Child relationships:

G_to_C_transversion	SO:1000026
Definition: A transversion from guanine to cytidine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: G_to_C_transversion is_a purine_to_pyrimidine_transversion	Child relationships:

G_to_T_transversion	SO:1000027
Definition: A transversion from guanine to thymine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: G_to_T_transversion is_a purine_to_pyrimidine_transversion	Child relationships:

GcvB_RNA	SO:0000379
Definition: A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: GcvB_RNA is_a DsrA_RNA	Child relationships:

H_ACA_box_snoRNA	SO:0000594
Definition: 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.
DBxref:external reference [http:////www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
Synonyms: [H/ACA_box_snoRNA]
Aspect: located_sequence_feature
Parent relationships: H_ACA_box_snoRNA is_a snoRNA	Child relationships:

H_ACA_box_snoRNA_primary_transcript	SO:0000596
Definition: A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: H_ACA_box_snoRNA_primary_transcript is_a snoRNA_primary_transcript	Child relationships:

H_pseudoknot	SO:0000592
Definition: A pseudoknot which contains two stems and at least two loops.
DBxref:external reference [http:////www.ncbi.nlm.nih.gov 80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]
Synonyms: [H-pseudoknot]
Aspect: located_sequence_feature
Parent relationships: H_pseudoknot is_a pseudoknot	Child relationships:

Hoogsteen_base_pair	SO:0000500
Definition: 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.
DBxref:PMID:12177293
Synonyms:
Aspect: located_sequence_feature
Parent relationships: Hoogsteen_base_pair is_a base_pair	Child relationships:

INR_motif	SO:0000014
Definition: 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.
DBxref:PMID:12651739
Synonyms:
Aspect: located_sequence_feature
Parent relationships: INR_motif is_a RNA_II_promotor_region	Child relationships:

J_C_cluster	SO:0000511
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.
DBxref:
Synonyms: [J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: C_gene part_of J_C_cluster J_gene part_of J_C_cluster

J_cluster	SO:0000513
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.
DBxref:
Synonyms: [J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of J_cluster

J_gene	SO:0000470
Definition: 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.
DBxref:
Synonyms: [J-GENE]
Aspect: located_sequence_feature
Parent relationships: J_gene part_of VDJ_J_cluster J_gene part_of VJ_J_C_cluster J_gene part_of V_D_J_cluster J_gene part_of V_VJ_J_C_cluster J_gene part_of V_D_J_C_cluster J_gene part_of V_D_DJ_J_C_cluster J_gene part_of V_DJ_J_cluster J_gene part_of V_J_C_cluster J_gene part_of V_D_DJ_J_cluster J_gene part_of V_VDJ_J_C_cluster J_gene is_a vertebrate_immunoglobulin_T_cell_receptor_segment J_gene part_of D_DJ_J_C_cluster J_gene part_of D_J_cluster J_gene part_of DJ_J_C_cluster J_gene part_of D_J_C_cluster J_gene part_of V_J_cluster J_gene part_of D_DJ_J_cluster J_gene part_of VJ_J_cluster J_gene part_of V_VDJ_J_cluster J_gene part_of DJ_J_cluster J_gene part_of J_C_cluster J_gene part_of J_cluster J_gene part_of V_DJ_J_C_cluster J_gene part_of VDJ_J_C_cluster J_gene part_of V_VJ_J_cluster	Child relationships:

J_gene_recombination_feature	SO:0000302
Definition: Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.
DBxref:
Synonyms: [J-RS]
Aspect: located_sequence_feature
Parent relationships: J_gene_recombination_feature is_a vertebrate_immune_system_gene_recombination_signal_feature	Child relationships: J_nonamer part_of J_gene_recombination_feature J_spacer part_of J_gene_recombination_feature J_heptamer part_of J_gene_recombination_feature

J_heptamer	SO:0000515
Definition: 7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
DBxref:
Synonyms: [J-HEPTAMER]
Aspect: located_sequence_feature
Parent relationships: J_heptamer part_of J_gene_recombination_feature J_heptamer is_a heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	Child relationships:

J_nonamer	SO:0000514
Definition: 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
DBxref:
Synonyms: [J-NONAMER]
Aspect: located_sequence_feature
Parent relationships: J_nonamer part_of J_gene_recombination_feature J_nonamer is_a nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	Child relationships:

J_spacer	SO:0000517
Definition: 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.
DBxref:
Synonyms: [J-SPACER]
Aspect: located_sequence_feature
Parent relationships: J_spacer part_of J_gene_recombination_feature J_spacer is_a vertebrate_immune_system_gene_recombination_spacer	Child relationships:

K_turn_RNA_motif	SO:0000023
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: K_turn_RNA_motif is_a asymmetric_RNA_internal_loop	Child relationships:

LINE_element	SO:0000194
Definition: 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.
DBxref:external reference [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
Synonyms: [Long interspersed element] [Long interspersed nuclear element]
Aspect: located_sequence_feature
Parent relationships: LINE_element is_a non_LTR_retrotransposon	Child relationships:

LTR_component	SO:0000848
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: LTR_component is_a repeat_component LTR_component part_of long_terminal_repeat	Child relationships: three_prime_LTR_component is_a LTR_component R_LTR_region is_a LTR_component U5_LTR_region is_a LTR_component five_prime_LTR_component is_a LTR_component U3_LTR_region is_a LTR_component

LTR_retrotransposon	SO:0000186
Definition: A retrotransposon flanked by long terminal repeat sequences.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: LTR_retrotransposon is_a retrotransposon	Child relationships: RR_tract is_a LTR_retrotransposon long_terminal_repeat part_of LTR_retrotransposon primer_binding_site part_of LTR_retrotransposon

MITE	SO:0000338
Definition: 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.
DBxref:external reference [http://www.pnas.org/cgi/content/full/97/18/10083]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: MITE is_a terminal_inverted_repeat_element	Child relationships:

MicF_RNA	SO:0000383
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: MicF_RNA is_a antisense_RNA	Child relationships:

ORF	SO:0000236
Definition: 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
DBxref:SO:ma SO:rb
Synonyms: [open_reading_frame]
Aspect: located_sequence_feature
Parent relationships: ORF is_a reading_frame	Child relationships: mini_gene is_a ORF

OxyS_RNA	SO:0000384
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: OxyS_RNA is_a small_regulatory_ncRNA	Child relationships:

PAC	SO:0000154
Definition: P1 Artificial Chromosome. These vectors can hold large inserts, typically 80-200 kb, and propagate in E. coli as a single copy episome.
DBxref:external reference [http:////www.ncbi.nlm.nih.gov/genome/guide/mouse/glossary.htm]
Synonyms: [P1]
Aspect: located_sequence_feature
Parent relationships: PAC is_a vector	Child relationships:

PCR_product	SO:0000006
Definition: A region amplified by a PCR reaction.
DBxref:SO:ke
Synonyms: [amplicon]
Aspect: located_sequence_feature
Parent relationships: PCR_product is_a reagent	Child relationships:

PSE_motif	SO:0000017
Definition: 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).
DBxref:PMID:12651739
Synonyms:
Aspect: located_sequence_feature
Parent relationships: PSE_motif is_a RNA_II_promotor_region	Child relationships:

QTL	SO:0000771
Definition: 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.
DBxref:external reference [http:// http://rgd.mcw.edu/tu/qtls/]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: QTL is_a region	Child relationships:

RFLP_fragment	SO:0000193
Definition: A polymorphism detectable by the size differences in DNA fragments generated by a restriction enzyme.
DBxref:PMID:6247908
Synonyms: [restriction_fragment_length_polymorphism]
Aspect: located_sequence_feature
Parent relationships: RFLP_fragment is_a restriction_fragment	Child relationships:

RNA_6S	SO:0000376
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]
Synonyms: [6S_RNA]
Aspect: located_sequence_feature
Parent relationships: RNA_6S is_a small_regulatory_ncRNA	Child relationships:

RNA_II_promotor_region	SO:0000844
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNA_II_promotor_region part_of RNApol_II_promoter RNA_II_promotor_region is_a promotor_region	Child relationships: BRE_motif is_a RNA_II_promotor_region INR_motif is_a RNA_II_promotor_region GC_rich_region is_a RNA_II_promotor_region CAAT_signal is_a RNA_II_promotor_region DPE_motif is_a RNA_II_promotor_region PSE_motif is_a RNA_II_promotor_region

RNA_aptamer	SO:0000033
Definition: RNA molecules that have been selected from random pools based on their ability to bind other molecules.
DBxref:external reference [http://aptamer.icmb.utexas.edu]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNA_aptamer is_a aptamer	Child relationships:

RNA_hairpin_loop	SO:0000019
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNA_hairpin_loop is_a RNA_motif	Child relationships:

RNA_hook_turn	SO:0000027
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNA_hook_turn is_a RNA_junction_loop	Child relationships:

RNA_internal_loop	SO:0000020
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNA_internal_loop is_a RNA_motif	Child relationships: symmetric_RNA_internal_loop is_a RNA_internal_loop asymmetric_RNA_internal_loop is_a RNA_internal_loop

RNA_junction_loop	SO:0000026
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNA_junction_loop is_a RNA_motif	Child relationships: RNA_hook_turn is_a RNA_junction_loop

RNA_motif	SO:0000715
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNA_motif is_a nucleotide_motif	Child relationships: RNA_hairpin_loop is_a RNA_motif RNA_junction_loop is_a RNA_motif RNA_internal_loop is_a RNA_motif

RNA_sequence_secondary_structure	SO:0000122
Definition: A folded RNA sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNA_sequence_secondary_structure is_a sequence_secondary_structure	Child relationships:

RNAi_reagent	SO:0000337
Definition: A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
DBxref:SO:rd
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNAi_reagent is_a oligo	Child relationships:

RNApol_III_promoter	SO:0000171
Definition: A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.
DBxref:SO:ke
Synonyms: [RNA_polymerase_C_promoter]
Aspect: located_sequence_feature
Parent relationships: RNApol_III_promoter is_a promoter	Child relationships: RNApol_III_promoter_type_3 is_a RNApol_III_promoter RNApol_III_promoter_type_1 is_a RNApol_III_promoter TATA_box part_of RNApol_III_promoter RNApol_III_promoter_type_2 is_a RNApol_III_promoter

RNApol_III_promoter_type_1	SO:0000617
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNApol_III_promoter_type_1 is_a RNApol_III_promoter	Child relationships: RNApol_III_promotor_type_1_region part_of RNApol_III_promoter_type_1

RNApol_III_promoter_type_2	SO:0000618
Definition: undefined
DBxref:
Synonyms: [tRNA_promoter]
Aspect: located_sequence_feature
Parent relationships: RNApol_III_promoter_type_2 is_a RNApol_III_promoter	Child relationships: RNApol_III_promotor_type_2_region part_of RNApol_III_promoter_type_2

RNApol_III_promoter_type_3	SO:0000621
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNApol_III_promoter_type_3 is_a RNApol_III_promoter	Child relationships:

RNApol_III_promotor_type_1_region	SO:0000845
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNApol_III_promotor_type_1_region is_a promotor_region RNApol_III_promotor_type_1_region part_of RNApol_III_promoter_type_1	Child relationships: C_box is_a RNApol_III_promotor_type_1_region

RNApol_III_promotor_type_2_region	SO:0000846
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNApol_III_promotor_type_2_region is_a promotor_region RNApol_III_promotor_type_2_region part_of RNApol_III_promoter_type_2	Child relationships: A_box is_a RNApol_III_promotor_type_2_region B_box is_a RNApol_III_promotor_type_2_region

RNApol_II_promoter	SO:0000170
Definition: A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
DBxref:SO:ke
Synonyms: [RNA_polymerase_B_promoter]
Aspect: located_sequence_feature
Parent relationships: RNApol_II_promoter is_a promoter	Child relationships: RNA_II_promotor_region part_of RNApol_II_promoter TATA_box part_of RNApol_II_promoter

RNApol_I_promoter	SO:0000169
Definition: A DNA sequence sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.
DBxref:SO:ke
Synonyms: [RNA_polymerase_A_promoter]
Aspect: located_sequence_feature
Parent relationships: RNApol_I_promoter is_a promoter	Child relationships:

RNase_MRP_RNA	SO:0000385
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNase_MRP_RNA is_a enzymatic_RNA	Child relationships:

RNase_P_RNA	SO:0000386
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNase_P_RNA is_a ribozyme	Child relationships:

RRE_RNA	SO:0000388
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RRE_RNA is_a small_regulatory_ncRNA	Child relationships:

RR_tract	SO:0000435
Definition: A polypurine tract within an LTR_retrotransposon.
DBxref:SO:ke
Synonyms: [LTR_retrotransposon_poly_purine_tract]
Aspect: located_sequence_feature
Parent relationships: RR_tract is_a LTR_retrotransposon	Child relationships:

R_LTR_region	SO:0000423
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: R_LTR_region is_a LTR_component	Child relationships: R_five_prime_LTR_region is_a R_LTR_region

R_five_prime_LTR_region	SO:0000427
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: R_five_prime_LTR_region is_a R_LTR_region R_five_prime_LTR_region is_a five_prime_LTR_component	Child relationships:

R_three_prime_LTR_region	SO:0000430
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: R_three_prime_LTR_region is_a three_prime_LTR_component	Child relationships:

RprA_RNA	SO:0000387
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RprA_RNA is_a small_regulatory_ncRNA	Child relationships:

SAGE_tag	SO:0000326
Definition: A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
DBxref:external reference [http:////www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: SAGE_tag is_a tag	Child relationships:

SECIS_element	SO:1001274
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: SECIS_element is_a recoding_stimulatory_region	Child relationships:

SINE_element	SO:0000206
Definition: A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.
DBxref:SO:ke
Synonyms: [Short interspersed element] [Short interspersed nuclear element]
Aspect: located_sequence_feature
Parent relationships: SINE_element is_a non_LTR_retrotransposon	Child relationships:

SL1_acceptor_site	SO:0000708
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: SL1_acceptor_site is_a trans_splice_acceptor_site	Child relationships:

SL2_acceptor_site	SO:0000709
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: SL2_acceptor_site is_a trans_splice_acceptor_site	Child relationships:

SNP	SO:0000694
Definition: 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.
DBxref:external reference [http:////www.cgr.ki.se/cgb/groups/brookes/Articles/essence_of_snps_article.pdf]
Synonyms: [single_nucleotide_polymorphism]
Aspect: located_sequence_feature
Parent relationships: SNP is_a point_mutation	Child relationships:

SRP_RNA	SO:0000590
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]
Synonyms: [7S RNA] [signal_recognition_particle_RNA]
Aspect: located_sequence_feature
Parent relationships: SRP_RNA is_a ncRNA	Child relationships:

SRP_RNA_primary_transcript	SO:0000589
Definition: A primary transcript encoding a signal recognition particle RNA.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: SRP_RNA_primary_transcript is_a nc_primary_transcript	Child relationships:

STS	SO:0000331
Definition: 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.
DBxref:external reference [http:////www.biospace.com]
Synonyms: [sequence_tag_site]
Aspect: located_sequence_feature
Parent relationships: STS is_a tag	Child relationships:

Sarcin_like_RNA_motif	SO:0000024
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: Sarcin_like_RNA_motif is_a asymmetric_RNA_internal_loop	Child relationships:

Shine_Dalgarno_sequence	SO:0000552
Definition: Region in 5' UTR where ribosome assembles on mRNA.
DBxref:SO:ke
Synonyms: [five_prime_ribosome_binding_site] [RBS] [Shine-Dalgarno_sequence]
Aspect: located_sequence_feature
Parent relationships: Shine_Dalgarno_sequence is_a ribosome_entry_site	Child relationships:

TATA_box	SO:0000174
Definition: 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).
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: TATA_box part_of RNApol_II_promoter TATA_box is_a promotor_region TATA_box part_of RNApol_III_promoter	Child relationships:

TF_binding_site	SO:0000235
Definition: A region of a molecule that binds to a transcription factor.
DBxref:SO:ke
Synonyms: [transcription_factor_binding_site]
Aspect: located_sequence_feature
Parent relationships: TF_binding_site is_a regulatory_region TF_binding_site is_a protein_binding_site	Child relationships:

TF_module	SO:0000727
Definition: A regulatory_region where more than 1 TF_binding_site together are regulatorily active
DBxref:SO:SG
Synonyms: [cis_regulatory_module] [CRM]
Aspect: located_sequence_feature
Parent relationships: TF_module is_a regulatory_region	Child relationships:

T_to_A_transversion	SO:1000021
Definition: A transversion from T to A.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: T_to_A_transversion is_a pyrimidine_to_purine_transversion	Child relationships:

T_to_C_transition	SO:1000013
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: T_to_C_transition is_a pyrimidine_transition	Child relationships:

T_to_G_transversion	SO:1000022
Definition: A transversion from T to G.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: T_to_G_transversion is_a pyrimidine_to_purine_transversion	Child relationships:

U11_snRNA	SO:0000398
Definition: 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.
DBxref:PMID:9622129
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U11_snRNA is_a snRNA	Child relationships:

U12_intron	SO:0000295
Definition: A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
DBxref:PMID:9428511
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U12_intron is_a spliceosomal_intron	Child relationships:

U12_snRNA	SO:0000399
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U12_snRNA is_a snRNA	Child relationships:

U14_snRNA	SO:0000403
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U14_snRNA is_a snRNA	Child relationships:

U1_snRNA	SO:0000391
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U1_snRNA is_a snRNA	Child relationships:

U2_intron	SO:0000184
Definition: A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
DBxref:PMID:9428511
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U2_intron is_a spliceosomal_intron	Child relationships:

U2_snRNA	SO:0000392
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U2_snRNA is_a snRNA	Child relationships:

U3_LTR_region	SO:0000424
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U3_LTR_region is_a LTR_component	Child relationships: U3_five_prime_LTR_region is_a U3_LTR_region

U3_five_prime_LTR_region	SO:0000429
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U3_five_prime_LTR_region is_a five_prime_LTR_component U3_five_prime_LTR_region is_a U3_LTR_region	Child relationships:

U3_three_prime_LTR_region	SO:0000431
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U3_three_prime_LTR_region is_a three_prime_LTR_component	Child relationships:

U4_snRNA	SO:0000393
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U4_snRNA is_a snRNA	Child relationships:

U4atac_snRNA	SO:0000394
Definition: 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).
DBxref:PMID:=12409455
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U4atac_snRNA is_a snRNA	Child relationships:

U5_LTR_region	SO:0000422
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U5_LTR_region is_a LTR_component	Child relationships: U5_five_prime_LTR_region is_a U5_LTR_region

U5_five_prime_LTR_region	SO:0000428
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U5_five_prime_LTR_region is_a U5_LTR_region U5_five_prime_LTR_region is_a five_prime_LTR_component	Child relationships:

U5_snRNA	SO:0000395
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U5_snRNA is_a snRNA	Child relationships:

U5_three_prime_LTR_region	SO:0000432
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U5_three_prime_LTR_region is_a three_prime_LTR_component	Child relationships:

U6_snRNA	SO:0000396
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U6_snRNA is_a snRNA	Child relationships:

U6atac_snRNA	SO:0000397
Definition: 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).
DBxref:external reference [http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=1 2409455&dopt=Abstract]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: U6atac_snRNA is_a snRNA	Child relationships:

UAA_stop_codon_signal	SO:1001283
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: UAA_stop_codon_signal is_a stop_codon_signal	Child relationships:

UAG_stop_codon_signal	SO:1001282
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: UAG_stop_codon_signal is_a stop_codon_signal	Child relationships:

UGA_stop_codon_signal	SO:1001285
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: UGA_stop_codon_signal is_a stop_codon_signal	Child relationships:

UTR	SO:0000203
Definition: Messenger RNA sequences that are untranslated and lie five prime and three prime to sequences which are translated.
DBxref:SO:ke
Synonyms: [untranslated_region]
Aspect: located_sequence_feature
Parent relationships: UTR is_a mRNA_region	Child relationships: five_prime_UTR is_a UTR untranslated_region_polyicistronic_mRNA is_a UTR UTR_region part_of UTR internal_UTR is_a UTR three_prime_UTR is_a UTR

UTR_intron	SO:0000446
Definition: Intron located in the untranslated region.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: UTR_intron is_a intron	Child relationships: three_prime_UTR_intron is_a UTR_intron five_prime_UTR_intron is_a UTR_intron

UTR_region	SO:0000837
Definition: A region og UTR.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: UTR_region part_of UTR UTR_region is_a mRNA_region	Child relationships: upstream_AUG_codon is_a UTR_region ribosome_entry_site is_a UTR_region

VDJ_C_cluster	SO:0000541
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene.
DBxref:
Synonyms: [(VDJ)-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: VDJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of VDJ_C_cluster VDJ_gene part_of VDJ_C_cluster

VDJ_J_C_cluster	SO:0000487
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.
DBxref:
Synonyms: [(VDJ)-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: VDJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of VDJ_J_C_cluster J_gene part_of VDJ_J_C_cluster VDJ_gene part_of VDJ_J_C_cluster

VDJ_J_cluster	SO:0000488
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.
DBxref:
Synonyms: [(VDJ)-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: VDJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: J_gene part_of VDJ_J_cluster VDJ_gene part_of VDJ_J_cluster

VDJ_gene	SO:0000574
Definition: 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)
DBxref:
Synonyms: [V-D-J-GENE]
Aspect: located_sequence_feature
Parent relationships: VDJ_gene part_of V_VDJ_J_C_cluster VDJ_gene part_of VDJ_J_cluster VDJ_gene part_of V_VDJ_cluster VDJ_gene part_of VDJ_C_cluster VDJ_gene is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment VDJ_gene part_of V_VDJ_J_cluster VDJ_gene part_of V_VDJ_C_cluster VDJ_gene part_of VDJ_J_C_cluster	Child relationships:

VD_gene	SO:0000510
Definition: 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).
DBxref:
Synonyms: [V_D_GENE]
Aspect: located_sequence_feature
Parent relationships: VD_gene is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	Child relationships:

VJ_C_cluster	SO:0000489
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.
DBxref:
Synonyms: [(VJ)-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: VJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of VJ_C_cluster VJ_gene part_of VJ_C_cluster

VJ_J_C_cluster	SO:0000490
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.
DBxref:
Synonyms: [(VJ)-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: VJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of VJ_J_C_cluster VJ_gene part_of VJ_J_C_cluster J_gene part_of VJ_J_C_cluster

VJ_J_cluster	SO:0000491
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.
DBxref:
Synonyms: [(VJ)-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: VJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: VJ_gene part_of VJ_J_cluster J_gene part_of VJ_J_cluster

VJ_gene	SO:0000576
Definition: 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)
DBxref:
Synonyms: [V-J-GENE]
Aspect: located_sequence_feature
Parent relationships: VJ_gene part_of VJ_J_C_cluster VJ_gene part_of V_VJ_J_C_cluster VJ_gene part_of VJ_C_cluster VJ_gene part_of V_VJ_cluster VJ_gene part_of VJ_J_cluster VJ_gene is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment VJ_gene part_of V_VJ_J_cluster VJ_gene part_of V_VJ_C_cluster	Child relationships:

V_DJ_C_cluster	SO:0000542
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene.
DBxref:
Synonyms: [V-(DJ)-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of V_DJ_C_cluster V_gene part_of V_DJ_C_cluster DJ_gene part_of V_DJ_C_cluster

V_DJ_J_C_cluster	SO:0000564
Definition: 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.
DBxref:
Synonyms: [V-(DJ)-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of V_DJ_J_C_cluster V_gene part_of V_DJ_J_C_cluster J_gene part_of V_DJ_J_C_cluster DJ_gene part_of V_DJ_J_C_cluster

