List of all SO terms

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variation_operation terms

A_to_C_transversion	SO:1000024 [is leaf node]
Definition: A transversion from adenine to cytidine.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: A_to_C_transversion is_a purine_to_pyrimidine_transversion	Child relationships:

A_to_G_transition	SO:1000015 [is leaf node]
Definition: A transition of an adenine to a guanine.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: A_to_G_transition is_a purine_transition	Child relationships:

A_to_T_transversion	SO:1000025 [is leaf node]
Definition: A transversion from adenine to thymine.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: A_to_T_transversion is_a purine_to_pyrimidine_transversion	Child relationships:

C_to_A_transversion	SO:1000019 [is leaf node]
Definition: A transversion from cytidine to adenine.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: C_to_A_transversion is_a pyrimidine_to_purine_transversion	Child relationships:

C_to_G_transversion	SO:1000020 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: variation_operation
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: variation_operation
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 [is leaf node]
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: variation_operation
Parent relationships: C_to_T_transition_at_pCpG_site is_a C_to_T_transition	Child relationships:

G_to_A_transition	SO:1000016 [is leaf node]
Definition: A transition of a guanine to an adenine.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: G_to_A_transition is_a purine_transition	Child relationships:

G_to_C_transversion	SO:1000026 [is leaf node]
Definition: A transversion from guanine to cytidine.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: G_to_C_transversion is_a purine_to_pyrimidine_transversion	Child relationships:

G_to_T_transversion	SO:1000027 [is leaf node]
Definition: A transversion from guanine to thymine.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: G_to_T_transversion is_a purine_to_pyrimidine_transversion	Child relationships:

SNP	SO:0000694 [is leaf node]
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: variation_operation
Parent relationships: SNP is_a point_mutation	Child relationships:

T_to_A_transversion	SO:1000021 [is leaf node]
Definition: A transversion from T to A.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: T_to_A_transversion is_a pyrimidine_to_purine_transversion	Child relationships:

T_to_C_transition	SO:1000013 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: variation_operation
Parent relationships: T_to_C_transition is_a pyrimidine_transition	Child relationships:

T_to_G_transversion	SO:1000022 [is leaf node]
Definition: A transversion from T to G.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: T_to_G_transversion is_a pyrimidine_to_purine_transversion	Child relationships:

complex_substitution	SO:1000005 [is leaf node]
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: variation_operation
Parent relationships: complex_substitution is_a substitution	Child relationships:

delete	SO:0000045
Definition: To remove a subsection of sequence.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: delete is_a variation_operation	Child relationships: deletion_junction position_of delete deletion sequence_of delete

insert	SO:0000046
Definition: To insert a subsection of sequence.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: insert is_a variation_operation	Child relationships: insertion sequence_of insert insertion_site position_of insert

invert	SO:0000047
Definition: To invert a subsection of sequence.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: invert is_a variation_operation	Child relationships: inversion sequence_of invert

partially_characterised_change_in_DNA_sequence	SO:1000004 [is leaf node]
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: variation_operation
Parent relationships: partially_characterised_change_in_DNA_sequence is_a uncharacterised_change_in_nucleotide_sequence	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: variation_operation
Parent relationships: point_mutation is_a substitution	Child relationships: transition is_a point_mutation transversion is_a point_mutation SNP is_a point_mutation

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: variation_operation
Parent relationships: purine_to_pyrimidine_transversion is_a transversion	Child relationships: A_to_T_transversion is_a purine_to_pyrimidine_transversion A_to_C_transversion is_a purine_to_pyrimidine_transversion G_to_T_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: variation_operation
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: variation_operation
Parent relationships: pyrimidine_to_purine_transversion is_a transversion	Child relationships: T_to_A_transversion is_a pyrimidine_to_purine_transversion C_to_G_transversion is_a pyrimidine_to_purine_transversion T_to_G_transversion is_a pyrimidine_to_purine_transversion C_to_A_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: variation_operation
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

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

simple_sequence_length_polymorphism	SO:0000207 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: variation_operation
Parent relationships: simple_sequence_length_polymorphism is_a sequence_length_variation	Child relationships:

substitute	SO:0000048
Definition: To substitute a subsection of sequence for another.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: substitute is_a variation_operation	Child relationships: substitution sequence_of substitute

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: variation_operation
Parent relationships: substitution sequence_of substitute substitution is_a region substitution is_a sequence_variant	Child relationships: uncharacterised_change_in_nucleotide_sequence is_a substitution point_mutation is_a substitution complex_substitution is_a substitution sequence_length_variation is_a substitution

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: variation_operation
Parent relationships: transition is_a point_mutation	Child relationships: pyrimidine_transition is_a transition purine_transition is_a transition

translocate	SO:0000049
Definition: To translocate a subsection of sequence.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: translocate is_a variation_operation	Child relationships: translocation sequence_of translocate translocation_site position_of translocate

translocation	SO:0000199 [is leaf node]
Definition: A region of nucleotide sequence that has translocated to a new position.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: translocation sequence_of translocate	Child relationships:

translocation_site	SO:0000691 [is leaf node]
Definition: The space between two bases in a sequence which marks the position where a translocation has occurred.
DBxref:SO:ke
Synonyms:
Aspect: variation_operation
Parent relationships: translocation_site position_of translocate	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: variation_operation
Parent relationships: transversion is_a point_mutation	Child relationships: pyrimidine_to_purine_transversion is_a transversion purine_to_pyrimidine_transversion is_a transversion

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: variation_operation
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

located_sequence_feature terms

ARS	SO:0000436 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: A_box part_of RNApol_III_promoter_type_2	Child relationships:

A_minor_RNA_motif	SO:0000022 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: A_minor_RNA_motif is_a asymmetric_RNA_internal_loop	Child relationships:

BAC	SO:0000153 [is leaf node]
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 part_of BAC_clone BAC is_a vector	Child relationships:

BAC_clone	SO:0000764
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: BAC_clone is_a clone	Child relationships: BAC part_of BAC_clone

BRE_motif	SO:0000016 [is leaf node]
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 part_of RNApol_II_promoter	Child relationships:

B_box	SO:0000620 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: B_box part_of RNApol_III_promoter_type_2	Child relationships:

CAAT_signal	SO:0000172 [is leaf node]
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 part_of RNApol_II_promoter	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 part_of mRNA	Child relationships: coding_start part_of CDS coding_end part_of CDS polypeptide derives_from CDS

CTG_start_codon	SO:1001273 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: C_box part_of RNApol_III_promoter_type_1	Child relationships:

CpG_island	SO:0000307 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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:

DNA_aptamer	SO:0000032 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: DNA_motif is_a nucleotide_motif	Child relationships:

DNA_sequence_secondary_structure	SO:0000142 [is leaf node]
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:

DNAaseI_hypersensitive_site	SO:0000685 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: DNAaseI_hypersensitive_site is_a nuclease_hypersensitive_site	Child relationships:

DPE_motif	SO:0000015 [is leaf node]
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 part_of RNApol_II_promoter	Child relationships:

D_gene_recombination_feature	SO:0000492
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: D_gene_recombination_feature is_a recombination_feature_of_vertebrate_immune_system_gene	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 [is leaf node]
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 [is leaf node]
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 derives_from mRNA EST is_a reagent	Child relationships:

EST_match	SO:0000668 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 part_of RNApol_II_promoter	Child relationships:

G_quartet	SO:0000003 [is leaf node]
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:

GcvB_RNA	SO:0000379 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 part_of RNApol_II_promoter	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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [J-RS]
Aspect: located_sequence_feature
Parent relationships: J_gene_recombination_feature is_a recombination_feature_of_vertebrate_immune_system_gene	Child relationships: J_heptamer part_of J_gene_recombination_feature J_spacer part_of J_gene_recombination_feature J_nonamer part_of J_gene_recombination_feature

J_heptamer	SO:0000515 [is leaf node]
Definition: 7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
DBxref:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [J-RS]
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 [is leaf node]
Definition: 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
DBxref:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms:
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 [is leaf node]
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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms:
Aspect: located_sequence_feature
Parent relationships: J_spacer part_of J_gene_recombination_feature J_spacer is_a spacer_of_recombination_feature_of_vertebrate_immune_system_gene	Child relationships:

K_turn_RNA_motif	SO:0000023 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: K_turn_RNA_motif is_a asymmetric_RNA_internal_loop	Child relationships:

MicF_RNA	SO:0000383 [is leaf node]
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 [is leaf node]
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:

OxyS_RNA	SO:0000384 [is leaf node]
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 [is leaf node]
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 part_of PAC_clone PAC is_a vector	Child relationships:

PAC_clone	SO:0000762
Definition: undefined
DBxref:
Synonyms: [P1_clone]
Aspect: located_sequence_feature
Parent relationships: PAC_clone is_a clone	Child relationships: PAC part_of PAC_clone

PCR_product	SO:0000006 [is leaf node]
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 [is leaf node]
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 part_of RNApol_II_promoter	Child relationships:

RFLP_fragment	SO:0000193 [is leaf node]
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 [is leaf node]
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_aptamer	SO:0000033 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNA_hairpin_loop is_a RNA_motif	Child relationships:

RNA_hook_turn	SO:0000027 [is leaf node]
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_junction_loop is_a RNA_motif RNA_internal_loop is_a RNA_motif RNA_hairpin_loop is_a RNA_motif

RNA_sequence_secondary_structure	SO:0000122 [is leaf node]
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 [is leaf node]
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 RNAi_reagent is_a reagent	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_1 is_a RNApol_III_promoter TATA_box part_of RNApol_III_promoter RNApol_III_promoter_type_3 is_a 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: C_box 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: B_box part_of RNApol_III_promoter_type_2 A_box part_of RNApol_III_promoter_type_2

