List of all SO terms

File created on Wed Oct 19 15:41:33 2005

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date: 14:10:2005 14:20
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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:
c