V_DJ_J_cluster	SO:0000519
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.
DBxref:
Synonyms: [V-(DJ)-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: V_gene part_of V_DJ_J_cluster J_gene part_of V_DJ_J_cluster DJ_gene part_of V_DJ_J_cluster

V_DJ_cluster	SO:0000518
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.
DBxref:
Synonyms: [V-(DJ)-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_DJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: V_gene part_of V_DJ_cluster DJ_gene part_of V_DJ_cluster

V_D_DJ_C_cluster	SO:0000527
Definition: 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.
DBxref:
Synonyms: [V-D-(DJ)-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_D_DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of V_D_DJ_C_cluster V_gene part_of V_D_DJ_C_cluster D_gene part_of V_D_DJ_C_cluster DJ_gene part_of V_D_DJ_C_cluster

V_D_DJ_J_C_cluster	SO:0000529
Definition: 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.
DBxref:
Synonyms: [V-D-(DJ)-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_D_DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of V_D_DJ_J_C_cluster V_gene part_of V_D_DJ_J_C_cluster D_gene part_of V_D_DJ_J_C_cluster J_gene part_of V_D_DJ_J_C_cluster DJ_gene part_of V_D_DJ_J_C_cluster

V_D_DJ_J_cluster	SO:0000530
Definition: 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.
DBxref:
Synonyms: [V-D-(DJ)-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_D_DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: V_gene part_of V_D_DJ_J_cluster D_gene part_of V_D_DJ_J_cluster J_gene part_of V_D_DJ_J_cluster DJ_gene part_of V_D_DJ_J_cluster

V_D_DJ_cluster	SO:0000528
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.
DBxref:
Synonyms: [V-D-(DJ)-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_D_DJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: V_gene part_of V_D_DJ_cluster D_gene part_of V_D_DJ_cluster DJ_gene part_of V_D_DJ_cluster

V_D_J_C_cluster	SO:0000531
Definition: 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.
DBxref:
Synonyms: [V-D-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_D_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of V_D_J_C_cluster V_gene part_of V_D_J_C_cluster D_gene part_of V_D_J_C_cluster J_gene part_of V_D_J_C_cluster

V_D_J_cluster	SO:0000532
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene.
DBxref:
Synonyms: [V-D-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_D_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: V_gene part_of V_D_J_cluster D_gene part_of V_D_J_cluster J_gene part_of V_D_J_cluster

V_J_C_cluster	SO:0000535
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene.
DBxref:
Synonyms: [V-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: C_gene part_of V_J_C_cluster V_gene part_of V_J_C_cluster J_gene part_of V_J_C_cluster

V_J_cluster	SO:0000534
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene.
DBxref:
Synonyms: [V-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: V_gene part_of V_J_cluster J_gene part_of V_J_cluster

V_VDJ_C_cluster	SO:0000520
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.
DBxref:
Synonyms: [V-(VDJ)-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_VDJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of V_VDJ_C_cluster V_gene part_of V_VDJ_C_cluster VDJ_gene part_of V_VDJ_C_cluster

V_VDJ_J_C_cluster	SO:0000565
Definition: 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.
DBxref:
Synonyms: [V-(VDJ)-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_VDJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of V_VDJ_J_C_cluster V_gene part_of V_VDJ_J_C_cluster J_gene part_of V_VDJ_J_C_cluster VDJ_gene part_of V_VDJ_J_C_cluster

V_VDJ_J_cluster	SO:0000522
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.
DBxref:
Synonyms: [V-(VDJ)-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_VDJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: V_gene part_of V_VDJ_J_cluster J_gene part_of V_VDJ_J_cluster VDJ_gene part_of V_VDJ_J_cluster

V_VDJ_cluster	SO:0000521
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.
DBxref:
Synonyms: [V-(VDJ)-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_VDJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: V_gene part_of V_VDJ_cluster VDJ_gene part_of V_VDJ_cluster

V_VJ_C_cluster	SO:0000523
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.
DBxref:
Synonyms: [V-(VJ)-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_VJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of V_VJ_C_cluster V_gene part_of V_VJ_C_cluster VJ_gene part_of V_VJ_C_cluster

V_VJ_J_C_cluster	SO:0000566
Definition: 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.
DBxref:
Synonyms: [V-(VJ)-J-C-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_VJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: C_gene part_of V_VJ_J_C_cluster V_gene part_of V_VJ_J_C_cluster VJ_gene part_of V_VJ_J_C_cluster J_gene part_of V_VJ_J_C_cluster

V_VJ_J_cluster	SO:0000525
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.
DBxref:
Synonyms: [V-(VJ)-J-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_VJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: V_gene part_of V_VJ_J_cluster VJ_gene part_of V_VJ_J_cluster J_gene part_of V_VJ_J_cluster

V_VJ_cluster	SO:0000524
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.
DBxref:
Synonyms: [V-(VJ)-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_VJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	Child relationships: V_gene part_of V_VJ_cluster VJ_gene part_of V_VJ_cluster

V_cluster	SO:0000526
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.
DBxref:
Synonyms: [V-CLUSTER]
Aspect: located_sequence_feature
Parent relationships: V_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: V_gene part_of V_cluster

V_gene	SO:0000466
Definition: Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.
DBxref:
Synonyms: [V_GENE] [variable_gene]
Aspect: located_sequence_feature
Parent relationships: V_gene part_of V_VDJ_cluster V_gene part_of V_D_J_cluster V_gene part_of V_D_DJ_C_cluster V_gene part_of V_VJ_J_C_cluster V_gene part_of V_D_J_C_cluster V_gene part_of V_D_DJ_J_C_cluster V_gene part_of V_DJ_J_cluster V_gene part_of V_cluster V_gene part_of V_J_C_cluster V_gene part_of V_DJ_C_cluster V_gene part_of V_D_DJ_J_cluster V_gene part_of V_VDJ_C_cluster V_gene part_of V_VJ_C_cluster V_gene part_of V_D_DJ_cluster V_gene part_of V_VDJ_J_C_cluster V_gene is_a vertebrate_immunoglobulin_T_cell_receptor_segment V_gene part_of V_VJ_cluster V_gene part_of V_J_cluster V_gene part_of V_VDJ_J_cluster V_gene part_of V_DJ_J_C_cluster V_gene part_of V_VJ_J_cluster V_gene part_of V_DJ_cluster	Child relationships:

V_gene_recombination_feature	SO:0000538
Definition: 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.
DBxref:
Synonyms: [V-RS]
Aspect: located_sequence_feature
Parent relationships: V_gene_recombination_feature is_a vertebrate_immune_system_gene_recombination_signal_feature	Child relationships: V_spacer part_of V_gene_recombination_feature V_nonamer part_of V_gene_recombination_feature V_heptamer part_of V_gene_recombination_feature

V_heptamer	SO:0000533
Definition: 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
DBxref:
Synonyms: [V-HEPTAMER]
Aspect: located_sequence_feature
Parent relationships: V_heptamer is_a heptamer_of_recombination_feature_of_vertebrate_immune_system_gene V_heptamer part_of V_gene_recombination_feature	Child relationships:

V_nonamer	SO:0000536
Definition: 9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
DBxref:
Synonyms: [V-NONAMER]
Aspect: located_sequence_feature
Parent relationships: V_nonamer is_a nonamer_of_recombination_feature_of_vertebrate_immune_system_gene V_nonamer part_of V_gene_recombination_feature	Child relationships:

V_spacer	SO:0000537
Definition: 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.
DBxref:
Synonyms: [V-SPACER]
Aspect: located_sequence_feature
Parent relationships: V_spacer is_a vertebrate_immune_system_gene_recombination_spacer V_spacer part_of V_gene_recombination_feature	Child relationships:

WC_base_pair	SO:0000029
Definition: The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.
DBxref:PMID:12177293
Synonyms: [Watson_Crick_based_pair]
Aspect: located_sequence_feature
Parent relationships: WC_base_pair is_a base_pair	Child relationships:

YAC	SO:0000152
Definition: Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: YAC is_a vector	Child relationships:

Y_RNA	SO:0000405
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: Y_RNA is_a ncRNA	Child relationships:

aberrant_processed_transcript	SO:0000681
Definition: A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: aberrant_processed_transcript is_a processed_transcript	Child relationships:

adaptive_island	SO:0000775
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: adaptive_island is_a genomic_island	Child relationships:

alanine_tRNA_primary_transcript	SO:0000211
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: alanine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

alanyl_tRNA	SO:0000254
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: alanyl_tRNA is_a tRNA	Child relationships:

amplification_origin	SO:0000750
Definition: An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: amplification_origin is_a origin_of_replication	Child relationships:

anchor_region	SO:0000931
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: anchor_region is_a guide_RNA_region	Child relationships:

antisense_RNA	SO:0000644
Definition: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: antisense_RNA is_a ncRNA	Child relationships: MicF_RNA is_a antisense_RNA

antisense_primary_transcript	SO:0000645
Definition: The reverse complement of the primary transcript.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: antisense_primary_transcript is_a primary_transcript	Child relationships:

aptamer	SO:0000031
Definition: DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.
DBxref:external reference [http://http://aptamer.icmb.utexas.edu]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: aptamer is_a oligo	Child relationships: RNA_aptamer is_a aptamer DNA_aptamer is_a aptamer

arginine_tRNA_primary_transcript	SO:0000212
Definition: A primary transcript encoding arginyl tRNA (SO:0000255).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: arginine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

asparagine_tRNA_primary_transcript	SO:0000213
Definition: A primary transcript encoding asparaginyl tRNA (SO:0000256).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: asparagine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

asparaginyl_tRNA	SO:0000256
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: asparaginyl_tRNA is_a tRNA	Child relationships:

aspartic_acid_tRNA_primary_transcript	SO:0000214
Definition: A primary transcript encoding aspartyl tRNA (SO:0000257).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: aspartic_acid_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

aspartyl_tRNA	SO:0000257
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: aspartyl_tRNA is_a tRNA	Child relationships:

assembly	SO:0000353
Definition: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: assembly is_a region	Child relationships: gap part_of assembly contig is_a assembly tiling_path is_a assembly supercontig is_a assembly ultracontig is_a assembly golden_path is_a assembly virtual_sequence is_a assembly

assembly_component	SO:0000143
Definition: A region of sequence which may be used to manufacture a longer assembled, sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: assembly_component is_a region	Child relationships: golden_path_fragment is_a assembly_component tiling_path_fragment is_a assembly_component gap is_a assembly_component contig is_a assembly_component read_pair is_a assembly_component read is_a assembly_component

asymmetric_RNA_internal_loop	SO:0000021
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: asymmetric_RNA_internal_loop is_a RNA_internal_loop	Child relationships: A_minor_RNA_motif is_a asymmetric_RNA_internal_loop K_turn_RNA_motif is_a asymmetric_RNA_internal_loop Sarcin_like_RNA_motif is_a asymmetric_RNA_internal_loop

attI_site	SO:0000367
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: attI_site is_a sequence_rearrangement_feature attI_site part_of integron	Child relationships:

attenuator	SO:0000140
Definition: A sequence segment located between the promoter and a structural gene that causes partial termination of transcription.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: attenuator is_a regulatory_region attenuator is_a gene_group_regulatory_region	Child relationships:

autocatalytically_spliced_intron	SO:0000588
Definition: A self spliced intron.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: autocatalytically_spliced_intron is_a intron autocatalytically_spliced_intron is_a ribozyme	Child relationships:

bacterial_RNApol_promoter	SO:0000613
Definition: A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: bacterial_RNApol_promoter is_a gene_group_regulatory_region bacterial_RNApol_promoter is_a promoter	Child relationships: bacterial_RNApol_promotor_region part_of bacterial_RNApol_promoter

bacterial_RNApol_promotor_region	SO:0000843
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: bacterial_RNApol_promotor_region is_a promotor_region bacterial_RNApol_promotor_region part_of bacterial_RNApol_promoter	Child relationships: minus_35_signal is_a bacterial_RNApol_promotor_region minus_10_signal is_a bacterial_RNApol_promotor_region

bacterial_terminator	SO:0000614
Definition: A terminator signal for bacterial transcription.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: bacterial_terminator is_a terminator	Child relationships:

base_pair	SO:0000028
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: base_pair is_a sequence_secondary_structure	Child relationships: reverse_Hoogsteen_base_pair is_a base_pair Hoogsteen_base_pair is_a base_pair sugar_edge_base_pair is_a base_pair WC_base_pair is_a base_pair

bidirectional_promotor	SO:0000568
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: bidirectional_promotor is_a promoter	Child relationships:

binding_site	SO:0000409
Definition: A region on the surface of a molecule that may interact with another molecule.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: binding_site is_a region	Child relationships: protein_binding_site is_a binding_site primer_binding_site is_a binding_site

blocked_reading_frame	SO:0000718
Definition: A reading_frame that is interupted by one or more stop codons; usually identified through intergenomic sequence comparisons.
DBxref:SO:rb
Synonyms:
Aspect: located_sequence_feature
Parent relationships: blocked_reading_frame is_a reading_frame	Child relationships:

branch_site	SO:0000611
Definition: 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.
DBxref:SO:ke
Synonyms: [branch_point]
Aspect: located_sequence_feature
Parent relationships: branch_site is_a spliceosomal_intron_region	Child relationships:

cDNA_clone	SO:0000317
Definition: Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
DBxref:external reference [http:////seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: cDNA_clone is_a clone	Child relationships:

cDNA_match	SO:0000689
Definition: A match against cDNA sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: cDNA_match is_a expressed_sequence_match	Child relationships:

canonical_five_prime_splice_site	SO:0000677
Definition: The canonical 5' splice site has the sequence "GT".
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: canonical_five_prime_splice_site is_a five_prime_splice_site canonical_five_prime_splice_site is_a canonical_splice_site	Child relationships:

canonical_splice_site	SO:0000675
Definition: The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: canonical_splice_site is_a splice_site	Child relationships: canonical_three_prime_splice_site is_a canonical_splice_site canonical_five_prime_splice_site is_a canonical_splice_site

canonical_three_prime_splice_site	SO:0000676
Definition: The canonical 3' splice site has the sequence "AG".
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: canonical_three_prime_splice_site is_a three_prime_splice_site canonical_three_prime_splice_site is_a canonical_splice_site	Child relationships:

cap	SO:0000581
Definition: 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.
DBxref:external reference [http:////seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: cap is_a region	Child relationships:

centromere	SO:0000577
Definition: A region of chromosome where the spindle fibers attach during mitosis and meiosis.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: centromere is_a chromosomal_structural_element	Child relationships:

chromosomal_regulatory_element	SO:0000626
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: chromosomal_regulatory_element is_a chromosome_region	Child relationships: matrix_attachment_site is_a chromosomal_regulatory_element

chromosomal_structural_element	SO:0000628
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: chromosomal_structural_element is_a chromosome_region	Child relationships: telomere is_a chromosomal_structural_element centromere is_a chromosomal_structural_element

chromosome	SO:0000340
Definition: Structural unit composed of long DNA molecule.
DBxref:external reference [http:////biotech.icmb.utexas.edu/search/dict-search.mhtml]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: chromosome is_a region	Child relationships: chromosome_region part_of chromosome

chromosome_arm	SO:0000105
Definition: 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.
DBxref:external reference [http:////www.exactsciences.com/cic/glossary/_index.htm]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: chromosome_arm is_a chromosome_region	Child relationships:

chromosome_band	SO:0000341
Definition: A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
DBxref:SO:ma
Synonyms: [cytological_band]
Aspect: located_sequence_feature
Parent relationships: chromosome_band is_a chromosome_region	Child relationships: interband is_a chromosome_band

chromosome_breakage_sequence	SO:0000670
Definition: A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: chromosome_breakage_sequence is_a sequence_rearrangement_feature	Child relationships:

chromosome_region	SO:0000830
Definition: A region of a chromosome
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: chromosome_region part_of chromosome chromosome_region is_a region	Child relationships: chromosomal_structural_element is_a chromosome_region chromosome_arm is_a chromosome_region introgressed_chromosome_region is_a chromosome_region chromosomal_regulatory_element is_a chromosome_region chromosome_band is_a chromosome_region

clip	SO:0000303
Definition: Part of the primary transcript that is clipped off during processing.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: clip is_a primary_transcript_region	Child relationships: five_prime_clip is_a clip three_prime_clip is_a clip

clone	SO:0000151
Definition: A piece of DNA that has been inserted in a vector so that it can be propagated in E. coli or some other organism.
DBxref:external reference [http:////www.geospiza.com/community/support/glossary/]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: clone is_a reagent	Child relationships: cDNA_clone is_a clone genomic_clone is_a clone vector part_of clone tiling_path_clone is_a clone

clone_insert	SO:0000753
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: clone_insert is_a reagent	Child relationships: clone_insert_end part_of clone_insert cloned_region part_of clone_insert clone_insert_start part_of clone_insert

clone_insert_end	SO:0000103
Definition: The end of the clone insert.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: clone_insert_end part_of clone_insert clone_insert_end is_a junction	Child relationships:

clone_insert_start	SO:0000179
Definition: The start of the clone insert.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: clone_insert_start part_of clone_insert clone_insert_start is_a junction	Child relationships:

cloned_region	SO:0000785
Definition: undefined
DBxref:
Synonyms: [cloned segment]
Aspect: located_sequence_feature
Parent relationships: cloned_region part_of clone_insert cloned_region is_a reagent	Child relationships:

coding_conserved_region	SO:0000332
Definition: Coding region of sequence similarity by descent from a common ancestor.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: coding_conserved_region is_a conserved_region	Child relationships:

coding_end	SO:0000327
Definition: The last base to be translated into protein. It does not include the stop codon.
DBxref:SO:ke
Synonyms: [translation_end]
Aspect: located_sequence_feature
Parent relationships: coding_end is_a CDS_region	Child relationships:

coding_exon	SO:0000195
Definition: An exon whereby at least one base is part of a codon, including the stop_codon.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: coding_exon is_a exon	Child relationships: five_prime_exon_coding_region is_a coding_exon three_prime_exon_coding_region is_a coding_exon interior_coding_exon is_a coding_exon

coding_start	SO:0000323
Definition: The first base to be translated into protein.
DBxref:SO:ke
Synonyms: [translation_start]
Aspect: located_sequence_feature
Parent relationships: coding_start is_a CDS_region	Child relationships:

codon	SO:0000360
Definition: 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.
DBxref:external reference [http:////genomics.phrma.org/lexicon/c.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: codon is_a mRNA_region	Child relationships: stop_codon is_a codon start_codon is_a codon recoded_codon is_a codon

complex_substitution	SO:1000005
Definition: 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.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: complex_substitution is_a substitution	Child relationships:

conjugative_transposon	SO:0000371
Definition: A transposon that encodes function required for conjugation.
DBxref:external reference [http:////www.sci.sdsu.edu/ ~ smaloy/Glossary/C.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: conjugative_transposon is_a DNA_transposon	Child relationships:

conserved_region	SO:0000330
Definition: Region of sequence similarity by descent from a common ancestor.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: conserved_region is_a region	Child relationships: nc_conserved_region is_a conserved_region coding_conserved_region is_a conserved_region

contig	SO:0000149
Definition: A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unvailable bases.
DBxref:SO:ls
Synonyms:
Aspect: located_sequence_feature
Parent relationships: contig is_a assembly contig part_of supercontig contig is_a assembly_component	Child relationships: read_pair part_of contig read part_of contig

contig_read	SO:0000476
Definition: A DNA sequencer read which is part of a contig.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: contig_read is_a read	Child relationships:

cosmid	SO:0000156
Definition: 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.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: cosmid is_a vector	Child relationships:

cross_genome_match	SO:0000177
Definition: A nucleotide match against a sequence from another organism.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: cross_genome_match is_a nucleotide_match	Child relationships:

cysteine_tRNA_primary_transcript	SO:0000215
Definition: A primary transcript encoding cysteinyl tRNA (SO:0000258).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: cysteine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

cysteinyl_tRNA	SO:0000258
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: cysteinyl_tRNA is_a tRNA	Child relationships:

databank_entry	SO:2000061
Definition: The sequence referred to by an entry in a databank such as Genbank or SwissProt.
DBxref:SO:ke
Synonyms: [accession]
Aspect: located_sequence_feature
Parent relationships: databank_entry is_a reagent	Child relationships:

decayed_exon	SO:0000464
Definition: A non-functional descendent of an exon.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: decayed_exon non_functional_homolog_of exon decayed_exon is_a pseudogenic_region	Child relationships:

dinucleotide_repeat_microsatellite_feature	SO:0000290
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: dinucleotide_repeat_microsatellite_feature is_a microsatellite	Child relationships:

direct_repeat	SO:0000314
Definition: A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: direct_repeat is_a repeat_region	Child relationships:

dispersed_repeat	SO:0000658
Definition: A repeat that is located at dispersed sites in the genome.
DBxref:SO:ke
Synonyms: [interspersed_repeat]
Aspect: located_sequence_feature
Parent relationships: dispersed_repeat is_a repeat_region	Child relationships:

distant_three_prime_recoding_signal	SO:1001287
Definition: A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon.
DBxref:external reference [http:////www.ncbi.nlm.nih.gov 80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: distant_three_prime_recoding_signal is_a three_prime_recoding_site	Child relationships:

ds_oligo	SO:0000442
Definition: A double stranded oligonucleotide.
DBxref:SO:ke
Synonyms: [double stranded oligonucleotide] [ds_oligonucleotide]
Aspect: located_sequence_feature
Parent relationships: ds_oligo is_a oligo	Child relationships:

edited_transcript_feature	SO:0000579
Definition: A locatable feature on a transcript that is edited.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: edited_transcript_feature is_a transcript_region	Child relationships: unedited_region is_a edited_transcript_feature editing_domain is_a edited_transcript_feature editing_block is_a edited_transcript_feature pre_edited_region is_a edited_transcript_feature

editing_block	SO:0000604
Definition: Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
DBxref:external reference [http:////www.rna.ucla/]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: editing_block is_a edited_transcript_feature	Child relationships:

editing_domain	SO:0000606
Definition: Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
DBxref:external reference [http:////www.rna.ucla/]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: editing_domain is_a edited_transcript_feature	Child relationships:

enhancer	SO:0000165
Definition: 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.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: enhancer is_a regulatory_region	Child relationships:

enzymatic_RNA	SO:0000372
Definition: A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: enzymatic_RNA is_a ncRNA	Child relationships: RNase_MRP_RNA is_a enzymatic_RNA telomerase_RNA is_a enzymatic_RNA ribozyme is_a enzymatic_RNA

episome	SO:0000768
Definition: A plasmid that may integrate with a chromosome.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: episome is_a plasmid	Child relationships:

exon	SO:0000147
Definition: 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).
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: exon is_a transcript_region	Child relationships: decayed_exon non_functional_homolog_of exon single_exon is_a exon interior_exon is_a exon coding_exon is_a exon three_prime_coding_exon is_a exon pseudogenic_exon non_functional_homolog_of exon five_prime_coding_exon is_a exon noncoding_exon is_a exon

exon_junction	SO:0000333
Definition: The boundary between two exons in a processed transcript.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: exon_junction is_a junction exon_junction part_of processed_transcript	Child relationships:

exon_region	SO:0000852
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: exon_region is_a transcript_region	Child relationships: three_prime_exon_noncoding_region is_a exon_region five_prime_exon_noncoding_region is_a exon_region

exonic_splice_enhancer	SO:0000683
Definition: Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.
DBxref:external reference [http:////www.ncbi.nlm.nih.gov 80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: exonic_splice_enhancer is_a splice_enhancer	Child relationships:

experimental_result_region	SO:0000703
Definition: A region of sequence implicated in an experimental result.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: experimental_result_region is_a remark	Child relationships:

expressed_sequence_match	SO:0000102
Definition: A match to an EST or cDNA sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: expressed_sequence_match is_a nucleotide_match	Child relationships: cDNA_match is_a expressed_sequence_match EST_match is_a expressed_sequence_match