RNApol_III_promoter_type_3	SO:0000621 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: RNApol_III_promoter_type_3 is_a RNApol_III_promoter	Child relationships:

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: INR_motif part_of RNApol_II_promoter TATA_box part_of RNApol_II_promoter PSE_motif part_of RNApol_II_promoter BRE_motif part_of RNApol_II_promoter CAAT_signal part_of RNApol_II_promoter GC_rich_region part_of RNApol_II_promoter DPE_motif part_of RNApol_II_promoter

RNApol_I_promoter	SO:0000169 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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:

RprA_RNA	SO:0000387 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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:

SL1_acceptor_site	SO:0000708 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: SL2_acceptor_site is_a trans_splice_acceptor_site	Child relationships:

SRP_RNA	SO:0000590 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: Region in 5' UTR where ribosome assembles on mRNA.
DBxref:SO:ke
Synonyms: [RBS] [Shine-Dalgarno_sequence] [five_prime_ribosome_binding_site]
Aspect: located_sequence_feature
Parent relationships: Shine_Dalgarno_sequence is_a ribosome_entry_site	Child relationships:

TATA_box	SO:0000174 [is leaf node]
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_III_promoter TATA_box part_of RNApol_II_promoter	Child relationships:

TF_binding_site	SO:0000235 [is leaf node]
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 [is leaf node]
Definition: A regulatory_region where more than 1 TF_binding_site together are regulatorily active
DBxref:SO:SG
Synonyms: [CRM] [cis_regulatory_module]
Aspect: located_sequence_feature
Parent relationships: TF_module is_a regulatory_region	Child relationships:

U11_snRNA	SO:0000398 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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:

U4_snRNA	SO:0000393 [is leaf node]
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 [is leaf node]
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_snRNA	SO:0000395 [is leaf node]
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:

U6_snRNA	SO:0000396 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 part_of mRNA	Child relationships: untranslated_region_polyicistronic_mRNA is_a UTR five_prime_UTR is_a UTR internal_UTR is_a UTR three_prime_UTR is_a UTR ribosome_entry_site part_of UTR upstream_AUG_codon part_of 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: five_prime_UTR_intron is_a UTR_intron three_prime_UTR_intron is_a UTR_intron

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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [V-RS]
Aspect: located_sequence_feature
Parent relationships: V_gene_recombination_feature is_a recombination_feature_of_vertebrate_immune_system_gene	Child relationships: V_heptamer part_of V_gene_recombination_feature V_spacer part_of V_gene_recombination_feature V_nonamer part_of V_gene_recombination_feature

V_heptamer	SO:0000533 [is leaf node]
Definition: 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
DBxref:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [V-RS]
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 [is leaf node]
Definition: 9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
DBxref:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [V-RS]
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 [is leaf node]
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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [V-RS]
Aspect: located_sequence_feature
Parent relationships: V_spacer is_a spacer_of_recombination_feature_of_vertebrate_immune_system_gene V_spacer part_of V_gene_recombination_feature	Child relationships:

WC_base_pair	SO:0000029 [is leaf node]
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 [is leaf node]
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 part_of YAC_clone YAC is_a vector	Child relationships:

YAC_clone	SO:0000760
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: YAC_clone is_a clone	Child relationships: YAC part_of YAC_clone

Y_RNA	SO:0000405 [is leaf node]
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 [is leaf node]
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:

alanine_tRNA_primary_transcript	SO:0000211 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: alanyl_tRNA is_a tRNA	Child relationships:

amplification_origin	SO:0000750 [is leaf node]
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:

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 [is leaf node]
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 aptamer is_a synthetic_sequence	Child relationships: RNA_aptamer is_a aptamer DNA_aptamer is_a aptamer

arginine_tRNA_primary_transcript	SO:0000212 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: asparaginyl_tRNA is_a tRNA	Child relationships:

aspartamine_tRNA_primary_transcript	SO:0000214 [is leaf node]
Definition: A primary transcript encoding aspartyl tRNA (SO:0000257).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: aspartamine_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

aspartyl_tRNA	SO:0000257 [is leaf node]
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: virtual_sequence is_a assembly supercontig is_a assembly tiling_path is_a assembly contig is_a assembly gap part_of assembly ultracontig is_a assembly golden_path 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: read is_a assembly_component read_pair is_a assembly_component golden_path_fragment is_a assembly_component contig is_a assembly_component tiling_path_fragment 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: Sarcin_like_RNA_motif is_a asymmetric_RNA_internal_loop K_turn_RNA_motif is_a asymmetric_RNA_internal_loop A_minor_RNA_motif is_a asymmetric_RNA_internal_loop

attI_site	SO:0000367 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: attI_site part_of integron	Child relationships:

attenuator	SO:0000140 [is leaf node]
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 [is leaf node]
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 promoter bacterial_RNApol_promoter is_a gene_group_regulatory_region	Child relationships: minus_10_signal part_of bacterial_RNApol_promoter minus_35_signal part_of bacterial_RNApol_promoter

bacterial_terminator	SO:0000614 [is leaf node]
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 sugar_edge_base_pair is_a base_pair WC_base_pair is_a base_pair Hoogsteen_base_pair is_a base_pair

bidirectional_promotor	SO:0000568 [is leaf node]
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

blocked_reading_frame	SO:0000718 [is leaf node]
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 [is leaf node]
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 part_of spliceosomal_intron	Child relationships:

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

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: genomically_contaminated_cDNA_clone is_a cDNA_clone partially_unprocessed_cDNA_clone is_a cDNA_clone genomic_polyA_primed_cDNA_clone is_a cDNA_clone chimeric_cDNA_clone is_a cDNA_clone cDNA part_of cDNA_clone

cDNA_match	SO:0000689 [is leaf node]
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 [is leaf node]
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 splice_donor_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_five_prime_splice_site is_a canonical_splice_site canonical_three_prime_splice_site is_a canonical_splice_site

canonical_three_prime_splice_site	SO:0000676 [is leaf node]
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 canonical_splice_site canonical_three_prime_splice_site is_a splice_acceptor_site	Child relationships:

cap	SO:0000581 [is leaf node]
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 adjacent_to mRNA	Child relationships:

centromere	SO:0000577 [is leaf node]
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:

chimeric_cDNA_clone	SO:0000362 [is leaf node]
Definition: A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: chimeric_cDNA_clone is_a cDNA_clone	Child relationships:

chromosomal_regulatory_element	SO:0000626
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: chromosomal_regulatory_element part_of chromosome	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 part_of chromosome	Child relationships: centromere is_a chromosomal_structural_element telomere 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: introgressed_chromosome part_of chromosome chromosome_arm part_of chromosome chromosomal_regulatory_element part_of chromosome chromosomal_structural_element part_of chromosome chromosome_band part_of chromosome

chromosome_arm	SO:0000105 [is leaf node]
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 part_of chromosome	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 part_of chromosome	Child relationships: interband is_a chromosome_band

chromosome_breakage_sequence	SO:0000670 [is leaf node]
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:

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 part_of primary_transcript	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: BAC_clone is_a clone YAC_clone is_a clone clone_insert part_of clone tiling_path_clone is_a clone genomic_clone is_a clone cosmid_clone is_a clone plasmid_clone is_a clone cDNA_clone is_a clone PAC_clone is_a clone fosmid_clone is_a clone vector part_of clone phagemid_clone is_a clone lambda_clone is_a clone

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

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

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

coding_conserved_region	SO:0000332 [is leaf node]
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 [is leaf node]
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 part_of CDS	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 interior_coding_exon is_a coding_exon three_prime_exon_coding_region is_a coding_exon

coding_start	SO:0000323 [is leaf node]
Definition: The first base to be translated into protein.
DBxref:SO:ke
Synonyms: [translation_start]
Aspect: located_sequence_feature
Parent relationships: coding_start part_of CDS	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 part_of mRNA	Child relationships: start_codon is_a codon stop_codon is_a codon recoded_codon is_a codon

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: coding_conserved_region is_a conserved_region syntenic_region is_a conserved_region nc_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 part_of supercontig contig is_a assembly_component contig is_a assembly	Child relationships: contig_read part_of contig read part_of contig read_pair part_of contig

contig_read	SO:0000476 [is leaf node]
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 contig_read part_of contig	Child relationships:

cosmid	SO:0000156 [is leaf node]
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 cosmid part_of cosmid_clone	Child relationships:

cosmid_clone	SO:0000765
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: cosmid_clone is_a clone	Child relationships: cosmid part_of cosmid_clone

cross_genome_match	SO:0000177 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: cysteinyl_tRNA is_a tRNA	Child relationships:

databank_entry	SO:2000061 [is leaf node]
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 [is leaf node]
Definition: A non-functional descendent of an exon.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: decayed_exon is_a pseudogenic_region decayed_exon non_functional_homolog_of exon	Child relationships:

deletion	SO:0000159 [is leaf node]
Definition: The sequence that is deleted.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: deletion is_a region deletion sequence_of delete deletion is_a sequence_variant	Child relationships:

deletion_junction	SO:0000687 [is leaf node]
Definition: The space between two bases in a sequence which marks the position where a deletion has occured.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: deletion_junction is_a junction deletion_junction position_of delete deletion_junction is_a sequence_variant	Child relationships:

dinucleotide_repeat_microsatellite_feature	SO:0000290 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: dinucleotide_repeat_microsatellite_feature is_a microsatellite	Child relationships:

direct_repeat	SO:0000314 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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:

double_stranded_cDNA	SO:0000758 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: double_stranded_cDNA is_a cDNA	Child relationships:

ds_oligo	SO:0000442 [is leaf node]
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 part_of transcript	Child relationships: unedited_region is_a edited_transcript_feature editing_block is_a edited_transcript_feature editing_domain is_a edited_transcript_feature pre_edited_region is_a edited_transcript_feature

editing_block	SO:0000604 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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: telomerase_RNA is_a enzymatic_RNA RNase_MRP_RNA is_a enzymatic_RNA ribozyme is_a enzymatic_RNA

episome	SO:0000768 [is leaf node]
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 part_of transcript	Child relationships: noncoding_exon is_a exon five_prime_coding_exon is_a exon coding_exon is_a exon single_exon is_a exon interior_exon is_a exon decayed_exon non_functional_homolog_of exon pseudogenic_exon non_functional_homolog_of exon three_prime_coding_exon is_a exon