external_transcribed_spacer_region	SO:0000640
Definition: Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: external_transcribed_spacer_region is_a transcribed_spacer_region	Child relationships:

five_prime_D_heptamer	SO:0000496
Definition: 7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
DBxref:
Synonyms: [5'D-HEPTAMER]
Aspect: located_sequence_feature
Parent relationships: five_prime_D_heptamer part_of five_prime_D_recombination_signal_sequence five_prime_D_heptamer is_a heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	Child relationships:

five_prime_D_nonamer	SO:0000497
Definition: 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.
DBxref:
Synonyms: [5'D-NONAMER]
Aspect: located_sequence_feature
Parent relationships: five_prime_D_nonamer part_of five_prime_D_recombination_signal_sequence five_prime_D_nonamer is_a nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	Child relationships:

five_prime_D_recombination_signal_sequence	SO:0000556
Definition: 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.
DBxref:
Synonyms: [5'RS] [five_prime_D-recombination_signal_sequence]
Aspect: located_sequence_feature
Parent relationships: five_prime_D_recombination_signal_sequence is_a D_gene_recombination_feature	Child relationships: five_prime_D_nonamer part_of five_prime_D_recombination_signal_sequence five_prime_D_spacer part_of five_prime_D_recombination_signal_sequence five_prime_D_heptamer part_of five_prime_D_recombination_signal_sequence

five_prime_D_spacer	SO:0000498
Definition: 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.
DBxref:
Synonyms: [5'-SPACER] [five_prime_D-spacer]
Aspect: located_sequence_feature
Parent relationships: five_prime_D_spacer part_of five_prime_D_recombination_signal_sequence five_prime_D_spacer is_a vertebrate_immune_system_gene_recombination_spacer	Child relationships:

five_prime_LTR	SO:0000425
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_LTR is_a long_terminal_repeat	Child relationships: five_prime_LTR_component part_of five_prime_LTR

five_prime_LTR_component	SO:0000850
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_LTR_component is_a LTR_component five_prime_LTR_component part_of five_prime_LTR	Child relationships: U3_five_prime_LTR_region is_a five_prime_LTR_component U5_five_prime_LTR_region is_a five_prime_LTR_component R_five_prime_LTR_region is_a five_prime_LTR_component

five_prime_UTR	SO:0000204
Definition: A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
DBxref:
Synonyms: [five_prime_untranslated_region]
Aspect: located_sequence_feature
Parent relationships: five_prime_UTR is_a UTR	Child relationships: five_prime_open_reading_frame part_of five_prime_UTR

five_prime_UTR_intron	SO:0000447
Definition: An intron located in the 5' UTR.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_UTR_intron is_a UTR_intron	Child relationships:

five_prime_clip	SO:0000555
Definition: 5' most region of a precursor transcript that is clipped off during processing.
DBxref:
Synonyms: [five_prime_-clip]
Aspect: located_sequence_feature
Parent relationships: five_prime_clip is_a clip	Child relationships:

five_prime_coding_exon	SO:0000200
Definition: The 5' most coding exon.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_coding_exon is_a exon	Child relationships: five_prime_exon_coding_region part_of five_prime_coding_exon five_prime_exon_noncoding_region part_of five_prime_coding_exon

five_prime_exon_coding_region	SO:0000196
Definition: The sequence of the 5' exon that encodes for protein.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_exon_coding_region is_a coding_exon five_prime_exon_coding_region part_of five_prime_coding_exon	Child relationships:

five_prime_exon_noncoding_region	SO:0000486
Definition: The sequence of the 5' exon preceeding the start codon.
DBxref:SO:ke
Synonyms: [five_prime_exon_noncoding_region]
Aspect: located_sequence_feature
Parent relationships: five_prime_exon_noncoding_region is_a exon_region five_prime_exon_noncoding_region part_of five_prime_coding_exon	Child relationships:

five_prime_intron	SO:0000190
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_intron is_a intron	Child relationships:

five_prime_noncoding_exon	SO:0000445
Definition: Non-coding exon in the 5' UTR.
DBxref:SO:ke
Synonyms: [five_prime_noncoding_exon]
Aspect: located_sequence_feature
Parent relationships: five_prime_noncoding_exon is_a noncoding_exon	Child relationships:

five_prime_open_reading_frame	SO:0000629
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_open_reading_frame part_of five_prime_UTR five_prime_open_reading_frame is_a mRNA_region	Child relationships:

five_prime_recoding_site	SO:1001280
Definition: The recoding signal found 5' of the redefined codon.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_recoding_site is_a recoding_stimulatory_region	Child relationships:

five_prime_splice_site	SO:0000163
Definition: The junction between the 3 prime end of an exon and the following intron.
DBxref:external reference [http:////www.ucl.ac.uk/ ~ ucbhjow/b241/glossary.html]
Synonyms: [donor] [donor_splice_site] [splice_donor_site]
Aspect: located_sequence_feature
Parent relationships: five_prime_splice_site is_a splice_site	Child relationships: trans_splice_donor_site is_a five_prime_splice_site non_canonical_five_prime_splice_site is_a five_prime_splice_site canonical_five_prime_splice_site is_a five_prime_splice_site

five_prime_terminal_inverted_repeat	SO:0000420
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_terminal_inverted_repeat is_a terminal_inverted_repeat	Child relationships:

flanking_region	SO:0000239
Definition: The DNA sequences extending on either side of a specific locus.
DBxref:external reference [http:////biotech.icmb.utexas.edu/search/dict-search.mhtml]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: flanking_region is_a region	Child relationships: transposable_element_flanking_region is_a flanking_region

flanking_three_prime_quadruplet_recoding_signal	SO:1001281
Definition: Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: flanking_three_prime_quadruplet_recoding_signal is_a three_prime_recoding_site	Child relationships:

foldback_element	SO:0000238
Definition: A transposable element with extensive secondary structure, characterised by large modular imperfect long inverted repeats
DBxref:external reference [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]
Synonyms: [long inverted repeat element] [LVR element]
Aspect: located_sequence_feature
Parent relationships: foldback_element is_a DNA_transposon	Child relationships:

forward_primer	SO:0000121
Definition: A single stranded oligo used for polymerase chain reaction.
DBxref:external reference [http:////mged.sourceforge.net/ontologies/MGEDontology.php]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: forward_primer is_a primer	Child relationships:

fosmid	SO:0000158
Definition: A cloning vector that utilises the E. coli F factor.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: fosmid is_a vector	Child relationships:

four_bp_start_codon	SO:1001269
Definition: A non-canonical start codon with 4 pase pairs.
DBxref:SO:ke
Synonyms: [4bp_start_codon]
Aspect: located_sequence_feature
Parent relationships: four_bp_start_codon is_a non_canonical_start_codon	Child relationships:

gap	SO:0000730
Definition: A gap in the sequence of known length. The unkown bases are filled in with N's.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: gap part_of assembly gap is_a assembly_component	Child relationships:

gene	SO:0000704
Definition: 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
DBxref:SO:rd
Synonyms:
Aspect: located_sequence_feature
Parent relationships: gene member_of gene_group gene is_a region	Child relationships: gene_component_region part_of gene gene_member_region member_of gene pseudogene non_functional_homolog_of gene

gene_array	SO:0005851
Definition: 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.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: gene_array is_a gene_group	Child relationships: gene_subarray is_a gene_array

gene_cassette	SO:0005853
Definition: A non-functional gene that, when captured by recombination forms a functional gene.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: gene_cassette is_a gene_group	Child relationships: gene_cassette_array is_a gene_cassette

gene_cassette_array	SO:0005854
Definition: An array of non-functional genes whose members, when captured by recombination form functional genes.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: gene_cassette_array is_a gene_cassette	Child relationships:

gene_component_region	SO:0000842
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: gene_component_region part_of gene gene_component_region is_a region	Child relationships: non_transcribed_region is_a gene_component_region

gene_group	SO:0005855
Definition: A collection of related genes.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: gene_group is_a region	Child relationships: gene_cassette is_a gene_group operon is_a gene_group gene_group_regulatory_region member_of gene_group regulon is_a gene_group gene_array is_a gene_group gene member_of gene_group

gene_group_regulatory_region	SO:0000752
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: gene_group_regulatory_region is_a regulatory_region gene_group_regulatory_region member_of gene_group	Child relationships: terminator is_a gene_group_regulatory_region attenuator is_a gene_group_regulatory_region bacterial_RNApol_promoter is_a gene_group_regulatory_region operator is_a gene_group_regulatory_region

gene_member_region	SO:0000831
Definition: A region of a gene.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: gene_member_region member_of gene gene_member_region is_a region	Child relationships: regulatory_region is_a gene_member_region transcript is_a gene_member_region

gene_subarray	SO:0005852
Definition: 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.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: gene_subarray is_a gene_array	Child relationships:

genomic_clone	SO:0000040
Definition: A clone of a DNA region of a genome.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: genomic_clone is_a clone	Child relationships:

genomic_island	SO:0000772
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: genomic_island is_a region	Child relationships: adaptive_island is_a genomic_island pathogenic_island is_a genomic_island metabolic_island is_a genomic_island symbiosis_island is_a genomic_island

glutamic_acid_tRNA_primary_transcript	SO:0000216
Definition: A primary transcript encoding glutaminyl tRNA (SO:0000260).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: glutamic_acid_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

glutamine_tRNA_primary_transcript	SO:0000217
Definition: A primary transcript encoding glutamyl tRNA (SO:0000260).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: glutamine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

glutaminyl_tRNA	SO:0000259
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: glutaminyl_tRNA is_a tRNA	Child relationships:

glutamyl_tRNA	SO:0000260
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: glutamyl_tRNA is_a tRNA	Child relationships:

glycine_tRNA_primary_transcript	SO:0000218
Definition: A primary transcript encoding glycyl tRNA (SO:0000263).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: glycine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

glycyl_tRNA	SO:0000261
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: glycyl_tRNA is_a tRNA	Child relationships:

golden_path	SO:0000688
Definition: A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
DBxref:SO:ls
Synonyms:
Aspect: located_sequence_feature
Parent relationships: golden_path is_a assembly	Child relationships: golden_path_fragment part_of golden_path

golden_path_fragment	SO:0000468
Definition: One of the pieces of sequence that make up a golden path.
DBxref:SO:rd
Synonyms:
Aspect: located_sequence_feature
Parent relationships: golden_path_fragment part_of golden_path golden_path_fragment is_a assembly_component	Child relationships:

group_1_intron_homing_endonuclease_target_region	SO:0000354
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: group_1_intron_homing_endonuclease_target_region is_a nuclease_sensitive_site	Child relationships:

group_IIA_intron	SO:0000381
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: group_IIA_intron is_a group_II_intron	Child relationships:

group_IIB_intron	SO:0000382
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: group_IIB_intron is_a group_II_intron	Child relationships:

group_II_intron	SO:0000603
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/Software/Rfam/browse/index.shtml]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: group_II_intron is_a intron	Child relationships: group_IIB_intron is_a group_II_intron group_IIA_intron is_a group_II_intron

group_I_intron	SO:0000587
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: group_I_intron is_a intron	Child relationships:

guide_RNA	SO:0000602
Definition: 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.
DBxref:external reference [http:////www.rna.ucla.edu/index.html]
Synonyms: [gRNA]
Aspect: located_sequence_feature
Parent relationships: guide_RNA is_a ncRNA	Child relationships: oligo_U_tail adjacent_to guide_RNA guide_RNA_region part_of guide_RNA

guide_RNA_region	SO:0000930
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: guide_RNA_region is_a processed_transcript_region guide_RNA_region part_of guide_RNA	Child relationships: anchor_region is_a guide_RNA_region

hammerhead_ribozyme	SO:0000380
Definition: 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.
DBxref:external reference [http://rnaworld.bio.ukans.edu/class/RNA/RNA00/RNA_World_3.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: hammerhead_ribozyme is_a ribozyme	Child relationships:

haplotype_block	SO:0000355
Definition: 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.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: haplotype_block is_a recombination_feature	Child relationships:

helitron	SO:0000544
Definition: 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.
DBxref:external reference [http:////www.pnas.org/cgi/content/full/100/11/6569]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: helitron is_a transposable_element	Child relationships:

heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000561
Definition: 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
DBxref:
Synonyms: [HEPTAMER]
Aspect: located_sequence_feature
Parent relationships: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene is_a vertebrate_immune_system_gene_recombination_signal_feature	Child relationships: three_prime_D_heptamer is_a heptamer_of_recombination_feature_of_vertebrate_immune_system_gene J_heptamer is_a heptamer_of_recombination_feature_of_vertebrate_immune_system_gene five_prime_D_heptamer is_a heptamer_of_recombination_feature_of_vertebrate_immune_system_gene V_heptamer is_a heptamer_of_recombination_feature_of_vertebrate_immune_system_gene

histidine_tRNA_primary_transcript	SO:0000219
Definition: A primary transcript encoding histidyl tRNA (SO:0000262).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: histidine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

histidyl_tRNA	SO:0000262
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: histidyl_tRNA is_a tRNA	Child relationships:

iDNA	SO:0000723
Definition: Genomic sequence removed from the genome, as a normal event, by a process of recombination.
DBxref:SO:ma
Synonyms: [intervening DNA]
Aspect: located_sequence_feature
Parent relationships: iDNA is_a recombination_feature	Child relationships:

indel	SO:1000032
Definition: A hybrid term (insertion/deletion) to describe sequence length change when the direction of the change is unspecified.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: indel is_a sequence_variant	Child relationships: nucleotide_insertion is_a indel nucleotide_deletion is_a indel

insulator	SO:0000627
Definition: undefined
DBxref:
Synonyms: [insulator_element]
Aspect: located_sequence_feature
Parent relationships: insulator is_a regulatory_region	Child relationships:

integrase_coding_region	SO:0000369
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: integrase_coding_region is_a sequence_rearrangement_feature integrase_coding_region part_of integron	Child relationships:

integrated_virus	SO:0000113
Definition: A viral sequence which has integrated into the host genome.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: integrated_virus is_a region	Child relationships:

integron	SO:0000365
Definition: DNA elements capable of mobilizing individual gene cassettes into bacterial chromosomes by site- specific recombination.
DBxref:external reference [http:////www.genomicglossaries.com/content/DNA.asp]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: integron is_a sequence_rearrangement_feature	Child relationships: attI_site part_of integron integrase_coding_region part_of integron

intein	SO:0000728
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: intein is_a polypeptide_region	Child relationships:

interband	SO:0000450
Definition: A light region between two darkly staining bands in a polytene chromosome.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: interband is_a chromosome_band	Child relationships:

intergenic_region	SO:0000605
Definition: The region between two known genes.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: intergenic_region is_a region	Child relationships:

interior_coding_exon	SO:0000004
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: interior_coding_exon is_a coding_exon	Child relationships:

interior_exon	SO:0000201
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: interior_exon is_a exon	Child relationships:

interior_intron	SO:0000191
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: interior_intron is_a intron	Child relationships:

internal_Shine_Dalgarno_sequence	SO:1001260
Definition: A Shine Delgarno sequence that is upstream of a non-5' CDS in a polycistronic mRNA.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: internal_Shine_Dalgarno_sequence is_a recoding_stimulatory_region internal_Shine_Dalgarno_sequence is_a internal_ribosome_entry_site	Child relationships:

internal_UTR	SO:0000241
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: internal_UTR is_a UTR	Child relationships:

internal_eliminated_sequence	SO:0000671
Definition: A sequence eliminated from the genome of ciliates during nuclear differentiation.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: internal_eliminated_sequence is_a sequence_rearrangement_feature	Child relationships:

internal_ribosome_entry_site	SO:0000243
Definition: Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
DBxref:SO:ke
Synonyms: [IRES]
Aspect: located_sequence_feature
Parent relationships: internal_ribosome_entry_site is_a ribosome_entry_site	Child relationships: internal_Shine_Dalgarno_sequence is_a internal_ribosome_entry_site

internal_transcribed_spacer_region	SO:0000639
Definition: Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: internal_transcribed_spacer_region is_a transcribed_spacer_region	Child relationships:

introgressed_chromosome_region	SO:0000664
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: introgressed_chromosome_region is_a chromosome_region	Child relationships:

intron	SO:0000188
Definition: A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: intron is_a primary_transcript_region	Child relationships: interior_intron is_a intron twintron is_a intron spliceosomal_intron is_a intron group_II_intron is_a intron UTR_intron is_a intron three_prime_intron is_a intron group_I_intron is_a intron five_prime_intron is_a intron autocatalytically_spliced_intron is_a intron

intronic_splice_enhancer	SO:0000320
Definition: Sequences within the intron that modulate splice site selection for some introns.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: intronic_splice_enhancer is_a splice_enhancer intronic_splice_enhancer is_a spliceosomal_intron_region	Child relationships:

inversion	SO:1000036
Definition: A continuous nucleotide sequence is inverted in the same position.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: inversion is_a sequence_variant inversion sequence_of invert inversion is_a region	Child relationships:

inverted_repeat	SO:0000294
Definition: The sequence is complementarily repeated on the opposite strand. Example: GCTGA-----TCAGC.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: inverted_repeat is_a repeat_region	Child relationships:

isoleucine_tRNA_primary_transcript	SO:0000220
Definition: A primary transcript encoding isoleucyl tRNA (SO:0000263).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: isoleucine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

isoleucyl_tRNA	SO:0000263
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: isoleucyl_tRNA is_a tRNA	Child relationships:

junction	SO:0000699
Definition: A junction refers to an interbase location of zero in a sequence.
DBxref:SO:ke
Synonyms: [boundary]
Aspect: located_sequence_feature
Parent relationships: junction is_a located_sequence_feature	Child relationships: clone_insert_end is_a junction deletion_junction is_a junction transcription_start_site is_a junction exon_junction is_a junction clone_insert_start is_a junction transcription_end_site is_a junction polyA_site is_a junction insertion_site is_a junction

lambda_vector	SO:0000754
Definition: The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
DBxref:ISBN:0-1767-2380-8
Synonyms:
Aspect: located_sequence_feature
Parent relationships: lambda_vector is_a vector	Child relationships:

large_subunit_rRNA	SO:0000651
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: large_subunit_rRNA is_a rRNA	Child relationships:

leucine_tRNA_primary_transcript	SO:0000221
Definition: A primary transcript encoding leucyl tRNA (SO:0000264).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: leucine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

leucyl_tRNA	SO:0000264
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: leucyl_tRNA is_a tRNA	Child relationships:

linkage_group	SO:0000018
Definition: A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.
DBxref:ISBN:038752046
Synonyms:
Aspect: located_sequence_feature
Parent relationships: linkage_group is_a region	Child relationships:

locus_control_region	SO:0000037
Definition: 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.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: locus_control_region is_a regulatory_region	Child relationships:

long_terminal_repeat	SO:0000286
Definition: A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.
DBxref:
Synonyms: [direct_terminal _repeat] [LTR]
Aspect: located_sequence_feature
Parent relationships: long_terminal_repeat part_of LTR_retrotransposon long_terminal_repeat is_a repeat_region	Child relationships: three_prime_LTR is_a long_terminal_repeat LTR_component part_of long_terminal_repeat five_prime_LTR is_a long_terminal_repeat

lysine_tRNA_primary_transcript	SO:0000222
Definition: A primary transcript encoding lysyl tRNA (SO:0000265).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: lysine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

lysyl_tRNA	SO:0000265
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: lysyl_tRNA is_a tRNA	Child relationships:

mRNA	SO:0000234
Definition: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
DBxref:SO:ma
Synonyms: [messenger_RNA]
Aspect: located_sequence_feature
Parent relationships: mRNA is_a processed_transcript	Child relationships: mRNA_region part_of mRNA riboswitch is_a mRNA EST derives_from mRNA

mRNA_region	SO:0000836
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: mRNA_region is_a processed_transcript_region mRNA_region part_of mRNA	Child relationships: UTR is_a mRNA_region codon is_a mRNA_region five_prime_open_reading_frame is_a mRNA_region UTR_region is_a mRNA_region CDS_region is_a mRNA_region CDS is_a mRNA_region recoding_stimulatory_region is_a mRNA_region

macronucleus_destined_segment	SO:0000672
Definition: A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: macronucleus_destined_segment is_a sequence_rearrangement_feature	Child relationships:

match	SO:0000343
Definition: A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: match is_a region	Child relationships: match_part is_a match match_set is_a match protein_match is_a match nucleotide_match is_a match

match_part	SO:0000039
Definition: A part of a match, for example an hsp from blast isa match_part.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: match_part part_of match_set match_part is_a match	Child relationships:

match_set	SO:0000038
Definition: A collection of match parts
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: match_set is_a match	Child relationships: match_part part_of match_set

matrix_attachment_site	SO:0000036
Definition: A DNA region that is required for the binding of chromatin to the nuclear matrix.
DBxref:SO:ma
Synonyms: [MAR] [scaffold_attachment_site] [SMAR]
Aspect: located_sequence_feature
Parent relationships: matrix_attachment_site is_a chromosomal_regulatory_element	Child relationships:

mature_peptide	SO:0000419
Definition: The coding sequence for the mature or final peptide or protein product following post-translational modification.
DBxref:external reference [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: mature_peptide is_a polypeptide_region	Child relationships:

metabolic_island	SO:0000774
Definition: A transmissible_element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: metabolic_island is_a genomic_island	Child relationships:

methionine_tRNA_primary_transcript	SO:0000223
Definition: A primary transcript encoding methionyl tRNA (SO:0000266).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: methionine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

methionyl_tRNA	SO:0000266
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: methionyl_tRNA is_a tRNA	Child relationships:

methylated_A	SO:0000161
Definition: A methylated adenine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: methylated_A is_a methylated_base_feature methylated_A is_a modified_RNA_base_feature	Child relationships:

methylated_C	SO:0000114
Definition: A methylated deoxy-cytosine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: methylated_C is_a methylated_base_feature	Child relationships:

methylated_base_feature	SO:0000306
Definition: A nucleotide modified by methylation.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: methylated_base_feature is_a modified_base_site	Child relationships: methylated_A is_a methylated_base_feature methylated_C is_a methylated_base_feature

methylation_guide_snoRNA	SO:0005841
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: methylation_guide_snoRNA is_a snoRNA	Child relationships:

methylation_guide_snoRNA_primary_transcript	SO:0000580
Definition: A primary transcript encoding a methylation guide small nucleolar RNA.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: methylation_guide_snoRNA_primary_transcript is_a snoRNA_primary_transcript	Child relationships:

miRNA	SO:0000276
Definition: 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.
DBxref:PMID:12592000
Synonyms: [micro_RNA]
Aspect: located_sequence_feature
Parent relationships: miRNA is_a small_regulatory_ncRNA	Child relationships:

miRNA_primary_transcript	SO:0000647
Definition: A primary transcript encoding a micro RNA.
DBxref:SO:ke
Synonyms: [micro_RNA_primary_transcript]
Aspect: located_sequence_feature
Parent relationships: miRNA_primary_transcript is_a nc_primary_transcript	Child relationships: stRNA_primary_transcript is_a miRNA_primary_transcript

microarray_oligo	SO:0000328
Definition: undefined
DBxref:
Synonyms: [microarray_oligonucleotide]
Aspect: located_sequence_feature
Parent relationships: microarray_oligo is_a tag microarray_oligo is_a probe microarray_oligo is_a oligo	Child relationships:

microsatellite	SO:0000289
Definition: A very short unit sequence of DNA (2 to 4 bp) that is repeated multiple times in tandem.
DBxref:external reference [http:////www.informatics.jax.org/silver/glossary.shtml]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: microsatellite is_a tandem_repeat	Child relationships: tetranucleotide_repeat_microsatellite_feature is_a microsatellite trinucleotide_repeat_microsatellite_feature is_a microsatellite dinucleotide_repeat_microsatellite_feature is_a microsatellite

mini_exon_donor_RNA	SO:0000635
Definition: A primary transcript that donates the spliced leader to other mRNA
DBxref:SO:ke
Synonyms: [mini-exon_donor_RNA]
Aspect: located_sequence_feature
Parent relationships: mini_exon_donor_RNA is_a primary_transcript	Child relationships: spliced_leader_RNA part_of mini_exon_donor_RNA

mini_gene	SO:0000815
Definition: By definition, minigenes are short open-reading framesn(ORF), usually encoding approximately 9 to 20 aminonacids, which are expressed in vivo (as distinct from beingnsynthesized as peptide or protein ex vivo and subsequentlyninjected). The in vivo synthesis confers a distinctnadvantage: the expressed sequences can enter bothnantigen presentation pathways, MHC I (inducing CD8+ T-ncells, which are usually cytotoxic T-lymphocytes (CTL))nand MHC II (inducing CD4+ T-cells, usually 'T-helpers'n(Th)); and can encounter B-cells, inducing antibodynresponses. Three main vector approaches have been usednto deliver minigenes: viral vectors, bacterial vectors andnplasmid DNA.
DBxref:external reference [http:////www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15992153&query_hl=2&itool=pubmed_docsum]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: mini_gene is_a ORF	Child relationships:

minisatellite	SO:0000643
Definition: A repetitive sequence spanning 500 to 20,000 base pairs (a repeat unit is 5 - 30 base pairs).
DBxref:external reference [http:////www.rerf.or.jp/eigo/glossary/minisate.htm]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: minisatellite is_a tandem_repeat	Child relationships:

minus_10_signal	SO:0000175
Definition: 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.
DBxref:
Synonyms: [-10_signal] [Pribnow_box]
Aspect: located_sequence_feature
Parent relationships: minus_10_signal is_a bacterial_RNApol_promotor_region	Child relationships:

minus_35_signal	SO:0000176
Definition: A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA.
DBxref:
Synonyms: [-35_signal]
Aspect: located_sequence_feature
Parent relationships: minus_35_signal is_a bacterial_RNApol_promotor_region	Child relationships:

modified_RNA_base_feature	SO:0000250
Definition: A post_transcriptionally modified base.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: modified_RNA_base_feature is_a transcript_region	Child relationships: methylated_A is_a modified_RNA_base_feature

modified_base_site	SO:0000305
Definition: A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: modified_base_site is_a region	Child relationships: methylated_base_feature is_a modified_base_site

morpholino	SO:0000034
Definition: 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.
DBxref:external reference [http://www.gene-tools.com/Morpholinos/morpholinos.HTML]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: morpholino is_a oligo	Child relationships:

ncRNA	SO:0000655
Definition: An mRNA sequence that does not encode for a protein rather the RNA molecule is the gene product.
DBxref:SO:ke
Synonyms: [noncoding_RNA]
Aspect: located_sequence_feature
Parent relationships: ncRNA is_a processed_transcript	Child relationships: SRP_RNA is_a ncRNA Y_RNA is_a ncRNA antisense_RNA is_a ncRNA tRNA is_a ncRNA guide_RNA is_a ncRNA stRNA is_a ncRNA siRNA is_a ncRNA enzymatic_RNA is_a ncRNA snoRNA is_a ncRNA small_regulatory_ncRNA is_a ncRNA scRNA is_a ncRNA rRNA is_a ncRNA vault_RNA is_a ncRNA snRNA is_a ncRNA rasiRNA is_a ncRNA

nc_conserved_region	SO:0000334
Definition: Non-coding region of sequence similarity by descent from a common ancestor.
DBxref:SO:ke
Synonyms: [noncoding_conserved_region]
Aspect: located_sequence_feature
Parent relationships: nc_conserved_region is_a conserved_region	Child relationships:

nc_primary_transcript	SO:0000483
Definition: A primary transcript that is never translated into a protein.
DBxref:SO:ke
Synonyms: [noncoding_primary_transcript]
Aspect: located_sequence_feature
Parent relationships: nc_primary_transcript is_a primary_transcript	Child relationships: miRNA_primary_transcript is_a nc_primary_transcript scRNA_primary_transcript is_a nc_primary_transcript rRNA_primary_transcript is_a nc_primary_transcript tmRNA_primary_transcript is_a nc_primary_transcript snoRNA_primary_transcript is_a nc_primary_transcript tRNA_primary_transcript is_a nc_primary_transcript SRP_RNA_primary_transcript is_a nc_primary_transcript snRNA_primary_transcript is_a nc_primary_transcript

non_LTR_retrotransposon	SO:0000189
Definition: A retrotransposon without long terminal repeat sequences.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: non_LTR_retrotransposon is_a retrotransposon	Child relationships: SINE_element is_a non_LTR_retrotransposon non_LTR_retrotransposon_polymeric_tract part_of non_LTR_retrotransposon LINE_element is_a non_LTR_retrotransposon

non_LTR_retrotransposon_polymeric_tract	SO:0000433
Definition: A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: non_LTR_retrotransposon_polymeric_tract part_of non_LTR_retrotransposon non_LTR_retrotransposon_polymeric_tract is_a repeat_component non_LTR_retrotransposon_polymeric_tract is_a repeat_region	Child relationships:

non_canonical_five_prime_splice_site	SO:0000679
Definition: A 5' splice site which does not have the sequence "GT".
DBxref:SO:ke
Synonyms: [non-canonical-five_prime_splice_site]
Aspect: located_sequence_feature
Parent relationships: non_canonical_five_prime_splice_site is_a five_prime_splice_site non_canonical_five_prime_splice_site is_a non_canonical_splice_site	Child relationships:

non_canonical_splice_site	SO:0000674
Definition: A splice site where the donor and acceptor sites differ from the canonical form.
DBxref:SO:ke
Synonyms: [non-canonical_splice_site]
Aspect: located_sequence_feature
Parent relationships: non_canonical_splice_site is_a splice_site	Child relationships: non_canonical_five_prime_splice_site is_a non_canonical_splice_site non_canonical_three_prime_splice_site is_a non_canonical_splice_site

non_canonical_start_codon	SO:0000680
Definition: A start codon that is not the usual AUG sequence.
DBxref:SO:ke
Synonyms: [non-canonical_start_codon] [non_ATG_start_codon]
Aspect: located_sequence_feature
Parent relationships: non_canonical_start_codon is_a start_codon	Child relationships: CTG_start_codon is_a non_canonical_start_codon four_bp_start_codon is_a non_canonical_start_codon

non_canonical_three_prime_splice_site	SO:0000678
Definition: A 3' splice site that does not have the sequence "AG".
DBxref:SO:ke
Synonyms: [non-canonical_three_prime_splice_site]
Aspect: located_sequence_feature
Parent relationships: non_canonical_three_prime_splice_site is_a non_canonical_splice_site non_canonical_three_prime_splice_site is_a three_prime_splice_site	Child relationships:

non_transcribed_region	SO:0000183
Definition: A region of the gene which is not transcribed.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: non_transcribed_region is_a gene_component_region	Child relationships:

nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000562
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene is_a vertebrate_immune_system_gene_recombination_signal_feature	Child relationships: J_nonamer is_a nonamer_of_recombination_feature_of_vertebrate_immune_system_gene five_prime_D_nonamer is_a nonamer_of_recombination_feature_of_vertebrate_immune_system_gene three_prime_D_nonamer is_a nonamer_of_recombination_feature_of_vertebrate_immune_system_gene V_nonamer is_a nonamer_of_recombination_feature_of_vertebrate_immune_system_gene

noncoding_exon	SO:0000198
Definition: An exon that does not contain any codons.
DBxref:SO:ke
Synonyms: [noncoding_exon]
Aspect: located_sequence_feature
Parent relationships: noncoding_exon is_a exon	Child relationships: five_prime_noncoding_exon is_a noncoding_exon three_prime_noncoding_exon is_a noncoding_exon

nuclease_binding_site	SO:0000059
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: nuclease_binding_site is_a protein_binding_site	Child relationships: restriction_enzyme_binding_site is_a nuclease_binding_site

nuclease_hypersensitive_site	SO:0000322
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: nuclease_hypersensitive_site is_a nuclease_sensitive_site	Child relationships: DNAaseI_hypersensitive_site is_a nuclease_hypersensitive_site

nuclease_sensitive_site	SO:0000684
Definition: A region of nucleotide sequence targeting by a nuclease enzyme.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: nuclease_sensitive_site is_a region	Child relationships: nuclease_hypersensitive_site is_a nuclease_sensitive_site group_1_intron_homing_endonuclease_target_region is_a nuclease_sensitive_site

nucleotide_deletion	SO:1000033
Definition: One or more continuous nucleotides are excised from the sequence.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: nucleotide_deletion is_a indel	Child relationships:

nucleotide_duplication	SO:1000035
Definition: 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.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: nucleotide_duplication is_a nucleotide_insertion	Child relationships:

nucleotide_insertion	SO:1000034
Definition: One or more nucleotides are added between two adjacent nucleotides in the sequence.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: nucleotide_insertion is_a indel	Child relationships: nucleotide_duplication is_a nucleotide_insertion

nucleotide_match	SO:0000347
Definition: A match against a nucleotide sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: nucleotide_match is_a match	Child relationships: cross_genome_match is_a nucleotide_match expressed_sequence_match is_a nucleotide_match translated_nucleotide_match is_a nucleotide_match

nucleotide_motif	SO:0000714
Definition: A region of nucleotide sequence corresponding to a known motif.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: nucleotide_motif is_a region	Child relationships: DNA_motif is_a nucleotide_motif RNA_motif is_a nucleotide_motif

oligo	SO:0000696
Definition: A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
DBxref:SO:ma
Synonyms: [oligonucleotide]
Aspect: located_sequence_feature
Parent relationships: oligo is_a reagent	Child relationships: RNAi_reagent is_a oligo ds_oligo is_a oligo microarray_oligo is_a oligo primer is_a oligo ss_oligo is_a oligo morpholino is_a oligo aptamer is_a oligo

oligo_U_tail	SO:0000609
Definition: The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).
DBxref:external reference [http:////www.rna.ucla.edu/]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: oligo_U_tail adjacent_to guide_RNA oligo_U_tail is_a region	Child relationships:

operator	SO:0000057
Definition: A regulatory element of an operon to which activators or repressors bind hereby effecting translation of genes in that operon.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: operator is_a gene_group_regulatory_region	Child relationships:

operon	SO:0000178
Definition: A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: operon is_a gene_group	Child relationships:

origin_of_replication	SO:0000296
Definition: The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: origin_of_replication is_a region	Child relationships: amplification_origin is_a origin_of_replication D_loop is_a origin_of_replication

origin_of_transfer	SO:0000724
Definition: A region of a DNA molecule whre transfer is initiated during the process of conjugation or mobilization.
DBxref:
Synonyms: [oriT]
Aspect: located_sequence_feature
Parent relationships: origin_of_transfer is_a region	Child relationships:

partially_characterised_change_in_DNA_sequence	SO:1000004
Definition: The nature of the mutation event is only partially characterised.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: partially_characterised_change_in_DNA_sequence is_a uncharacterised_change_in_nucleotide_sequence	Child relationships:

pathogenic_island	SO:0000773
Definition: 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.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pathogenic_island is_a genomic_island	Child relationships:

phagemid	SO:0000157
Definition: 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.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: phagemid is_a vector	Child relationships:

phenylalanine_tRNA_primary_transcript	SO:0000224
Definition: A primary transcript encoding phenylalanyl tRNA (SO:0000267).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: phenylalanine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

phenylalanyl_tRNA	SO:0000267
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: phenylalanyl_tRNA is_a tRNA	Child relationships:

plasmid	SO:0000155
Definition: A self-replicating circular DNA molecule that is distinct from a chromosome in the organism.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: plasmid is_a reagent	Child relationships: episome is_a plasmid

plasmid_vector	SO:0000755
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: plasmid_vector is_a vector	Child relationships:

point_mutation	SO:1000008
Definition: A mutation event where a single DNA nucleotide changes into another nucleotide.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: point_mutation is_a substitution	Child relationships: transition is_a point_mutation transversion is_a point_mutation SNP is_a point_mutation

polyA_sequence	SO:0000610
Definition: Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: polyA_sequence is_a region	Child relationships:

polyA_signal_sequence	SO:0000551
Definition: The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: polyA_signal_sequence is_a regulatory_region	Child relationships:

polyA_site	SO:0000553
Definition: The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: polyA_site is_a junction polyA_site part_of processed_transcript	Child relationships:

polypeptide	SO:0000104
Definition: A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversable denaturation.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: polypeptide derives_from CDS polypeptide is_a region	Child relationships: polypeptide_region part_of polypeptide

polypeptide_domain	SO:0000417
Definition: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
DBxref:external reference [http://www.molbiol.bbsrc.ac.uk/new_protein/domains.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: polypeptide_domain is_a polypeptide_region	Child relationships:

polypeptide_region	SO:0000839
Definition: A region of sequence that can be translated into polypeptide sequence. This sequence can be reprsenseted as nucleotide or aminoacid. This sequence must be part of an mRNA sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: polypeptide_region part_of polypeptide polypeptide_region is_a region	Child relationships: intein is_a polypeptide_region signal_peptide is_a polypeptide_region polypeptide_domain is_a polypeptide_region transit_peptide is_a polypeptide_region mature_peptide is_a polypeptide_region

polypyrimidine_tract	SO:0000612
Definition: The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
DBxref:external reference [http:////nar.oupjournals.org/cgi/content/full/25/4/888]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: polypyrimidine_tract is_a spliceosomal_intron_region	Child relationships:

possible_assembly_error	SO:0000702
Definition: A region of sequence where there may have been an error in the assembly.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: possible_assembly_error is_a sequence_difference	Child relationships:

possible_base_call_error	SO:0000701
Definition: A region of sequence where the validity of the base calling is questionable.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: possible_base_call_error is_a sequence_difference	Child relationships:

pre_edited_mRNA	SO:0000932
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pre_edited_mRNA is_a protein_coding_primary_transcript	Child relationships:

pre_edited_region	SO:0000583
Definition: The region of a transcript that will be edited.
DBxref:external reference [http:////www.rna.ucla.edu]
Synonyms: [pre-edited_region]
Aspect: located_sequence_feature
Parent relationships: pre_edited_region is_a edited_transcript_feature	Child relationships:

primary_transcript	SO:0000185
Definition: 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).
DBxref:
Synonyms: [precursor_RNA]
Aspect: located_sequence_feature
Parent relationships: primary_transcript is_a transcript	Child relationships: primary_transcript_region part_of primary_transcript antisense_primary_transcript is_a primary_transcript mini_exon_donor_RNA is_a primary_transcript processed_transcript derives_from primary_transcript protein_coding_primary_transcript is_a primary_transcript nc_primary_transcript is_a primary_transcript

primary_transcript_region	SO:0000835
Definition: A region of a primary transcript.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: primary_transcript_region part_of primary_transcript primary_transcript_region is_a transcript_region	Child relationships: splice_site is_a primary_transcript_region intron is_a primary_transcript_region transcription_start_site is_a primary_transcript_region spliceosomal_intron_region is_a primary_transcript_region spliced_leader_RNA is_a primary_transcript_region transcription_end_site is_a primary_transcript_region rRNA_primary_transcript_region is_a primary_transcript_region clip is_a primary_transcript_region

primer	SO:0000112
Definition: A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase.
DBxref:external reference [http:////www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/glossary.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: primer is_a oligo	Child relationships: forward_primer is_a primer reverse_primer is_a primer sequencing_primer is_a primer

primer_binding_site	SO:0005850
Definition: Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.
DBxref:external reference [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: primer_binding_site part_of LTR_retrotransposon primer_binding_site is_a binding_site	Child relationships:

probe	SO:0000051
Definition: A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: probe is_a reagent	Child relationships: microarray_oligo is_a probe

processed_transcript	SO:0000233
Definition: A transcript which has undergone processing to remove parts such as introns and transcribed_spacer_regions.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: processed_transcript is_a transcript processed_transcript derives_from primary_transcript	Child relationships: ncRNA is_a processed_transcript exon_junction part_of processed_transcript mRNA is_a processed_transcript aberrant_processed_transcript is_a processed_transcript polyA_site part_of processed_transcript

processed_transcript_region	SO:0000834
Definition: A region of a processed transcript.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: processed_transcript_region is_a transcript_region	Child relationships: mRNA_region is_a processed_transcript_region tmRNA_region is_a processed_transcript_region guide_RNA_region is_a processed_transcript_region

proline_tRNA_primary_transcript	SO:0000225
Definition: A primary transcript encoding prolyl tRNA (SO:0000268).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: proline_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

prolyl_tRNA	SO:0000268
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: prolyl_tRNA is_a tRNA	Child relationships:

promoter	SO:0000167
Definition: The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: promoter is_a regulatory_region	Child relationships: bidirectional_promotor is_a promoter RNApol_II_promoter is_a promoter RNApol_I_promoter is_a promoter bacterial_RNApol_promoter is_a promoter RNApol_III_promoter is_a promoter

promotor_region	SO:0000832
Definition: A region of sequence which is part of a promotor.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: promotor_region is_a regulatory_region	Child relationships: RNApol_III_promotor_type_2_region is_a promotor_region RNA_II_promotor_region is_a promotor_region TATA_box is_a promotor_region RNApol_III_promotor_type_1_region is_a promotor_region bacterial_RNApol_promotor_region is_a promotor_region

protein_binding_site	SO:0000410
Definition: A region of a molecule that binds to a protein.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: protein_binding_site is_a binding_site	Child relationships: TF_binding_site is_a protein_binding_site nuclease_binding_site is_a protein_binding_site

protein_coding_primary_transcript	SO:0000120
Definition: A primary transcript that, at least in part, encodes one or more proteins.
DBxref:SO:ke
Synonyms: [pre-mRNA]
Aspect: located_sequence_feature
Parent relationships: protein_coding_primary_transcript is_a primary_transcript	Child relationships: pre_edited_mRNA is_a protein_coding_primary_transcript

protein_match	SO:0000349
Definition: A match against a protein sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: protein_match is_a match	Child relationships:

pseudogene	SO:0000336
Definition: 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).
DBxref:external reference [http:////www.ucl.ac.uk/ ~ ucbhjow/b241/glossary.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pseudogene is_a pseudogenic_region pseudogene non_functional_homolog_of gene	Child relationships: pseudogenic_transcript part_of pseudogene

pseudogenic_exon	SO:0000507
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pseudogenic_exon non_functional_homolog_of exon pseudogenic_exon is_a pseudogenic_region pseudogenic_exon part_of pseudogenic_transcript	Child relationships:

pseudogenic_rRNA	SO:0000777
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pseudogenic_rRNA is_a pseudogenic_region	Child relationships:

pseudogenic_region	SO:0000462
Definition: A non-functional descendent of a functional entitity.
DBxref:SO:cjm
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pseudogenic_region is_a region	Child relationships: decayed_exon is_a pseudogenic_region pseudogene is_a pseudogenic_region pseudogenic_tRNA is_a pseudogenic_region pseudogenic_transcript is_a pseudogenic_region pseudogenic_exon is_a pseudogenic_region pseudogenic_rRNA is_a pseudogenic_region

pseudogenic_tRNA	SO:0000778
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pseudogenic_tRNA is_a pseudogenic_region	Child relationships:

pseudogenic_transcript	SO:0000516
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pseudogenic_transcript part_of pseudogene pseudogenic_transcript non_functional_homolog_of transcript pseudogenic_transcript is_a pseudogenic_region	Child relationships: pseudogenic_exon part_of pseudogenic_transcript

pseudoknot	SO:0000591
Definition: A stem-loop RNA structure where nucleotides in the loop participate in complementary interactions with a region of RNA downstream of the stem-loop.
DBxref:external reference [http:////www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pseudoknot is_a sequence_secondary_structure	Child relationships: H_pseudoknot is_a pseudoknot recoding_pseudoknot is_a pseudoknot

purine_to_pyrimidine_transversion	SO:1000023
Definition: Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: purine_to_pyrimidine_transversion is_a transversion	Child relationships: G_to_T_transversion is_a purine_to_pyrimidine_transversion A_to_T_transversion is_a purine_to_pyrimidine_transversion A_to_C_transversion is_a purine_to_pyrimidine_transversion G_to_C_transversion is_a purine_to_pyrimidine_transversion

purine_transition	SO:1000014
Definition: A substitution of a purine, A or G, for another purine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: purine_transition is_a transition	Child relationships: A_to_G_transition is_a purine_transition G_to_A_transition is_a purine_transition

pyrimidine_to_purine_transversion	SO:1000018
Definition: Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pyrimidine_to_purine_transversion is_a transversion	Child relationships: T_to_G_transversion is_a pyrimidine_to_purine_transversion T_to_A_transversion is_a pyrimidine_to_purine_transversion C_to_A_transversion is_a pyrimidine_to_purine_transversion C_to_G_transversion is_a pyrimidine_to_purine_transversion

pyrimidine_transition	SO:1000010
Definition: A substitution of a pyrimidine, C or T, for another pyrimidine.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pyrimidine_transition is_a transition	Child relationships: C_to_T_transition is_a pyrimidine_transition T_to_C_transition is_a pyrimidine_transition

pyrrolysyl_tRNA	SO:0000766
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pyrrolysyl_tRNA is_a tRNA	Child relationships:

rRNA	SO:0000252
Definition: RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
DBxref:
Synonyms: [ribsomal_RNA]
Aspect: located_sequence_feature
Parent relationships: rRNA is_a ncRNA	Child relationships: rRNA_28S is_a rRNA rRNA_5.8S is_a rRNA large_subunit_rRNA is_a rRNA rRNA_5S is_a rRNA rRNA_18S is_a rRNA small_subunit_rRNA is_a rRNA

rRNA_18S	SO:0000407
Definition: 18S_rRNA -A large polynucleotide which functions as a part of the small subunit of the ribosome
DBxref:SO:ke
Synonyms: [16S_rRNA]
Aspect: located_sequence_feature
Parent relationships: rRNA_18S is_a rRNA	Child relationships:

rRNA_28S	SO:0000653
Definition: A component of the large ribosomal subunit.
DBxref:SO:ke
Synonyms: [23S_rRNA] [28S_rRNA]
Aspect: located_sequence_feature
Parent relationships: rRNA_28S is_a rRNA	Child relationships:

rRNA_5.8S	SO:0000375
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]
Synonyms: [5.8S_rRNA]
Aspect: located_sequence_feature
Parent relationships: rRNA_5.8S is_a rRNA	Child relationships:

rRNA_5S	SO:0000652
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: rRNA_5S is_a rRNA	Child relationships:

rRNA_cleavage_snoRNA	SO:0005843
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: rRNA_cleavage_snoRNA is_a snoRNA	Child relationships:

rRNA_cleavage_snoRNA_primary_transcript	SO:0000582
Definition: A primary transcript encoding an rRNA cleavage snoRNA.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: rRNA_cleavage_snoRNA_primary_transcript is_a snoRNA_primary_transcript	Child relationships:

rRNA_large_subunit_primary_transcript	SO:0000325
Definition: A primary transcript encoding a large ribosomal subunit RNA.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: rRNA_large_subunit_primary_transcript is_a rRNA_primary_transcript	Child relationships:

rRNA_primary_transcript	SO:0000209
Definition: A primary transcript encoding a ribosomal RNA.
DBxref:SO:ke
Synonyms: [ribosomal_RNA_primary_transcript]
Aspect: located_sequence_feature
Parent relationships: rRNA_primary_transcript is_a nc_primary_transcript	Child relationships: rRNA_small_subunit_primary_transcript is_a rRNA_primary_transcript rRNA_large_subunit_primary_transcript is_a rRNA_primary_transcript rRNA_primary_transcript_region part_of rRNA_primary_transcript