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

exonic_splice_enhancer	SO:0000683 [is leaf node]
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 [is leaf node]
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: EST_match is_a expressed_sequence_match cDNA_match is_a expressed_sequence_match

external_transcribed_spacer_region	SO:0000640 [is leaf node]
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 [is leaf node]
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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [five_prime_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 [is leaf node]
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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [five_prime_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [five_prime_D-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_heptamer part_of five_prime_D_recombination_signal_sequence 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_spacer	SO:0000498 [is leaf node]
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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [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 spacer_of_recombination_feature_of_vertebrate_immune_system_gene	Child relationships:

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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 part_of five_prime_coding_exon five_prime_exon_coding_region is_a coding_exon	Child relationships:

five_prime_exon_noncoding_region	SO:0000486 [is leaf node]
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 part_of five_prime_coding_exon	Child relationships:

five_prime_intron	SO:0000190 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_intron is_a intron	Child relationships:

five_prime_noncoding_exon	SO:0000445 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: five_prime_open_reading_frame part_of five_prime_UTR	Child relationships:

five_prime_recoding_site	SO:1001280 [is leaf node]
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:

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 [is leaf node]
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:

forward_primer	SO:0000121 [is leaf node]
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 [is leaf node]
Definition: A cloning vector that utilises the E. coli F factor.
DBxref:SO:ma
Synonyms:
Aspect: located_sequence_feature
Parent relationships: fosmid part_of fosmid_clone fosmid is_a vector	Child relationships:

fosmid_clone	SO:0000763
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: fosmid_clone is_a clone	Child relationships: fosmid part_of fosmid_clone

four_bp_start_codon	SO:1001269 [is leaf node]
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 [is leaf node]
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 is_a junction gap part_of assembly	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: regulatory_region member_of gene pseudogene non_functional_homolog_of gene transcript member_of gene non_transcribed_region part_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 [is leaf node]
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_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: regulon is_a gene_group gene_cassette is_a gene_group gene_array is_a gene_group operon is_a gene_group gene member_of gene_group gene_group_regulatory_region member_of gene_group

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

gene_subarray	SO:0005852 [is leaf node]
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 [is leaf node]
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_polyA_primed_cDNA_clone	SO:0000415 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: genomic_polyA_primed_cDNA_clone is_a cDNA_clone	Child relationships:

genomically_contaminated_cDNA_clone	SO:0000414 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: genomically_contaminated_cDNA_clone is_a cDNA_clone	Child relationships:

glutamine_tRNA_primary_transcript	SO:0000217 [is leaf node]
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:

glutaminic_acid_tRNA_primary_transcript	SO:0000216 [is leaf node]
Definition: A primary transcript encoding glutaminyl tRNA (SO:0000260).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: glutaminic_acid_tRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

glutaminyl_tRNA	SO:0000259 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: glutaminyl_tRNA is_a tRNA	Child relationships:

glutamyl_tRNA	SO:0000260 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: glutamyl_tRNA is_a tRNA	Child relationships:

glycinetRNA_primary_transcript	SO:0000218 [is leaf node]
Definition: A primary transcript encoding glycyl tRNA (SO:0000263).
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: glycinetRNA_primary_transcript is_a tRNA_primary_transcript	Child relationships:

glycyl_tRNA	SO:0000261 [is leaf node]
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 [is leaf node]
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 is_a assembly_component golden_path_fragment part_of golden_path	Child relationships:

group_1_intron_homing_endonuclease_target_region	SO:0000354 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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_IIA_intron is_a group_II_intron group_IIB_intron is_a group_II_intron

group_I_intron	SO:0000587 [is leaf node]
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

hammerhead_ribozyme	SO:0000380 [is leaf node]
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 [is leaf node]
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:

heptamer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000561
Definition: 7 nucleotide regulation site, like CTCATGC, in 5' UTR (SO:0000204) of a V-gene, VD-gene, VDJ-gene, or VJ-gene of an immunoglobulin/T-cell receptor gene.
DBxref:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms:
Aspect: located_sequence_feature
Parent relationships: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene is_a recombination_feature_of_vertebrate_immune_system_gene	Child relationships: V_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 three_prime_D_heptamer is_a heptamer_of_recombination_feature_of_vertebrate_immune_system_gene

histidine_tRNA_primary_transcript	SO:0000219 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: histidyl_tRNA is_a tRNA	Child relationships:

iDNA	SO:0000723 [is leaf node]
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

insertion	SO:0000667 [is leaf node]
Definition: A region of sequence identified as having been inserted.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: insertion is_a region insertion is_a sequence_variant insertion sequence_of insert	Child relationships:

insertion_site	SO:0000366
Definition: The junction where an insertion occurred.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: insertion_site is_a junction insertion_site is_a sequence_variant insertion_site position_of insert	Child relationships: transposable_element_insertion_site is_a insertion_site

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

integrase_coding_region	SO:0000369 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: integrase_coding_region part_of integron	Child relationships:

integrated_virus	SO:0000113 [is leaf node]
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: integrase_coding_region part_of integron attI_site part_of integron

intein	SO:0000728 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: intein part_of polypeptide	Child relationships:

interband	SO:0000450 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: interior_coding_exon is_a coding_exon	Child relationships:

interior_exon	SO:0000201 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: interior_exon is_a exon	Child relationships:

interior_intron	SO:0000191 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: interior_intron is_a intron	Child relationships:

internal_Shine_Dalgarno_sequence	SO:1001260 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: internal_UTR is_a UTR	Child relationships:

internal_eliminated_sequence	SO:0000671 [is leaf node]
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 [is leaf node]
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	SO:0000664 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: introgressed_chromosome part_of chromosome	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 part_of primary_transcript	Child relationships: interior_intron is_a intron autocatalytically_spliced_intron is_a intron five_prime_intron is_a intron group_II_intron is_a intron three_prime_intron is_a intron twintron is_a intron group_I_intron is_a intron spliceosomal_intron is_a intron UTR_intron is_a intron

intronic_splice_enhancer	SO:0000320 [is leaf node]
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 part_of spliceosomal_intron	Child relationships:

inversion	SO:1000036 [is leaf node]
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 region inversion sequence_of invert inversion is_a sequence_variant	Child relationships:

inverted_repeat	SO:0000294 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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: deletion_junction is_a junction transcription_start_site is_a junction polyA_site is_a junction insertion_site is_a junction transcription_end_site is_a junction splice_site is_a junction clone_insert_end is_a junction exon_junction is_a junction gap is_a junction clone_insert_start is_a junction

lambda_clone	SO:0000160
Definition: A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
DBxref:ISBN:0-1767-2380-8
Synonyms:
Aspect: located_sequence_feature
Parent relationships: lambda_clone is_a clone	Child relationships: lambda_vector part_of lambda_clone

lambda_vector	SO:0000754 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: lambda_vector is_a vector lambda_vector part_of lambda_clone	Child relationships:

large_subunit_rRNA	SO:0000651 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: large_subunit_rRNA is_a rRNA	Child relationships:

leucine_tRNA_primary_transcript	SO:0000221 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: leucyl_tRNA is_a tRNA	Child relationships:

linkage_group	SO:0000018 [is leaf node]
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 [is leaf node]
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:

lysine_tRNA_primary_transcript	SO:0000222 [is leaf node]
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 [is leaf node]
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: codon part_of mRNA recoding_stimulatory_region part_of mRNA cap adjacent_to mRNA EST derives_from mRNA riboswitch is_a mRNA polyA_sequence adjacent_to mRNA CDS part_of mRNA UTR part_of mRNA

macronucleus_destined_segment	SO:0000672 [is leaf node]
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: nucleotide_match is_a match protein_match is_a match match_part is_a match match_set is_a match

match_part	SO:0000039 [is leaf node]
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 is_a match match_part part_of match_set	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 [is leaf node]
Definition: A DNA region that is required for the binding of chromatin to the nuclear matrix.
DBxref:SO:ma
Synonyms: [MAR] [SMAR] [scaffold_attachment_site]
Aspect: located_sequence_feature
Parent relationships: matrix_attachment_site is_a chromosomal_regulatory_element	Child relationships:

mature_peptide	SO:0000419 [is leaf node]
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 part_of polypeptide	Child relationships:

methionine_tRNA_primary_transcript	SO:0000223 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: methionyl_tRNA is_a tRNA	Child relationships:

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

methylated_C	SO:0000114 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms: [microarray_oligonucleotide]
Aspect: located_sequence_feature
Parent relationships: microarray_oligo is_a oligo microarray_oligo is_a probe microarray_oligo is_a tag	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: trinucleotide_repeat_microsatellite_feature is_a microsatellite tetranucleotide_repeat_microsatellite_feature is_a microsatellite dinucleotide_repeat_microsatellite_feature is_a microsatellite

mini_exon_donor_RNA	SO:0000635
Definition: The 3' site of a mini-exon which is trans-spliced on to the 5'end of a mature 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

minisatellite	SO:0000643 [is leaf node]
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 [is leaf node]
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 part_of bacterial_RNApol_promoter	Child relationships:

minus_35_signal	SO:0000176 [is leaf node]
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 part_of bacterial_RNApol_promoter	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 part_of transcript	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 [is leaf node]
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 morpholino is_a synthetic_sequence	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: scRNA is_a ncRNA small_regulatory_ncRNA is_a ncRNA rRNA is_a ncRNA enzymatic_RNA is_a ncRNA rasiRNA is_a ncRNA Y_RNA is_a ncRNA stRNA is_a ncRNA snoRNA is_a ncRNA SRP_RNA is_a ncRNA vault_RNA is_a ncRNA guide_RNA is_a ncRNA snRNA is_a ncRNA siRNA is_a ncRNA antisense_RNA is_a ncRNA tRNA is_a ncRNA

nc_conserved_region	SO:0000334 [is leaf node]
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: tmRNA_primary_transcript is_a nc_primary_transcript snRNA_primary_transcript is_a nc_primary_transcript miRNA_primary_transcript is_a nc_primary_transcript scRNA_primary_transcript is_a nc_primary_transcript tRNA_primary_transcript is_a nc_primary_transcript SRP_RNA_primary_transcript is_a nc_primary_transcript snoRNA_primary_transcript is_a nc_primary_transcript rRNA_primary_transcript is_a nc_primary_transcript

non_canonical_five_prime_splice_site	SO:0000679 [is leaf node]
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 splice_donor_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_three_prime_splice_site is_a non_canonical_splice_site non_canonical_five_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: four_bp_start_codon is_a non_canonical_start_codon CTG_start_codon is_a non_canonical_start_codon

non_canonical_three_prime_splice_site	SO:0000678 [is leaf node]
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 splice_acceptor_site non_canonical_three_prime_splice_site is_a non_canonical_splice_site	Child relationships:

non_transcribed_region	SO:0000183 [is leaf node]
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 region non_transcribed_region part_of gene	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 recombination_feature_of_vertebrate_immune_system_gene	Child relationships: five_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 three_prime_D_nonamer is_a nonamer_of_recombination_feature_of_vertebrate_immune_system_gene J_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: three_prime_noncoding_exon is_a noncoding_exon five_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: group_1_intron_homing_endonuclease_target_region is_a nuclease_sensitive_site nuclease_hypersensitive_site is_a nuclease_sensitive_site

nucleotide_deletion	SO:1000033 [is leaf node]
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 [is leaf node]
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: translated_nucleotide_match is_a nucleotide_match expressed_sequence_match is_a nucleotide_match cross_genome_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: RNA_motif is_a nucleotide_motif DNA_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: ss_oligo is_a oligo aptamer is_a oligo microarray_oligo is_a oligo primer is_a oligo ds_oligo is_a oligo RNAi_reagent is_a oligo morpholino is_a oligo

oligo_U_tail	SO:0000609 [is leaf node]
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	Child relationships:

operator	SO:0000057 [is leaf node]
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 [is leaf node]
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: D_loop is_a origin_of_replication amplification_origin is_a origin_of_replication

origin_of_transfer	SO:0000724 [is leaf node]
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_unprocessed_cDNA_clone	SO:0000416 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: partially_unprocessed_cDNA_clone is_a cDNA_clone	Child relationships:

phagemid	SO:0000157 [is leaf node]
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 phagemid part_of phagemid_clone	Child relationships:

phagemid_clone	SO:0000761
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: phagemid_clone is_a clone	Child relationships: phagemid part_of phagemid_clone

phenylalanine_tRNA_primary_transcript	SO:0000224 [is leaf node]
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 [is leaf node]
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_clone	SO:0000759
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: plasmid_clone is_a clone	Child relationships: plasmid_vector part_of plasmid_clone

plasmid_vector	SO:0000755 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: plasmid_vector is_a vector plasmid_vector part_of plasmid_clone	Child relationships:

polyA_sequence	SO:0000610 [is leaf node]
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 adjacent_to mRNA	Child relationships:

polyA_signal_sequence	SO:0000551 [is leaf node]
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 [is leaf node]
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 part_of processed_transcript polyA_site is_a junction	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	Child relationships: intein part_of polypeptide transit_peptide part_of polypeptide signal_peptide part_of polypeptide polypeptide_domain part_of polypeptide mature_peptide part_of polypeptide

polypeptide_domain	SO:0000417 [is leaf node]
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 part_of polypeptide	Child relationships:

polypyrimidine_tract	SO:0000612 [is leaf node]
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 part_of spliceosomal_intron	Child relationships:

possible_assembly_error	SO:0000702 [is leaf node]
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 [is leaf node]
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_region	SO:0000583 [is leaf node]
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: antisense_primary_transcript is_a primary_transcript transcription_start_site part_of primary_transcript processed_transcript derives_from primary_transcript clip part_of primary_transcript transcription_end_site part_of primary_transcript splice_site part_of primary_transcript intron part_of primary_transcript protein_coding_primary_transcript is_a primary_transcript nc_primary_transcript is_a primary_transcript mini_exon_donor_RNA is_a primary_transcript

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 sequencing_primer is_a primer reverse_primer is_a primer

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: mRNA is_a processed_transcript polyA_site part_of processed_transcript exon_junction part_of processed_transcript ncRNA is_a processed_transcript aberrant_processed_transcript is_a processed_transcript

proline_tRNA_primary_transcript	SO:0000225 [is leaf node]
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 [is leaf node]
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_III_promoter is_a promoter RNApol_II_promoter is_a promoter bacterial_RNApol_promoter is_a promoter RNApol_I_promoter is_a promoter

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: nuclease_binding_site is_a protein_binding_site TF_binding_site is_a protein_binding_site

protein_coding_primary_transcript	SO:0000120 [is leaf node]
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:

protein_match	SO:0000349 [is leaf node]
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 non_functional_homolog_of gene pseudogene is_a pseudogenic_region	Child relationships: pseudogenic_transcript part_of pseudogene

pseudogenic_exon	SO:0000507 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: pseudogenic_exon is_a pseudogenic_region pseudogenic_exon part_of pseudogenic_transcript pseudogenic_exon non_functional_homolog_of exon	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: pseudogene is_a pseudogenic_region pseudogenic_transcript is_a pseudogenic_region decayed_exon is_a pseudogenic_region pseudogenic_exon is_a pseudogenic_region

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

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: large_subunit_rRNA is_a rRNA rRNA_18S is_a rRNA rRNA_5S is_a rRNA rRNA_28S is_a rRNA small_subunit_rRNA is_a rRNA rRNA_5.8S is_a rRNA

rRNA_18S	SO:0000407 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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: transcribed_spacer_region part_of rRNA_primary_transcript rRNA_large_subunit_primary_transcript is_a rRNA_primary_transcript rRNA_small_subunit_primary_transcript is_a rRNA_primary_transcript

rRNA_small_subunit_primary_transcript	SO:0000255 [is leaf node]
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 [is leaf node]
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 is_a assembly_component read part_of contig	Child relationships: contig_read is_a read

read_pair	SO:0000007 [is leaf node]
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 is_a assembly_component read_pair part_of contig	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: ORF is_a reading_frame blocked_reading_frame 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: oligo is_a reagent plasmid is_a reagent probe is_a reagent tag is_a reagent restriction_fragment is_a reagent clone is_a reagent cDNA is_a reagent databank_entry is_a reagent EST is_a reagent rescue_fragment is_a reagent vector is_a reagent RNAi_reagent is_a reagent PCR_product is_a reagent

recoded_codon	SO:0000145 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: recoded_codon is_a codon	Child relationships:

recoding_pseudoknot	SO:0000545 [is leaf node]
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 part_of recoding_stimulatory_region recoding_pseudoknot is_a pseudoknot	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 part_of mRNA	Child relationships: internal_Shine_Dalgarno_sequence is_a recoding_stimulatory_region stop_codon_signal is_a recoding_stimulatory_region SECIS_element is_a recoding_stimulatory_region recoding_pseudoknot part_of recoding_stimulatory_region five_prime_recoding_site is_a recoding_stimulatory_region three_prime_recoding_site 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: haplotype_block is_a recombination_feature recombination_hotspot is_a recombination_feature iDNA is_a recombination_feature sequence_rearrangement_feature 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: recombination_feature_of_vertebrate_immune_system_gene is_a recombination_feature_of_rearranged_gene

recombination_feature_of_vertebrate_immune_system_gene	SO:0000301
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: recombination_feature_of_vertebrate_immune_system_gene is_a recombination_feature_of_rearranged_gene	Child relationships: spacer_of_recombination_feature_of_vertebrate_immune_system_gene is_a recombination_feature_of_vertebrate_immune_system_gene heptamer_of_recombination_feature_of_vertebrate_immune_system_gene is_a recombination_feature_of_vertebrate_immune_system_gene J_gene_recombination_feature is_a recombination_feature_of_vertebrate_immune_system_gene D_gene_recombination_feature is_a recombination_feature_of_vertebrate_immune_system_gene nonamer_of_recombination_feature_of_vertebrate_immune_system_gene is_a recombination_feature_of_vertebrate_immune_system_gene V_gene_recombination_feature is_a recombination_feature_of_vertebrate_immune_system_gene