rRNA_primary_transcript_region	SO:0000838
Definition: A region of an rRNA primary transcript
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: rRNA_primary_transcript_region is_a primary_transcript_region rRNA_primary_transcript_region part_of rRNA_primary_transcript	Child relationships: transcribed_spacer_region is_a rRNA_primary_transcript_region

rRNA_small_subunit_primary_transcript	SO:0000255
Definition: A primary transcript encoding a small ribosomal subunit RNA.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: rRNA_small_subunit_primary_transcript is_a rRNA_primary_transcript	Child relationships:

rasiRNA	SO:0000454
Definition: A small, 17-28-nt, small interfering RNA derived from transcripts ofrepetitive elements.
DBxref:external reference [http:////www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]
Synonyms: [repeat associated small interfering RNA]
Aspect: located_sequence_feature
Parent relationships: rasiRNA is_a ncRNA	Child relationships:

read	SO:0000150
Definition: 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.
DBxref:SO:rd
Synonyms:
Aspect: located_sequence_feature
Parent relationships: read part_of contig read is_a assembly_component	Child relationships: contig_read is_a read

read_pair	SO:0000007
Definition: A pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
DBxref:SO:ls
Synonyms:
Aspect: located_sequence_feature
Parent relationships: read_pair part_of contig read_pair is_a assembly_component	Child relationships:

reading_frame	SO:0000717
Definition: 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.
DBxref:SO:rb
Synonyms:
Aspect: located_sequence_feature
Parent relationships: reading_frame is_a region	Child relationships: blocked_reading_frame is_a reading_frame ORF is_a reading_frame

reagent	SO:0000695
Definition: A sequence used in experiment.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: reagent is_a region	Child relationships: restriction_fragment is_a reagent PCR_product is_a reagent cloned_region is_a reagent vector is_a reagent clone is_a reagent EST is_a reagent plasmid is_a reagent probe is_a reagent tag is_a reagent clone_insert is_a reagent databank_entry is_a reagent oligo is_a reagent

recoded_codon	SO:0000145
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: recoded_codon is_a codon	Child relationships:

recoding_pseudoknot	SO:0000545
Definition: 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.
DBxref:external reference [http:////www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: recoding_pseudoknot is_a pseudoknot recoding_pseudoknot part_of recoding_stimulatory_region	Child relationships:

recoding_stimulatory_region	SO:1001268
Definition: A site in an mRNA sequence that stimulates the recoding of the same mRNA.
DBxref:external reference [http:////www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]
Synonyms: [recoding_stimulatory_signal]
Aspect: located_sequence_feature
Parent relationships: recoding_stimulatory_region is_a mRNA_region	Child relationships: three_prime_recoding_site is_a recoding_stimulatory_region internal_Shine_Dalgarno_sequence is_a recoding_stimulatory_region recoding_pseudoknot part_of recoding_stimulatory_region five_prime_recoding_site is_a recoding_stimulatory_region stop_codon_signal is_a recoding_stimulatory_region SECIS_element is_a recoding_stimulatory_region

recombination_feature	SO:0000298
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: recombination_feature is_a region	Child relationships: recombination_hotspot is_a recombination_feature sequence_rearrangement_feature is_a recombination_feature iDNA is_a recombination_feature haplotype_block is_a recombination_feature

recombination_feature_of_rearranged_gene	SO:0000300
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: recombination_feature_of_rearranged_gene is_a specific_recombination_site	Child relationships: vertebrate_immune_system_gene_recombination_feature is_a recombination_feature_of_rearranged_gene

recombination_hotspot	SO:0000339
Definition: A region in a genome whioch promotes recombination.
DBxref:SO:rd
Synonyms:
Aspect: located_sequence_feature
Parent relationships: recombination_hotspot is_a recombination_feature	Child relationships:

region	SO:0000001
Definition: Continuous sequence.
DBxref:SO:ke
Synonyms: [sequence]
Aspect: located_sequence_feature
Parent relationships: region is_a located_sequence_feature	Child relationships: chromosome_region is_a region reagent is_a region flanking_region is_a region polypeptide is_a region cap is_a region nucleotide_motif is_a region modified_base_site is_a region gene_member_region is_a region pseudogenic_region is_a region match is_a region linkage_group is_a region CpG_island is_a region binding_site is_a region ARS is_a region genomic_island is_a region polyA_sequence is_a region sequence_secondary_structure is_a region repeat_component is_a region origin_of_transfer is_a region nuclease_sensitive_site is_a region QTL is_a region conserved_region is_a region gene_component_region is_a region insertion is_a region repeat_region is_a region retron is_a region assembly_component is_a region reading_frame is_a region chromosome is_a region gene is_a region inversion is_a region assembly is_a region substitution is_a region deletion is_a region remark is_a region recombination_feature is_a region integrated_virus is_a region polypeptide_region is_a region gene_group is_a region oligo_U_tail is_a region transcript_region is_a region origin_of_replication is_a region intergenic_region is_a region

regulatory_region	SO:0005836
Definition: A DNA sequence that controls the expression of a gene.
DBxref:external reference [http:////www.genpromag.com/scripts/glossary.asp?LETTER=R]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: regulatory_region is_a gene_member_region	Child relationships: splice_enhancer is_a regulatory_region terminator is_a regulatory_region attenuator is_a regulatory_region TF_module is_a regulatory_region locus_control_region is_a regulatory_region insulator is_a regulatory_region promoter is_a regulatory_region promotor_region is_a regulatory_region TF_binding_site is_a regulatory_region polyA_signal_sequence is_a regulatory_region gene_group_regulatory_region is_a regulatory_region silencer is_a regulatory_region enhancer is_a regulatory_region

regulon	SO:1001284
Definition: A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal.
DBxref:ISBN:0198506732
Synonyms:
Aspect: located_sequence_feature
Parent relationships: regulon is_a gene_group	Child relationships:

remark	SO:0000700
Definition: A comment about the sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: remark is_a region	Child relationships: experimental_result_region is_a remark sequence_difference is_a remark

repeat_component	SO:0000840
Definition: A region of a repeated sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: repeat_component part_of repeat_region repeat_component is_a region	Child relationships: non_LTR_retrotransposon_polymeric_tract is_a repeat_component LTR_component is_a repeat_component

repeat_family	SO:0000187
Definition: A group of characterized repeat sequences.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: repeat_family is_a repeat_region	Child relationships: transposable_element is_a repeat_family

repeat_region	SO:0000657
Definition: A region of sequence containing one or more repeat units.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: repeat_region is_a region	Child relationships: direct_repeat is_a repeat_region inverted_repeat is_a repeat_region long_terminal_repeat is_a repeat_region satellite_DNA is_a repeat_region non_LTR_retrotransposon_polymeric_tract is_a repeat_region transposable_element_target_site_duplication is_a repeat_region tandem_repeat is_a repeat_region repeat_family is_a repeat_region repeat_component part_of repeat_region repeat_unit is_a repeat_region terminal_inverted_repeat is_a repeat_region dispersed_repeat is_a repeat_region

repeat_unit	SO:0000726
Definition: A single repeat element.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: repeat_unit is_a repeat_region	Child relationships:

restriction_enzyme_binding_site	SO:0000061
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: restriction_enzyme_binding_site is_a nuclease_binding_site	Child relationships:

restriction_fragment	SO:0000412
Definition: Any of the individual polynucleotide sequences produced by digestion of DNA with a restriction endonuclease.
DBxref:external reference [http:////www.agron.missouri.edu/cgi-bin/sybgw_mdb/mdb3/Term/119]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: restriction_fragment is_a reagent	Child relationships: RFLP_fragment is_a restriction_fragment

retron	SO:1001275
Definition: Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: retron is_a region	Child relationships:

retrotransposon	SO:0000180
Definition: A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.
DBxref:external reference [http:////www.genpromag.com/scripts/glossary.asp?LETTER=R]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: retrotransposon is_a transposable_element	Child relationships: non_LTR_retrotransposon is_a retrotransposon LTR_retrotransposon is_a retrotransposon

reverse_Hoogsteen_base_pair	SO:0000501
Definition: A type of non-canonical base-pairing.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: reverse_Hoogsteen_base_pair is_a base_pair	Child relationships:

reverse_primer	SO:0000132
Definition: A single stranded oligo used for polymerase chain reaction.
DBxref:external reference [http:////mged.sourceforge.net/ontologies/MGEDontology.php]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: reverse_primer is_a primer	Child relationships:

ribosome_entry_site	SO:0000139
Definition: Region in mRNA where ribosome assembles.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: ribosome_entry_site is_a UTR_region	Child relationships: Shine_Dalgarno_sequence is_a ribosome_entry_site internal_ribosome_entry_site is_a ribosome_entry_site

riboswitch	SO:0000035
Definition: 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.
DBxref:PMID:2820954
Synonyms:
Aspect: located_sequence_feature
Parent relationships: riboswitch is_a mRNA	Child relationships:

ribozyme	SO:0000374
Definition: An RNA with catalytic activity.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: ribozyme is_a enzymatic_RNA	Child relationships: hammerhead_ribozyme is_a ribozyme RNase_P_RNA is_a ribozyme autocatalytically_spliced_intron is_a ribozyme

satellite_DNA	SO:0000005
Definition: 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.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: satellite_DNA is_a repeat_region	Child relationships: tandem_repeat part_of satellite_DNA

scRNA	SO:0000013
Definition: Any one of several small cytoplasmic RNA moleculespresent in the cytoplasm and sometimes nucleus of a eukaryote.
DBxref:external reference [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: scRNA is_a ncRNA	Child relationships:

scRNA_primary_transcript	SO:0000012
Definition: The primary transcript of any one of several small cytoplasmic RNA moleculespresent in the cytoplasm and sometimes nucleus of a eukaryote.
DBxref:external reference [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]
Synonyms: [small_cytoplasmic_RNA]
Aspect: located_sequence_feature
Parent relationships: scRNA_primary_transcript is_a nc_primary_transcript	Child relationships:

selenocysteine_tRNA_primary_transcript	SO:0005856
Definition: A primary transcript encoding seryl tRNA (SO:000269).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: selenocysteine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

selenocysteinyl_tRNA	SO:0005857
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: selenocysteinyl_tRNA is_a tRNA	Child relationships:

sequence_difference	SO:0000413
Definition: A region where the sequences differs from that of a specified sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: sequence_difference is_a remark	Child relationships: possible_assembly_error is_a sequence_difference possible_base_call_error is_a sequence_difference

sequence_length_variation	SO:0000248
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: sequence_length_variation is_a substitution	Child relationships: simple_sequence_length_polymorphism is_a sequence_length_variation

sequence_rearrangement_feature	SO:0000669
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: sequence_rearrangement_feature is_a recombination_feature	Child relationships: chromosome_breakage_sequence is_a sequence_rearrangement_feature attI_site is_a sequence_rearrangement_feature integron is_a sequence_rearrangement_feature integrase_coding_region is_a sequence_rearrangement_feature internal_eliminated_sequence is_a sequence_rearrangement_feature macronucleus_destined_segment is_a sequence_rearrangement_feature specific_recombination_site is_a sequence_rearrangement_feature

sequence_secondary_structure	SO:0000002
Definition: A folded sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: sequence_secondary_structure is_a region	Child relationships: base_pair is_a sequence_secondary_structure G_quartet is_a sequence_secondary_structure DNA_sequence_secondary_structure is_a sequence_secondary_structure pseudoknot is_a sequence_secondary_structure RNA_sequence_secondary_structure is_a sequence_secondary_structure stem_loop is_a sequence_secondary_structure

sequence_variant	SO:0000109
Definition: A region of sequence where variation has been observed.
DBxref:SO:ke
Synonyms: [mutation]
Aspect: located_sequence_feature
Parent relationships: sequence_variant is_a located_sequence_feature	Child relationships: insertion is_a sequence_variant deletion_junction is_a sequence_variant indel is_a sequence_variant insertion_site is_a sequence_variant inversion is_a sequence_variant deletion is_a sequence_variant substitution is_a sequence_variant translocation is_a sequence_variant translocation_site is_a sequence_variant

sequencing_primer	SO:0000107
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: sequencing_primer is_a primer	Child relationships:

serine_tRNA_primary_transcript	SO:0000226
Definition: A primary transcript encoding seryl tRNA (SO:000269).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: serine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

seryl_tRNA	SO:0000269
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: seryl_tRNA is_a tRNA	Child relationships:

siRNA	SO:0000646
Definition: 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.
DBxref:PMID:12592000
Synonyms: [small_interfering_RNA]
Aspect: located_sequence_feature
Parent relationships: siRNA is_a ncRNA	Child relationships:

signal_peptide	SO:0000418
Definition: The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
DBxref:external reference [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
Synonyms: [signal peptide coding sequence]
Aspect: located_sequence_feature
Parent relationships: signal_peptide is_a polypeptide_region	Child relationships:

silencer	SO:0000625
Definition: Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: silencer is_a regulatory_region	Child relationships:

simple_sequence_length_polymorphism	SO:0000207
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: simple_sequence_length_polymorphism is_a sequence_length_variation	Child relationships:

single_exon	SO:0005845
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: single_exon is_a exon	Child relationships:

site_specific_recombination_target_region	SO:0000342
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: site_specific_recombination_target_region is_a specific_recombination_site	Child relationships: FLP_recombination_target_region is_a site_specific_recombination_target_region Cre_recombination_target_region is_a site_specific_recombination_target_region DNA_invertase_target_sequence is_a site_specific_recombination_target_region

small_regulatory_ncRNA	SO:0000370
Definition: A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: small_regulatory_ncRNA is_a ncRNA	Child relationships: spot_42_RNA is_a small_regulatory_ncRNA miRNA is_a small_regulatory_ncRNA CsrB_RsmB_RNA is_a small_regulatory_ncRNA RprA_RNA is_a small_regulatory_ncRNA OxyS_RNA is_a small_regulatory_ncRNA DsrA_RNA is_a small_regulatory_ncRNA RRE_RNA is_a small_regulatory_ncRNA tmRNA is_a small_regulatory_ncRNA RNA_6S is_a small_regulatory_ncRNA

small_subunit_rRNA	SO:0000650
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: small_subunit_rRNA is_a rRNA	Child relationships:

snRNA	SO:0000274
Definition: Small non-coding RNA in the nucleoplasm. A small nuclear RNA molecule involved in pre-mRNA splicing and processing
DBxref:
Synonyms: [small_nuclear_RNA]
Aspect: located_sequence_feature
Parent relationships: snRNA is_a ncRNA	Child relationships: U12_snRNA is_a snRNA U4_snRNA is_a snRNA U2_snRNA is_a snRNA U11_snRNA is_a snRNA U1_snRNA is_a snRNA U5_snRNA is_a snRNA snRNA_4.5S is_a snRNA U14_snRNA is_a snRNA U6_snRNA is_a snRNA U4atac_snRNA is_a snRNA U6atac_snRNA is_a snRNA

snRNA_4.5S	SO:0005839
Definition: undefined
DBxref:
Synonyms: [4.5S_snRNA]
Aspect: located_sequence_feature
Parent relationships: snRNA_4.5S is_a snRNA	Child relationships:

snRNA_4.5S_primary_transcript	SO:0005837
Definition: A primary transcript encoding a 4.5S snRNA.
DBxref:SO:ke
Synonyms: [4.5S_snRNA_primary_transcript]
Aspect: located_sequence_feature
Parent relationships: snRNA_4.5S_primary_transcript is_a snRNA_primary_transcript	Child relationships:

snRNA_primary_transcript	SO:0000231
Definition: A primary transcript encoding a small nuclear mRNA (SO:0000274).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: snRNA_primary_transcript is_a nc_primary_transcript	Child relationships: snRNA_4.5S_primary_transcript is_a snRNA_primary_transcript

snoRNA	SO:0000275
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]
Synonyms: [small_nucleolar_RNA]
Aspect: located_sequence_feature
Parent relationships: snoRNA is_a ncRNA	Child relationships: rRNA_cleavage_snoRNA is_a snoRNA methylation_guide_snoRNA is_a snoRNA C_D_box_snoRNA is_a snoRNA H_ACA_box_snoRNA is_a snoRNA

snoRNA_primary_transcript	SO:0000232
Definition: A primary transcript encoding a small nucleolar mRNA (SO:0000275).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: snoRNA_primary_transcript is_a nc_primary_transcript	Child relationships: C_D_box_snoRNA_primary_transcript is_a snoRNA_primary_transcript methylation_guide_snoRNA_primary_transcript is_a snoRNA_primary_transcript H_ACA_box_snoRNA_primary_transcript is_a snoRNA_primary_transcript rRNA_cleavage_snoRNA_primary_transcript is_a snoRNA_primary_transcript

specific_recombination_site	SO:0000299
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: specific_recombination_site is_a sequence_rearrangement_feature	Child relationships: recombination_feature_of_rearranged_gene is_a specific_recombination_site site_specific_recombination_target_region is_a specific_recombination_site

splice_enhancer	SO:0000344
Definition: Region of a transcript that regulates splicing.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: splice_enhancer is_a regulatory_region	Child relationships: exonic_splice_enhancer is_a splice_enhancer intronic_splice_enhancer is_a splice_enhancer

splice_site	SO:0000162
Definition: The position where intron is excised.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: splice_site is_a primary_transcript_region	Child relationships: five_prime_splice_site is_a splice_site non_canonical_splice_site is_a splice_site three_prime_splice_site is_a splice_site canonical_splice_site is_a splice_site

spliced_leader_RNA	SO:0000636
Definition: undefined
DBxref:
Synonyms: [mini-exon]
Aspect: located_sequence_feature
Parent relationships: spliced_leader_RNA is_a primary_transcript_region spliced_leader_RNA part_of mini_exon_donor_RNA	Child relationships:

spliceosomal_intron	SO:0000662
Definition: An intron which is spliced by the spliceosome.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: spliceosomal_intron is_a intron	Child relationships: U12_intron is_a spliceosomal_intron spliceosomal_intron_region part_of spliceosomal_intron U2_intron is_a spliceosomal_intron

spliceosomal_intron_region	SO:0000841
Definition: A region within an intron.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: spliceosomal_intron_region is_a primary_transcript_region spliceosomal_intron_region part_of spliceosomal_intron	Child relationships: polypyrimidine_tract is_a spliceosomal_intron_region branch_site is_a spliceosomal_intron_region intronic_splice_enhancer is_a spliceosomal_intron_region

spot_42_RNA	SO:0000389
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: spot_42_RNA is_a small_regulatory_ncRNA	Child relationships:

ss_oligo	SO:0000441
Definition: A single stranded oligonucleotide.
DBxref:SO:ke
Synonyms: [single stranded oligonucleotide.new synonym] [ss_oligonucleotide]
Aspect: located_sequence_feature
Parent relationships: ss_oligo is_a oligo	Child relationships:

stRNA	SO:0000649
Definition: Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans.
DBxref:PMID:11081512
Synonyms: [small_temporal_RNA]
Aspect: located_sequence_feature
Parent relationships: stRNA is_a ncRNA	Child relationships:

stRNA_primary_transcript	SO:0000648
Definition: A primary transcript encoding a small temporal mRNA (SO:0000649).
DBxref:SO:ke
Synonyms: [small_temporal_RNA_primary_transcript]
Aspect: located_sequence_feature
Parent relationships: stRNA_primary_transcript is_a miRNA_primary_transcript	Child relationships:

start_codon	SO:0000318
Definition: First codon to be translated by a ribosome.
DBxref:SO:ke
Synonyms: [initiation codon]
Aspect: located_sequence_feature
Parent relationships: start_codon is_a codon	Child relationships: non_canonical_start_codon is_a start_codon

stem_loop	SO:0000313
Definition: A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: stem_loop is_a sequence_secondary_structure	Child relationships:

stop_codon	SO:0000319
Definition: In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: stop_codon is_a codon	Child relationships:

stop_codon_signal	SO:1001288
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: stop_codon_signal is_a recoding_stimulatory_region	Child relationships: UGA_stop_codon_signal is_a stop_codon_signal UAG_stop_codon_signal is_a stop_codon_signal UAA_stop_codon_signal is_a stop_codon_signal

substitution	SO:1000002
Definition: Any change in genomic DNA caused by a single event.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: substitution is_a sequence_variant substitution sequence_of substitute substitution is_a region	Child relationships: point_mutation is_a substitution complex_substitution is_a substitution sequence_length_variation is_a substitution uncharacterised_change_in_nucleotide_sequence is_a substitution

sugar_edge_base_pair	SO:0000030
Definition: A type of non-canonical base-pairing.
DBxref:PMID:12177293
Synonyms:
Aspect: located_sequence_feature
Parent relationships: sugar_edge_base_pair is_a base_pair	Child relationships:

supercontig	SO:0000148
Definition: One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
DBxref:SO:ls
Synonyms: [scaffold]
Aspect: located_sequence_feature
Parent relationships: supercontig is_a assembly supercontig part_of ultracontig	Child relationships: contig part_of supercontig

symbiosis_island	SO:0000776
Definition: A transmissible_element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: symbiosis_island is_a genomic_island	Child relationships:

symmetric_RNA_internal_loop	SO:0000025
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: symmetric_RNA_internal_loop is_a RNA_internal_loop	Child relationships:

tRNA	SO:0000253
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005] ISBN:0198506732
Synonyms: [transfer_RNA]
Aspect: located_sequence_feature
Parent relationships: tRNA is_a ncRNA	Child relationships: alanyl_tRNA is_a tRNA glutaminyl_tRNA is_a tRNA prolyl_tRNA is_a tRNA glutamyl_tRNA is_a tRNA methionyl_tRNA is_a tRNA asparaginyl_tRNA is_a tRNA threonyl_tRNA is_a tRNA glycyl_tRNA is_a tRNA valyl_tRNA is_a tRNA tyrosyl_tRNA is_a tRNA cysteinyl_tRNA is_a tRNA isoleucyl_tRNA is_a tRNA seryl_tRNA is_a tRNA leucyl_tRNA is_a tRNA selenocysteinyl_tRNA is_a tRNA tryptophanyl_tRNA is_a tRNA pyrrolysyl_tRNA is_a tRNA lysyl_tRNA is_a tRNA aspartyl_tRNA is_a tRNA histidyl_tRNA is_a tRNA phenylalanyl_tRNA is_a tRNA

tRNA_primary_transcript	SO:0000210
Definition: A primary transcript encoding a transfer RNA (SO:0000253.)
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tRNA_primary_transcript is_a nc_primary_transcript	Child relationships: glutamic_acid_tRNA_primary_transcript is_a tRNA_primary_transcript alanine_tRNA_primary_transcript is_a tRNA_primary_transcript valine_tRNA_primary_transcript is_a tRNA_primary_transcript lysine_tRNA_primary_transcript is_a tRNA_primary_transcript arginine_tRNA_primary_transcript is_a tRNA_primary_transcript isoleucine_tRNA_primary_transcript is_a tRNA_primary_transcript selenocysteine_tRNA_primary_transcript is_a tRNA_primary_transcript phenylalanine_tRNA_primary_transcript is_a tRNA_primary_transcript histidine_tRNA_primary_transcript is_a tRNA_primary_transcript tyrosine_tRNA_primary_transcript is_a tRNA_primary_transcript threonine_tRNA_primary_transcript is_a tRNA_primary_transcript leucine_tRNA_primary_transcript is_a tRNA_primary_transcript serine_tRNA_primary_transcript is_a tRNA_primary_transcript aspartic_acid_tRNA_primary_transcript is_a tRNA_primary_transcript cysteine_tRNA_primary_transcript is_a tRNA_primary_transcript proline_tRNA_primary_transcript is_a tRNA_primary_transcript glycine_tRNA_primary_transcript is_a tRNA_primary_transcript tryptophan_tRNA_primary_transcript is_a tRNA_primary_transcript asparagine_tRNA_primary_transcript is_a tRNA_primary_transcript glutamine_tRNA_primary_transcript is_a tRNA_primary_transcript methionine_tRNA_primary_transcript is_a tRNA_primary_transcript

tag	SO:0000324
Definition: A nucleotide sequence that may be used to identify a larger sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tag is_a reagent	Child relationships: SAGE_tag is_a tag STS is_a tag microarray_oligo is_a tag

tandem_repeat	SO:0000705
Definition: Two or more adjacent copies of a DNA sequence.
DBxref:external reference [http:////www.sci.sdsu.edu/ ~ smaloy/Glossary/T.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tandem_repeat part_of satellite_DNA tandem_repeat is_a repeat_region	Child relationships: minisatellite is_a tandem_repeat microsatellite is_a tandem_repeat

telomerase_RNA	SO:0000390
Definition: The RNA component of telomerase, a reverse transcriptase that synthesises telomeric DNA.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: telomerase_RNA is_a enzymatic_RNA	Child relationships:

telomere	SO:0000624
Definition: A specific structure at the end of a linear chromosome, required for the integrity and maintenence of the end,
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: telomere is_a chromosomal_structural_element	Child relationships:

terminal_inverted_repeat	SO:0000481
Definition: An inverted repeat (SO:0000294) occuring at the termini of a DNA transposon.
DBxref:SO:ke
Synonyms: [TIR]
Aspect: located_sequence_feature
Parent relationships: terminal_inverted_repeat part_of terminal_inverted_repeat_element terminal_inverted_repeat is_a repeat_region	Child relationships: three_prime_terminal_inverted_repeat is_a terminal_inverted_repeat five_prime_terminal_inverted_repeat is_a terminal_inverted_repeat

terminal_inverted_repeat_element	SO:0000208
Definition: A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.
DBxref:external reference [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: terminal_inverted_repeat_element is_a DNA_transposon	Child relationships: terminal_inverted_repeat part_of terminal_inverted_repeat_element MITE is_a terminal_inverted_repeat_element

terminator	SO:0000141
Definition: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: terminator is_a regulatory_region terminator is_a gene_group_regulatory_region	Child relationships: bacterial_terminator is_a terminator terminator_of_type_2_RNApol_III_promoter is_a terminator

terminator_of_type_2_RNApol_III_promoter	SO:0000615
Definition: A terminator signal for RNA polymerase III transcription.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: terminator_of_type_2_RNApol_III_promoter is_a terminator	Child relationships:

tetranucleotide_repeat_microsatellite_feature	SO:0000641
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tetranucleotide_repeat_microsatellite_feature is_a microsatellite	Child relationships:

three_prime_D_heptamer	SO:0000493
Definition: 7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
DBxref:
Synonyms: [3'D-HEPTAMER]
Aspect: located_sequence_feature
Parent relationships: three_prime_D_heptamer is_a heptamer_of_recombination_feature_of_vertebrate_immune_system_gene three_prime_D_heptamer part_of three_prime_D_recombination_signal_sequence	Child relationships:

three_prime_D_nonamer	SO:0000494
Definition: A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
DBxref:
Synonyms: [3'D-NOMAMER]
Aspect: located_sequence_feature
Parent relationships: three_prime_D_nonamer part_of three_prime_D_recombination_signal_sequence three_prime_D_nonamer is_a nonamer_of_recombination_feature_of_vertebrate_immune_system_gene	Child relationships:

three_prime_D_recombination_signal_sequence	SO:0000570
Definition: 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.
DBxref:
Synonyms: [3'D-RS] [three_prime_D-recombination_signal_sequence]
Aspect: located_sequence_feature
Parent relationships: three_prime_D_recombination_signal_sequence is_a D_gene_recombination_feature	Child relationships: three_prime_D_heptamer part_of three_prime_D_recombination_signal_sequence three_prime_D_nonamer part_of three_prime_D_recombination_signal_sequence three_prime_D_spacer part_of three_prime_D_recombination_signal_sequence

three_prime_D_spacer	SO:0000495
Definition: A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.
DBxref:
Synonyms: [3'D-SPACER]
Aspect: located_sequence_feature
Parent relationships: three_prime_D_spacer part_of three_prime_D_recombination_signal_sequence three_prime_D_spacer is_a vertebrate_immune_system_gene_recombination_spacer	Child relationships:

three_prime_LTR	SO:0000426
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_LTR is_a long_terminal_repeat	Child relationships: three_prime_LTR_component part_of three_prime_LTR

three_prime_LTR_component	SO:0000849
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_LTR_component part_of three_prime_LTR three_prime_LTR_component is_a LTR_component	Child relationships: U3_three_prime_LTR_region is_a three_prime_LTR_component R_three_prime_LTR_region is_a three_prime_LTR_component U5_three_prime_LTR_region is_a three_prime_LTR_component

three_prime_UTR	SO:0000205
Definition: A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
DBxref:
Synonyms: [three_prime_untranslated_region]
Aspect: located_sequence_feature
Parent relationships: three_prime_UTR is_a UTR	Child relationships:

three_prime_UTR_intron	SO:0000448
Definition: An intron located in the 3' UTR.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_UTR_intron is_a UTR_intron	Child relationships:

three_prime_clip	SO:0000557
Definition: 3'-most region of a precursor transcript that is clipped off during processing.
DBxref:
Synonyms: [3'-clip]
Aspect: located_sequence_feature
Parent relationships: three_prime_clip is_a clip	Child relationships:

three_prime_coding_exon	SO:0000202
Definition: The exon that is most 3-prime on a given transcript.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_coding_exon is_a exon	Child relationships: three_prime_exon_noncoding_region part_of three_prime_coding_exon three_prime_exon_coding_region part_of three_prime_coding_exon

three_prime_exon_coding_region	SO:0000197
Definition: The sequence of the 3' exon that encodes for protein.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_exon_coding_region is_a coding_exon three_prime_exon_coding_region part_of three_prime_coding_exon	Child relationships:

three_prime_exon_noncoding_region	SO:0000484
Definition: The sequence of the 3' exon that is not coding.
DBxref:SO:ke
Synonyms: [three_prime_exon_noncoding_region]
Aspect: located_sequence_feature
Parent relationships: three_prime_exon_noncoding_region is_a exon_region three_prime_exon_noncoding_region part_of three_prime_coding_exon	Child relationships:

three_prime_intron	SO:0000192
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_intron is_a intron	Child relationships:

three_prime_noncoding_exon	SO:0000444
Definition: Non-coding exon in the 3' UTR.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_noncoding_exon is_a noncoding_exon	Child relationships:

three_prime_recoding_site	SO:1001277
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_recoding_site is_a recoding_stimulatory_region	Child relationships: flanking_three_prime_quadruplet_recoding_signal is_a three_prime_recoding_site distant_three_prime_recoding_signal is_a three_prime_recoding_site three_prime_repeat_recoding_signal is_a three_prime_recoding_site three_prime_stem_loop_structure is_a three_prime_recoding_site

three_prime_repeat_recoding_signal	SO:1001286
Definition: It is a downstream sequence important for recoding that contains repetitive elements.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_repeat_recoding_signal is_a three_prime_recoding_site	Child relationships:

three_prime_splice_site	SO:0000164
Definition: The junction between the 3 prime end of an intron and the following exon.
DBxref:external reference [http:////www.ucl.ac.uk/ ~ ucbhjow/b241/glossary.html]
Synonyms: [acceptor] [acceptor_splice_site] [splice_acceptor_site]
Aspect: located_sequence_feature
Parent relationships: three_prime_splice_site is_a splice_site	Child relationships: canonical_three_prime_splice_site is_a three_prime_splice_site trans_splice_acceptor_site is_a three_prime_splice_site non_canonical_three_prime_splice_site is_a three_prime_splice_site

three_prime_stem_loop_structure	SO:1001279
Definition: The stem-loop secondary structural element downstream of the redefined region.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_stem_loop_structure is_a three_prime_recoding_site	Child relationships:

three_prime_terminal_inverted_repeat	SO:0000421
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_terminal_inverted_repeat is_a terminal_inverted_repeat	Child relationships:

threonine_tRNA_primary_transcript	SO:0000227
Definition: A primary transcript encoding threonyl tRNA (SO:000270).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: threonine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

threonyl_tRNA	SO:0000270
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: threonyl_tRNA is_a tRNA	Child relationships:

tiling_path	SO:0000472
Definition: A set of regions which overlap with minimal polymorphism to form a linear sequence.
DBxref:CJM:SO
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tiling_path is_a assembly	Child relationships: tiling_path_fragment part_of tiling_path

tiling_path_clone	SO:0000480
Definition: 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.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tiling_path_clone is_a tiling_path_fragment tiling_path_clone is_a clone	Child relationships:

tiling_path_fragment	SO:0000474
Definition: A piece of sequence that makes up a tiling_path.SO:0000472.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tiling_path_fragment part_of tiling_path tiling_path_fragment is_a assembly_component	Child relationships: tiling_path_clone is_a tiling_path_fragment

tmRNA	SO:0000584
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]
Synonyms: [10Sa_RNA] [ssrA]
Aspect: located_sequence_feature
Parent relationships: tmRNA is_a small_regulatory_ncRNA	Child relationships: tmRNA_region part_of tmRNA

tmRNA_acceptor_piece	SO:0000770
Definition: 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.
DBxref:Indiana:kw
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tmRNA_acceptor_piece is_a tmRNA_region	Child relationships:

tmRNA_coding_piece	SO:0000769
Definition: 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.
DBxref:Indiana:kw
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tmRNA_coding_piece is_a tmRNA_region	Child relationships:

tmRNA_primary_transcript	SO:0000586
Definition: A primary transcript encoding a tmRNA (SO:0000584).
DBxref:SO:ke
Synonyms: [10Sa_RNA_primary_transcript] [ssrA_RNA_primary_transcript]
Aspect: located_sequence_feature
Parent relationships: tmRNA_primary_transcript is_a nc_primary_transcript	Child relationships:

tmRNA_region	SO:0000847
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tmRNA_region is_a processed_transcript_region tmRNA_region part_of tmRNA	Child relationships: tmRNA_acceptor_piece is_a tmRNA_region tmRNA_coding_piece is_a tmRNA_region

trans_splice_acceptor_site	SO:0000706
Definition: The process that produces mature transcripts by combining exons of independent pre-mRNA molecules. The acceptor site lies on the 3' of these molecules.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: trans_splice_acceptor_site is_a three_prime_splice_site	Child relationships: SL2_acceptor_site is_a trans_splice_acceptor_site SL1_acceptor_site is_a trans_splice_acceptor_site

trans_splice_donor_site	SO:0000707
Definition: The site at which trans-splicing occurs.
DBxref:SO:ke
Synonyms: [trans-splice_donor_site]
Aspect: located_sequence_feature
Parent relationships: trans_splice_donor_site is_a five_prime_splice_site	Child relationships:

transcribed_spacer_region	SO:0000638
Definition: Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
DBxref:external reference [http:////oregonstate.edu/instruction/bb492/general/glossary.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transcribed_spacer_region is_a rRNA_primary_transcript_region	Child relationships: external_transcribed_spacer_region is_a transcribed_spacer_region internal_transcribed_spacer_region is_a transcribed_spacer_region

transcript	SO:0000673
Definition: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transcript is_a gene_member_region	Child relationships: pseudogenic_transcript non_functional_homolog_of transcript transcript_region part_of transcript processed_transcript is_a transcript primary_transcript is_a transcript

transcript_region	SO:0000833
Definition: A region of a transcript.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transcript_region part_of transcript transcript_region is_a region	Child relationships: edited_transcript_feature is_a transcript_region primary_transcript_region is_a transcript_region exon is_a transcript_region processed_transcript_region is_a transcript_region modified_RNA_base_feature is_a transcript_region exon_region is_a transcript_region

transcription_end_site	SO:0000616
Definition: The site where transcription ends.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transcription_end_site is_a primary_transcript_region transcription_end_site is_a junction	Child relationships:

transcription_start_site	SO:0000315
Definition: The site where transcription begins.
DBxref:SO:ke
Synonyms: [TSS]
Aspect: located_sequence_feature
Parent relationships: transcription_start_site is_a primary_transcript_region transcription_start_site is_a junction	Child relationships:

transit_peptide	SO:0000725
Definition: 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.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transit_peptide is_a polypeptide_region	Child relationships:

transition	SO:1000009
Definition: 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.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transition is_a point_mutation	Child relationships: pyrimidine_transition is_a transition purine_transition is_a transition

translated_nucleotide_match	SO:0000181
Definition: A match against a translated sequence.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: translated_nucleotide_match is_a nucleotide_match	Child relationships:

translocation	SO:0000199
Definition: A region of nucleotide sequence that has translocated to a new position.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: translocation is_a sequence_variant translocation sequence_of translocate	Child relationships:

translocation_site	SO:0000691
Definition: The space between two bases in a sequence which marks the position where a translocation has occurred.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: translocation_site is_a sequence_variant translocation_site position_of translocate	Child relationships:

transposable_element	SO:0000101
Definition: A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
DBxref:external reference [http:////www.sci.sdsu.edu/ ~ smaloy/Glossary/T.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transposable_element is_a repeat_family	Child relationships: helitron is_a transposable_element DNA_transposon is_a transposable_element retrotransposon is_a transposable_element

transposable_element_flanking_region	SO:0000364
Definition: The region of sequence surrounding a transposible element.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transposable_element_flanking_region is_a flanking_region	Child relationships:

transposable_element_target_site_duplication	SO:0000434
Definition: A sequence of DNA that is duplicated when a transposable element inserts; usually found at each end the insertion.
DBxref:external reference [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transposable_element_target_site_duplication is_a repeat_region	Child relationships:

transversion	SO:1000017
Definition: Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transversion is_a point_mutation	Child relationships: pyrimidine_to_purine_transversion is_a transversion purine_to_pyrimidine_transversion is_a transversion

trinucleotide_repeat_microsatellite_feature	SO:0000291
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: trinucleotide_repeat_microsatellite_feature is_a microsatellite	Child relationships:

tryptophan_tRNA_primary_transcript	SO:0000228
Definition: A primary transcript encoding tryptophanyl tRNA (SO:000271).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tryptophan_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

tryptophanyl_tRNA	SO:0000271
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tryptophanyl_tRNA is_a tRNA	Child relationships:

twintron	SO:0000406
Definition: An intron within an intron.
DBxref:PMID:1899376
Synonyms:
Aspect: located_sequence_feature
Parent relationships: twintron is_a intron	Child relationships:

tyrosine_tRNA_primary_transcript	SO:0000229
Definition: A primary transcript encoding tyrosyl tRNA (SO:000272).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tyrosine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

tyrosyl_tRNA	SO:0000272
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tyrosyl_tRNA is_a tRNA	Child relationships:

ultracontig	SO:0000719
Definition: 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.
DBxref:FB:WG
Synonyms:
Aspect: located_sequence_feature
Parent relationships: ultracontig is_a assembly	Child relationships: supercontig part_of ultracontig

uncharacterised_change_in_nucleotide_sequence	SO:1000007
Definition: The nature of the mutation event is either uncharacterised or only partially characterised.
DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: uncharacterised_change_in_nucleotide_sequence is_a substitution	Child relationships: partially_characterised_change_in_DNA_sequence is_a uncharacterised_change_in_nucleotide_sequence

unedited_region	SO:0000607
Definition: The region of an edited transcript that will not be edited.
DBxref:external reference [http:////www.rna.ucla.edu/]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: unedited_region is_a edited_transcript_feature	Child relationships:

untranslated_region_polyicistronic_mRNA	SO:0000242
Definition: The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: untranslated_region_polyicistronic_mRNA is_a UTR	Child relationships:

upstream_AUG_codon	SO:0000630
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: upstream_AUG_codon is_a UTR_region	Child relationships:

valine_tRNA_primary_transcript	SO:0000230
Definition: A primary transcript encoding valyl tRNA (SO:000273).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: valine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

valyl_tRNA	SO:0000273
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: valyl_tRNA is_a tRNA	Child relationships:

vault_RNA	SO:0000404
Definition: 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.
DBxref:external reference [http:////www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: vault_RNA is_a ncRNA	Child relationships:

vector	SO:0000440
Definition: A DNA molecule that can be used to transfer DNA molecules between organisms.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: vector is_a reagent vector part_of clone	Child relationships: phagemid is_a vector plasmid_vector is_a vector PAC is_a vector cosmid is_a vector YAC is_a vector fosmid is_a vector BAC is_a vector lambda_vector is_a vector

vertebrate_immune_system_gene_recombination_feature	SO:0000301
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: vertebrate_immune_system_gene_recombination_feature is_a recombination_feature_of_rearranged_gene	Child relationships: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster is_a vertebrate_immune_system_gene_recombination_feature vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment is_a vertebrate_immune_system_gene_recombination_feature vertebrate_immune_system_gene_recombination_spacer is_a vertebrate_immune_system_gene_recombination_feature vertebrate_immunoglobulin_T_cell_receptor_segment is_a vertebrate_immune_system_gene_recombination_feature vertebrate_immune_system_gene_recombination_signal_feature is_a vertebrate_immune_system_gene_recombination_feature vertebrate_immunoglobulin_T_cell_receptor_gene_cluster is_a vertebrate_immune_system_gene_recombination_feature

vertebrate_immune_system_gene_recombination_signal_feature	SO:0000939
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: vertebrate_immune_system_gene_recombination_signal_feature is_a vertebrate_immune_system_gene_recombination_feature	Child relationships: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene is_a vertebrate_immune_system_gene_recombination_signal_feature J_gene_recombination_feature is_a vertebrate_immune_system_gene_recombination_signal_feature D_gene_recombination_feature is_a vertebrate_immune_system_gene_recombination_signal_feature nonamer_of_recombination_feature_of_vertebrate_immune_system_gene is_a vertebrate_immune_system_gene_recombination_signal_feature V_gene_recombination_feature is_a vertebrate_immune_system_gene_recombination_signal_feature

vertebrate_immune_system_gene_recombination_spacer	SO:0000563
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: vertebrate_immune_system_gene_recombination_spacer is_a vertebrate_immune_system_gene_recombination_feature	Child relationships: J_spacer is_a vertebrate_immune_system_gene_recombination_spacer five_prime_D_spacer is_a vertebrate_immune_system_gene_recombination_spacer V_spacer is_a vertebrate_immune_system_gene_recombination_spacer three_prime_D_spacer is_a vertebrate_immune_system_gene_recombination_spacer

vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	SO:0000482
Definition: undefined
DBxref:
Synonyms: [vertebrate_immunoglobulin/T-cell_receptor_gene-cluster]
Aspect: located_sequence_feature
Parent relationships: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster is_a vertebrate_immune_system_gene_recombination_feature	Child relationships: D_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster D_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster D_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster V_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster V_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster V_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster

vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster	SO:0000938
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster is_a vertebrate_immune_system_gene_recombination_feature	Child relationships: D_DJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster VDJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_VDJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster VJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_D_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_D_DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_VJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster VDJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_D_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_D_DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster D_DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_D_DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_VDJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_VJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_D_DJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_VDJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster D_DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster VJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_VJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster VJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster D_DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_VDJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster VDJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_VJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster V_DJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster

vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment	SO:0000936
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment is_a vertebrate_immune_system_gene_recombination_feature	Child relationships: VD_gene is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment VJ_gene is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment VDJ_gene is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment DJ_gene is_a vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment

vertebrate_immunoglobulin_T_cell_receptor_segment	SO:0000460
Definition: undefined
DBxref:
Synonyms: [vertebrate_immunoglobulin/T-cell_receptor_gene]
Aspect: located_sequence_feature
Parent relationships: vertebrate_immunoglobulin_T_cell_receptor_segment is_a vertebrate_immune_system_gene_recombination_feature	Child relationships: C_gene is_a vertebrate_immunoglobulin_T_cell_receptor_segment V_gene is_a vertebrate_immunoglobulin_T_cell_receptor_segment D_gene is_a vertebrate_immunoglobulin_T_cell_receptor_segment J_gene is_a vertebrate_immunoglobulin_T_cell_receptor_segment

virtual_sequence	SO:0000499
Definition: A continous piece of sequence similar to the 'virtual contig' concept of ensembl.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: virtual_sequence is_a assembly	Child relationships:

chromosome_variation terms

Robertsonian_fusion	SO:1000043
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: Robertsonian_fusion is_a chromosomal_translocation	Child relationships:

aneuploid	SO:0000054
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: aneuploid is_a chromosome_number_variation	Child relationships: hypoploid is_a aneuploid hyperploid is_a aneuploid

aneuploid_chromosome	SO:0000550
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: aneuploid_chromosome is_a chromosome_structure_variation	Child relationships: chromosomal_duplication is_a aneuploid_chromosome inversion_derived_aneuploid_chromosome is_a aneuploid_chromosome chromosomal_deletion is_a aneuploid_chromosome

assortment_derived_aneuploid	SO:0000803
Definition: A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.
DBxref:fb:gm
Synonyms:
Aspect: chromosome_variation
Parent relationships: assortment_derived_aneuploid is_a chromosome_variation	Child relationships:

assortment_derived_deficiency	SO:0000802
Definition: A multi-chromosome deficiency aberration generated by reassortment of other aberration components.
DBxref:FB:gm
Synonyms:
Aspect: chromosome_variation
Parent relationships: assortment_derived_deficiency is_a chromosome_variation	Child relationships:

assortment_derived_deficiency_plus_duplication	SO:0000801
Definition: A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.
DBxref:FB:gm
Synonyms:
Aspect: chromosome_variation
Parent relationships: assortment_derived_deficiency_plus_duplication is_a chromosome_variation	Child relationships:

assortment_derived_duplication	SO:0000800
Definition: A multi-chromosome duplication aberration generated by reassortment of other aberration components.
DBxref:FB:gm
Synonyms:
Aspect: chromosome_variation
Parent relationships: assortment_derived_duplication is_a chromosome_variation	Child relationships:

autosynaptic_chromosome	SO:1000136
Definition: undefined
DBxref:
Synonyms: [(Drosophila)A]
Aspect: chromosome_variation
Parent relationships: autosynaptic_chromosome is_a chromosome_structure_variation	Child relationships: laevosynaptic_chromosome is_a autosynaptic_chromosome dexstrosynaptic_chromosome is_a autosynaptic_chromosome

bipartite_duplication	SO:1000149
Definition: 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.
DBxref:fb:reference_manual
Synonyms: [(Drosophila)bDp]
Aspect: chromosome_variation
Parent relationships: bipartite_duplication is_a interchromosomal_mutation	Child relationships:

bipartite_inversion	SO:1000151
Definition: Three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed).
DBxref:fb:reference_manual
Synonyms: [(Drosophila)bIn]
Aspect: chromosome_variation
Parent relationships: bipartite_inversion is_a chromosomal_inversion	Child relationships:

chromosomal_deletion	SO:1000029
Definition: undefined
DBxref:
Synonyms: [(bacteria)&Dgr;] [(Drosophila)Df] [(fungi)D]
Aspect: chromosome_variation
Parent relationships: chromosomal_deletion is_a aneuploid_chromosome chromosomal_deletion is_a intrachromosomal_mutation	Child relationships: inversion_derived_deficiency_plus_duplication is_a chromosomal_deletion inversion_derived_deficiency_plus_aneuploid is_a chromosomal_deletion inversion_derived_bipartite_deficiency is_a chromosomal_deletion deficient_translocation is_a chromosomal_deletion deficient_inversion is_a chromosomal_deletion

chromosomal_duplication	SO:1000037
Definition: undefined
DBxref:
Synonyms: [(Drosophila)Dp] [(fungi)Dp]
Aspect: chromosome_variation
Parent relationships: chromosomal_duplication is_a chromosome_structure_variation chromosomal_duplication is_a aneuploid_chromosome	Child relationships: interchromosomal_duplication is_a chromosomal_duplication insertional_duplication is_a chromosomal_duplication free_duplication is_a chromosomal_duplication intrachromosomal_duplication is_a chromosomal_duplication