recombination_hotspot	SO:0000339 [is leaf node]
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: regulatory_region is_a region binding_site is_a region remark is_a region non_transcribed_region is_a region chromosome is_a region recombination_feature is_a region flanking_region is_a region assembly is_a region reagent is_a region gene_group is_a region assembly_component is_a region modified_base_site is_a region pseudogenic_region is_a region match is_a region sequence_secondary_structure is_a region ARS is_a region deletion is_a region insertion is_a region CpG_island is_a region origin_of_replication is_a region repeat_region is_a region nuclease_sensitive_site is_a region gene is_a region reading_frame is_a region linkage_group is_a region substitution is_a region conserved_region is_a region origin_of_transfer is_a region intergenic_region is_a region inversion is_a region integrated_virus is_a region nucleotide_motif 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 region regulatory_region member_of gene	Child relationships: attenuator is_a regulatory_region TF_module is_a regulatory_region silencer is_a regulatory_region promoter is_a regulatory_region splice_enhancer is_a regulatory_region terminator is_a regulatory_region insulator is_a regulatory_region TF_binding_site is_a regulatory_region enhancer is_a regulatory_region polyA_signal_sequence is_a regulatory_region locus_control_region is_a regulatory_region gene_group_regulatory_region is_a regulatory_region

regulon	SO:1001284 [is leaf node]
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_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: tandem_repeat is_a repeat_region terminal_inverted_repeat is_a repeat_region inverted_repeat is_a repeat_region repeat_family is_a repeat_region transposable_element_target_site_duplication is_a repeat_region long_terminal_repeat is_a repeat_region dispersed_repeat is_a repeat_region non_LTR_retrotransposon_polymeric_tract is_a repeat_region repeat_unit is_a repeat_region direct_repeat is_a repeat_region satellite_DNA is_a repeat_region

repeat_unit	SO:0000726 [is leaf node]
Definition: A single repeat element.
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: repeat_unit is_a repeat_region	Child relationships:

rescue_fragment	SO:0000411 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: rescue_fragment is_a reagent	Child relationships:

restriction_enzyme_binding_site	SO:0000061 [is leaf node]
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

reverse_Hoogsteen_base_pair	SO:0000501 [is leaf node]
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 [is leaf node]
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 part_of UTR	Child relationships: internal_ribosome_entry_site is_a ribosome_entry_site Shine_Dalgarno_sequence is_a ribosome_entry_site

riboswitch	SO:0000035 [is leaf node]
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: autocatalytically_spliced_intron is_a ribozyme RNase_P_RNA is_a ribozyme hammerhead_ribozyme 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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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_rearrangement_feature	SO:0000669
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: sequence_rearrangement_feature is_a recombination_feature	Child relationships: integron is_a sequence_rearrangement_feature macronucleus_destined_segment is_a sequence_rearrangement_feature chromosome_breakage_sequence is_a sequence_rearrangement_feature specific_recombination_site is_a sequence_rearrangement_feature internal_eliminated_sequence 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: RNA_sequence_secondary_structure is_a sequence_secondary_structure G_quartet is_a sequence_secondary_structure stem_loop is_a sequence_secondary_structure pseudoknot is_a sequence_secondary_structure DNA_sequence_secondary_structure is_a sequence_secondary_structure base_pair 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: indel is_a sequence_variant deletion_junction is_a sequence_variant substitution is_a sequence_variant insertion is_a sequence_variant deletion is_a sequence_variant inversion is_a sequence_variant insertion_site is_a sequence_variant

sequencing_primer	SO:0000107 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: sequencing_primer is_a primer	Child relationships:

serine_tRNA_primary_transcript	SO:0000226 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: seryl_tRNA is_a tRNA	Child relationships:

siRNA	SO:0000646 [is leaf node]
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 [is leaf node]
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 part_of polypeptide	Child relationships:

silencer	SO:0000625 [is leaf node]
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:

single_exon	SO:0005845 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: single_exon is_a exon	Child relationships:

single_stranded_cDNA	SO:0000757 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: single_stranded_cDNA is_a cDNA	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 DNA_invertase_target_sequence is_a site_specific_recombination_target_region Cre_recombination_target_region 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: tmRNA is_a small_regulatory_ncRNA miRNA is_a small_regulatory_ncRNA RNA_6S is_a small_regulatory_ncRNA RprA_RNA is_a small_regulatory_ncRNA DsrA_RNA is_a small_regulatory_ncRNA RRE_RNA is_a small_regulatory_ncRNA CsrB_RsmB_RNA is_a small_regulatory_ncRNA spot_42_RNA is_a small_regulatory_ncRNA OxyS_RNA is_a small_regulatory_ncRNA

small_subunit_rRNA	SO:0000650 [is leaf node]
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: U5_snRNA is_a snRNA U12_snRNA is_a snRNA U2_snRNA is_a snRNA U6atac_snRNA is_a snRNA U4atac_snRNA is_a snRNA U1_snRNA is_a snRNA U14_snRNA is_a snRNA U6_snRNA is_a snRNA U11_snRNA is_a snRNA U4_snRNA is_a snRNA snRNA_4.5S is_a snRNA

snRNA_4.5S	SO:0005839 [is leaf node]
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 [is leaf node]
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: H_ACA_box_snoRNA is_a snoRNA rRNA_cleavage_snoRNA is_a snoRNA C_D_box_snoRNA is_a snoRNA methylation_guide_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: H_ACA_box_snoRNA_primary_transcript is_a snoRNA_primary_transcript rRNA_cleavage_snoRNA_primary_transcript is_a snoRNA_primary_transcript C_D_box_snoRNA_primary_transcript is_a snoRNA_primary_transcript methylation_guide_snoRNA_primary_transcript is_a snoRNA_primary_transcript

spacer_of_recombination_feature_of_vertebrate_immune_system_gene	SO:0000563
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: spacer_of_recombination_feature_of_vertebrate_immune_system_gene is_a recombination_feature_of_vertebrate_immune_system_gene	Child relationships: V_spacer is_a spacer_of_recombination_feature_of_vertebrate_immune_system_gene J_spacer is_a spacer_of_recombination_feature_of_vertebrate_immune_system_gene three_prime_Dspacer is_a spacer_of_recombination_feature_of_vertebrate_immune_system_gene five_prime_D_spacer is_a spacer_of_recombination_feature_of_vertebrate_immune_system_gene

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: site_specific_recombination_target_region is_a specific_recombination_site recombination_feature_of_rearranged_gene is_a specific_recombination_site

splice_acceptor_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]
Aspect: located_sequence_feature
Parent relationships: splice_acceptor_site is_a splice_site	Child relationships: canonical_three_prime_splice_site is_a splice_acceptor_site non_canonical_three_prime_splice_site is_a splice_acceptor_site trans_splice_acceptor_site is_a splice_acceptor_site

splice_donor_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]
Aspect: located_sequence_feature
Parent relationships: splice_donor_site is_a splice_site	Child relationships: trans_splice_donor_site is_a splice_donor_site canonical_five_prime_splice_site is_a splice_donor_site non_canonical_five_prime_splice_site is_a splice_donor_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 junction splice_site part_of primary_transcript	Child relationships: splice_donor_site is_a splice_site canonical_splice_site is_a splice_site splice_acceptor_site is_a splice_site non_canonical_splice_site is_a splice_site

spliced_leader_RNA	SO:0000636 [is leaf node]
Definition: undefined
DBxref:
Synonyms: [mini-exon]
Aspect: located_sequence_feature
Parent relationships: 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: intronic_splice_enhancer part_of spliceosomal_intron branch_site part_of spliceosomal_intron U2_intron is_a spliceosomal_intron U12_intron is_a spliceosomal_intron polypyrimidine_tract part_of spliceosomal_intron

spot_42_RNA	SO:0000389 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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

sugar_edge_base_pair	SO:0000030 [is leaf node]
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

symmetric_RNA_internal_loop	SO:0000025 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: symmetric_RNA_internal_loop is_a RNA_internal_loop	Child relationships:

syntenic_region	SO:0005858 [is leaf node]
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]
Synonyms:
Aspect: located_sequence_feature
Parent relationships: syntenic_region is_a conserved_region	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: asparaginyl_tRNA is_a tRNA glutamyl_tRNA is_a tRNA lysyl_tRNA is_a tRNA glutaminyl_tRNA is_a tRNA selenocysteinyl_tRNA is_a tRNA methionyl_tRNA is_a tRNA phenylalanyl_tRNA is_a tRNA leucyl_tRNA is_a tRNA glycyl_tRNA is_a tRNA valyl_tRNA is_a tRNA threonyl_tRNA is_a tRNA seryl_tRNA is_a tRNA alanyl_tRNA is_a tRNA tryptophanyl_tRNA is_a tRNA histidyl_tRNA is_a tRNA tyrosyl_tRNA is_a tRNA cysteinyl_tRNA is_a tRNA isoleucyl_tRNA is_a tRNA prolyl_tRNA is_a tRNA aspartyl_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: cysteine_tRNA_primary_transcript is_a tRNA_primary_transcript histidine_tRNA_primary_transcript is_a tRNA_primary_transcript methionine_tRNA_primary_transcript is_a tRNA_primary_transcript isoleucine_tRNA_primary_transcript is_a tRNA_primary_transcript lysine_tRNA_primary_transcript is_a tRNA_primary_transcript asparagine_tRNA_primary_transcript is_a tRNA_primary_transcript proline_tRNA_primary_transcript is_a tRNA_primary_transcript aspartamine_tRNA_primary_transcript is_a tRNA_primary_transcript glutamine_tRNA_primary_transcript is_a tRNA_primary_transcript glutaminic_acid_tRNA_primary_transcript is_a tRNA_primary_transcript alanine_tRNA_primary_transcript is_a tRNA_primary_transcript tryptophan_tRNA_primary_transcript is_a tRNA_primary_transcript selenocysteine_tRNA_primary_transcript is_a tRNA_primary_transcript leucine_tRNA_primary_transcript is_a tRNA_primary_transcript threonine_tRNA_primary_transcript is_a tRNA_primary_transcript glycinetRNA_primary_transcript is_a tRNA_primary_transcript phenylalanine_tRNA_primary_transcript is_a tRNA_primary_transcript tyrosine_tRNA_primary_transcript is_a tRNA_primary_transcript valine_tRNA_primary_transcript is_a tRNA_primary_transcript arginine_tRNA_primary_transcript is_a tRNA_primary_transcript serine_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 microarray_oligo is_a tag STS 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 [is leaf node]
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 [is leaf node]
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:

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: terminator_of_type_2_RNApol_III_promoter is_a terminator bacterial_terminator is_a terminator

terminator_of_type_2_RNApol_III_promoter	SO:0000615 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: 7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
DBxref:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [three_prime_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 [is leaf node]
Definition: 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
DBxref:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [three_prime_D-nonamer]
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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
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_nonamer part_of three_prime_D_recombination_signal_sequence three_prime_D_heptamer part_of three_prime_D_recombination_signal_sequence three_prime_Dspacer part_of three_prime_D_recombination_signal_sequence

three_prime_Dspacer	SO:0000495 [is leaf node]
Definition: undefined
DBxref:
Synonyms: [three_prime_D-spacer]
Aspect: located_sequence_feature
Parent relationships: three_prime_Dspacer is_a spacer_of_recombination_feature_of_vertebrate_immune_system_gene three_prime_Dspacer part_of three_prime_D_recombination_signal_sequence	Child relationships:

three_prime_UTR	SO:0000205 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 part_of three_prime_coding_exon three_prime_exon_coding_region is_a coding_exon	Child relationships:

three_prime_exon_noncoding_region	SO:0000484 [is leaf node]
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 part_of three_prime_coding_exon	Child relationships:

three_prime_intron	SO:0000192 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: three_prime_intron is_a intron	Child relationships:

three_prime_noncoding_exon	SO:0000444 [is leaf node]
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: three_prime_repeat_recoding_signal is_a three_prime_recoding_site three_prime_stem_loop_structure is_a three_prime_recoding_site distant_three_prime_recoding_signal is_a three_prime_recoding_site flanking_three_prime_quadruplet_recoding_signal is_a three_prime_recoding_site

three_prime_repeat_recoding_signal	SO:1001286 [is leaf node]
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_stem_loop_structure	SO:1001279 [is leaf node]
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:

threonine_tRNA_primary_transcript	SO:0000227 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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.A minimal_tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly attempting to minimize the overlap between adjacent clones. (LS)
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tiling_path_clone is_a clone tiling_path_clone is_a tiling_path_fragment	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 is_a assembly_component tiling_path_fragment part_of tiling_path	Child relationships: tiling_path_clone is_a tiling_path_fragment

tmRNA	SO:0000584 [is leaf node]
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_primary_transcript	SO:0000586 [is leaf node]
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:

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 splice_acceptor_site	Child relationships: SL1_acceptor_site is_a trans_splice_acceptor_site SL2_acceptor_site is_a trans_splice_acceptor_site

trans_splice_donor_site	SO:0000707 [is leaf node]
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 splice_donor_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 part_of rRNA_primary_transcript	Child relationships: internal_transcribed_spacer_region is_a transcribed_spacer_region external_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 member_of gene	Child relationships: processed_transcript is_a transcript pseudogenic_transcript non_functional_homolog_of transcript edited_transcript_feature part_of transcript modified_RNA_base_feature part_of transcript exon part_of transcript primary_transcript is_a transcript

transcription_end_site	SO:0000616 [is leaf node]
Definition: The site where transcription ends.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transcription_end_site is_a junction transcription_end_site part_of primary_transcript	Child relationships:

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

transit_peptide	SO:0000725 [is leaf node]
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 part_of polypeptide	Child relationships:

translated_nucleotide_match	SO:0000181 [is leaf node]
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:

transposable_element_flanking_region	SO:0000364 [is leaf node]
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_insertion_site	SO:0000368 [is leaf node]
Definition: The junction in a genome where a transposable_element has inserted.
DBxref:SO:ke
Synonyms:
Aspect: located_sequence_feature
Parent relationships: transposable_element_insertion_site is_a insertion_site	Child relationships:

transposable_element_target_site_duplication	SO:0000434 [is leaf node]
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:

trinucleotide_repeat_microsatellite_feature	SO:0000291 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: tryptophanyl_tRNA is_a tRNA	Child relationships:

twintron	SO:0000406 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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

unedited_region	SO:0000607 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: upstream_AUG_codon part_of UTR	Child relationships:

valine_tRNA_primary_transcript	SO:0000230 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: located_sequence_feature
Parent relationships: valyl_tRNA is_a tRNA	Child relationships:

vault_RNA	SO:0000404 [is leaf node]
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 part_of clone vector is_a reagent	Child relationships: lambda_vector is_a vector phagemid is_a vector PAC is_a vector YAC is_a vector fosmid is_a vector plasmid_vector is_a vector BAC is_a vector cosmid is_a vector

virtual_sequence	SO:0000499 [is leaf node]
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

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

LINE_element	SO:0000194 [is leaf node]
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: chromosome_variation
Parent relationships: LINE_element is_a non_LTR_retrotransposon	Child relationships:

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

MITE	SO:0000338 [is leaf node]
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: chromosome_variation
Parent relationships: MITE is_a terminal_inverted_repeat_element	Child relationships:

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

R_LTR_region	SO:0000423
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: R_LTR_region part_of long_terminal_repeat	Child relationships: R_five_prime_LTR_region is_a R_LTR_region

R_five_prime_LTR_region	SO:0000427 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: R_five_prime_LTR_region is_a R_LTR_region R_five_prime_LTR_region part_of five_prime_LTR	Child relationships:

R_three_prime_LTR_region	SO:0000430 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: R_three_prime_LTR_region part_of three_prime_LTR	Child relationships:

Robertsonian_fusion	SO:1000043 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: Robertsonian_fusion is_a chromosomal_translocation	Child relationships:

SINE_element	SO:0000206 [is leaf node]
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: chromosome_variation
Parent relationships: SINE_element is_a non_LTR_retrotransposon	Child relationships:

U3_LTR_region	SO:0000424
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: U3_LTR_region part_of long_terminal_repeat	Child relationships: U3_five_prime_LTR_region is_a U3_LTR_region

U3_five_prime_LTR_region	SO:0000429 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: U3_five_prime_LTR_region is_a U3_LTR_region U3_five_prime_LTR_region part_of five_prime_LTR	Child relationships:

U3_three_prime_LTR_region	SO:0000431 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: U3_three_prime_LTR_region part_of three_prime_LTR	Child relationships:

U5_LTR_region	SO:0000422
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: U5_LTR_region part_of long_terminal_repeat	Child relationships: U5_five_prime_LTR_region is_a U5_LTR_region

U5_five_prime_LTR_region	SO:0000428 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: U5_five_prime_LTR_region part_of five_prime_LTR U5_five_prime_LTR_region is_a U5_LTR_region	Child relationships:

U5_three_prime_LTR_region	SO:0000432 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: U5_three_prime_LTR_region part_of three_prime_LTR	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: inversion_derived_aneuploid_chromosome is_a aneuploid_chromosome chromosomal_deletion is_a aneuploid_chromosome chromosomal_duplication is_a aneuploid_chromosome

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

bipartite_duplication	SO:1000149 [is leaf node]
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 [is leaf node]
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: [(Drosophila)Df] [(bacteria)&Dgr;] [(fungi)D]
Aspect: chromosome_variation
Parent relationships: chromosomal_deletion is_a intrachromosomal_mutation chromosomal_deletion is_a aneuploid_chromosome	Child relationships: deficient_inversion is_a chromosomal_deletion inversion_derived_deficiency_plus_aneuploid is_a chromosomal_deletion deficient_translocation is_a chromosomal_deletion inversion_derived_deficiency_plus_duplication is_a chromosomal_deletion inversion_derived_bipartite_deficiency 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: insertional_duplication is_a chromosomal_duplication free_duplication is_a chromosomal_duplication intrachromosomal_duplication is_a chromosomal_duplication interchromosomal_duplication is_a chromosomal_duplication

chromosomal_inversion	SO:1000030
Definition: undefined
DBxref:
Synonyms: [(Drosophila)In] [(bacteria)IN] [(fungi)In]
Aspect: chromosome_variation
Parent relationships: chromosomal_inversion is_a intrachromosomal_mutation	Child relationships: deficient_inversion is_a chromosomal_inversion inverted_intrachromosomal_transposition is_a chromosomal_inversion inverted_ring_chromosome is_a chromosomal_inversion paracentric_inversion is_a chromosomal_inversion inversion_cum_translocation is_a chromosomal_inversion pericentric_inversion is_a chromosomal_inversion bipartite_inversion 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: cyclic_translocation is_a chromosomal_translocation reciprocal_chromosomal_translocation is_a chromosomal_translocation inversion_cum_translocation is_a chromosomal_translocation deficient_translocation is_a chromosomal_translocation translocation_element part_of chromosomal_translocation Robertsonian_fusion is_a chromosomal_translocation

chromosome_fission	SO:1000141 [is leaf node]
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: complex_chromosomal_mutation is_a chromosome_structure_variation intrachromosomal_mutation is_a chromosome_structure_variation interchromosomal_mutation is_a chromosome_structure_variation compound_chromosome is_a chromosome_structure_variation free_chromosome_arm is_a chromosome_structure_variation uncharacterised_chromosomal_mutation is_a chromosome_structure_variation transposition is_a chromosome_structure_variation autosynaptic_chromosome is_a chromosome_structure_variation chromosomal_duplication is_a chromosome_structure_variation aneuploid_chromosome is_a chromosome_structure_variation

complex_chromosomal_mutation	SO:1000146 [is leaf node]
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: homo_compound_chromosome is_a compound_chromosome hetero_compound_chromosome is_a compound_chromosome compound_chromosome_arm is_a compound_chromosome

compound_chromosome_arm	SO:0000060 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: compound_chromosome_arm is_a compound_chromosome	Child relationships:

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

cyclic_translocation	SO:1000150 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: deficient_interchromosomal_transposition is_a interchromosomal_transposition	Child relationships:

deficient_intrachromosomal_transposition	SO:0000062 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: deficient_intrachromosomal_transposition is_a intrachromosomal_transposition	Child relationships:

deficient_inversion	SO:1000171 [is leaf node]
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_inversion deficient_inversion is_a chromosomal_deletion	Child relationships:

deficient_translocation	SO:1000147 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: dexstrosynaptic_chromosome is_a autosynaptic_chromosome	Child relationships:

direct_tandem_duplication	SO:1000039 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: direct_tandem_duplication is_a tandem_duplication	Child relationships:

five_prime_LTR	SO:0000425
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: five_prime_LTR is_a long_terminal_repeat	Child relationships: U5_five_prime_LTR_region part_of five_prime_LTR U3_five_prime_LTR_region part_of five_prime_LTR R_five_prime_LTR_region part_of five_prime_LTR

five_prime_terminal_inverted_repeat	SO:0000420 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: five_prime_terminal_inverted_repeat is_a terminal_inverted_repeat	Child relationships:

foldback_element	SO:0000238 [is leaf node]
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: [LVR element] [long inverted repeat element]
Aspect: chromosome_variation
Parent relationships: foldback_element is_a DNA_transposon	Child relationships:

foreign_transposable_element	SO:0000720 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: foreign_transposable_element is_a transposable_element	Child relationships:

free_chromosome_arm	SO:0000065 [is leaf node]
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 [is leaf node]
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:

helitron	SO:0000544 [is leaf node]
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: chromosome_variation
Parent relationships: helitron is_a transposable_element	Child relationships:

hetero_compound_chromosome	SO:1000140 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms: [homo-compound_chromosome]
Aspect: chromosome_variation
Parent relationships: homo_compound_chromosome is_a compound_chromosome	Child relationships:

hyperploid	SO:0000055 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: hyperploid is_a aneuploid	Child relationships:

hypoploid	SO:0000056 [is leaf node]
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: uninverted_insertional_duplication is_a insertional_duplication unoriented_insertional_duplication is_a insertional_duplication inverted_insertional_duplication is_a insertional_duplication

interchromosomal_duplication	SO:0000457 [is leaf node]
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: interchromosomal_transposition is_a interchromosomal_mutation bipartite_duplication is_a interchromosomal_mutation chromosomal_translocation is_a interchromosomal_mutation

interchromosomal_transposition	SO:1000155
Definition: undefined
DBxref:
Synonyms: [(Drosophila)Tp]
Aspect: chromosome_variation
Parent relationships: interchromosomal_transposition is_a interchromosomal_mutation interchromosomal_transposition is_a transposition	Child relationships: deficient_interchromosomal_transposition is_a interchromosomal_transposition unorientated_interchromosomal_transposition is_a interchromosomal_transposition inverted_interchromosomal_transposition is_a interchromosomal_transposition uninverted_interchromosomal_transposition is_a interchromosomal_transposition

intrachromosomal_duplication	SO:1000038
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: intrachromosomal_duplication is_a intrachromosomal_mutation intrachromosomal_duplication is_a chromosomal_duplication	Child relationships: tandem_duplication is_a intrachromosomal_duplication intrachromosomal_transposition is_a intrachromosomal_duplication inversion_derived_bipartite_duplication is_a intrachromosomal_duplication inversion_derived_deficiency_plus_duplication is_a intrachromosomal_duplication inversion_derived_duplication_plus_aneuploid 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: intrachromosomal_duplication is_a intrachromosomal_mutation chromosome_fission is_a intrachromosomal_mutation transposable_element is_a intrachromosomal_mutation ring_chromosome is_a intrachromosomal_mutation chromosomal_inversion is_a intrachromosomal_mutation chromosomal_deletion is_a intrachromosomal_mutation

intrachromosomal_transposition	SO:1000041
Definition: undefined
DBxref:
Synonyms: [(Drosophila)Tp]
Aspect: chromosome_variation
Parent relationships: intrachromosomal_transposition is_a intrachromosomal_duplication intrachromosomal_transposition is_a transposition	Child relationships: inverted_intrachromosomal_transposition is_a intrachromosomal_transposition uninverted_intrachromosomal_transposition is_a intrachromosomal_transposition unorientated_intrachromosomal_transposition is_a intrachromosomal_transposition deficient_intrachromosomal_transposition is_a intrachromosomal_transposition

inversion_cum_translocation	SO:1000148 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: inverted_tandem_duplication is_a tandem_duplication	Child relationships:

laevosynaptic_chromosome	SO:1000143 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: laevosynaptic_chromosome is_a autosynaptic_chromosome	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: [LTR] [direct_terminal _repeat]
Aspect: chromosome_variation
Parent relationships: long_terminal_repeat part_of LTR_retrotransposon long_terminal_repeat is_a repeat_region	Child relationships: U3_LTR_region part_of long_terminal_repeat three_prime_LTR is_a long_terminal_repeat R_LTR_region part_of long_terminal_repeat five_prime_LTR is_a long_terminal_repeat U5_LTR_region part_of long_terminal_repeat

non_LTR_retrotransposon	SO:0000189
Definition: A retrotransposon without long terminal repeat sequences.
DBxref:SO:ke
Synonyms:
Aspect: chromosome_variation
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 [is leaf node]
Definition: A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.
DBxref:SO:ke
Synonyms:
Aspect: chromosome_variation
Parent relationships: non_LTR_retrotransposon_polymeric_tract part_of non_LTR_retrotransposon non_LTR_retrotransposon_polymeric_tract is_a repeat_region	Child relationships:

paracentric_inversion	SO:1000047 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: paracentric_inversion is_a chromosomal_inversion	Child relationships:

partially_characterised_chromosomal_mutation	SO:1000175 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: partially_characterised_chromosomal_mutation is_a uncharacterised_chromosomal_mutation	Child relationships:

pericentric_inversion	SO:1000046 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: pericentric_inversion is_a chromosomal_inversion	Child relationships:

primer_binding_site	SO:0005850 [is leaf node]
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: chromosome_variation
Parent relationships: primer_binding_site part_of LTR_retrotransposon	Child relationships:

reciprocal_chromosomal_translocation	SO:1000048 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: reciprocal_chromosomal_translocation is_a chromosomal_translocation	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: chromosome_variation
Parent relationships: retrotransposon is_a transposable_element	Child relationships: non_LTR_retrotransposon is_a retrotransposon LTR_retrotransposon is_a retrotransposon

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

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: chromosome_variation
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: chromosome_variation
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

three_prime_LTR	SO:0000426
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: three_prime_LTR is_a long_terminal_repeat	Child relationships: U5_three_prime_LTR_region part_of three_prime_LTR R_three_prime_LTR_region part_of three_prime_LTR U3_three_prime_LTR_region part_of three_prime_LTR

three_prime_terminal_inverted_repeat	SO:0000421 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: three_prime_terminal_inverted_repeat is_a terminal_inverted_repeat	Child relationships:

translocation_element	SO:0000686 [is leaf node]
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 part_of chromosomal_translocation	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: chromosome_variation
Parent relationships: transposable_element is_a intrachromosomal_mutation transposable_element is_a repeat_family	Child relationships: DNA_transposon is_a transposable_element foreign_transposable_element is_a transposable_element retrotransposon is_a transposable_element helitron is_a transposable_element

transposition	SO:0000453
Definition: undefined
DBxref:
Synonyms:
Aspect: chromosome_variation
Parent relationships: transposition is_a chromosome_structure_variation	Child relationships: interchromosomal_transposition is_a transposition intrachromosomal_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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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 [is leaf node]
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:

sequence_attribute terms

CDS_independently_known	SO:1001246 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: CDS_independently_known is_a status_of_coding_sequence	Child relationships:

CDS_predicted	SO:1001254
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: CDS_predicted is_a status_of_coding_sequence	Child relationships: CDS_supported_by_EST_or_cDNA_data is_a CDS_predicted CDS_supported_by_domain_match_data is_a CDS_predicted CDS_supported_by_sequence_similarity_data is_a CDS_predicted orphan_CDS is_a CDS_predicted

CDS_supported_by_EST_or_cDNA_data	SO:1001259 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: CDS_supported_by_EST_or_cDNA_data is_a CDS_predicted	Child relationships:

CDS_supported_by_domain_match_data	SO:1001249 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: CDS_supported_by_domain_match_data is_a CDS_predicted	Child relationships:

CDS_supported_by_sequence_similarity_data	SO:1001251 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: CDS_supported_by_sequence_similarity_data is_a CDS_predicted	Child relationships:

C_D_box_snoRNA_gene	SO:0000585 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: C_D_box_snoRNA_gene is_a snoRNA_gene	Child relationships:

C_cluster	SO:0000558
Definition: Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.
DBxref:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [constant_gene]
Aspect: sequence_attribute
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 [is leaf node]
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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [constant_gene]
Aspect: sequence_attribute
Parent relationships: C_gene part_of V_J_C_cluster C_gene part_of V_DJ_C_cluster C_gene part_of DJ_C_cluster C_gene part_of J_C_cluster C_gene part_of D_DJ_C_cluster C_gene part_of V_DJ_J_C_cluster C_gene part_of V_D_DJ_J_C_cluster C_gene part_of V_VJ_C_cluster C_gene part_of D_J_C_cluster C_gene part_of V_VJ_J_C_cluster C_gene part_of V_VDJ_J_C_cluster C_gene part_of VDJ_J_C_cluster C_gene part_of V_VDJ_C_cluster C_gene is_a vertebrate_immunoglobulin_T_cell_receptor_gene C_gene part_of V_D_DJ_C_cluster C_gene part_of VJ_C_cluster C_gene part_of D_DJ_J_C_cluster C_gene part_of DJ_J_C_cluster C_gene part_of VDJ_C_cluster C_gene part_of V_D_J_C_cluster C_gene part_of VJ_J_C_cluster C_gene part_of C_cluster	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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [(DJ)-C-cluster]
Aspect: sequence_attribute
Parent relationships: DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_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: undefined
DBxref:
Synonyms: [(DJ)-J-C-cluster]
Aspect: sequence_attribute
Parent relationships: DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of DJ_J_C_cluster C_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [(DJ)-J-cluster]
Aspect: sequence_attribute
Parent relationships: DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of DJ_J_cluster DJ_gene part_of DJ_J_cluster

DJ_gene	SO:0000572 [is leaf node]
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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms:
Aspect: sequence_attribute
Parent relationships: DJ_gene part_of D_DJ_J_cluster DJ_gene part_of V_DJ_J_cluster DJ_gene is_a vertebrate_immunoglobulin_T_cell_receptor_gene DJ_gene part_of V_DJ_C_cluster DJ_gene part_of DJ_C_cluster DJ_gene part_of D_DJ_C_cluster DJ_gene part_of V_DJ_J_C_cluster DJ_gene part_of V_D_DJ_J_C_cluster DJ_gene part_of V_D_DJ_C_cluster DJ_gene part_of DJ_J_cluster DJ_gene part_of DJ_J_C_cluster DJ_gene part_of V_D_DJ_cluster DJ_gene part_of D_DJ_J_C_cluster DJ_gene part_of D_DJ_cluster DJ_gene part_of V_DJ_cluster DJ_gene part_of V_D_DJ_J_cluster	Child relationships:

DNA	SO:0000352 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: DNA is_a nucleic_acid	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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [D-(DJ)-C-cluster]
Aspect: sequence_attribute
Parent relationships: D_DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [D-(DJ)-J-C-cluster]
Aspect: sequence_attribute
Parent relationships: D_DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of D_DJ_J_C_cluster C_gene part_of D_DJ_J_C_cluster D_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [D-(DJ)-J-cluster]
Aspect: sequence_attribute
Parent relationships: D_DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of D_DJ_J_cluster D_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [D-(DJ)-cluster]
Aspect: sequence_attribute
Parent relationships: D_DJ_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [D-J-C-cluster]
Aspect: sequence_attribute
Parent relationships: D_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of D_J_C_cluster C_gene part_of D_J_C_cluster D_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [D-J-cluster]
Aspect: sequence_attribute
Parent relationships: D_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of D_J_cluster D_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms:
Aspect: sequence_attribute
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 [is leaf node]
Definition: Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
DBxref:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms:
Aspect: sequence_attribute
Parent relationships: D_gene part_of D_DJ_J_cluster D_gene is_a vertebrate_immunoglobulin_T_cell_receptor_gene D_gene part_of D_DJ_C_cluster D_gene part_of V_D_DJ_J_C_cluster D_gene part_of V_D_DJ_C_cluster D_gene part_of V_D_DJ_cluster D_gene part_of D_DJ_J_C_cluster D_gene part_of V_D_J_cluster D_gene part_of D_J_C_cluster D_gene part_of D_cluster D_gene part_of V_D_J_C_cluster D_gene part_of D_DJ_cluster D_gene part_of D_J_cluster D_gene part_of V_D_DJ_J_cluster	Child relationships:

FRT_flanked_sequence	SO:0000361 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: FRT_flanked_sequence is_a sequence_by_flanking_target_attribute	Child relationships:

H_ACA_box_snoRNA_gene	SO:0000608 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: H_ACA_box_snoRNA_gene is_a snoRNA_gene	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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [J-C-cluster]
Aspect: sequence_attribute
Parent relationships: J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of J_C_cluster C_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms:
Aspect: sequence_attribute
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 [is leaf node]
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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms:
Aspect: sequence_attribute
Parent relationships: J_gene part_of V_J_C_cluster J_gene part_of D_DJ_J_cluster J_gene part_of J_C_cluster J_gene part_of V_DJ_J_C_cluster J_gene part_of V_D_DJ_J_C_cluster J_gene part_of V_VJ_J_cluster J_gene part_of V_D_J_cluster J_gene part_of D_J_C_cluster J_gene part_of V_VJ_J_C_cluster J_gene part_of V_VDJ_J_C_cluster J_gene part_of VDJ_J_C_cluster J_gene part_of D_J_cluster J_gene part_of V_J_cluster J_gene part_of J_cluster J_gene part_of VDJ_J_cluster J_gene part_of V_D_DJ_J_cluster J_gene is_a vertebrate_immunoglobulin_T_cell_receptor_gene J_gene part_of V_DJ_J_cluster J_gene part_of DJ_J_cluster J_gene part_of DJ_J_C_cluster J_gene part_of D_DJ_J_C_cluster J_gene part_of V_VDJ_J_cluster J_gene part_of V_D_J_C_cluster J_gene part_of VJ_J_C_cluster J_gene part_of VJ_J_cluster	Child relationships:

RNA	SO:0000356 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: RNA is_a nucleic_acid	Child relationships:

SRP_RNA_gene	SO:0000642 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: SRP_RNA_gene is_a non_protein_coding_gene	Child relationships:

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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [(VDJ)-C-cluster]
Aspect: sequence_attribute
Parent relationships: VDJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: VDJ_gene part_of VDJ_C_cluster C_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [(VDJ)-J-C-cluster]
Aspect: sequence_attribute
Parent relationships: VDJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of VDJ_J_C_cluster VDJ_gene part_of VDJ_J_C_cluster C_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [(VDJ)-J-cluster]
Aspect: sequence_attribute
Parent relationships: VDJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of VDJ_J_cluster VDJ_gene part_of VDJ_J_cluster

VDJ_gene	SO:0000574 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: VDJ_gene part_of V_VDJ_J_C_cluster VDJ_gene part_of VDJ_J_C_cluster VDJ_gene part_of V_VDJ_C_cluster VDJ_gene is_a vertebrate_immunoglobulin_T_cell_receptor_gene VDJ_gene part_of V_VDJ_J_cluster VDJ_gene part_of V_VDJ_cluster VDJ_gene part_of VDJ_C_cluster VDJ_gene part_of VDJ_J_cluster	Child relationships:

VD_gene	SO:0000510 [is leaf node]
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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms:
Aspect: sequence_attribute
Parent relationships: VD_gene is_a vertebrate_immunoglobulin_T_cell_receptor_gene	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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [(VJ)-C-cluster]
Aspect: sequence_attribute
Parent relationships: VJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: VJ_gene part_of VJ_C_cluster C_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [(VJ)-J-C-cluster]
Aspect: sequence_attribute
Parent relationships: VJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: VJ_gene part_of VJ_J_C_cluster J_gene part_of VJ_J_C_cluster C_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [(VJ)-J-cluster]
Aspect: sequence_attribute
Parent relationships: VJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: VJ_gene part_of VJ_J_cluster J_gene part_of VJ_J_cluster

VJ_gene	SO:0000576 [is leaf node]
Definition: undefined
DBxref:
Synonyms:
Aspect: sequence_attribute
Parent relationships: VJ_gene is_a vertebrate_immunoglobulin_T_cell_receptor_gene VJ_gene part_of VJ_J_C_cluster VJ_gene part_of V_VJ_J_cluster VJ_gene part_of V_VJ_C_cluster VJ_gene part_of VJ_J_cluster VJ_gene part_of VJ_C_cluster VJ_gene part_of V_VJ_J_C_cluster VJ_gene part_of V_VJ_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms:
Aspect: sequence_attribute
Parent relationships: V_DJ_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: V_gene part_of V_DJ_C_cluster C_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [V-(DJ)-J-C-cluster]
Aspect: sequence_attribute
Parent relationships: V_DJ_J_C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of V_DJ_J_C_cluster V_gene part_of V_DJ_J_C_cluster C_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:ftp://ftp.cines.fr/IMGT/ftable_doc.html
Synonyms: [V-(DJ)-J-cluster]
Aspect: sequence_attribute
Parent relationships: V_DJ_J_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster	Child relationships: J_gene part_of V_DJ_J_cluster V_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:ftp://ft