chromosomal_inversion	SO:1000030
Definition: undefined
DBxref:
Synonyms: [(bacteria)IN] [(Drosophila)In] [(fungi)In]
Aspect: chromosome_variation
Parent relationships: chromosomal_inversion is_a intrachromosomal_mutation	Child relationships: inverted_ring_chromosome is_a chromosomal_inversion inversion_cum_translocation is_a chromosomal_inversion pericentric_inversion is_a chromosomal_inversion bipartite_inversion is_a chromosomal_inversion paracentric_inversion is_a chromosomal_inversion deficient_inversion is_a chromosomal_inversion inverted_intrachromosomal_transposition is_a chromosomal_inversion

chromosomal_translocation	SO:1000044
Definition: undefined
DBxref:
Synonyms: [(Drosophila)T] [(fungi)T]
Aspect: chromosome_variation
Parent relationships: chromosomal_translocation is_a interchromosomal_mutation	Child relationships: inversion_cum_translocation is_a chromosomal_translocation Robertsonian_fusion is_a chromosomal_translocation translocation_element is_a chromosomal_translocation deficient_translocation is_a chromosomal_translocation cyclic_translocation is_a chromosomal_translocation reciprocal_chromosomal_translocation is_a chromosomal_translocation

chromosome_fission	SO:1000141
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: chromosome_fission is_a intrachromosomal_mutation	Child relationships:

chromosome_number_variation	SO:1000182
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: chromosome_number_variation is_a chromosome_variation	Child relationships: aneuploid is_a chromosome_number_variation

chromosome_structure_variation	SO:1000183
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: chromosome_structure_variation is_a chromosome_variation	Child relationships: autosynaptic_chromosome is_a chromosome_structure_variation aneuploid_chromosome is_a chromosome_structure_variation complex_chromosomal_mutation is_a chromosome_structure_variation compound_chromosome is_a chromosome_structure_variation intrachromosomal_mutation is_a chromosome_structure_variation transposition is_a chromosome_structure_variation chromosomal_duplication is_a chromosome_structure_variation free_chromosome_arm is_a chromosome_structure_variation uncharacterised_chromosomal_mutation is_a chromosome_structure_variation interchromosomal_mutation is_a chromosome_structure_variation

complex_chromosomal_mutation	SO:1000146
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: complex_chromosomal_mutation is_a chromosome_structure_variation	Child relationships:

compound_chromosome	SO:1000042
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: compound_chromosome is_a chromosome_structure_variation	Child relationships: compound_chromosome_arm is_a compound_chromosome hetero_compound_chromosome is_a compound_chromosome homo_compound_chromosome is_a compound_chromosome

compound_chromosome_arm	SO:0000060
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: compound_chromosome_arm is_a compound_chromosome	Child relationships:

cyclic_translocation	SO:1000150
Definition: 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.
DBxref:fb:reference_manual
Synonyms:
Aspect: chromosome_variation
Parent relationships: cyclic_translocation is_a chromosomal_translocation	Child relationships:

deficient_interchromosomal_transposition	SO:0000063
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: deficient_interchromosomal_transposition is_a interchromosomal_transposition	Child relationships:

deficient_intrachromosomal_transposition	SO:0000062
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: deficient_intrachromosomal_transposition is_a intrachromosomal_transposition	Child relationships:

deficient_inversion	SO:1000171
Definition: Three breaks in the same chromosome; one central region lost, the other inverted.
DBxref:fb:reference_manual
Synonyms: [(Drosophila)Df] [(Drosophila)DfIn]
Aspect: chromosome_variation
Parent relationships: deficient_inversion is_a chromosomal_deletion deficient_inversion is_a chromosomal_inversion	Child relationships:

deficient_translocation	SO:1000147
Definition: A translocation in which one of the four broken ends loses a segment before re-joining.
DBxref:fb:reference_manual
Synonyms: [(Drosophila)Df] [(Drosophila)DfT]
Aspect: chromosome_variation
Parent relationships: deficient_translocation is_a chromosomal_translocation deficient_translocation is_a chromosomal_deletion	Child relationships:

dexstrosynaptic_chromosome	SO:1000142
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: dexstrosynaptic_chromosome is_a autosynaptic_chromosome	Child relationships:

direct_tandem_duplication	SO:1000039
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: direct_tandem_duplication is_a tandem_duplication	Child relationships:

free_chromosome_arm	SO:0000065
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: free_chromosome_arm is_a chromosome_structure_variation	Child relationships:

free_duplication	SO:1000144
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: free_duplication is_a chromosomal_duplication	Child relationships: free_ring_duplication is_a free_duplication

free_ring_duplication	SO:1000145
Definition: undefined
DBxref:
Synonyms: [(Drosophila)R]
Aspect: chromosome_variation
Parent relationships: free_ring_duplication is_a free_duplication free_ring_duplication is_a ring_chromosome	Child relationships:

hetero_compound_chromosome	SO:1000140
Definition: undefined
DBxref:
Synonyms: [hetero-compound_chromosome]
Aspect: chromosome_variation
Parent relationships: hetero_compound_chromosome is_a compound_chromosome	Child relationships:

homo_compound_chromosome	SO:1000138
Definition: undefined
DBxref:
Synonyms: [homo-compound_chromosome]
Aspect: chromosome_variation
Parent relationships: homo_compound_chromosome is_a compound_chromosome	Child relationships:

hyperploid	SO:0000055
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: hyperploid is_a aneuploid	Child relationships:

hypoploid	SO:0000056
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: hypoploid is_a aneuploid	Child relationships:

insertional_duplication	SO:1000154
Definition: undefined
DBxref:
Synonyms: [(Drosophila)Dpp]
Aspect: chromosome_variation
Parent relationships: insertional_duplication is_a chromosomal_duplication	Child relationships: unoriented_insertional_duplication is_a insertional_duplication uninverted_insertional_duplication is_a insertional_duplication inverted_insertional_duplication is_a insertional_duplication

interchromosomal_duplication	SO:0000457
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: interchromosomal_duplication is_a chromosomal_duplication	Child relationships:

interchromosomal_mutation	SO:1000031
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: interchromosomal_mutation is_a chromosome_structure_variation	Child relationships: chromosomal_translocation is_a interchromosomal_mutation interchromosomal_transposition is_a interchromosomal_mutation bipartite_duplication is_a interchromosomal_mutation

interchromosomal_transposition	SO:1000155
Definition: undefined
DBxref:
Synonyms: [(Drosophila)Tp]
Aspect: chromosome_variation
Parent relationships: interchromosomal_transposition is_a transposition interchromosomal_transposition is_a interchromosomal_mutation	Child relationships: unorientated_interchromosomal_transposition is_a interchromosomal_transposition inverted_interchromosomal_transposition is_a interchromosomal_transposition uninverted_interchromosomal_transposition is_a interchromosomal_transposition deficient_interchromosomal_transposition is_a interchromosomal_transposition

intrachromosomal_duplication	SO:1000038
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: intrachromosomal_duplication is_a chromosomal_duplication intrachromosomal_duplication is_a intrachromosomal_mutation	Child relationships: intrachromosomal_transposition is_a intrachromosomal_duplication inversion_derived_deficiency_plus_duplication is_a intrachromosomal_duplication tandem_duplication is_a intrachromosomal_duplication inversion_derived_duplication_plus_aneuploid is_a intrachromosomal_duplication inversion_derived_bipartite_duplication is_a intrachromosomal_duplication

intrachromosomal_mutation	SO:1000028
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: intrachromosomal_mutation is_a chromosome_structure_variation	Child relationships: chromosome_fission is_a intrachromosomal_mutation intrachromosomal_duplication is_a intrachromosomal_mutation chromosomal_deletion is_a intrachromosomal_mutation ring_chromosome is_a intrachromosomal_mutation chromosomal_inversion is_a intrachromosomal_mutation

intrachromosomal_transposition	SO:1000041
Definition: undefined
DBxref:
Synonyms: [(Drosophila)Tp]
Aspect: chromosome_variation
Parent relationships: intrachromosomal_transposition is_a transposition intrachromosomal_transposition is_a intrachromosomal_duplication	Child relationships: deficient_intrachromosomal_transposition is_a intrachromosomal_transposition unorientated_intrachromosomal_transposition is_a intrachromosomal_transposition uninverted_intrachromosomal_transposition is_a intrachromosomal_transposition inverted_intrachromosomal_transposition is_a intrachromosomal_transposition

inversion_cum_translocation	SO:1000148
Definition: 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.
DBxref:fb:reference_manual
Synonyms: [(Drosophila)InT] [(Drosophila)T] [inversion-cum-translocation]
Aspect: chromosome_variation
Parent relationships: inversion_cum_translocation is_a chromosomal_translocation inversion_cum_translocation is_a chromosomal_inversion	Child relationships:

inversion_derived_aneuploid_chromosome	SO:0000567
Definition: A chromosome may be generated by recombination between two inverversions; presumed to have a deficiency or duplication at each end of the inversion.
DBxref:FB:km
Synonyms:
Aspect: chromosome_variation
Parent relationships: inversion_derived_aneuploid_chromosome is_a aneuploid_chromosome	Child relationships:

inversion_derived_bipartite_deficiency	SO:0000461
Definition: A chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.
DBxref:FB:km
Synonyms:
Aspect: chromosome_variation
Parent relationships: inversion_derived_bipartite_deficiency is_a chromosomal_deletion	Child relationships:

inversion_derived_bipartite_duplication	SO:0000547
Definition: A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion.
DBxref:FB:km
Synonyms:
Aspect: chromosome_variation
Parent relationships: inversion_derived_bipartite_duplication is_a intrachromosomal_duplication	Child relationships:

inversion_derived_deficiency_plus_aneuploid	SO:0000512
Definition: 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.
DBxref:FB:km
Synonyms:
Aspect: chromosome_variation
Parent relationships: inversion_derived_deficiency_plus_aneuploid is_a chromosomal_deletion	Child relationships:

inversion_derived_deficiency_plus_duplication	SO:0000465
Definition: 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.
DBxref:FB:km
Synonyms:
Aspect: chromosome_variation
Parent relationships: inversion_derived_deficiency_plus_duplication is_a intrachromosomal_duplication inversion_derived_deficiency_plus_duplication is_a chromosomal_deletion	Child relationships:

inversion_derived_duplication_plus_aneuploid	SO:0000549
Definition: 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.
DBxref:FB:km
Synonyms:
Aspect: chromosome_variation
Parent relationships: inversion_derived_duplication_plus_aneuploid is_a intrachromosomal_duplication	Child relationships:

inverted_insertional_duplication	SO:1000153
Definition: 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.
DBxref:fb:reference_manual
Synonyms: [(Drosophila)iDp]
Aspect: chromosome_variation
Parent relationships: inverted_insertional_duplication is_a insertional_duplication	Child relationships:

inverted_interchromosomal_transposition	SO:1000156
Definition: undefined
DBxref:
Synonyms: [(Drosophila)iTp]
Aspect: chromosome_variation
Parent relationships: inverted_interchromosomal_transposition is_a interchromosomal_transposition	Child relationships:

inverted_intrachromosomal_transposition	SO:1000158
Definition: 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.
DBxref:fb:reference_manual
Synonyms: [(Drosophila)iTp]
Aspect: chromosome_variation
Parent relationships: inverted_intrachromosomal_transposition is_a intrachromosomal_transposition inverted_intrachromosomal_transposition is_a chromosomal_inversion	Child relationships:

inverted_ring_chromosome	SO:0000439
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: inverted_ring_chromosome is_a ring_chromosome inverted_ring_chromosome is_a chromosomal_inversion	Child relationships:

inverted_tandem_duplication	SO:1000040
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: inverted_tandem_duplication is_a tandem_duplication	Child relationships:

laevosynaptic_chromosome	SO:1000143
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: laevosynaptic_chromosome is_a autosynaptic_chromosome	Child relationships:

paracentric_inversion	SO:1000047
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: paracentric_inversion is_a chromosomal_inversion	Child relationships:

partially_characterised_chromosomal_mutation	SO:1000175
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: partially_characterised_chromosomal_mutation is_a uncharacterised_chromosomal_mutation	Child relationships:

pericentric_inversion	SO:1000046
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: pericentric_inversion is_a chromosomal_inversion	Child relationships:

reciprocal_chromosomal_translocation	SO:1000048
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: reciprocal_chromosomal_translocation is_a chromosomal_translocation	Child relationships:

ring_chromosome	SO:1000045
Definition: undefined
DBxref:
Synonyms: [(Drosophila)R] [(fungi)C]
Aspect: chromosome_variation
Parent relationships: ring_chromosome is_a intrachromosomal_mutation	Child relationships: inverted_ring_chromosome is_a ring_chromosome free_ring_duplication is_a ring_chromosome

tandem_duplication	SO:1000173
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: tandem_duplication is_a intrachromosomal_duplication	Child relationships: direct_tandem_duplication is_a tandem_duplication inverted_tandem_duplication is_a tandem_duplication

translocation_element	SO:0000686
Definition: 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.
DBxref:SO:ma
Synonyms:
Aspect: chromosome_variation
Parent relationships: translocation_element is_a chromosomal_translocation	Child relationships:

transposition	SO:0000453
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: transposition is_a chromosome_structure_variation	Child relationships: intrachromosomal_transposition is_a transposition interchromosomal_transposition is_a transposition

uncharacterised_chromosomal_mutation	SO:1000170
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: uncharacterised_chromosomal_mutation is_a chromosome_structure_variation	Child relationships: partially_characterised_chromosomal_mutation is_a uncharacterised_chromosomal_mutation

uninverted_insertional_duplication	SO:1000152
Definition: 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.
DBxref:fb:reference_manual
Synonyms: [(Drosophila)eDp]
Aspect: chromosome_variation
Parent relationships: uninverted_insertional_duplication is_a insertional_duplication	Child relationships:

uninverted_interchromosomal_transposition	SO:1000157
Definition: undefined
DBxref:
Synonyms: [(Drosophila)eTp]
Aspect: chromosome_variation
Parent relationships: uninverted_interchromosomal_transposition is_a interchromosomal_transposition	Child relationships:

uninverted_intrachromosomal_transposition	SO:1000159
Definition: 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.
DBxref:fb:reference_manual
Synonyms: [(Drosophila)eTp]
Aspect: chromosome_variation
Parent relationships: uninverted_intrachromosomal_transposition is_a intrachromosomal_transposition	Child relationships:

unorientated_interchromosomal_transposition	SO:1000161
Definition: undefined
DBxref:
Synonyms: [(Drosophila)uTp]
Aspect: chromosome_variation
Parent relationships: unorientated_interchromosomal_transposition is_a interchromosomal_transposition	Child relationships:

unorientated_intrachromosomal_transposition	SO:1000162
Definition: 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.
DBxref:fb:reference_manual
Synonyms: [(Drosophila)uTp]
Aspect: chromosome_variation
Parent relationships: unorientated_intrachromosomal_transposition is_a intrachromosomal_transposition	Child relationships:

unoriented_insertional_duplication	SO:1000160
Definition: 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.
DBxref:fb:reference_manual
Synonyms: [(Drosophila)uDp]
Aspect: chromosome_variation
Parent relationships: unoriented_insertional_duplication is_a insertional_duplication	Child relationships:

cross product terms:

CDS_independently_known	SO:1001246
Aspect: Cross Product
Definition: A CDS with the evidence status of being independently known.
DBxref:SO:xp
intersection of is_a CDS
intersection of has_quality independently_known

CDS_predicted	SO:1001254
Aspect: Cross Product
Definition: A CDS that is predicted.
DBxref:SO:ke
intersection of is_a CDS
intersection of has_quality predicted

CDS_supported_by_EST_or_cDNA_data	SO:1001259
Aspect: Cross Product
Definition: A CDS that is supported by similarity to EST or cDNA data.
DBxref:SO:xp
intersection of is_a CDS_supported_by_sequence_similarity_data
intersection of has_quality supported_by_EST_or_cDNA

CDS_supported_by_domain_match_data	SO:1001249
Aspect: Cross Product
Definition: A CDS that is supported by domain similarity.
DBxref:SO:xp
intersection of is_a CDS_supported_by_sequence_similarity_data
intersection of has_quality supported_by_domain_match

CDS_supported_by_sequence_similarity_data	SO:1001251
Aspect: Cross Product
Definition: A CDS that is supported by sequence similarity data.
DBxref:SO:xp
intersection of is_a CDS
intersection of has_quality supported_by_sequence_similarity

allelically_excluded_gene	SO:0000897
Aspect: Cross Product
Definition: A gene that is allelically_excluded
DBxref:SO:xp
intersection of is_a epigenetically_modified_gene
intersection of has_quality allelically_excluded

alternatively_spliced_transcript	SO:1001187
Aspect: Cross Product
Definition: A transcript that is alternatively spliced.
DBxref:SO:xp
intersection of is_a transcript
intersection of has_quality alternatively_spliced

apicoplast_gene	SO:0000091
Aspect: Cross Product
Definition: A gene from apicoplast sequence.
DBxref:SO:xp
intersection of is_a plastid_gene
intersection of has_origin apicoplast_sequence

capped_mRNA	SO:0000862
Aspect: Cross Product
Definition: An mRNA that is capped
DBxref:SO:xp
intersection of is_a mRNA
intersection of adjacent_to cap
intersection of has_quality capped

capped_primary_transcript	SO:0000861
Aspect: Cross Product
Definition: A primary transcript that is capped.
DBxref:SO:xp
intersection of is_a primary_transcript
intersection of adjacent_to cap
intersection of has_quality capped

chimeric_cDNA_clone	SO:0000810
Aspect: Cross Product
Definition: A cDNA clone invalidated because it is chimeric.
DBxref:SO:xp
intersection of is_a invalidated_cDNA_clone
intersection of has_quality invalidated_by_chimeric_cDNA

chloroplast_chromosome	SO:0000820
Aspect: Cross Product
Definition: A chromsome originating in a chloroplast.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin chloroplast_sequence

chromoplast_chromosome	SO:0000821
Aspect: Cross Product
Definition: A chromsome originating in a chromoplast.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin chromoplast_sequence

chromoplast_gene	SO:0000093
Aspect: Cross Product
Definition: A gene from chromoplast_sequence.
DBxref:SO:xp
intersection of is_a plastid_gene
intersection of has_origin chromoplast_sequence

cloned_cDNA_insert	SO:0000913
Aspect: Cross Product
Definition: A clone insert made from cDNA.
DBxref:SO:xp
intersection of is_a clone_insert
intersection of has_quality cloned_cDNA

cloned_genomic_insert	SO:0000914
Aspect: Cross Product
Definition: A clone insert made from genomic DNA.
DBxref:SO:xp
intersection of is_a clone_insert
intersection of has_origin cloned_genomic

ct_gene	SO:0000092
Aspect: Cross Product
Definition: A gene from chloroplast sequence.
DBxref:SO:xp
intersection of is_a plastid_gene
intersection of has_origin chloroplast_sequence

cyanelle_chromosome	SO:0000822
Aspect: Cross Product
Definition: A chromosome originating in a cyanelle.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin cyanelle_sequence

cyanelle_gene	SO:0000094
Aspect: Cross Product
Definition: A gene from cyanelle sequence.
DBxref:SO:xp
intersection of is_a plastid_gene
intersection of has_origin cyanelle_sequence

dicistronic_mRNA	SO:0000716
Aspect: Cross Product
Definition: An mRNA that has the quality dicistronic.
DBxref:SO:ke
intersection of is_a mRNA
intersection of has_quality dicistronic

dicistronic_primary_transcript	SO:1001197
Aspect: Cross Product
Definition: A primary transcript that has the quality dicistronic.
DBxref:SO:xp
intersection of is_a primary_transcript
intersection of has_quality dicistronic

dicistronic_transcript	SO:0000079
Aspect: Cross Product
Definition: A transcript that is dicistronic.
DBxref:SO:ke
intersection of is_a transcript
intersection of has_quality dicistronic

edited_CDS	SO:0000935
Aspect: Cross Product
Definition: A CDS that is edited.
DBxref:SO:xp
intersection of is_a CDS
intersection of associated_with edit_operation
intersection of has_quality edited

edited_mRNA	SO:0000929
Aspect: Cross Product
Definition: An mRNA that is edited.
DBxref:SO:xp
intersection of is_a edited_transcript
intersection of associated_with edit_operation
intersection of has_quality edited

edited_transcript	SO:0000873
Aspect: Cross Product
Definition: A transcript that is edited.
DBxref:SO:ke
intersection of is_a transcript
intersection of has_quality edited

edited_transcript_by A_to_I_substitution	SO:0000874
Aspect: Cross Product
Definition: A transcript that has been edited by A to I substitution.
DBxref:SO:ke
intersection of is_a edited_transcript
intersection of associated_with substitute_A_to_I

endogenous_retroviral_gene	SO:0000100
Aspect: Cross Product
Definition: A proviral gene with origin endogenous retrovirus.
DBxref:SO:xp
intersection of is_a proviral_gene
intersection of has_origin endogenous_retroviral_sequence

engineered_episome	SO:0000779
Aspect: Cross Product
Definition: An episome that is engineered.
DBxref:SO:xp
intersection of is_a episome
intersection of has_quality engineered

engineered_foreign_gene	SO:0000281
Aspect: Cross Product
Definition: A gene that is engineered and foreign.
DBxref:SO:xp
intersection of is_a engineered_gene
intersection of has_quality engineered
intersection of has_quality foreign

engineered_foreign_region	SO:0000805
Aspect: Cross Product
Definition: A region that is engineered and foreign.
DBxref:SO:xp
intersection of is_a region
intersection of has_quality engineered
intersection of has_quality foreign

engineered_foreign_repetitive_element	SO:0000293
Aspect: Cross Product
Definition: A repetitive element that is engineered and foreign.
DBxref:SO:xp
intersection of is_a repeat_region
intersection of has_quality engineered
intersection of has_quality foreign

engineered_foreign_transposable_element	SO:0000799
Aspect: Cross Product
Definition: A transposable_element that is engineereed and foreign.
DBxref:SO:mc
intersection of is_a transposable_element
intersection of has_quality engineered
intersection of has_quality foreign

engineered_foreign_transposable_element_gene	SO:0000283
Aspect: Cross Product
Definition: A transposible_element that is engineered and foreign.
DBxref:SO:xp
intersection of is_a transposable_element_gene
intersection of has_quality engineered
intersection of has_quality foreign

engineered_fusion_gene	SO:0000288
Aspect: Cross Product
Definition: A fusion gene that is engineered.
DBxref:SO:xp
intersection of is_a fusion_gene
intersection of is_a gene
intersection of has_quality engineered
intersection of has_quality fusion

engineered_gene	SO:0000280
Aspect: Cross Product
Definition: A gene that is engineered.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality engineered

engineered_insert	SO:0000915
Aspect: Cross Product
Definition: A clone insert that is engineered.
DBxref:SO:xp
intersection of is_a clone_insert
intersection of has_quality engineered

engineered_plasmid	SO:0000637
Aspect: Cross Product
Definition: A plasmid that is engineered.
DBxref:SO:xp
intersection of is_a plasmid
intersection of has_quality engineered

engineered_region	SO:0000804
Aspect: Cross Product
Definition: A region that is engineered.
DBxref:SO:xp
intersection of is_a region
intersection of has_quality engineered

engineered_rescue_region	SO:0000794
Aspect: Cross Product
Definition: A rescue region that is engineered.
DBxref:SO:xp
intersection of is_a rescue_region
intersection of has_quality engineered

engineered_tag	SO:0000807
Aspect: Cross Product
Definition: A tag that is engineered.
DBxref:SO:xp
intersection of is_a tag
intersection of has_quality engineered

engineered_transposable_element	SO:0000798
Aspect: Cross Product
Definition: TE that has been modified by manipulations in vitro.
DBxref:SO:mc
intersection of is_a transposable_element
intersection of has_quality engineered

enhancer_bound_by_factor	SO:0000166
Aspect: Cross Product
Definition: An enhancer bound by a factor.
DBxref:SO:xp
intersection of is_a enhancer
intersection of has_quality bound_by_factor

epigenetically_modified_gene	SO:0000898
Aspect: Cross Product
Definition: A gene that is epigenetically modified.
DBxref:SO:ke
intersection of is_a gene
intersection of has_quality epigenetically_modified

exemplar_mRNA	SO:0000734
Aspect: Cross Product
Definition: 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.
DBxref:
intersection of is_a mRNA
intersection of has_quality exemplar

floxed_gene	SO:0000363
Aspect: Cross Product
Definition: A transgene that is floxed.
DBxref:SO:xp
intersection of is_a transgene
intersection of has_quality floxed

foreign_gene	SO:0000285
Aspect: Cross Product
Definition: A gene that is foreign.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality foreign

foreign_transposable_element	SO:0000720
Aspect: Cross Product
Definition: A transposable element that is foreign.
DBxref:SO:ke
intersection of is_a transposable_element
intersection of has_quality foreign

fusion_gene	SO:0000287
Aspect: Cross Product
Definition: A gene that is a fusion.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality fusion

gene_rearranged_at_DNA_level	SO:0000138
Aspect: Cross Product
Definition: An epigenetically modified gene, rearranged at the DNA level.
DBxref:SO:xp
intersection of is_a epigenetically_modified_gene
intersection of has_quality rearranged_at_DNA_level

gene_silenced_by_DNA_methylation	SO:0000129
Aspect: Cross Product
Definition: A silenced gene silenced DNA methylation.
DBxref:SO:xp
intersection of is_a gene_silenced_by_DNA_modification
intersection of has_quality silenced_by_DNA_methylation

gene_silenced_by_DNA_modification	SO:0000128
Aspect: Cross Product
Definition: A silenced gene by DNA modification.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality silenced_by_DNA_modification

gene_with_dicistronic_mRNA	SO:0000722
Aspect: Cross Product
Definition: A gene that encodes a polycisronic mRNA.
DBxref:SO:xp
intersection of is_a gene_with_dicistronic_transcript
intersection of associated_with dicistronic_mRNA

gene_with_dicistronic_primary_transcript	SO:0000721
Aspect: Cross Product
Definition: A gene that encodes a dicistronic primary transcript.
DBxref:SO:xp
intersection of is_a gene_with_dicistronic_transcript
intersection of associated_with dicistronic_primary_transcript

gene_with_dicistronic_transcript	SO:0000692
Aspect: Cross Product
Definition: A gene that encodes a dicistronic transcript.
DBxref:SO:xp
intersection of is_a gene_with_polycistronic_transcript
intersection of associated_with dicistronic_transcript

gene_with_edited_transcript	SO:0000548
Aspect: Cross Product
Definition: A gene that encodes a transcript that is edited.
DBxref:SO:xp
intersection of is_a gene
intersection of associated_with edited_transcript

gene_with_mRNA_recoded_by_translational_bypass	SO:0000711
Aspect: Cross Product
Definition: A gene with mRNA recoded by translational bypass.
DBxref:SO:xp
intersection of is_a gene_with_recoded_mRNA
intersection of associated_with recoded_by_translational_bypass

gene_with_mRNA_with_frameshift	SO:0000455
Aspect: Cross Product
Definition: A gene that encodes an mRNA with a frameshift.
DBxref:SO:xp
intersection of is_a gene
intersection of associated_with frameshift

gene_with_polyadenylated_mRNA	SO:0000451
Aspect: Cross Product
Definition: A gene that encodes a polyadenylated mRNA.
DBxref:SO:xp
intersection of is_a gene
intersection of associated_with polyadenylated_mRNA

gene_with_polycistronic_transcript	SO:0000690
Aspect: Cross Product
Definition: A gene that encodes a polycistronic transcript.
DBxref:SO:xp
intersection of is_a gene
intersection of associated_with polycistronic_transcript

gene_with_recoded_mRNA	SO:0000693
Aspect: Cross Product
Definition: A gene that encodes an mRNA that is recoded.
DBxref:SO:xp
intersection of is_a gene
intersection of associated_with recoded_mRNA

gene_with_stop_codon_read_through	SO:0000697
Aspect: Cross Product
Definition: A gene that encodes a transcript with stop codon readthrough.
DBxref:SO:xp
intersection of is_a gene_with_recoded_mRNA
intersection of associated_with stop_codon_read_through

gene_with_stop_codon_redefined_as_pyrrolysine	SO:0000698
Aspect: Cross Product
Definition: A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.
DBxref:SO:xp
intersection of is_a gene_with_stop_codon_read_through
intersection of associated_with stop_codon_redefined_as_pyrrolysine

gene_with_stop_codon_redefined_as_selenocysteine	SO:0000710
Aspect: Cross Product
Definition: A gene encoding an mRNA that has the stop codon redefined as selenocysteine.
DBxref:SO:xp
intersection of is_a gene_with_stop_codon_read_through
intersection of associated_with stop_codon_redefined_as_selenocysteine

gene_with_trans_spliced_transcript	SO:0000459
Aspect: Cross Product
Definition: A gene with a transcript that is trans-spliced.
DBxref:SO:xp
intersection of is_a gene
intersection of associated_with trans_spliced_transcript

gene_with_transcript_with_translational_frameshift	SO:0000712
Aspect: Cross Product
Definition: A gene encoding a transcript that has a translational frameshift.
DBxref:SO:xp
intersection of is_a gene_with_recoded_mRNA
intersection of associated_with translational_frameshift

genomically_contaminated_cDNA_clone	SO:0000811
Aspect: Cross Product
Definition: A cDNA clone invalidated by genomic contamination.
DBxref:SO:xp
intersection of is_a invalidated_cDNA_clone
intersection of has_quality invalidated_by_genomic_contamination

homologous_region	SO:0000853
Aspect: Cross Product
Definition: A region that is homologous to another region.
DBxref:SO:ke
intersection of is_a conserved_region
intersection of has_quality conserved

intermediate_edited_mRNA	SO:0000934
Aspect: Cross Product
Definition: A pre-edited mRNA that has been partially edited.
DBxref:SO:xp
intersection of is_a pre_edited_mRNA
intersection of associated_with guide_RNA
intersection of associated_with edit_operation
intersection of has_quality intermediate

invalidated_cDNA_clone	SO:0000809
Aspect: Cross Product
Definition: A cDNA clone that is invalid.
DBxref:SO:xp
intersection of is_a cDNA_clone
intersection of has_quality invalidated

kinetoplast_chromosome	SO:0000826
Aspect: Cross Product
Definition: A chromosome with origine in the kinetoplast.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin kinetoplast_sequence

kinetoplast_gene	SO:0000089
Aspect: Cross Product
Definition: A gene located in kinetoplast sequence.
DBxref:SO:xp
intersection of is_a mt_gene
intersection of has_origin kinetoplast_sequence

leucoplast_chromosome	SO:0000823
Aspect: Cross Product
Definition: A chromosome with origin in a leucoplast.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin leucoplast_sequence

leucoplast_gene	SO:0000095
Aspect: Cross Product
Definition: A plastid gene from leucoplast sequence.
DBxref:SO:xp
intersection of is_a plastid_gene
intersection of has_origin leucoplast_sequence

mRNA_recoded_by_codon_redefinition	SO:1001265
Aspect: Cross Product
Definition: A gene whose mRNA is recoded by an alteration of codon meaning.
DBxref:SO:ma
intersection of is_a mRNA
intersection of has_quality codon_redefined

mRNA_recoded_by_translational_bypass	SO:1001264
Aspect: Cross Product
Definition: mRNA is translated by ribosomes that suspend translation at a particular codon and resume translation at a particular non-overlapping downstream codon.
DBxref:external reference [http:////www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]
intersection of is_a mRNA
intersection of has_quality recoded_by_translational_bypass

mRNA_with_frameshift	SO:0000108
Aspect: Cross Product
Definition: An mRNA with a frameshift
DBxref:SO:xp
intersection of is_a mRNA
intersection of has_quality frameshift

mRNA_with_minus_1_frameshift	SO:0000282
Aspect: Cross Product
Definition: An mRNA with a minus 1 frameshift
DBxref:SO:xp
intersection of is_a mRNA_with_frameshift
intersection of has_quality minus_1_frameshift

mRNA_with_minus_2_frameshift	SO:0000335
Aspect: Cross Product
Definition: A mRNA with a minus 2 frameshift.
DBxref:SO:ke
intersection of is_a mRNA_with_frameshift
intersection of has_quality minus_2_frameshift

mRNA_with_plus_1_frameshift	SO:0000321
Aspect: Cross Product
Definition: An mRNA with a plus 1 frameshift
DBxref:SO:ke
intersection of is_a mRNA_with_frameshift
intersection of has_quality plus_1_frameshift

mRNA_with_plus_2_frameshift	SO:0000329
Aspect: Cross Product
Definition: AAn mRNA with a plus 2 frameshift.
DBxref:SO:xp
intersection of is_a mRNA_with_frameshift
intersection of has_quality plus_2_framshift

macronuclear_chromosome	SO:0000824
Aspect: Cross Product
Definition: A chromosome originating in a macronucleus.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin macronuclear_sequence

maternally_imprinted_gene	SO:0000888
Aspect: Cross Product
Definition: A gene that is maternally_imprinted.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality maternally_imprinted

maxi_circle_gene	SO:0000654
Aspect: Cross Product
Definition: A mitochondrial gene located in a maxicircle.
DBxref:SO:xp
intersection of is_a mt_gene
intersection of has_origin maxicircle_sequence

maxicircle_chromosome	SO:0000827
Aspect: Cross Product
Definition: A chromosome originating in a maxi-circle.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin maxicircle_sequence

micronuclear_chromosome	SO:0000825
Aspect: Cross Product
Definition: A chromosome originating in a micronucleus.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin micronuclear_sequence

mitochondrial_chromosome	SO:0000819
Aspect: Cross Product
Definition: A chromosome originating in a mitochondria.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin mitochondrial_sequence

monocistronic_mRNA	SO:0000633
Aspect: Cross Product
Definition: An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
DBxref:SO:rd
intersection of is_a mRNA
intersection of has_quality monocistronic

monocistronic_primary_transcript	SO:0000632
Aspect: Cross Product
Definition: A primary transcript encoding for more than one gene product.
DBxref:SO:ke
intersection of is_a primary_transcript
intersection of has_quality monocistronic

monocistronic_transcript	SO:0000665
Aspect: Cross Product
Definition: A transcript that is monocistronic
DBxref:SO:xp
intersection of is_a transcript
intersection of has_quality monocistronic

mt_gene	SO:0000088
Aspect: Cross Product
Definition: A gene located in mitochondrial sequence.
DBxref:SO:xp
intersection of is_a gene
intersection of has_origin mitochondrial_sequence

natural_transposable_element	SO:0000797
Aspect: Cross Product
Definition: TE that exists (or existed) in nature.
DBxref:SO:mc
intersection of is_a transposable_element
intersection of has_quality natural

negatively_autoregulated_gene	SO:0000891
Aspect: Cross Product
Definition: A gene that is negatively autoreguated.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality negatively_autoregulated

nuclear_chromosome	SO:0000828
Aspect: Cross Product
Definition: A chromosome originating in a nucleus.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin chromosome

nuclear_gene	SO:0000087
Aspect: Cross Product
Definition: A gene from nuclear sequence.
DBxref:SO:xp
intersection of is_a gene
intersection of has_origin nuclear_sequence

nuclear_mt_pseudogene	SO:0001044
Aspect: Cross Product
Definition: A pseudogene that is nuclear/mitochondrial.
DBxref:SO:xp
intersection of is_a pseudogene
intersection of has_quality nuclear_mitochondrial

nucleomorph_gene	SO:0000097
Aspect: Cross Product
Definition: A gene from nucleomorph sequence.
DBxref:SO:xp
intersection of is_a gene
intersection of has_origin nucleomorphic_sequence

nucleomorphic_chromosome	SO:0000829
Aspect: Cross Product
Definition: A chromosome originating in a nucleomorph.
DBxref:SO:xp
intersection of is_a chromosome
intersection of has_origin nucleomorphic_sequence

orphan_CDS	SO:1001247
Aspect: Cross Product
Definition: A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.
DBxref:SO:ma
intersection of is_a CDS_predicted
intersection of has_origin orphan

orthologous_region	SO:0000855
Aspect: Cross Product
Definition: A homologous_region that is orthologous to another region.
DBxref:SO:ke
intersection of is_a homologous_region
intersection of has_quality orthologous

paralogous_region	SO:0000854
Aspect: Cross Product
Definition: A homologous_region that is paralogous to another region.
DBxref:SO:ke
intersection of is_a homologous_region
intersection of has_quality paralogous

partially_processed_cDNA_clone	SO:0000813
Aspect: Cross Product
Definition: A cDNA invalidated clone by partial processing.
DBxref:SO:xp
intersection of is_a invalidated_cDNA_clone
intersection of has_quality invalidated_by_partial_processing

paternally_imprinted_gene	SO:0000889
Aspect: Cross Product
Definition: A gene that is paternally imprinted.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality paternally_imprinted

plasmid_gene	SO:0000098
Aspect: Cross Product
Definition: A gene from plasmid sequence.
DBxref:SO:xp
intersection of is_a gene
intersection of has_origin plasmid_sequence

plastid_gene	SO:0000090
Aspect: Cross Product
Definition: A gene from plastid sequence.
DBxref:SO:xp
intersection of is_a gene
intersection of has_origin plastid_sequence

polyA_primed_cDNA_clone	SO:0000812
Aspect: Cross Product
Definition: A cDNA clone invalidated by polyA priming.
DBxref:SO:xp
intersection of is_a invalidated_cDNA_clone
intersection of has_quality invalidated_by_genomic_polyA_primed_cDNA

polyadenylated_mRNA	SO:0000871
Aspect: Cross Product
Definition: An mRNA that is polyadenylated.
DBxref:SO:xp
intersection of is_a mRNA
intersection of adjacent_to polyA_sequence
intersection of has_quality polyadenylated

polycistronic_mRNA	SO:0000634
Aspect: Cross Product
Definition: An mRNA that encodes multiple proteins from at least two non-overlapping regions.
DBxref:SO:rd
intersection of is_a mRNA
intersection of has_quality polycistronic

polycistronic_primary_transcript	SO:0000631
Aspect: Cross Product
Definition: A primary transcript encoding for more than one gene product.
DBxref:SO:ke
intersection of is_a primary_transcript
intersection of has_quality polycistronic

polycistronic_transcript	SO:0000078
Aspect: Cross Product
Definition: A transcript that is polycistronic.
DBxref:SO:xp
intersection of is_a transcript
intersection of has_quality polycistronic

positively_autoregulated_gene	SO:0000892
Aspect: Cross Product
Definition: A gene that is positively autoregulated.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality positively_autoregulated

post_translationally_regulated_gene	SO:0000890
Aspect: Cross Product
Definition: A gene that is post translationally regulated.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality post_translationally_regulated

processed_pseudogene	SO:0000043
Aspect: Cross Product
Definition: A pseudogene that is processed.
DBxref:SO:xp
intersection of is_a pseudogene
intersection of has_quality processed

proplastid_gene	SO:0000096
Aspect: Cross Product
Definition: A gene from proplastid sequence.
DBxref:SO:ke
intersection of is_a plastid_gene
intersection of has_origin proplastid_sequence

proviral_gene	SO:0000099
Aspect: Cross Product
Definition: A gene from proviral sequence.
DBxref:SO:xp
intersection of is_a gene
intersection of has_origin proviral_sequence

pseudogene_by_unequal_crossing_over	SO:0000044
Aspect: Cross Product
Definition: A pseudogene caused by unequal crossing over at recombination.
DBxref:SO:ke
intersection of is_a pseudogene
intersection of has_quality unequally_crossed_over

recoded_mRNA	SO:1001261
Aspect: Cross Product
Definition: A gene coding an mRNA which is recoded before translation, usually by special cis-acting signals.
DBxref:external reference [http:////www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]
intersection of is_a mRNA
intersection of has_quality recoded

recombinationally_inverted_gene	SO:0000373
Aspect: Cross Product
Definition: A recombinationally rearranged gene by inversion.
DBxref:SO:xp
intersection of is_a recombinationally_rearranged_gene
intersection of associated_with invert

recombinationally_rearranged_gene	SO:0000456
Aspect: Cross Product
Definition: A gene that is recombinationally rearranged.
DBxref:SO:ke
intersection of is_a gene
intersection of has_quality recombinationally_rearranged

recombinationally_rearranged_vertebrate_immune_system_gene	SO:0000941
Aspect: Cross Product
Definition: A recombinationally rearranged gene of the vertibrate immune system.
DBxref:SO:xp
intersection of is_a recombinationally_rearranged_gene
intersection of associated_with vertebrate_immune_system_gene_recombination_feature

rescue_gene	SO:0000816
Aspect: Cross Product
Definition: A gene that rescues.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality rescue

rescue_mini_gene	SO:0000795
Aspect: Cross Product
Definition: A mini_gene that rescues.
DBxref:SO:xp
intersection of is_a mini_gene
intersection of has_quality rescue

rescue_region	SO:0000411
Aspect: Cross Product
Definition: A region that rescues.
DBxref:SO:xp
intersection of is_a reagent
intersection of has_quality rescue

silenced_gene	SO:0000127
Aspect: Cross Product
Definition: A gene that is silenced.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality silenced

syntenic_region	SO:0005858
Aspect: Cross Product
Definition: A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.
DBxref:external reference [http:////tbase.jax.org/docs/glossary.html]
intersection of is_a conserved_region
intersection of has_quality syntenic

trans_spliced_mRNA	SO:0000872
Aspect: Cross Product
Definition: An mRNA that is trans-spliced
DBxref:SO:xp
intersection of is_a mRNA
intersection of adjacent_to spliced_leader_RNA
intersection of has_quality trans_spliced

trans_spliced_transcript	SO:0000479
Aspect: Cross Product
Definition: A transcript that is trans-spliced.
DBxref:SO:xp
intersection of is_a transcript
intersection of has_quality trans_spliced

transcript_bound_by_nucleic_acid	SO:0000278
Aspect: Cross Product
Definition: A transcript that is bound by anucleic acid.
DBxref:SO:xp
intersection of is_a transcript
intersection of has_quality bound_by_nucleic_acid

transcript_bound_by_protein	SO:0000279
Aspect: Cross Product
Definition: A transcript that is bound by a protein.
DBxref:SO:xp
intersection of is_a transcript
intersection of has_quality bound_by_protein

transcript_with_translational_frameshift	SO:0000118
Aspect: Cross Product
Definition: A transcript with a translational frameshift
DBxref:SO:xp
intersection of is_a transcript
intersection of has_quality translational_frameshift

transgene	SO:0000902
Aspect: Cross Product
Definition: A gene that is transgenic.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality transgenic

transgenic_transposable_element	SO:0000796
Aspect: Cross Product
Definition: TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.
DBxref:SO:mc
intersection of is_a transposable_element
intersection of has_quality transgenic

translationally_regulated_gene	SO:0000896
Aspect: Cross Product
Definition: A gene that is translationally regulated.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality translationally_regulated

transposable_element_gene	SO:0000111
Aspect: Cross Product
Definition: 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.
DBxref:SO:ke
intersection of is_a gene
intersection of part_of transposable_element

validated_cDNA_clone	SO:0000808
Aspect: Cross Product
Definition: undefined
DBxref:
intersection of is_a clone
intersection of is_a cDNA_clone
intersection of has_quality validated

wild_type_rescue_gene	SO:0000818
Aspect: Cross Product
Definition: A gene that rescues.
DBxref:SO:xp
intersection of is_a gene
intersection of has_quality wild_type

Aspects:

Sequence_Ontology	SO:0000000
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships:	Child relationships: consequences_of_mutation is_a Sequence_Ontology chromosome_variation is_a Sequence_Ontology sequence_attribute is_a Sequence_Ontology located_sequence_feature is_a Sequence_Ontology operation is_a Sequence_Ontology

chromosome_variation	SO:0000240
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships: chromosome_variation is_a Sequence_Ontology	Child relationships: chromosome_structure_variation is_a chromosome_variation assortment_derived_deficiency is_a chromosome_variation assortment_derived_duplication is_a chromosome_variation chromosome_number_variation is_a chromosome_variation assortment_derived_aneuploid is_a chromosome_variation assortment_derived_deficiency_plus_duplication is_a chromosome_variation

consequences_of_mutation	SO:1000132
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships: consequences_of_mutation is_a Sequence_Ontology	Child relationships: mutation_affecting_transcript is_a consequences_of_mutation mutation_affecting_gene_structure is_a consequences_of_mutation mutation_affecting_regulatory_region is_a consequences_of_mutation mutation_affecting_splicing is_a consequences_of_mutation mutation_affecting_translational_product is_a consequences_of_mutation

located_sequence_feature	SO:0000110
Definition: A biological feature that can be attributed to a region of biological sequence.
DBxref:SO:ke
Synonyms:
Aspect: root
Parent relationships: located_sequence_feature is_a Sequence_Ontology	Child relationships: sequence_variant is_a located_sequence_feature junction is_a located_sequence_feature region is_a located_sequence_feature

operation	SO:0000041
Definition: An operation that can be applied to a sequence, that results in a chnage.
DBxref:SO:ke
Synonyms:
Aspect: root
Parent relationships: operation is_a Sequence_Ontology	Child relationships: insert is_a operation delete is_a operation edit_operation is_a operation translocate is_a operation invert is_a operation substitute is_a operation

sequence_attribute	SO:0000400
Definition: An attribute describes a quality of sequence.
DBxref:SO:ke
Synonyms:
Aspect: root
Parent relationships: sequence_attribute is_a Sequence_Ontology	Child relationships: polymer_type is_a sequence_attribute sequence_location is_a sequence_attribute feature_attribute is_a sequence_attribute

List of all the relationships used in this ontology

part_of	part_of
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships:	Child relationships: member_of is_a part_of

has_quality	has_quality
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships:	Child relationships:

derives_from	derives_from
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships:	Child relationships:

has_origin	has_origin
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships:	Child relationships:

non_functional_homolog_of	non_functional_homolog_of
Definition: A relationship between a pseudogenic feature and its functional ancestor.
DBxref:SO:ke
Synonyms:
Aspect: root
Parent relationships: non_functional_homolog_of is_a homologous_to	Child relationships:

similar_to	similar_to
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships:	Child relationships: homologous_to is_a similar_to

position_of	position_of
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships:	Child relationships:

orthologous_to	orthologous_to
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships: orthologous_to is_a homologous_to	Child relationships:

genome_of	genome_of
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships:	Child relationships:

associated_with	associated_with
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships:	Child relationships:

paralogous_to	paralogous_to
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships: paralogous_to is_a homologous_to	Child relationships:

sequence_of	sequence_of
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships:	Child relationships:

homologous_to	homologous_to
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships: homologous_to is_a similar_to	Child relationships: orthologous_to is_a homologous_to paralogous_to is_a homologous_to non_functional_homolog_of is_a homologous_to

member_of	member_of
Definition: undefined
DBxref:
Synonyms:
Aspect: root
Parent relationships: member_of is_a part_of	Child relationships:

adjacent_to	adjacent_to
Definition: A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence.
DBxref:SO:ke
Synonyms:
Aspect: root
Parent relationships:	Child relationships: