part_of
Example: amino_acid part_of polypeptide.
sequence
X part_of Y if X is a subregion of Y.
URL:http://precedings.nature.com/documents/3495/version/1
http://precedings.nature.com/documents/3495/version/1
adjacent_to
sequence
A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
SO:ke
http://purl.org/obo/owl/SO#SO_ke
associated_with
This relationship is vague and up for discussion.
sequence
complete_evidence_for_feature
If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
sequence
B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
connects_on
Example: A splice_junction connects_on exon, exon, mature_transcript.
sequence
X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
contained_by
The inverse is contains. Example: intein contained_by immature_peptide_region.
sequence
X contained_by Y iff X starts after start of Y and X ends before end of Y.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
contains
Example: pre_miRNA contains miRNA_loop.
sequence
The inverse of contained_by.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
derives_from
sequence
disconnected_from
Example: intron disconnected from exon {on primary_transcript}.
sequence
X is disconnected_from Y iff it is not the case that X overlaps Y.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
edited_from
sequence
edited_to
sequence
evidence_for_feature
This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
sequence
B is evidence_for_feature A, if an instance of B supports the existence of A.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
exemplar_of
Tracker id: 2594157.
sequence
X is exemplar of Y if X is the best evidence for Y.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
finished_by
Example CDS finished_by stop_codon.
sequence
Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
finishes
Example: stop_codon finishes CDS.
sequence
X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
gained
A relation with which to annotate the changes in a variant sequence with respect to a reference.nFor example a variant transcript may gain a stop codon not present in the reference sequence.
sequence
X gained Y if X is a variant_of X' and Y part of X but not X'.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
genome_of
sequence
guided_by
sequence
guides
sequence
has_integral_part
Example: mRNA has_integral_part CDS.
sequence
X has_integral_part Y if and only if: X has_part Y and Y part_of X.
URL:http://precedings.nature.com/documents/3495/version/1
http://precedings.nature.com/documents/3495/version/1
has_origin
sequence
has_part
Example: operon has_part gene.
sequence
Inverse of part_of.
URL:http://precedings.nature.com/documents/3495/version/1
http://precedings.nature.com/documents/3495/version/1
has_quality
The relationship between a feature and an attribute.
sequence
homologous_to
sequence
integral_part_of
Example: exon integral_part_of transcript.
sequence
X integral_part_of Y if and only if: X part_of Y and Y has_part X.
URL:http://precedings.nature.com/documents/3495/version/1
http://precedings.nature.com/documents/3495/version/1
is_consecutive_sequence_of
Example: region is consecutive_sequence of base.
sequence
R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
lost
A relation with which to annotate the changes in a variant sequence with respect to a reference.nFor example a variant transcript may have lost a stop codon present in the reference sequence.
sequence
X lost Y if X is a variant_of X' and Y part of X' but not X.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
maximally_overlaps
Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.
sequence
A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
member_of
A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
sequence
non_functional_homolog_of
sequence
A relationship between a pseudogenic feature and its functional ancestor.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
orthologous_to
sequence
overlaps
Example: coding_exon overlaps CDS.
sequence
X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
paralogous_to
sequence
partial_evidence_for_feature
sequence
B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
position_of
sequence
processed_from
Example: miRNA processed_from miRNA_primary_transcript.
sequence
Inverse of processed_into.
URL:http://precedings.nature.com/documents/3495/version/1
http://precedings.nature.com/documents/3495/version/1
processed_into
Example: miRNA_primary_transcript processed into miRNA.
sequence
X is processed_into Y if a region X is modified to create Y.
URL:http://precedings.nature.com/documents/3495/version/1
http://precedings.nature.com/documents/3495/version/1
recombined_from
sequence
recombined_to
sequence
sequence_of
sequence
similar_to
sequence
started_by
Example: CDS started_by start_codon.
sequence
X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
starts
Example: start_codon starts CDS.
sequence
X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
PMID:20226267
http://purl.org/obo/owl/PMID#PMID_20226267
trans_spliced_from
sequence
trans_spliced_to
sequence
transcribed_from
Example: primary_transcript transcribed_from gene.
sequence
X is transcribed_from Y if X is synthesized from template Y.
URL:http://precedings.nature.com/documents/3495/version/1
http://precedings.nature.com/documents/3495/version/1
transcribed_to
Example: gene transcribed_to primary_transcript.
sequence
Inverse of transcribed_from.
URL:http://precedings.nature.com/documents/3495/version/1
http://precedings.nature.com/documents/3495/version/1
translates_to
Example: codon translates_to amino_acid.
sequence
Inverse of translation _of.
URL:http://precedings.nature.com/documents/3495/version/1
http://precedings.nature.com/documents/3495/version/1
translation_of
Example: Polypeptide translation_of CDS.
sequence
X is translation of Y if X is translated by ribosome to create Y.
URL:http://precedings.nature.com/documents/3495/version/1
http://precedings.nature.com/documents/3495/version/1
variant_of
Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.
sequence
A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
SO:immuno_workshop
http://purl.org/obo/owl/SO#SO_immuno_workshop
Sequence_Ontology
sequence
region
sequence
sequence
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence_secondary_structure
sequence
A folded sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence secondary structure
G_quartet
sequence
URL:http://en.wikipedia.org/wiki/G-quadruplex
http://en.wikipedia.org/wiki/G-quadruplex
G quartet
G_quadruplex
guanine tetrad
G-tetrad
G-quartet
G-quadruplex
G tetrad
G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.
URL:http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract
http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract
interior_coding_exon
sequence
interior coding exon
satellite_DNA
sequence
URL:http://en.wikipedia.org/wiki/Satellite_DNA
http://en.wikipedia.org/wiki/Satellite_DNA
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.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
satellite DNA
PCR_product
This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
sequence
URL:http://en.wikipedia.org/wiki/RAPD
http://en.wikipedia.org/wiki/RAPD
PCR product
amplicon
A region amplified by a PCR reaction.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
read_pair
sequence
read-pair
One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
SO:ls
http://purl.org/obo/owl/SO#SO_ls
mate pair
gene_sensu_your_favorite_organism
sequence
gene_class
sequence
protein_coding
sequence
protein-coding
non_protein_coding
sequence
non protein-coding
scRNA_primary_transcript
sequence
scRNA primary transcript
small cytoplasmic RNA
small_cytoplasmic_RNA
small cytoplasmic RNA transcript
The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote.
URL:http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html
http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html
scRNA transcript
scRNA
sequence
A small non coding RNA sequence, present in the cytoplasm.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
small cytoplasmic RNA
INR_motif
Binds TAF1, TAF2.
sequence
A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.
PMID:12651739
http://purl.org/obo/owl/PMID#PMID_12651739
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
initiator motif
initiator
INR motif
DMp2
DPE_motif
Binds TAF6, TAF9.
sequence
downstream core promoter element
A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
PMID:12651739:12537576
http://purl.org/obo/owl/PMID#PMID_12651739:12537576
DPE motif
CRWMGCGWKCGCTTS
BREu_motif
Binds TFIIB.
sequence
A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.
PMID:12651739
http://purl.org/obo/owl/PMID#PMID_12651739
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
BREu motif
transcription factor B-recognition element
BREu
TFIIB recognition element
B-recognition element
BRE motif
PSE_motif
sequence
A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G).
PMID:12651739
http://purl.org/obo/owl/PMID#PMID_12651739
proximal sequence element
PSE motif
linkage_group
sequence
URL:http://en.wikipedia.org/wiki/Linkage_group
http://en.wikipedia.org/wiki/Linkage_group
linkage group
A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.
ISBN:038752046
http://purl.org/obo/owl/ISBN#ISBN_038752046
RNA_internal_loop
sequence
A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RNA internal loop
asymmetric_RNA_internal_loop
sequence
asymmetric RNA internal loop
An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
A_minor_RNA_motif
sequence
A minor RNA motif
A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
K_turn_RNA_motif
sequence
kink-turn motif
kink turn
K-turn
K turn RNA motif
The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/K-turn
http://en.wikipedia.org/wiki/K-turn
sarcin_like_RNA_motif
sequence
sarcin like RNA motif
A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.
URL:http://www.ncbi.nlm.nih.gov/pubmed/7897662
http://www.ncbi.nlm.nih.gov/pubmed/7897662
sarcin/ricin domain
sarcin/ricin loop
sarcin/ricin RNA domain
symmetric_RNA_internal_loop
sequence
An internal RNA loop where the extent of the loop on both stands is the same size.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
A-minor RNA motif
RNA_junction_loop
sequence
RNA junction loop
RNA_hook_turn
sequence
hook turn
hook-turn motif
RNA hook turn
base_pair
sequence
base pair
URL:http://en.wikipedia.org/wiki/Base_pair
http://en.wikipedia.org/wiki/Base_pair
WC_base_pair
sequence
Watson-Crick pair
The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.
PMID:12177293
http://purl.org/obo/owl/PMID#PMID_12177293
WC base pair
Watson Crick base pair
canonical base pair
Watson-Crick base pair
sugar_edge_base_pair
sequence
A type of non-canonical base-pairing.
PMID:12177293
http://purl.org/obo/owl/PMID#PMID_12177293
sugar edge base pair
aptamer
sequence
DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.
URL:http://aptamer.icmb.utexas.edu
http://aptamer.icmb.utexas.edu
URL:http://en.wikipedia.org/wiki/Aptamer
http://en.wikipedia.org/wiki/Aptamer
DNA_aptamer
sequence
DNA aptamer
DNA molecules that have been selected from random pools based on their ability to bind other molecules.
http:aptamer.icmb.utexas.edu
http://purl.org/obo/owl/http#http_aptamer.icmb.utexas.edu
RNA_aptamer
sequence
RNA aptamer
RNA molecules that have been selected from random pools based on their ability to bind other molecules.
URL:http://aptamer.icmb.utexas.edu
http://aptamer.icmb.utexas.edu
morpholino_oligo
sequence
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.
URL:http://www.gene-tools.com/
http://www.gene-tools.com/
morpholino oligo
morpholino
morphant
riboswitch
sequence
A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites.
PMID:2820954
http://purl.org/obo/owl/PMID#PMID_2820954
URL:http://en.wikipedia.org/wiki/Riboswitch
http://en.wikipedia.org/wiki/Riboswitch
riboswitch RNA
matrix_attachment_site
sequence
URL:http://en.wikipedia.org/wiki/Matrix_attachment_site
http://en.wikipedia.org/wiki/Matrix_attachment_site
scaffold matrix attachment region
MAR
scaffold attachment site
SMAR
nuclear matrix association region
matrix attachment site
matrix attachment region
matrix association region
nuclear matrix attachment site
S/MAR
S/MAR element
A DNA region that is required for the binding of chromatin to the nuclear matrix.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
locus_control_region
sequence
locus control element
locus control region
LCR
A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/Locus_control_region
http://en.wikipedia.org/wiki/Locus_control_region
match_set
sequence
A collection of match parts.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
match_part
sequence
A part of a match, for example an hsp from blast is a match_part.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
match part
genomic_clone
sequence
A clone of a DNA region of a genome.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
genomic clone
sequence_operation
sequence
An operation that can be applied to a sequence, that results in a change.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence operation
pseudogene_attribute
sequence
An attribute of a pseudogene (SO:0000336).
SO:ma
http://purl.org/obo/owl/SO#SO_ma
pseudogene attribute
processed_pseudogene
Please not the synonym R psi M uses the spelled out form of the greek letter.
sequence
processed pseudogene
A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
pseudogene by reverse transcription
R psi G
retropseudogene
pseudogene_by_unequal_crossing_over
sequence
pseudogene by unequal crossing over
A pseudogene caused by unequal crossing over at recombination.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
delete
sequence
To remove a subsection of sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insert
sequence
To insert a subsection of sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
invert
sequence
To invert a subsection of sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
substitute
sequence
To substitute a subsection of sequence for another.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translocate
sequence
To translocate a subsection of sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene_part
sequence
A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
probe
sequence
URL:http://en.wikipedia.org/wiki/Hybridization_probe
http://en.wikipedia.org/wiki/Hybridization_probe
A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
assortment_derived_deficiency
sequence
assortment-derived_deficiency
sequence_variant_affecting_regulatory_region
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
A sequence_variant_effect which changes the regulatory region of a gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mutation affecting regulatory region
sequence variant affecting regulatory region
aneuploid
sequence
URL:http://en.wikipedia.org/wiki/Aneuploid
http://en.wikipedia.org/wiki/Aneuploid
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
hyperploid
sequence
URL:http://en.wikipedia.org/wiki/Hyperploid
http://en.wikipedia.org/wiki/Hyperploid
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
hypoploid
sequence
URL:http://en.wikipedia.org/wiki/Hypoploid
http://en.wikipedia.org/wiki/Hypoploid
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
operator
sequence
A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
operator segment
URL:http://en.wikipedia.org/wiki/Operator_(biology)#Operator
http://en.wikipedia.org/wiki/Operator_(biology)#Operator
assortment_derived_aneuploid
sequence
assortment-derived_aneuploid
nuclease_binding_site
sequence
A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
nuclease binding site
compound_chromosome_arm
FLAG - this term is should probably be a part of rather than an is_a.
sequence
compound chromosome arm
restriction_enzyme_binding_site
A region of a molecule that binds to a restriction enzyme.
sequence
restriction endonuclease binding site
restriction enzyme binding site
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
deficient_intrachromosomal_transposition
sequence
An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
deficient intrachromosomal transposition
deficient_interchromosomal_transposition
sequence
deficient interchromosomal transposition
An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene_by_transcript_attribute
This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.
sequence
free_chromosome_arm
sequence
free chromosome arm
A chromosome structure variation whereby an arm exists as an individual chromosome element.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene_by_polyadenylation_attribute
sequence
gene_to_gene_feature
sequence
gene to gene feature
overlapping
sequence
An attribute describing a gene that has a sequence that overlaps the sequence of another gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inside_intron
sequence
An attribute to describe a gene when it is located within the intron of another gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inside intron
inside_intron_antiparallel
sequence
An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inside intron antiparallel
inside_intron_parallel
sequence
inside intron parallel
An attribute to describe a gene when it is located within the intron of another gene and on the same strand.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
end_overlapping_gene
sequence
five_prime_three_prime_overlap
sequence
An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
five prime-three prime overlap
five_prime_five_prime_overlap
sequence
An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
five prime-five prime overlap
three_prime_three_prime_overlap
sequence
three prime-three prime overlap
An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
three_prime_five_prime_overlap
sequence
An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
5' 3' overlap
three prime five prime overlap
antisense
sequence
URL:http://en.wikipedia.org/wiki/Antisense
http://en.wikipedia.org/wiki/Antisense
A region sequence that is complementary to a sequence of messenger RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polycistronic_transcript
sequence
A transcript that is polycistronic.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
polycistronic transcript
dicistronic_transcript
sequence
A transcript that is dicistronic.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
dicistronic transcript
operon_member
sequence
operon member
gene_array_member
sequence
gene array member
processed_transcript_attribute
sequence
macronuclear_sequence
sequence
macronuclear sequence
micronuclear_sequence
sequence
micronuclear sequence
gene_by_genome_location
sequence
gene_by_organelle_of_genome
sequence
nuclear_gene
sequence
A gene from nuclear sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
nuclear gene
URL:http://en.wikipedia.org/wiki/Nuclear_gene
http://en.wikipedia.org/wiki/Nuclear_gene
mt_gene
sequence
mt gene
A gene located in mitochondrial sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
mitochondrial gene
URL:http://en.wikipedia.org/wiki/Mitochondrial_gene
http://en.wikipedia.org/wiki/Mitochondrial_gene
kinetoplast_gene
sequence
kinetoplast gene
A gene located in kinetoplast sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
plastid_gene
sequence
A gene from plastid sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
plastid gene
apicoplast_gene
sequence
A gene from apicoplast sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
apicoplast gene
ct_gene
sequence
ct gene
chloroplast gene
A gene from chloroplast sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
chromoplast_gene
sequence
chromoplast gene
A gene from chromoplast_sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
cyanelle_gene
sequence
cyanelle gene
A gene from cyanelle sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
leucoplast_gene
sequence
leucoplast gene
A plastid gene from leucoplast sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
proplastid_gene
sequence
A gene from proplastid sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
proplastid gene
nucleomorph_gene
sequence
nucleomorph gene
A gene from nucleomorph sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
plasmid_gene
sequence
A gene from plasmid sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
plasmid gene
proviral_gene
sequence
A gene from proviral sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
proviral gene
endogenous_retroviral_gene
sequence
A proviral gene with origin endogenous retrovirus.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
endogenous retroviral gene
transposable_element
sequence
URL:http://en.wikipedia.org/wiki/Transposable_element
http://en.wikipedia.org/wiki/Transposable_element
A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
URL:http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
transposon
transposable element
expressed_sequence_match
sequence
A match to an EST or cDNA sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
expressed sequence match
clone_insert_end
sequence
clone insert end
The end of the clone insert.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.
SO:0000358
sequence
protein
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/Polypeptide
http://en.wikipedia.org/wiki/Polypeptide
chromosome_arm
sequence
chromosome arm
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.
URL:http://www.medterms.com/script/main/art.asp?articlekey=5152
http://www.medterms.com/script/main/art.asp?articlekey=5152
non_capped_primary_transcript
sequence
sequencing_primer
sequence
sequencing primer
mRNA_with_frameshift
sequence
frameshifted mRNA
An mRNA with a frameshift.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
mRNA with frameshift
sequence_variant_obs
sequence
A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mutation
sequence_feature
sequence
located_sequence_feature
sequence feature
located sequence feature
An extent of biological sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transposable_element_gene
sequence
A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transposable element gene
primer
sequence
DNA primer
primer oligonucleotide
primer polynucleotide
URL:http://en.wikipedia.org/wiki/Primer_(molecular_biology)
http://en.wikipedia.org/wiki/Primer_(molecular_biology)
An oligo to which new deoxyribonucleotides can be added by DNA polymerase.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
primer sequence
proviral_region
sequence
proviral region
proviral sequence
A viral sequence which has integrated into a host genome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
methylated_C
sequence
methylated cytosine base
methylated cytosine
methylated C
A methylated deoxy-cytosine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
methylated cytosine residue
transcript_feature
sequence
edited
sequence
An attribute describing a sequence that is modified by editing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript_with_readthrough_stop_codon
sequence
transcript_with_translational_frameshift
sequence
transcript with translational frameshift
A transcript with a translational frameshift.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
regulated
sequence
An attribute to describe a sequence that is regulated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
protein_coding_primary_transcript
May contain introns.
sequence
protein coding primary transcript
A primary transcript that, at least in part, encodes one or more proteins.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
pre mRNA
forward_primer
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
A single stranded oligo used for polymerase chain reaction.
URL:http://mged.sourceforge.net/ontologies/MGEDontology.php
http://mged.sourceforge.net/ontologies/MGEDontology.php
forward primer
forward DNA primer
forward primer oligo
DNA forward primer
forward primer oligonucleotide
forward primer polynucleotide
forward primer sequence
RNA_sequence_secondary_structure
sequence
A folded RNA sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RNA sequence secondary structure
transcriptionally_regulated
By:<protein_id>.
sequence
An attribute describing a gene that is regulated at transcription.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
transcriptionally regulated
transcriptionally_constitutive
sequence
Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcriptionally constitutive
transcriptionally_induced
sequence
transcriptionally induced
An inducer molecule is required for transcription to occur.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcriptionally_repressed
sequence
transcriptionally repressed
A repressor molecule is required for transcription to stop.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
silenced_gene
sequence
A gene that is silenced.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
silenced gene
gene_silenced_by_DNA_modification
sequence
gene silenced by DNA modification
A gene that is silenced by DNA modification.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene_silenced_by_DNA_methylation
sequence
A gene that is silenced by DNA methylation.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene silenced by DNA methylation
methylation-silenced gene
post_translationally_regulated
sequence
post-translationally regulated
post translationally regulated
An attribute describing a gene that is regulated after it has been translated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translationally_regulated
sequence
An attribute describing a gene that is regulated as it is translated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translationally regulated
reverse_primer
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
A single stranded oligo used for polymerase chain reaction.
URL:http://mged.sourceforge.net/ontologies/MGEDontology.php
http://mged.sourceforge.net/ontologies/MGEDontology.php
DNA reverse primer
reverse DNA primer
reverse primer
reverse primer oligo
reverse primer oligonucleotide
reverse primer sequence
epigenetically_modified
sequence
epigenetically modified
This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
genomically_imprinted
sequence
http:http://en.wikipedia.org/wiki/Genomic_imprinting
http://purl.org/obo/owl/http#http_http://en.wikipedia.org/wiki/Genomic_imprinting
imprinted
Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
genomically imprinted
maternally_imprinted
sequence
The maternal copy of the gene is modified, rendering it transcriptionally silent.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
maternally imprinted
paternally_imprinted
sequence
The paternal copy of the gene is modified, rendering it transcriptionally silent.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
paternally imprinted
allelically_excluded
Examples are x-inactivation and immunoglobulin formation.
sequence
allelically excluded
Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene_rearranged_at_DNA_level
sequence
An epigenetically modified gene, rearranged at the DNA level.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene rearranged at DNA level
ribosome_entry_site
sequence
ribosome entry site
Region in mRNA where ribosome assembles.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
attenuator
sequence
URL:http://en.wikipedia.org/wiki/Attenuator
http://en.wikipedia.org/wiki/Attenuator
A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
SO:as
http://purl.org/obo/owl/SO#SO_as
attenuator sequence
terminator
sequence
URL:http://en.wikipedia.org/wiki/Terminator_(genetics)
http://en.wikipedia.org/wiki/Terminator_(genetics)
The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
terminator sequence
DNA_sequence_secondary_structure
sequence
DNA sequence secondary structure
A folded DNA sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
assembly_component
sequence
A region of known length which may be used to manufacture a longer region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
assembly component
primary_transcript_attribute
sequence
recoded_codon
sequence
A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
recoded codon
capped
sequence
An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
exon
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
URL:http://en.wikipedia.org/wiki/Exon
http://en.wikipedia.org/wiki/Exon
A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
supercontig
sequence
One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
SO:ls
http://purl.org/obo/owl/SO#SO_ls
scaffold
contig
sequence
URL:http://en.wikipedia.org/wiki/Contig
http://en.wikipedia.org/wiki/Contig
A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
SO:ls
http://purl.org/obo/owl/SO#SO_ls
read
sequence
A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
SO:rd
http://purl.org/obo/owl/SO#SO_rd
clone
sequence
http:http://en.wikipedia.org/wiki/Clone_(genetics)
http://purl.org/obo/owl/http#http_http://en.wikipedia.org/wiki/Clone_(genetics)
A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
YAC
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
yeast artificial chromosome
BAC
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
bacterial artificial chromosome
PAC
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome.
sequence
P1 artificial chromosome
The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.
URL:http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome
http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome
URL:http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome
http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome
P1
plasmid
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
plasmid sequence
cosmid
Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
cosmid vector
A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/Cosmid
http://en.wikipedia.org/wiki/Cosmid
phagemid
sequence
URL:http://en.wikipedia.org/wiki/Phagemid
http://en.wikipedia.org/wiki/Phagemid
phagemid vector
A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
fosmid
Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.
sequence
URL:http://en.wikipedia.org/wiki/Fosmid
http://en.wikipedia.org/wiki/Fosmid
fosmid vector
A cloning vector that utilizes the E. coli F factor.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
deletion
sequence
SO:1000033
nucleotide_deletion
nucleotide deletion
The point at which one or more contiguous nucleotides were excised.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
loinc:LA6692-3
http://purl.org/obo/owl/loinc#loinc_LA6692-3
URL:http://en.wikipedia.org/wiki/Nucleotide_deletion
http://en.wikipedia.org/wiki/Nucleotide_deletion
deleted_sequence
lambda_clone
sequence
A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
ISBN:0-1767-2380-8
http://purl.org/obo/owl/ISBN#ISBN_0-1767-2380-8
methylated_A
sequence
methylated adenine
methylated A
A modified RNA base in which adenine has been methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
methylated adenine residue
methylated adenine base
splice_site
With spliceosomal introns, the splice sites bind the spliceosomal machinery.
sequence
splice site
Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Splice_site
http://en.wikipedia.org/wiki/Splice_site
five_prime_cis_splice_site
sequence
5' splice site
donor splice site
Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.
URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
SO:ke
http://purl.org/obo/owl/SO#SO_ke
donor
splice donor site
five prime splice site
three_prime_cis_splice_site
sequence
acceptor
splice acceptor site
acceptor splice site
3' splice site
Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
three prime splice site
enhancer
An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.
sequence
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.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
URL:http://en.wikipedia.org/wiki/Enhancer_(genetics)
http://en.wikipedia.org/wiki/Enhancer_(genetics)
enhancer_bound_by_factor
sequence
enhancer bound by factor
An enhancer bound by a factor.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
promoter
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
sequence
URL:http://en.wikipedia.org/wiki/Promoter
http://en.wikipedia.org/wiki/Promoter
promoter sequence
A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
SO:regcreative
http://purl.org/obo/owl/SO#SO_regcreative
restriction_enzyme_cut_site
sequence
A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
RNApol_I_promoter
sequence
A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RNA polymerase A promoter
RNApol I promoter
pol I promoter
polymerase I promoter
RNApol_II_promoter
sequence
polymerase II promoter
pol II promoter
RNA polymerase B promoter
RNApol II promoter
A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RNApol_III_promoter
sequence
A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RNA polymerase C promoter
RNApol III promoter
pol III promoter
polymerase III promoter
CAAT_signal
sequence
URL:http://en.wikipedia.org/wiki/CAAT_box
http://en.wikipedia.org/wiki/CAAT_box
CAAT-box
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.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
CAAT signal
CAAT box
GC_rich_promoter_region
sequence
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.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
GC-rich region
GC rich promoter region
TATA_box
Binds TBP.
sequence
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).
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
URL:http://en.wikipedia.org/wiki/TATA_box
http://en.wikipedia.org/wiki/TATA_box
TATA box
Goldstein-Hogness box
minus_10_signal
sequence
URL:http://en.wikipedia.org/wiki/Pribnow_box
http://en.wikipedia.org/wiki/Pribnow_box
Pribnow box
Pribnow Schaller box
-10 signal
minus 10 signal
Pribnow-Schaller box
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. This region is associated with sigma factor 70.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
minus_35_signal
sequence
-35 signal
minus 35 signal
A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
cross_genome_match
sequence
A nucleotide match against a sequence from another organism.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
cross genome match
operon
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/Operon
http://en.wikipedia.org/wiki/Operon
clone_insert_start
sequence
The start of the clone insert.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
clone insert start
retrotransposon
sequence
A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.
URL:http://www.dddmag.com/Glossary.aspx#r
http://www.dddmag.com/Glossary.aspx#r
retrotransposon element
class I transposon
URL:http://en.wikipedia.org/wiki/Retrotransposon
http://en.wikipedia.org/wiki/Retrotransposon
class I
translated_nucleotide_match
sequence
A match against a translated sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translated nucleotide match
DNA_transposon
sequence
A transposon where the mechanism of transposition is via a DNA intermediate.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
class II
class II transposon
DNA transposon
non_transcribed_region
sequence
non transcribed region
nontranscribed sequence
nontranscribed region
A region of the gene which is not transcribed.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
non-transcribed sequence
U2_intron
May have either GT-AG or AT-AG 5' and 3' boundaries.
sequence
A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
PMID:9428511
http://purl.org/obo/owl/PMID#PMID_9428511
U2 intron
primary_transcript
sequence
precursor RNA
primary transcript
A transcript that in its initial state requires modification to be functional.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/Primary_transcript
http://en.wikipedia.org/wiki/Primary_transcript
LTR_retrotransposon
sequence
long terminal repeat retrotransposon
LTR retrotransposon
A retrotransposon flanked by long terminal repeat sequences.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
repeat_family
sequence
A group of characterized repeat sequences.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
intron
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
URL:http://en.wikipedia.org/wiki/Intron
http://en.wikipedia.org/wiki/Intron
A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
non_LTR_retrotransposon
sequence
non LTR retrotransposon
A retrotransposon without long terminal repeat sequences.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
five_prime_intron
sequence
five prime intron
5' intron sequence
5' intron
interior_intron
sequence
interior intron
three_prime_intron
sequence
three prime intron
3' intron
3' intron sequence
RFLP_fragment
sequence
A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
GOC:pj
http://purl.org/obo/owl/GOC#GOC_pj
restriction fragment length polymorphism
RFLP
RFLP fragment
URL:http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism
http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism
LINE_element
sequence
Long interspersed element
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.
URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
LINE element
LINE
Long interspersed nuclear element
coding_exon
sequence
coding exon
An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
five_prime_coding_exon_coding_region
sequence
five prime exon coding region
The sequence of the five_prime_coding_exon that codes for protein.
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
three_prime_coding_exon_coding_region
sequence
three prime exon coding region
The sequence of the three_prime_coding_exon that codes for protein.
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
noncoding_exon
sequence
noncoding exon
An exon that does not contain any codons.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translocation
sequence
translocated sequence
transchr
URL:http://www.ncbi.nlm.nih.gov/dbvar/
http://www.ncbi.nlm.nih.gov/dbvar/
A region of nucleotide sequence that has translocated to a new position.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
five_prime_coding_exon
sequence
five prime coding exon
5' coding exon
The 5' most coding exon.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
interior_exon
sequence
An exon that is bounded by 5' and 3' splice sites.
PMID:10373547
http://purl.org/obo/owl/PMID#PMID_10373547
interior exon
three_prime_coding_exon
sequence
3' coding exon
three prime coding exon
The coding exon that is most 3-prime on a given transcript.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
UTR
sequence
Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
untranslated region
five_prime_UTR
sequence
five_prime_untranslated_region
URL:http://en.wikipedia.org/wiki/5'_UTR
http://en.wikipedia.org/wiki/5'_UTR
A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
5' UTR
five prime UTR
three_prime_UTR
sequence
three prime UTR
three prime untranslated region
URL:http://en.wikipedia.org/wiki/Three_prime_untranslated_region
http://en.wikipedia.org/wiki/Three_prime_untranslated_region
A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
SINE_element
sequence
A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
SINE element
Short interspersed nuclear element
Short interspersed element
URL:http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element
http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element
simple_sequence_length_variation
sequence
simple sequence length variation
SSLP
simple sequence length polymorphism
terminal_inverted_repeat_element
sequence
A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.
URL:http://www.genetics.org/cgi/reprint/156/4/1983.pdf
http://www.genetics.org/cgi/reprint/156/4/1983.pdf
TIR element
terminal inverted repeat element
rRNA_primary_transcript
sequence
A primary transcript encoding a ribosomal RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ribosomal RNA primary transcript
rRNA primary transcript
tRNA_primary_transcript
sequence
tRNA primary transcript
A primary transcript encoding a transfer RNA (SO:0000253).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
alanine_tRNA_primary_transcript
sequence
alanine tRNA primary transcript
A primary transcript encoding alanyl tRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
arginine_tRNA_primary_transcript
sequence
A primary transcript encoding arginyl tRNA (SO:0000255).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
arginine tRNA primary transcript
asparagine_tRNA_primary_transcript
sequence
asparagine tRNA primary transcript
A primary transcript encoding asparaginyl tRNA (SO:0000256).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
aspartic_acid_tRNA_primary_transcript
sequence
A primary transcript encoding aspartyl tRNA (SO:0000257).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
aspartic acid tRNA primary transcript
cysteine_tRNA_primary_transcript
sequence
A primary transcript encoding cysteinyl tRNA (SO:0000258).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cysteine tRNA primary transcript
glutamic_acid_tRNA_primary_transcript
sequence
A primary transcript encoding glutaminyl tRNA (SO:0000260).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
glutamic acid tRNA primary transcript
glutamine_tRNA_primary_transcript
sequence
A primary transcript encoding glutamyl tRNA (SO:0000260).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
glutamine tRNA primary transcript
glycine_tRNA_primary_transcript
sequence
glycine tRNA primary transcript
A primary transcript encoding glycyl tRNA (SO:0000263).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
histidine_tRNA_primary_transcript
sequence
histidine tRNA primary transcript
A primary transcript encoding histidyl tRNA (SO:0000262).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
isoleucine_tRNA_primary_transcript
sequence
A primary transcript encoding isoleucyl tRNA (SO:0000263).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
isoleucine tRNA primary transcript
leucine_tRNA_primary_transcript
sequence
A primary transcript encoding leucyl tRNA (SO:0000264).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
leucine tRNA primary transcript
lysine_tRNA_primary_transcript
sequence
A primary transcript encoding lysyl tRNA (SO:0000265).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
lysine tRNA primary transcript
methionine_tRNA_primary_transcript
sequence
methionine tRNA primary transcript
A primary transcript encoding methionyl tRNA (SO:0000266).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
phenylalanine_tRNA_primary_transcript
sequence
phenylalanine tRNA primary transcript
A primary transcript encoding phenylalanyl tRNA (SO:0000267).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
proline_tRNA_primary_transcript
sequence
A primary transcript encoding prolyl tRNA (SO:0000268).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
proline tRNA primary transcript
serine_tRNA_primary_transcript
sequence
A primary transcript encoding seryl tRNA (SO:000269).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
serine tRNA primary transcript
threonine_tRNA_primary_transcript
sequence
threonine tRNA primary transcript
A primary transcript encoding threonyl tRNA (SO:000270).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tryptophan_tRNA_primary_transcript
sequence
A primary transcript encoding tryptophanyl tRNA (SO:000271).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tryptophan tRNA primary transcript
tyrosine_tRNA_primary_transcript
sequence
tyrosine tRNA primary transcript
A primary transcript encoding tyrosyl tRNA (SO:000272).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
valine_tRNA_primary_transcript
sequence
A primary transcript encoding valyl tRNA (SO:000273).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
valine tRNA primary transcript
snRNA_primary_transcript
sequence
snRNA primary transcript
A primary transcript encoding a small nuclear RNA (SO:0000274).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
snoRNA_primary_transcript
sequence
snoRNA primary transcript
A primary transcript encoding a small nucleolar mRNA (SO:0000275).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mature_transcript
A processed transcript cannot contain introns.
sequence
A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mature transcript
URL:http://en.wikipedia.org/wiki/Mature_transcript
http://en.wikipedia.org/wiki/Mature_transcript
mRNA
An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/MRNA
http://en.wikipedia.org/wiki/MRNA
messenger RNA
TF_binding_site
sequence
transcription factor binding site
TF binding site
A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667].
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ORF
The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
open reading frame
The in-frame 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.
SGD:rb
http://purl.org/obo/owl/SGD#SGD_rb
SO:ma
http://purl.org/obo/owl/SO#SO_ma
transcript_attribute
sequence
transcript attribute
foldback_element
sequence
foldback element
long inverted repeat element
A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats.
URL:http://www.genetics.org/cgi/reprint/156/4/1983.pdf
http://www.genetics.org/cgi/reprint/156/4/1983.pdf
LVR element
flanking_region
sequence
flanking region
The sequences extending on either side of a specific region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
chromosome_variation
sequence
chromosome variation
internal_UTR
sequence
A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
internal UTR
untranslated_region_polycistronic_mRNA
sequence
untranslated region polycistronic mRNA
The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
internal_ribosome_entry_site
sequence
Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
IRES
internal ribosome entry sequence
URL:http://en.wikipedia.org/wiki/Internal_ribosome_entry_site
http://en.wikipedia.org/wiki/Internal_ribosome_entry_site
internal ribosomal entry sequence
internal ribosomal entry site
internal ribosome entry site
four_cutter_restriction_site
sequence
four-cutter_restriction_sit
4-cutter_restriction_site
mRNA_by_polyadenylation_status
sequence
polyadenylated
sequence
A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mRNA_not_polyadenylated
sequence
sequence_length_variation
sequence
sequence length variation
six_cutter_restriction_site
sequence
6-cutter_restriction_site
six-cutter_restriction_site
modified_RNA_base_feature
sequence
A post_transcriptionally modified base.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified RNA base feature
eight_cutter_restriction_site
sequence
eight-cutter_restriction_site
8-cutter_restriction_site
rRNA
sequence
ribosomal RNA
RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
ISBN:0198506732
http://purl.org/obo/owl/ISBN#ISBN_0198506732
ribosomal ribonucleic acid
URL:http://en.wikipedia.org/wiki/RRNA
http://en.wikipedia.org/wiki/RRNA
tRNA
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
transfer ribonucleic acid
transfer RNA
URL:http://en.wikipedia.org/wiki/TRNA
http://en.wikipedia.org/wiki/TRNA
Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.
ISBN:0198506732
http://purl.org/obo/owl/ISBN#ISBN_0198506732
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005
alanyl_tRNA
sequence
A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
alanyl-transfer RNA
alanyl tRNA
alanyl-transfer ribonucleic acid
rRNA_small_subunit_primary_transcript
sequence
rRNA small subunit primary transcript
A primary transcript encoding a small ribosomal subunit RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
asparaginyl_tRNA
sequence
asparaginyl tRNA
asparaginyl-transfer ribonucleic acid
asparaginyl-transfer RNA
A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
aspartyl_tRNA
sequence
A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
aspartyl-transfer RNA
aspartyl tRNA
aspartyl-transfer ribonucleic acid
cysteinyl_tRNA
sequence
cysteinyl-transfer ribonucleic acid
cysteinyl-transfer RNA
cysteinyl tRNA
A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
glutaminyl_tRNA
sequence
glutaminyl tRNA
A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
glutaminyl-transfer ribonucleic acid
glutaminyl-transfer RNA
glutamyl_tRNA
sequence
glutamyl tRNA
glutamyl-transfer ribonucleic acid
glutamyl-transfer RNA
A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
glycyl_tRNA
sequence
glycyl-transfer RNA
glycyl-transfer ribonucleic acid
A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
glycyl tRNA
histidyl_tRNA
sequence
histidyl-transfer ribonucleic acid
histidyl-transfer RNA
histidyl tRNA
A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
isoleucyl_tRNA
sequence
A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
isoleucyl tRNA
isoleucyl-transfer ribonucleic acid
isoleucyl-transfer RNA
leucyl_tRNA
sequence
leucyl tRNA
leucyl-transfer ribonucleic acid
A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
leucyl-transfer RNA
lysyl_tRNA
sequence
lysyl-transfer ribonucleic acid
lysyl tRNA
A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
lysyl-transfer RNA
methionyl_tRNA
sequence
methionyl tRNA
methionyl-transfer ribonucleic acid
A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
methionyl-transfer RNA
phenylalanyl_tRNA
sequence
phenylalanyl tRNA
phenylalanyl-transfer ribonucleic acid
phenylalanyl-transfer RNA
A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
prolyl_tRNA
sequence
prolyl-transfer RNA
prolyl-transfer ribonucleic acid
prolyl tRNA
A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
seryl_tRNA
sequence
seryl-transfer ribonucleic acid
A tRNA sequence that has a serine anticodon, and a 3' serine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
seryl-transfer RNA
seryl tRNA
threonyl_tRNA
sequence
threonyl-transfer ribonucleic acid
A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
threonyl tRNA
threonyl-transfer RNA
tryptophanyl_tRNA
sequence
tryptophanyl-transfer RNA
A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tryptophanyl tRNA
tryptophanyl-transfer ribonucleic acid
tyrosyl_tRNA
sequence
A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tyrosyl tRNA
tyrosyl-transfer RNA
tyrosyl-transfer ribonucleic acid
valyl_tRNA
sequence
A tRNA sequence that has a valine anticodon, and a 3' valine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
valyl tRNA
valyl-transfer RNA
valyl-transfer ribonucleic acid
snRNA
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
WB:ems
http://purl.org/obo/owl/WB#WB_ems
PMID:11733745
http://purl.org/obo/owl/PMID#PMID_11733745
URL:http://en.wikipedia.org/wiki/SnRNA
http://en.wikipedia.org/wiki/SnRNA
small nuclear RNA
snoRNA
sequence
A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.
GOC:kgc
http://purl.org/obo/owl/GOC#GOC_kgc
small nucleolar RNA
URL:http://en.wikipedia.org/wiki/SnoRNA
http://en.wikipedia.org/wiki/SnoRNA
miRNA
sequence
URL:http://en.wikipedia.org/wiki/MiRNA
http://en.wikipedia.org/wiki/MiRNA
microRNA
Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
PMID:12592000
http://purl.org/obo/owl/PMID#PMID_12592000
micro RNA
bound_by_factor
Formerly called transcript_by_bound_factor.
sequence
An attribute describing a sequence that is bound by another molecule.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
bound by factor
transcript_bound_by_nucleic_acid
Formerly called transcript_by_bound_nucleic_acid.
sequence
transcript bound by nucleic acid
A transcript that is bound by a nucleic acid.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
transcript_bound_by_protein
Formerly called transcript_by_bound_protein.
sequence
A transcript that is bound by a protein.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
transcript bound by protein
engineered_gene
sequence
engineered gene
A gene that is engineered.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered_foreign_gene
sequence
A gene that is engineered and foreign.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered foreign gene
mRNA_with_minus_1_frameshift
sequence
An mRNA with a minus 1 frameshift.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
mRNA with minus 1 frameshift
engineered_foreign_transposable_element_gene
sequence
A transposable_element that is engineered and foreign.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered foreign transposable element gene
type_I_enzyme_restriction_site
sequence
The recognition site is bipartite and interrupted.
URL:http://www.promega.com
http://www.promega.com
foreign_gene
sequence
A gene that is foreign.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
foreign gene
long_terminal_repeat
sequence
LTR
direct terminal repeat
long terminal repeat
URL:http://en.wikipedia.org/wiki/Long_terminal_repeat
http://en.wikipedia.org/wiki/Long_terminal_repeat
A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
fusion_gene
sequence
URL:http://en.wikipedia.org/wiki/Fusion_gene
http://en.wikipedia.org/wiki/Fusion_gene
fusion gene
A gene that is a fusion.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered_fusion_gene
sequence
A fusion gene that is engineered.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered fusion gene
microsatellite
sequence
VNTR
microsatellite marker
microsatellite locus
A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem.
URL:http://www.informatics.jax.org/silver/glossary.shtml
http://www.informatics.jax.org/silver/glossary.shtml
URL:http://en.wikipedia.org/wiki/Microsatellite
http://en.wikipedia.org/wiki/Microsatellite
dinucleotide_repeat_microsatellite_feature
sequence
dinucleotide repeat microsatellite marker
dinucleotide repeat microsatellite locus
dinucleotide repeat microsatellite feature
dinucleotide repeat microsatellite
trinucleotide_repeat_microsatellite_feature
sequence
rinucleotide repeat microsatellite
trinucleotide repeat microsatellite feature
trinucleotide repeat microsatellite locus
dinucleotide repeat microsatellite marker
repetitive_element
sequence
engineered_foreign_repetitive_element
sequence
engineered foreign repetitive element
A repetitive element that is engineered and foreign.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
inverted_repeat
sequence
The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inverted repeat sequence
inverted repeat
URL:http://en.wikipedia.org/wiki/Inverted_repeat
http://en.wikipedia.org/wiki/Inverted_repeat
U12_intron
May have either GT-AC or AT-AC 5' and 3' boundaries.
sequence
U12 intron
U12-dependent intron
A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
PMID:9428511
http://purl.org/obo/owl/PMID#PMID_9428511
origin_of_replication
sequence
ori
The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
origin of replication
URL:http://en.wikipedia.org/wiki/Origin_of_replication
http://en.wikipedia.org/wiki/Origin_of_replication
D_loop
sequence
displacement loop
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.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
D-loop
URL:http://en.wikipedia.org/wiki/D_loop
http://en.wikipedia.org/wiki/D_loop
recombination_feature
sequence
recombination feature
specific_recombination_site
sequence
specific recombination site
recombination_feature_of_rearranged_gene
sequence
recombination feature of rearranged gene
vertebrate_immune_system_gene_recombination_feature
sequence
vertebrate immune system gene recombination feature
J_gene_recombination_feature
sequence
J-RS
J gene recombination feature
Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
clip
sequence
Part of the primary transcript that is clipped off during processing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
type_II_enzyme_restriction_site
sequence
The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site.
URL:http://www.promega.com
http://www.promega.com
modified_base
Modified base:<modified_base>.
sequence
A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
modified base site
methylated_base_feature
sequence
A nucleotide modified by methylation.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
methylated base feature
CpG_island
sequence
Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
SO:rd
http://purl.org/obo/owl/SO#SO_rd
URL:http://en.wikipedia.org/wiki/CpG_island
http://en.wikipedia.org/wiki/CpG_island
CG island
CpG island
sequence_feature_locating_method
sequence
computed_feature
sequence
predicted_ab_initio_computation
sequence
computed_feature_by_similarity
similar to:<sequence_id>
sequence
.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
experimentally_determined
sequence
Attribute to describe a feature that has been experimentally verified.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
experimentally determined
stem_loop
SO:0000019
sequence
RNA_hairpin_loop
URL:http://en.wikipedia.org/wiki/Stem_loop
http://en.wikipedia.org/wiki/Stem_loop
stem loop
stem-loop
A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
direct_repeat
sequence
URL:http://en.wikipedia.org/wiki/Direct_repeat
http://en.wikipedia.org/wiki/Direct_repeat
A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
direct repeat
TSS
sequence
The first base where RNA polymerase begins to synthesize the RNA transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcription start site
CDS
sequence
A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
coding sequence
cDNA_clone
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
cDNA clone
Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
URL:http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html
http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html
start_codon
sequence
URL:http://en.wikipedia.org/wiki/Start_codon
http://en.wikipedia.org/wiki/Start_codon
start codon
initiation codon
First codon to be translated by a ribosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
stop_codon
sequence
stop codon
In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Stop_codon
http://en.wikipedia.org/wiki/Stop_codon
intronic_splice_enhancer
sequence
intronic splice enhancer
Sequences within the intron that modulate splice site selection for some introns.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mRNA_with_plus_1_frameshift
sequence
mRNA with plus 1 frameshift
An mRNA with a plus 1 frameshift.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nuclease_hypersensitive_site
sequence
nuclease hypersensitive site
coding_start
sequence
translation start
coding start
translation initiation site
The first base to be translated into protein.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tag
sequence
A nucleotide sequence that may be used to identify a larger sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
rRNA_large_subunit_primary_transcript
sequence
rRNA large subunit primary transcript
A primary transcript encoding a large ribosomal subunit RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
SAGE_tag
sequence
A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract
SAGE tag
coding_end
sequence
coding end
translation_end
translation termination site
The last base to be translated into protein. It does not include the stop codon.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
microarray_oligo
sequence
microarray oligo
microarray oligonucleotide
mRNA_with_plus_2_frameshift
sequence
mRNA with plus 2 frameshift
An mRNA with a plus 2 frameshift.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
conserved_region
sequence
conserved region
Region of sequence similarity by descent from a common ancestor.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Conserved_region
http://en.wikipedia.org/wiki/Conserved_region
STS
sequence
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.
URL:http://www.biospace.com
http://www.biospace.com
sequence tag site
coding_conserved_region
sequence
Coding region of sequence similarity by descent from a common ancestor.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
coding conserved region
exon_junction
sequence
exon junction
The boundary between two exons in a processed transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nc_conserved_region
sequence
Non-coding region of sequence similarity by descent from a common ancestor.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nc conserved region
noncoding conserved region
mRNA_with_minus_2_frameshift
sequence
A mRNA with a minus 2 frameshift.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mRNA with minus 2 frameshift
pseudogene
sequence
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).
URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
URL:http://en.wikipedia.org/wiki/Pseudogene
http://en.wikipedia.org/wiki/Pseudogene
RNAi_reagent
sequence
RNAi reagent
A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
SO:rd
http://purl.org/obo/owl/SO#SO_rd
MITE
sequence
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.
URL:http://www.pnas.org/cgi/content/full/97/18/10083
http://www.pnas.org/cgi/content/full/97/18/10083
miniature inverted repeat transposable element
recombination_hotspot
sequence
A region in a genome which promotes recombination.
SO:rd
http://purl.org/obo/owl/SO#SO_rd
URL:http://en.wikipedia.org/wiki/Recombination_hotspot
http://en.wikipedia.org/wiki/Recombination_hotspot
recombination hotspot
chromosome
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
URL:http://en.wikipedia.org/wiki/Chromosome
http://en.wikipedia.org/wiki/Chromosome
Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
chromosome_band
sequence
A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
cytological band
cytoband
chromosome band
URL:http://en.wikipedia.org/wiki/Cytological_band
http://en.wikipedia.org/wiki/Cytological_band
site_specific_recombination_target_region
sequence
site specific recombination target region
match
sequence
A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
splice_enhancer
sequence
splice enhancer
Region of a transcript that regulates splicing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
EST
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
expressed sequence tag
A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
loxP_site
sequence
loxP site
Cre-recombination target region
nucleotide_match
sequence
A match against a nucleotide sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nucleotide match
nucleic_acid
sequence
nucleic acid
URL:http://en.wikipedia.org/wiki/Nucleic_acid
http://en.wikipedia.org/wiki/Nucleic_acid
An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
CHEBI:33696
http://purl.org/obo/owl/CHEBI#CHEBI_33696
protein_match
sequence
protein match
A match against a protein sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
FRT_site
sequence
FLP recombination target region
An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
FRT site
synthetic_sequence
sequence
An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
synthetic sequence
DNA
sequence
An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
sequence_assembly
sequence
A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
sequence assembly
URL:http://en.wikipedia.org/wiki/Sequence_assembly
http://en.wikipedia.org/wiki/Sequence_assembly
group_1_intron_homing_endonuclease_target_region
sequence
group 1 intron homing endonuclease target region
A region of intronic nucleotide sequence targeted by a nuclease enzyme.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
haplotype_block
sequence
haplotype block
A region of the genome which is co-inherited as the result of the lack of historic recombination within it.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
RNA
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
flanked
sequence
An attribute describing a region that is bounded either side by a particular kind of region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
floxed
sequence
An attribute describing sequence that is flanked by Lox-P sites.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Floxed
http://en.wikipedia.org/wiki/Floxed
codon
sequence
URL:http://en.wikipedia.org/wiki/Codon
http://en.wikipedia.org/wiki/Codon
A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://www.everythingbio.com/glos/definition.php?word=codon
http://www.everythingbio.com/glos/definition.php?word=codon
FRT_flanked
sequence
An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
FRT flanked
invalidated_by_chimeric_cDNA
sequence
invalidated by chimeric cDNA
A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
floxed_gene
sequence
A transgene that is floxed.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
floxed gene
transposable_element_flanking_region
sequence
The region of sequence surrounding a transposable element.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transposable element flanking region
integron
sequence
A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.
SO:as
http://purl.org/obo/owl/SO#SO_as
URL:http://en.wikipedia.org/wiki/Integron
http://en.wikipedia.org/wiki/Integron
insertion_site
sequence
The junction where an insertion occurred.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insertion site
attI_site
sequence
A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.
SO:as
http://purl.org/obo/owl/SO#SO_as
attI site
transposable_element_insertion_site
sequence
The junction in a genome where a transposable_element has inserted.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transposable element insertion site
integrase_coding_region
sequence
small_regulatory_ncRNA
sequence
small regulatory ncRNA
A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
conjugative_transposon
sequence
A transposon that encodes function required for conjugation.
URL:http://www.sci.sdsu.edu/~smaloy/Glossary/C.html
http://www.sci.sdsu.edu/~smaloy/Glossary/C.html
conjugative transposon
enzymatic_RNA
This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts.
sequence
enzymatic RNA
An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
recombinationally_inverted_gene
sequence
A recombinationally rearranged gene by inversion.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
recombinationally inverted gene
ribozyme
sequence
An RNA with catalytic activity.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/Ribozyme
http://en.wikipedia.org/wiki/Ribozyme
rRNA_5_8S
sequence
5.8S LSU rRNA
5.8S rRNA
5.8S ribosomal RNA
URL:http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA
http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA
rRNA 5 8S
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002
RNA_6S
sequence
RNA 6S
6S RNA
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013
URL:http://en.wikipedia.org/wiki/6S_RNA
http://en.wikipedia.org/wiki/6S_RNA
CsrB_RsmB_RNA
sequence
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018
CsrB-RsmB RNA
CsrB RsmB RNA
DsrA_RNA
sequence
DsrA RNA
URL:http://en.wikipedia.org/wiki/DsrA_RNA
http://en.wikipedia.org/wiki/DsrA_RNA
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014
GcvB_RNA
sequence
GcvB RNA
A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022
URL:http://en.wikipedia.org/wiki/GcvB_RNA
http://en.wikipedia.org/wiki/GcvB_RNA
hammerhead_ribozyme
sequence
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.
PMID:2436805
http://purl.org/obo/owl/PMID#PMID_2436805
URL:http://en.wikipedia.org/wiki/Hammerhead_ribozyme
http://en.wikipedia.org/wiki/Hammerhead_ribozyme
hammerhead ribozyme
group_IIA_intron
sequence
group IIA intron
group_IIB_intron
sequence
group IIB intron
MicF_RNA
sequence
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033
MicF RNA
URL:http://en.wikipedia.org/wiki/MicF_RNA
http://en.wikipedia.org/wiki/MicF_RNA
OxyS_RNA
sequence
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035
OxyS RNA
URL:http://en.wikipedia.org/wiki/OxyS_RNA
http://en.wikipedia.org/wiki/OxyS_RNA
RNase_MRP_RNA
sequence
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030
RNase MRP RNA
RNase_P_RNA
sequence
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 characterized 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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010
RNase P RNA
RprA_RNA
sequence
URL:http://en.wikipedia.org/wiki/RprA_RNA
http://en.wikipedia.org/wiki/RprA_RNA
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034
RprA RNA
RRE_RNA
sequence
RRE RNA
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036
spot_42_RNA
sequence
spot-42 RNA
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021
URL:http://en.wikipedia.org/wiki/Spot_42_RNA
http://en.wikipedia.org/wiki/Spot_42_RNA
telomerase_RNA
sequence
URL:http://en.wikipedia.org/wiki/Telomerase_RNA
http://en.wikipedia.org/wiki/Telomerase_RNA
The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025
telomerase RNA
U1_snRNA
sequence
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003
small nuclear RNA U1
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
URL:http://en.wikipedia.org/wiki/U1_snRNA
http://en.wikipedia.org/wiki/U1_snRNA
snRNA U1
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
U1 small nuclear RNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
U1 snRNA
U2_snRNA
sequence
U2 snRNA
URL:http://en.wikipedia.org/wiki/U2_snRNA
http://en.wikipedia.org/wiki/U2_snRNA
U2 small nuclear RNA
RSC:CB
http://purl.org/obo/owl/RSC#RSC_CB
snRNA U2
RSC:CB
http://purl.org/obo/owl/RSC#RSC_CB
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004
small nuclear RNA U2
RSC:CB
http://purl.org/obo/owl/RSC#RSC_CB
U4_snRNA
sequence
U4 small nuclear RNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015
U4 snRNA
small nuclear RNA U4
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
snRNA U4
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
URL:http://en.wikipedia.org/wiki/U4_snRNA
http://en.wikipedia.org/wiki/U4_snRNA
U4atac_snRNA
sequence
An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
PMID:=12409455
http://purl.org/obo/owl/PMID#PMID_=12409455
small nuclear RNA U4atac
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
snRNA U4atac
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
U4atac small nuclear RNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
U4atac snRNA
U5_snRNA
sequence
snRNA U5
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
URL:http://en.wikipedia.org/wiki/U5_snRNA
http://en.wikipedia.org/wiki/U5_snRNA
U5 small nuclear RNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
U5 snRNA
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020
small nuclear RNA U5
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
U6_snRNA
sequence
small nuclear RNA U6
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
URL:http://en.wikipedia.org/wiki/U6_snRNA
http://en.wikipedia.org/wiki/U6_snRNA
U6 small nuclear RNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
snRNA U6
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015
U6 snRNA
U6atac_snRNA
sequence
U6atac snRNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
U6atac small nuclear RNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
snRNA U6atac
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract
U11_snRNA
sequence
URL:http://en.wikipedia.org/wiki/U11_snRNA
http://en.wikipedia.org/wiki/U11_snRNA
small nuclear RNA U11
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
snRNA U11
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
U11 small nuclear RNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
PMID:9622129
http://purl.org/obo/owl/PMID#PMID_9622129
U11 snRNA
U12_snRNA
sequence
U12 snRNA
URL:http://en.wikipedia.org/wiki/U12_snRNA
http://en.wikipedia.org/wiki/U12_snRNA
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007
U12 small nuclear RNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
snRNA U12
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
small nuclear RNA U12
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
sequence_attribute
sequence
sequence attribute
An attribute describes a quality of sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene_attribute
sequence
gene attribute
enhancer_attribute
sequence
U14_snoRNA
An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
SO:0005839
sequence
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.
PMID:2551119
http://purl.org/obo/owl/PMID#PMID_2551119
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016
U14 snoRNA
U14 small nucleolar RNA
snoRNA U14
small nucleolar RNA U14
vault_RNA
sequence
vault RNA
A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006
URL:http://en.wikipedia.org/wiki/Vault_RNA
http://en.wikipedia.org/wiki/Vault_RNA
Y_RNA
sequence
Y RNA
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019
URL:http://en.wikipedia.org/wiki/Y_RNA
http://en.wikipedia.org/wiki/Y_RNA
twintron
sequence
URL:http://en.wikipedia.org/wiki/Twintron
http://en.wikipedia.org/wiki/Twintron
An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
PMID:7823908
http://purl.org/obo/owl/PMID#PMID_7823908
PMID:1899376
http://purl.org/obo/owl/PMID#PMID_1899376
rRNA_18S
sequence
A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/18S_ribosomal_RNA
http://en.wikipedia.org/wiki/18S_ribosomal_RNA
18S ribosomal RNA
18S rRNA
rRNA 18S
site
sequence
The interbase position where something (eg an aberration) occurred.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
binding_site
See GO:0005488 : binding.
sequence
BS:00033
URL:http://en.wikipedia.org/wiki/Binding_site
http://en.wikipedia.org/wiki/Binding_site
A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:ke
http://purl.org/obo/owl/SO#SO_ke
binding_or_interaction_site
site
protein_binding_site
See GO:0042277 : peptide binding.
sequence
A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
protein binding site
rescue_region
sequence
rescue region
A region that rescues.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
rescue fragment
rescue segment
restriction_fragment
sequence
A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
restriction fragment
URL:http://en.wikipedia.org/wiki/Restriction_fragment
http://en.wikipedia.org/wiki/Restriction_fragment
sequence_difference
sequence
sequence difference
A region where the sequence differs from that of a specified sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
invalidated_by_genomic_contamination
sequence
An attribute to describe a feature that is invalidated due to genomic contamination.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
invalidated by genomic contamination
invalidated_by_genomic_polyA_primed_cDNA
sequence
invalidated by genomic polyA primed cDNA
An attribute to describe a feature that is invalidated due to polyA priming.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
invalidated_by_partial_processing
sequence
invalidated by partial processing
An attribute to describe a feature that is invalidated due to partial processing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide_domain
Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
SO:0001069
BS:00012
BS:00134
sequence
domain
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
np_bind
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
DNA_bind
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
ca_bind
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
zn_fing
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
structural domain
polypeptide domain
polypeptide_structural_domain
signal_peptide
Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
BS:00159
sequence
URL:http://en.wikipedia.org/wiki/Signal_peptide
http://en.wikipedia.org/wiki/Signal_peptide
signal
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
signal peptide coding sequence
signal peptide
The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
mature_protein_region
This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
sequence
BS:00149
The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
SO:cb
http://purl.org/obo/owl/SO#SO_cb
mature peptide
mature protein region
chain
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
five_prime_terminal_inverted_repeat
sequence
5' TIR
five prime terminal inverted repeat
three_prime_terminal_inverted_repeat
sequence
3' TIR
three prime terminal inverted repeat
U5_LTR_region
sequence
U5 LTR region
U5 long terminal repeat region
R_LTR_region
sequence
R long terminal repeat region
R LTR region
U3_LTR_region
sequence
U3 long terminal repeat region
U3 LTR region
five_prime_LTR
sequence
five prime LTR
5' LTR
5' long terminal repeat
three_prime_LTR
sequence
3' long terminal repeat
three prime LTR
3' LTR
R_five_prime_LTR_region
sequence
R 5' long term repeat region
R five prime LTR region
U5_five_prime_LTR_region
sequence
U5 5' long terminal repeat region
U5 five prime LTR region
U3_five_prime_LTR_region
sequence
U3 five prime LTR region
U3 5' long term repeat region
R_three_prime_LTR_region
sequence
R three prime LTR region
R 3' long terminal repeat region
U3_three_prime_LTR_region
sequence
U3 three prime LTR region
U3 3' long terminal repeat region
U5_three_prime_LTR_region
sequence
U5 3' long terminal repeat region
U5 three prime LTR region
non_LTR_retrotransposon_polymeric_tract
sequence
non LTR retrotransposon polymeric tract
A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
target_site_duplication
sequence
target site duplication
A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.
URL:http://www.koko.gov.my/CocoaBioTech/Glossaryt.html
http://www.koko.gov.my/CocoaBioTech/Glossaryt.html
RR_tract
sequence
A polypurine tract within an LTR_retrotransposon.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RR tract
LTR retrotransposon poly purine tract
ARS
sequence
autonomously replicating sequence
A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
assortment_derived_duplication
sequence
gene_not_polyadenylated
sequence
inverted_ring_chromosome
sequence
inverted ring chromosome
vector_replicon
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
vector replicon
A replicon that has been modified to act as a vector for foreign sequence.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
vector
URL:http://en.wikipedia.org/wiki/Vector_(molecular_biology)
http://en.wikipedia.org/wiki/Vector_(molecular_biology)
ss_oligo
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
ss oligo
single stranded oligonucleotide
single strand oligonucleotide
single strand oligo
A single stranded oligonucleotide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ss oligonucleotide
ds_oligo
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
double stranded oligonucleotide
ds oligo
ds-oligonucleotide
A double stranded oligonucleotide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polymer_attribute
sequence
polymer attribute
An attribute to describe the kind of biological sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
three_prime_noncoding_exon
sequence
Non-coding exon in the 3' UTR.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
three prime noncoding exon
five_prime_noncoding_exon
sequence
five prime noncoding exon
5' nc exon
5' non coding exon
Non-coding exon in the 5' UTR.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
UTR_intron
sequence
Intron located in the untranslated region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
UTR intron
five_prime_UTR_intron
sequence
five prime UTR intron
An intron located in the 5' UTR.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
three_prime_UTR_intron
sequence
three prime UTR intron
An intron located in the 3' UTR.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
random_sequence
sequence
random sequence
A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
interband
sequence
chromosome interband
A light region between two darkly staining bands in a polytene chromosome.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
gene_with_polyadenylated_mRNA
sequence
A gene that encodes a polyadenylated mRNA.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene with polyadenylated mRNA
transgene_attribute
sequence
chromosomal_transposition
sequence
transposition
chromosomal transposition
A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
rasiRNA
sequence
repeat associated small interfering RNA
URL:http://en.wikipedia.org/wiki/RasiRNA
http://en.wikipedia.org/wiki/RasiRNA
A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
URL:http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284
http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284
gene_with_mRNA_with_frameshift
sequence
A gene that encodes an mRNA with a frameshift.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene with mRNA with frameshift
recombinationally_rearranged_gene
sequence
recombinationally rearranged gene
A gene that is recombinationally rearranged.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
interchromosomal_duplication
sequence
interchromosomal duplication
A chromosome duplication involving an insertion from another chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
D_gene_segment
sequence
Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D gene
D-GENE
gene_with_trans_spliced_transcript
sequence
A gene with a transcript that is trans-spliced.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene with trans spliced transcript
vertebrate_immunoglobulin_T_cell_receptor_segment
I am using the term segment instead of gene here to avoid confusion with the region 'gene'.
sequence
vertebrate immunoglobulin T cell receptor segment
vertebrate_immunoglobulin/T-cell receptor gene
inversion_derived_bipartite_deficiency
sequence
A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.
FB:km
http://purl.org/obo/owl/FB#FB_km
inversion derived bipartite deficiency
pseudogenic_region
sequence
A non-functional descendent of a functional entity.
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
pseudogenic region
encodes_alternately_spliced_transcripts
sequence
encodes alternately spliced transcripts
A gene that encodes more than one transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
decayed_exon
sequence
decayed exon
A non-functional descendant of an exon.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inversion_derived_deficiency_plus_duplication
sequence
inversion derived deficiency plus duplication
A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.
FB:km
http://purl.org/obo/owl/FB#FB_km
V_gene_segment
sequence
V gene
variable_gene
V-GENE
Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
post_translationally_regulated_by_protein_stability
sequence
post-translationally regulated by protein stability
post translationally regulated by protein stability
An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
golden_path_fragment
sequence
golden path fragment
One of the pieces of sequence that make up a golden path.
SO:rd
http://purl.org/obo/owl/SO#SO_rd
post_translationally_regulated_by_protein_modification
sequence
post-translationally regulated by protein modification
post translationally regulated by protein modification
An attribute describing a gene sequence where the resulting protein is modified to regulate it.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
J_gene_segment
sequence
J gene
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
J-GENE
autoregulated
sequence
The gene product is involved in its own transcriptional regulation.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tiling_path
sequence
tiling path
A set of regions which overlap with minimal polymorphism to form a linear sequence.
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
negatively_autoregulated
sequence
negatively autoregulated
The gene product is involved in its own transcriptional regulation where it decreases transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tiling_path_fragment
sequence
A piece of sequence that makes up a tiling_path (SO:0000472).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tiling path fragment
positively_autoregulated
sequence
positively autoregulated
The gene product is involved in its own transcriptional regulation, where it increases transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
contig_read
sequence
A DNA sequencer read which is part of a contig.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
contig read
polycistronic_gene
sequence
A gene that is polycistronic.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
C_gene_segment
sequence
constant gene
C_GENE
C gene
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).
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
trans_spliced_transcript
sequence
trans-spliced transcript
trans spliced transcript
A transcript that is trans-spliced.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
tiling_path_clone
sequence
tiling path clone
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.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
terminal_inverted_repeat
sequence
TIR
terminal inverted repeat
An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
sequence
vertebrate_immunoglobulin/T-cell receptor gene cluster
vertebrate immunoglobulin T cell receptor gene cluster
nc_primary_transcript
sequence
A primary transcript that is never translated into a protein.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nc primary transcript
noncoding primary transcript
three_prime_coding_exon_noncoding_region
sequence
three prime coding exon noncoding region
three_prime_exon_noncoding_region
The sequence of the 3' exon that is not coding.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
DJ_J_cluster
sequence
(DJ)-J-CLUSTER
DJ J cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
five_prime_coding_exon_noncoding_region
sequence
five prime coding exon noncoding region
five_prime_exon_noncoding_region
The sequence of the 5' exon preceding the start codon.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
VDJ_J_C_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VDJ J C cluster
(VDJ)-J-C-CLUSTER
VDJ_J_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
(VDJ)-J-CLUSTER
VDJ J cluster
VJ_C_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VJ C cluster
(VJ)-C-CLUSTER
VJ_J_C_cluster
sequence
VJ J C cluster
(VJ)-J-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VJ_J_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
(VJ)-J-CLUSTER
VJ J cluster
D_gene_recombination_feature
sequence
D gene recombination feature
three_prime_D_heptamer
sequence
7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
3'D-HEPTAMER
three prime D heptamer
three_prime_D_nonamer
sequence
three prime D nonamer
3'D-NOMAMER
A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
three_prime_D_spacer
sequence
3'D-SPACER
three prime D spacer
A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
five_prime_D_heptamer
sequence
7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
five prime D heptamer
5'D-HEPTAMER
five_prime_D_nonamer
sequence
5'D-NONAMER
five prime D nonamer
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
five_prime_D_spacer
sequence
five prime D spacer
5'-SPACER
five prime D-spacer
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
virtual_sequence
sequence
A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
virtual sequence
Hoogsteen_base_pair
sequence
A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds.
PMID:12177293
http://purl.org/obo/owl/PMID#PMID_12177293
Hoogsteen base pair
URL:http://en.wikipedia.org/wiki/Hoogsteen_base_pair
http://en.wikipedia.org/wiki/Hoogsteen_base_pair
reverse_Hoogsteen_base_pair
sequence
reverse Hoogsteen base pair
A type of non-canonical base-pairing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcribed_region
This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
sequence
A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
alternately_spliced_gene_encodeing_one_transcript
sequence
D_DJ_C_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D DJ C cluster
D-(DJ)-C-CLUSTER
D_DJ_cluster
sequence
D DJ cluster
D-(DJ)-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D_DJ_J_C_cluster
sequence
D DJ J C cluster
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D-(DJ)-J-C-CLUSTER
pseudogenic_exon
This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
sequence
A non functional descendant of an exon, part of a pseudogene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
pseudogenic exon
D_DJ_J_cluster
sequence
D DJ J cluster
D-(DJ)-J-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D_J_C_cluster
sequence
D-J-C-CLUSTER
D J C cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VD_gene_segment
sequence
V_D_GENE
VD gene
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).
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
J_C_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
J C cluster
J-C-CLUSTER
inversion_derived_deficiency_plus_aneuploid
sequence
A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion.
FB:km
http://purl.org/obo/owl/FB#FB_km
inversion derived deficiency plus aneuploid
J_cluster
sequence
J cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
J-CLUSTER
J_nonamer
sequence
J nonamer
9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
J-NONAMER
J_heptamer
sequence
J-HEPTAMER
7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
J heptamer
pseudogenic_transcript
This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
sequence
A non functional descendant of a transcript, part of a pseudogene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
pseudogenic transcript
J_spacer
sequence
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
J spacer
J-SPACER
V_DJ_cluster
sequence
V-(DJ)-CLUSTER
V DJ cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_DJ_J_cluster
sequence
V DJ J cluster
V-(DJ)-J-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_VDJ_C_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-(VDJ)-C-CLUSTER
V VDJ C cluster
V_VDJ_cluster
sequence
V VDJ cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-(VDJ)-CLUSTER
V_VDJ_J_cluster
sequence
V VDJ J cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-(VDJ)-J-CLUSTER
V_VJ_C_cluster
sequence
V VJ C cluster
V-(VJ)-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_VJ_cluster
sequence
V VJ cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-(VJ)-CLUSTER
V_VJ_J_cluster
sequence
V VJ J cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-(VJ)-J-CLUSTER
V_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V cluster
V-CLUSTER
V_D_DJ_C_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-D-(DJ)-C-CLUSTER
V D DJ C cluster
V_D_DJ_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-D-(DJ)-CLUSTER
V D DJ cluster
V_D_DJ_J_C_cluster
sequence
V D DJ J C cluster
V-D-(DJ)-J-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_D_DJ_J_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-D-(DJ)-J-CLUSTER
V D DJ J cluster
V_D_J_C_cluster
sequence
V D J C cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-D-J-C-CLUSTER
V_D_J_cluster
sequence
V D J cluster
V-D-J-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_heptamer
sequence
7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-HEPTAMER
V heptamer
V_J_cluster
sequence
V-J-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V J cluster
V_J_C_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V J C cluster
V-J-C-CLUSTER
V_nonamer
sequence
9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-NONAMER
V nonamer
V_spacer
sequence
V spacer
V-SPACER
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_gene_recombination_feature
sequence
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V-RS
V gene recombination feature
DJ_C_cluster
sequence
DJ C cluster
(DJ)-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
DJ_J_C_cluster
sequence
(DJ)-J-C-CLUSTER
DJ J C cluster
Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VDJ_C_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VDJ C cluster
(VDJ)-C-CLUSTER
V_DJ_C_cluster
sequence
V-(DJ)-C-CLUSTER
V DJ C cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
alternately_spliced_gene_encoding_greater_than_one_transcript
sequence
helitron
sequence
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.
URL:http://www.pnas.org/cgi/content/full/100/11/6569
http://www.pnas.org/cgi/content/full/100/11/6569
URL:http://en.wikipedia.org/wiki/Helitron
http://en.wikipedia.org/wiki/Helitron
ISCR
recoding_pseudoknot
sequence
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.
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937
recoding pseudoknot
designed_sequence
sequence
designed sequence
inversion_derived_bipartite_duplication
sequence
inversion derived bipartite duplication
A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion.
FB:km
http://purl.org/obo/owl/FB#FB_km
gene_with_edited_transcript
sequence
gene with edited transcript
A gene that encodes a transcript that is edited.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
inversion_derived_duplication_plus_aneuploid
sequence
inversion derived duplication plus aneuploid
A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion.
FB:km
http://purl.org/obo/owl/FB#FB_km
aneuploid_chromosome
Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila.
sequence
aneuploid chromosome
A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polyA_signal_sequence
sequence
polyA signal sequence
polyadenylation termination signal
poly(A) signal
The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
Shine_Dalgarno_sequence
Not found in Eukaryotic sequence.
sequence
A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
SO:jh
http://purl.org/obo/owl/SO#SO_jh
five prime ribosome binding site
URL:http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence
http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence
RBS
Shine Dalgarno sequence
Shine-Dalgarno sequence
polyA_site
sequence
SO:0001430
The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
polyadenylation site
polyA cleavage site
polyA junction
polyA site
polyA_junction
assortment_derived_deficiency_plus_duplication
sequence
five_prime_clip
sequence
5' clip
five prime clip
5' most region of a precursor transcript that is clipped off during processing.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
five_prime_D_recombination_signal_sequence
sequence
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
5'RS
five prime D-recombination signal sequence
five prime D recombination signal sequence
three_prime_clip
sequence
three prime clip
3'-clip
3'-most region of a precursor transcript that is clipped off during processing.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
C_cluster
sequence
C-CLUSTER
C cluster
Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D_cluster
sequence
D-CLUSTER
D cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D_J_cluster
sequence
D-J-CLUSTER
D J cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
sequence
HEPTAMER
heptamer of recombination feature of vertebrate immune system gene
Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
sequence
nonamer of recombination feature of vertebrate immune system gene
vertebrate_immune_system_gene_recombination_spacer
sequence
vertebrate immune system gene recombination spacer
V_DJ_J_C_cluster
sequence
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V DJ J C cluster
V-(DJ)-J-C-CLUSTER
V_VDJ_J_C_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V VDJ J C cluster
V-(VDJ)-J-C-CLUSTER
V_VJ_J_C_cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V VJ J C cluster
V-(VJ)-J-C-CLUSTER
inversion_derived_aneuploid_chromosome
sequence
A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion.
FB:km
http://purl.org/obo/owl/FB#FB_km
inversion derived aneuploid chromosome
bidirectional_promoter
sequence
bidirectional promoter
retrotransposed
GO:0003964 RNA-directed DNA polymerase activity.
sequence
SO:0100042
An attribute of a feature that occurred as the product of a reverse transcriptase mediated event.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Retrotransposed
http://en.wikipedia.org/wiki/Retrotransposed
three_prime_D_recombination_signal_sequence
sequence
3'D-RS
three_prime_D-recombination_signal_sequence
three prime D recombination signal sequence
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
miRNA_encoding
sequence
miRNA encoding
DJ_gene_segment
sequence
D-J-GENE
DJ gene
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.
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
rRNA_encoding
sequence
rRNA encoding
VDJ_gene_segment
sequence
V-D-J-GENE
VDJ gene
Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
scRNA_encoding
sequence
scRNA encoding
VJ_gene_segment
sequence
Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VJ gene
V-J-GENE
centromere
sequence
URL:http://en.wikipedia.org/wiki/Centromere
http://en.wikipedia.org/wiki/Centromere
A region of chromosome where the spindle fibers attach during mitosis and meiosis.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
snoRNA_encoding
sequence
snoRNA encoding
edited_transcript_feature
sequence
edited transcript feature
A locatable feature on a transcript that is edited.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
methylation_guide_snoRNA_primary_transcript
sequence
A primary transcript encoding a methylation guide small nucleolar RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
methylation guide snoRNA primary transcript
cap
sequence
URL:http://en.wikipedia.org/wiki/5%27_cap
http://en.wikipedia.org/wiki/5%27_cap
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.
URL:http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html
http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html
rRNA_cleavage_snoRNA_primary_transcript
sequence
A primary transcript encoding an rRNA cleavage snoRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
rRNA cleavage snoRNA primary transcript
pre_edited_region
sequence
The region of a transcript that will be edited.
URL:http://dna.kdna.ucla.edu/rna/index.aspx
http://dna.kdna.ucla.edu/rna/index.aspx
pre-edited region
pre edited region
tmRNA
sequence
A 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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023
ssrA
10Sa RNA
URL:http://en.wikipedia.org/wiki/TmRNA
http://en.wikipedia.org/wiki/TmRNA
C_D_box_snoRNA_encoding
sequence
C/D box snoRNA encoding
tmRNA_primary_transcript
sequence
tmRNA primary transcript
A primary transcript encoding a tmRNA (SO:0000584).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
10Sa RNA primary transcript
ssrA RNA primary transcript
group_I_intron
GO:0000372.
sequence
group I intron
URL:http://en.wikipedia.org/wiki/Group_I_intron
http://en.wikipedia.org/wiki/Group_I_intron
Group I catalytic introns are large self-splicing ribozymes. They catalyze 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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028
autocatalytically_spliced_intron
sequence
autocatalytically spliced intron
A self spliced intron.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
SRP_RNA_primary_transcript
sequence
SRP RNA primary transcript
A primary transcript encoding a signal recognition particle RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
SRP_RNA
sequence
signal recognition particle RNA
7S RNA
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017
SRP RNA
pseudoknot
sequence
URL:http://en.wikipedia.org/wiki/Pseudoknot
http://en.wikipedia.org/wiki/Pseudoknot
A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
H_pseudoknot
sequence
hairpin-type pseudoknot
A pseudoknot which contains two stems and at least two loops.
URL:http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract
H pseudoknot
classical pseudoknot
H-type pseudoknot
H-pseudoknot
C_D_box_snoRNA
sequence
box C/D snoRNA
C/D box snoRNA
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'.
URL:http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
C D box snoRNA
H_ACA_box_snoRNA
sequence
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.
URL:http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
box H/ACA snoRNA
H ACA box snoRNA
H/ACA box snoRNA
C_D_box_snoRNA_primary_transcript
sequence
A primary transcript encoding a small nucleolar RNA of the box C/D family.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
C/D box snoRNA primary transcript
H_ACA_box_snoRNA_primary_transcript
sequence
H ACA box snoRNA primary transcript
A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript_edited_by_U_insertion/deletion
sequence
The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
URL:http://www.rna.ucla.edu/index.html
http://www.rna.ucla.edu/index.html
edited_by_C_insertion_and_dinucleotide_insertion
sequence
transcript_edited_by_C-insertion_and_dinucleotide_insertion
edited_by_C_to_U_substitution
sequence
edited_by_A_to_I_substitution
sequence
edited_by_G_addition
sequence
guide_RNA
sequence
URL:http://en.wikipedia.org/wiki/Guide_RNA
http://en.wikipedia.org/wiki/Guide_RNA
guide RNA
gRNA
A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
URL:http://www.rna.ucla.edu/index.html
http://www.rna.ucla.edu/index.html
group_II_intron
GO:0000373.
sequence
URL:http://en.wikipedia.org/wiki/Group_II_intron
http://en.wikipedia.org/wiki/Group_II_intron
group II intron
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.
URL:http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml
http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml
editing_block
sequence
editing block
Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
URL:http://dna.kdna.ucla.edu/rna/index.aspx
http://dna.kdna.ucla.edu/rna/index.aspx
intergenic_region
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
intergenic region
URL:http://en.wikipedia.org/wiki/Intergenic_region
http://en.wikipedia.org/wiki/Intergenic_region
A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
editing_domain
sequence
Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
URL:http://dna.kdna.ucla.edu/rna/index.aspx
http://dna.kdna.ucla.edu/rna/index.aspx
editing domain
unedited_region
sequence
The region of an edited transcript that will not be edited.
URL:http://dna.kdna.ucla.edu/rna/index.aspx
http://dna.kdna.ucla.edu/rna/index.aspx
unedited region
H_ACA_box_snoRNA_encoding
sequence
H ACA box snoRNA encoding
oligo_U_tail
sequence
oligo U tail
The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).
URL:http://www.rna.ucla.edu/
http://www.rna.ucla.edu/
polyA_sequence
sequence
polyA sequence
Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
branch_site
sequence
A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
branch point
branch site
branch_point
polypyrimidine_tract
sequence
URL:http://en.wikipedia.org/wiki/Polypyrimidine_tract
http://en.wikipedia.org/wiki/Polypyrimidine_tract
polypyrimidine tract
The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
URL:http://nar.oupjournals.org/cgi/content/full/25/4/888
http://nar.oupjournals.org/cgi/content/full/25/4/888
bacterial_RNApol_promoter
sequence
A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
bacterial RNApol promoter
bacterial_terminator
sequence
A terminator signal for bacterial transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
bacterial terminator
terminator_of_type_2_RNApol_III_promoter
sequence
A terminator signal for RNA polymerase III transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
terminator of type 2 RNApol III promoter
transcription_end_site
sequence
The base where transcription ends.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcription end site
RNApol_III_promoter_type_1
sequence
RNApol III promoter type 1
RNApol_III_promoter_type_2
sequence
RNApol III promoter type 2
tRNA promoter
A_box
Binds TFIIIC.
sequence
A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
A-box
URL:http://en.wikipedia.org/wiki/A-box
http://en.wikipedia.org/wiki/A-box
B_box
Binds TFIIIC.
sequence
A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
B-box
RNApol_III_promoter_type_3
sequence
RNApol III promoter type 3
C_box
sequence
C-box
An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
snRNA_encoding
sequence
snRNA encoding
telomere
sequence
A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
telomeric DNA
URL:http://en.wikipedia.org/wiki/Telomere
http://en.wikipedia.org/wiki/Telomere
telomeric sequence
silencer
sequence
URL:http://en.wikipedia.org/wiki/Silencer_(DNA)
http://en.wikipedia.org/wiki/Silencer_(DNA)
A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
chromosomal_regulatory_element
sequence
chromosomal regulatory element
insulator
sequence
URL:http://en.wikipedia.org/wiki/Insulator_(genetics)
http://en.wikipedia.org/wiki/Insulator_(genetics)
A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
SO:regcreative
http://purl.org/obo/owl/SO#SO_regcreative
insulator element
chromosomal_structural_element
sequence
chromosomal structural element
five_prime_open_reading_frame
sequence
five prime open reading frame
upstream_AUG_codon
sequence
A start codon upstream of the ORF.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
upstream AUG codon
polycistronic_primary_transcript
sequence
A primary transcript encoding for more than one gene product.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polycistronic primary transcript
monocistronic_primary_transcript
sequence
monocistronic primary transcript
A primary transcript encoding for one gene product.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
monocistronic_mRNA
sequence
URL:http://en.wikipedia.org/wiki/Monocistronic_mRNA
http://en.wikipedia.org/wiki/Monocistronic_mRNA
An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
SO:rd
http://purl.org/obo/owl/SO#SO_rd
monocistronic processed transcript
monocistronic mRNA
polycistronic_mRNA
sequence
polycistronic processed transcript
polycistronic mRNA
URL:http://en.wikipedia.org/wiki/Polycistronic_mRNA
http://en.wikipedia.org/wiki/Polycistronic_mRNA
An mRNA that encodes multiple proteins from at least two non-overlapping regions.
SO:rd
http://purl.org/obo/owl/SO#SO_rd
mini_exon_donor_RNA
sequence
A primary transcript that donates the spliced leader to other mRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mini exon donor RNA
mini-exon donor RNA
spliced_leader_RNA
sequence
spliced leader RNA
mini-exon
engineered_plasmid
sequence
A plasmid that is engineered.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered plasmid gene
engineered plasmid
transcribed_spacer_region
sequence
transcribed spacer region
Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
URL:http://oregonstate.edu/instruction/bb492/general/glossary.html
http://oregonstate.edu/instruction/bb492/general/glossary.html
internal_transcribed_spacer_region
sequence
Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
internal transcribed spacer region
external_transcribed_spacer_region
sequence
external transcribed spacer region
Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tetranucleotide_repeat_microsatellite_feature
sequence
tetranucleotide repeat microsatellite feature
SRP_RNA_encoding
sequence
SRP RNA encoding
minisatellite
sequence
A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
URL:http://www.informatics.jax.org/silver/glossary.shtml
http://www.informatics.jax.org/silver/glossary.shtml
URL:http://en.wikipedia.org/wiki/Minisatellite
http://en.wikipedia.org/wiki/Minisatellite
antisense_RNA
sequence
URL:http://en.wikipedia.org/wiki/Antisense_RNA
http://en.wikipedia.org/wiki/Antisense_RNA
antisense RNA
Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
antisense_primary_transcript
sequence
antisense primary transcript
The reverse complement of the primary transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
siRNA
sequence
URL:http://en.wikipedia.org/wiki/SiRNA
http://en.wikipedia.org/wiki/SiRNA
small interfering RNA
A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.
PMID:12592000
http://purl.org/obo/owl/PMID#PMID_12592000
miRNA_primary_transcript
sequence
A primary transcript encoding a micro RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
miRNA primary transcript
micro RNA primary transcript
stRNA_primary_transcript
sequence
A primary transcript encoding a small temporal mRNA (SO:0000649).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
small temporal RNA primary transcript
stRNA primary transcript
stRNA
sequence
Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans.
PMID:11081512
http://purl.org/obo/owl/PMID#PMID_11081512
small temporal RNA
URL:http://en.wikipedia.org/wiki/StRNA
http://en.wikipedia.org/wiki/StRNA
small_subunit_rRNA
sequence
small subunit rRNA
Ribosomal RNA transcript that structures the small subunit of the ribosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
SSU RNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
SSU rRNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
large_subunit_rRNA
sequence
large subunit rRNA
LSU RNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
Ribosomal RNA transcript that structures the large subunit of the ribosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
LSU rRNA
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
rRNA_5S
sequence
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 stabilizes 5S rRNA until it is required for transcription.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001
URL:http://en.wikipedia.org/wiki/5S_ribosomal_RNA
http://en.wikipedia.org/wiki/5S_ribosomal_RNA
5S ribosomal RNA
5S LSU rRNA
rRNA 5S
5S rRNA
rRNA_28S
sequence
28S LSU rRNA
rRNA 28S
URL:http://en.wikipedia.org/wiki/28S_ribosomal_RNA
http://en.wikipedia.org/wiki/28S_ribosomal_RNA
28S ribosomal RNA
28S rRNA
A component of the large ribosomal subunit.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
maxicircle_gene
sequence
maxicircle gene
maxi-circle gene
A mitochondrial gene located in a maxicircle.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
ncRNA
A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
sequence
noncoding RNA
An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/NcRNA
http://en.wikipedia.org/wiki/NcRNA
stRNA_encoding
sequence
stRNA encoding
repeat_region
sequence
A region of sequence containing one or more repeat units.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
repeat region
dispersed_repeat
sequence
A repeat that is located at dispersed sites in the genome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Interspersed_repeat
http://en.wikipedia.org/wiki/Interspersed_repeat
dispersed repeat
interspersed repeat
tmRNA_encoding
sequence
tmRNA encoding
DNA_invertase_target_sequence
sequence
intron_attribute
sequence
spliceosomal_intron
GO:0000398.
sequence
spliceosomal intron
An intron which is spliced by the spliceosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tRNA_encoding
sequence
tRNA encoding
introgressed_chromosome_region
sequence
introgressed chromosome region
monocistronic_transcript
sequence
A transcript that is monocistronic.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
monocistronic transcript
mobile_intron
sequence
An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mobile intron
insertion
sequence
SO:1000034
loinc:LA6687-3
http://purl.org/obo/owl/loinc#loinc_LA6687-3
nucleotide insertion
nucleotide_insertion
The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insertion
URL:http://www.ncbi.nlm.nih.gov/dbvar/
http://www.ncbi.nlm.nih.gov/dbvar/
EST_match
sequence
A match against an EST sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
EST match
sequence_rearrangement_feature
sequence
sequence rearrangement feature
chromosome_breakage_sequence
sequence
A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
chromosome breakage sequence
internal_eliminated_sequence
sequence
internal eliminated sequence
A sequence eliminated from the genome of ciliates during nuclear differentiation.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
macronucleus_destined_segment
sequence
A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
macronucleus destined segment
transcript
sequence
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/RNA
http://en.wikipedia.org/wiki/RNA
non_canonical_splice_site
sequence
A splice site where the donor and acceptor sites differ from the canonical form.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
non-canonical splice site
non canonical splice site
canonical_splice_site
sequence
The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
canonical splice site
canonical_three_prime_splice_site
sequence
canonical three prime splice site
canonical 3' splice site
The canonical 3' splice site has the sequence "AG".
SO:ke
http://purl.org/obo/owl/SO#SO_ke
canonical_five_prime_splice_site
sequence
The canonical 5' splice site has the sequence "GT".
SO:ke
http://purl.org/obo/owl/SO#SO_ke
canonical 5' splice site
canonical five prime splice site
non_canonical_three_prime_splice_site
sequence
non canonical 3' splice site
A 3' splice site that does not have the sequence "AG".
SO:ke
http://purl.org/obo/owl/SO#SO_ke
non canonical three prime splice site
non-canonical three prime splice site
non_canonical_five_prime_splice_site
sequence
non-canonical five prime splice site
non canonical five prime splice site
non canonical 5' splice site
A 5' splice site which does not have the sequence "GT".
SO:ke
http://purl.org/obo/owl/SO#SO_ke
non_canonical_start_codon
sequence
A start codon that is not the usual AUG sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
non ATG start codon
non-canonical start codon
non canonical start codon
aberrant_processed_transcript
sequence
A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
aberrant processed transcript
splicing_feature
sequence
exonic_splice_enhancer
sequence
Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.
URL:http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract
exonic splice enhancer
nuclease_sensitive_site
sequence
A region of nucleotide sequence targeted by a nuclease enzyme.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
nuclease sensitive site
DNAseI_hypersensitive_site
sequence
DHS
DNAseI hypersensitive site
translocation_element
sequence
A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
translocation element
deletion_junction
sequence
deletion junction
The space between two bases in a sequence which marks the position where a deletion has occurred.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
golden_path
sequence
golden path
A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
SO:ls
http://purl.org/obo/owl/SO#SO_ls
cDNA_match
sequence
A match against cDNA sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cDNA match
gene_with_polycistronic_transcript
sequence
A gene that encodes a polycistronic transcript.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene with polycistronic transcript
cleaved_initiator_methionine
BS:00067
sequence
The initiator methionine that has been cleaved from a mature polypeptide sequence.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
initiator methionine
init_met
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
cleaved initiator methionine
gene_with_dicistronic_transcript
sequence
A gene that encodes a dicistronic transcript.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene with dicistronic transcript
gene_with_recoded_mRNA
sequence
gene with recoded mRNA
A gene that encodes an mRNA that is recoded.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
SNP
sequence
single nucleotide polymorphism
SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
reagent
Requested by Lynn Crosby, jan 2006.
sequence
A sequence used in experiment.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
oligo
sequence
oligonucleotide
A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/Oligonucleotide
http://en.wikipedia.org/wiki/Oligonucleotide
gene_with_stop_codon_read_through
sequence
A gene that encodes a transcript with stop codon readthrough.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene with stop codon read through
gene_with_stop_codon_redefined_as_pyrrolysine
sequence
gene with stop codon redefined as pyrrolysine
A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
junction
A junction is a boundary between regions. A boundary has an extent of zero.
sequence
A sequence_feature with an extent of zero.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
boundary
breakpoint
remark
sequence
A comment about the sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
possible_base_call_error
sequence
possible base call error
A region of sequence where the validity of the base calling is questionable.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
possible_assembly_error
sequence
possible assembly error
A region of sequence where there may have been an error in the assembly.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
experimental_result_region
sequence
A region of sequence implicated in an experimental result.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
experimental result region
gene
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
sequence
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
SO:immuno_workshop
http://purl.org/obo/owl/SO#SO_immuno_workshop
URL:http://en.wikipedia.org/wiki/Gene
http://en.wikipedia.org/wiki/Gene
tandem_repeat
sequence
Two or more adjcent copies of a region (of length greater than 1).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
URL:http://en.wikipedia.org/wiki/Tandem_repeat
http://en.wikipedia.org/wiki/Tandem_repeat
tandem repeat
trans_splice_acceptor_site
This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
sequence
The 3' splice site of the acceptor primary transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
trans splice acceptor site
3' trans splice site
trans_splice_donor_site
SL RNA contains a donor site.
sequence
trans splice donor site
5 prime trans splice site
trans-splice donor site
The 5' five prime splice site region of the donor RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
SL1_acceptor_site
sequence
A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL1 acceptor site
SL2_acceptor_site
sequence
SL2 acceptor site
A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
gene_with_stop_codon_redefined_as_selenocysteine
sequence
A gene encoding an mRNA that has the stop codon redefined as selenocysteine.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene with stop codon redefined as selenocysteine
gene_with_mRNA_recoded_by_translational_bypass
sequence
gene with mRNA recoded by translational bypass
A gene with mRNA recoded by translational bypass.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene_with_transcript_with_translational_frameshift
sequence
A gene encoding a transcript that has a translational frameshift.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene with transcript with translational frameshift
DNA_motif
sequence
URL:http://en.wikipedia.org/wiki/DNA_motif
http://en.wikipedia.org/wiki/DNA_motif
A motif that is active in the DNA form of the sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
DNA motif
nucleotide_motif
sequence
nucleotide motif
A region of nucleotide sequence corresponding to a known motif.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RNA_motif
sequence
RNA motif
A motif that is active in RNA sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
dicistronic_mRNA
sequence
An mRNA that has the quality dicistronic.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
dicistronic mRNA
dicistronic processed transcript
reading_frame
This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
sequence
reading frame
URL:http://en.wikipedia.org/wiki/Reading_frame
http://en.wikipedia.org/wiki/Reading_frame
A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
SGD:rb
http://purl.org/obo/owl/SGD#SGD_rb
blocked_reading_frame
Term requested by Rama from SGD.
sequence
A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons.
SGD:rb
http://purl.org/obo/owl/SGD#SGD_rb
blocked reading frame
ultracontig
sequence
An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
FB:WG
http://purl.org/obo/owl/FB#FB_WG
superscaffold
foreign_transposable_element
requested by Michael on 19 Nov 2004.
sequence
A transposable element that is foreign.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
foreign transposable element
gene_with_dicistronic_primary_transcript
Requested by Michael, 19 nov 2004.
sequence
A gene that encodes a dicistronic primary transcript.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene with dicistronic primary transcript
gene_with_dicistronic_mRNA
Requested by MA nov 19 2004.
sequence
A gene that encodes a polycistronic mRNA.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene with dicistronic processed transcript
gene with dicistronic mRNA
iDNA
sequence
Genomic sequence removed from the genome, as a normal event, by a process of recombination.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/IDNA
http://en.wikipedia.org/wiki/IDNA
intervening DNA
oriT
sequence
origin of transfer
URL:http://en.wikipedia.org/wiki/Origin_of_transfer
http://en.wikipedia.org/wiki/Origin_of_transfer
A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
transit_peptide
Added to bring SO inline with the embl ddbj genbank feature table. Old definition before biosapiens: 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.
sequence
BS:00055
transit
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
signal
transit peptide
The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
repeat_unit
Added to comply with the feature table. A single repeat.
sequence
The simplest repeated component of a repeat region. A single repeat.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
repeat unit
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
CRM
Requested by Stepen Grossmann Dec 2004.
sequence
A regulatory_region where more than 1 TF_binding_site together are regulatorily active.
SO:SG
http://purl.org/obo/owl/SO#SO_SG
cis regulatory module
TF module
intein
Intein-mediated protein splicing occurs after mRNA has been translated into a protein.
sequence
A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Intein
http://en.wikipedia.org/wiki/Intein
protein intron
intein_containing
sequence
intein containing
An attribute of protein-coding genes where the initial protein product contains an intein.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gap
sequence
A gap in the sequence of known length. The unknown bases are filled in with N's.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
fragmentary
Term added because of request by MO people.
sequence
An attribute to describe a feature that is incomplete.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
fragment
predicted
sequence
URL:http://en.wikipedia.org/wiki/Predicted
http://en.wikipedia.org/wiki/Predicted
An attribute describing an unverified region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
feature_attribute
sequence
An attribute describing a located_sequence_feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
feature attribute
exemplar_mRNA
Added for the MO people.
sequence
An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.
URL:http://mged.sourceforge.net/ontologies/MGEDontology.php
http://mged.sourceforge.net/ontologies/MGEDontology.php
exemplar mRNA
sequence_location
sequence
sequence location
organelle_sequence
sequence
organelle sequence
mitochondrial_sequence
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
mitochondrial sequence
nuclear_sequence
sequence
nuclear sequence
nucleomorphic_sequence
sequence
nucleomorphic sequence
plastid_sequence
sequence
plastid sequence
kinetoplast
SO:0000826
sequence
kinetoplast_chromosome
A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species.
PMID:8395055
http://purl.org/obo/owl/PMID#PMID_8395055
URL:http://en.wikipedia.org/wiki/Kinetoplast
http://en.wikipedia.org/wiki/Kinetoplast
maxicircle
SO:0000827
sequence
maxicircle_chromosome
A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.
PMID:8395055
http://purl.org/obo/owl/PMID#PMID_8395055
apicoplast_sequence
sequence
apicoplast sequence
chromoplast_sequence
sequence
chromoplast sequence
chloroplast_sequence
sequence
chloroplast sequence
cyanelle_sequence
sequence
cyanelle sequence
leucoplast_sequence
sequence
leucoplast sequence
proplastid_sequence
sequence
proplastid sequence
plasmid_location
sequence
plasmid location
amplification_origin
sequence
amplification origin
An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
proviral_location
sequence
proviral location
gene_group_regulatory_region
sequence
gene group regulatory region
clone_insert
sequence
clone insert
The region of sequence that has been inserted and is being propagated by the clone.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
lambda_vector
sequence
The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
ISBN:0-1767-2380-8
http://purl.org/obo/owl/ISBN#ISBN_0-1767-2380-8
lambda vector
plasmid_vector
sequence
URL:http://en.wikipedia.org/wiki/Plasmid_vector#Vectors
http://en.wikipedia.org/wiki/Plasmid_vector#Vectors
plasmid vector
cDNA
sequence
complementary DNA
DNA synthesized by reverse transcriptase using RNA as a template.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
URL:http://en.wikipedia.org/wiki/CDNA
http://en.wikipedia.org/wiki/CDNA
single_stranded_cDNA
sequence
single-strand cDNA
single strand cDNA
single stranded cDNA
double_stranded_cDNA
sequence
double stranded cDNA
double-strand cDNA
double strand cDNA
plasmid_clone
sequence
YAC_clone
sequence
phagemid_clone
sequence
PAC_clone
sequence
P1_clone
fosmid_clone
sequence
BAC_clone
sequence
cosmid_clone
sequence
pyrrolysyl_tRNA
sequence
pyrrolysyl-transfer RNA
pyrrolysyl-transfer ribonucleic acid
pyrrolysyl tRNA
A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
clone_insert_start
sequence
episome
sequence
A plasmid that may integrate with a chromosome.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
tmRNA_coding_piece
Added in response to comment from Kelly Williams from Indiana. Nov 2005.
sequence
The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
doi:10.1093/nar/gkh795
http://purl.org/obo/owl/doi#doi_10.1093/nar/gkh795
issn:1362-4962
http://purl.org/obo/owl/issn#issn_1362-4962
Indiana:kw
http://purl.org/obo/owl/Indiana#Indiana_kw
tmRNA coding piece
tmRNA_acceptor_piece
Added in response to Kelly Williams from Indiana. Date: Nov 2005.
sequence
The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
doi:10.1093/nar/gkh795
http://purl.org/obo/owl/doi#doi_10.1093/nar/gkh795
Indiana:kw
http://purl.org/obo/owl/Indiana#Indiana_kw
tmRNA acceptor piece
QTL
Added in respose to request by Simon Twigger November 14th 2005.
sequence
quantitative trait locus
A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
URL:http://rgd.mcw.edu/tu/qtls/
http://rgd.mcw.edu/tu/qtls/
genomic_island
Genomic islands are transmissible elements characterized by large size (>10kb).
sequence
A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
Phigo:at
http://purl.org/obo/owl/Phigo#Phigo_at
genomic island
URL:http://en.wikipedia.org/wiki/Genomic_island
http://en.wikipedia.org/wiki/Genomic_island
pathogenic_island
Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
sequence
pathogenic island
Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
metabolic_island
Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.
sequence
A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
metabolic island
adaptive_island
The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
sequence
adaptive island
An adaptive island is a genomic island that provides an adaptive advantage to the host.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
symbiosis_island
Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149.
sequence
symbiosis island
A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
pseudogenic_rRNA
Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
sequence
A non functional descendent of an rRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
pseudogenic rRNA
pseudogenic_tRNA
Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
sequence
pseudogenic tRNA
A non functional descendent of a tRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
engineered_episome
Requested by Lynn Crosby Jan 2006.
sequence
An episome that is engineered.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered episome
transposable_element_attribute
Added by KE Jan 2006 to capture the kinds of attributes of TEs
sequence
transgenic
sequence
Attribute describing sequence that has been integrated with foreign sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
natural
sequence
An attribute describing a feature that occurs in nature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
engineered
sequence
An attribute to describe a region that was modified in vitro.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
foreign
sequence
An attribute to describe a region from another species.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cloned_region
Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.
sequence
cloned segment
cloned region
reagent_attribute
Added jan 2006 by KE.
sequence
reagent attribute
clone_attribute
sequence
cloned
sequence
validated
sequence
An attribute to describe a feature that has been proven.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
invalidated
sequence
An attribute describing a feature that is invalidated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cloned_genomic
sequence
cloned_cDNA
sequence
engineered_DNA
sequence
engineered_rescue_region
sequence
A rescue region that is engineered.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered rescue region
engineered rescue segment
engineered rescue fragment
rescue_mini_gene
sequence
A mini_gene that rescues.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
rescue mini-gene
rescue mini gene
transgenic_transposable_element
Modified as requested by Lynn - FB. May 2007.
sequence
TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.
FB:mc
http://purl.org/obo/owl/FB#FB_mc
transgenic transposable element
natural_transposable_element
sequence
TE that exists (or existed) in nature.
FB:mc
http://purl.org/obo/owl/FB#FB_mc
natural transposable element
engineered_transposable_element
sequence
engineered transposable element
TE that has been modified by manipulations in vitro.
FB:mc
http://purl.org/obo/owl/FB#FB_mc
engineered_foreign_transposable_element
sequence
A transposable_element that is engineered and foreign.
FB:mc
http://purl.org/obo/owl/FB#FB_mc
engineered foreign transposable element
assortment_derived_duplication
sequence
assortment derived duplication
A multi-chromosome duplication aberration generated by reassortment of other aberration components.
FB:gm
http://purl.org/obo/owl/FB#FB_gm
assortment_derived_deficiency_plus_duplication
sequence
assortment derived deficiency plus duplication
A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.
FB:gm
http://purl.org/obo/owl/FB#FB_gm
assortment_derived_deficiency
sequence
A multi-chromosome deficiency aberration generated by reassortment of other aberration components.
FB:gm
http://purl.org/obo/owl/FB#FB_gm
assortment-derived deficiency
assortment_derived_aneuploid
sequence
A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.
FB:gm
http://purl.org/obo/owl/FB#FB_gm
assortment derived aneuploid
engineered_region
sequence
A region that is engineered.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered region
construct
engineered sequence
engineered_foreign_region
sequence
engineered foreign region
A region that is engineered and foreign.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
fusion
sequence
engineered_tag
sequence
A tag that is engineered.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered tag
validated_cDNA_clone
sequence
A cDNA clone that has been validated.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
validated cDNA clone
invalidated_cDNA_clone
sequence
invalidated cDNA clone
A cDNA clone that is invalid.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
chimeric_cDNA_clone
sequence
chimeric cDNA clone
A cDNA clone invalidated because it is chimeric.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
genomically_contaminated_cDNA_clone
sequence
genomically contaminated cDNA clone
A cDNA clone invalidated by genomic contamination.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
polyA_primed_cDNA_clone
sequence
A cDNA clone invalidated by polyA priming.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
polyA primed cDNA clone
partially_processed_cDNA_clone
sequence
A cDNA invalidated clone by partial processing.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
partially processed cDNA clone
rescue
sequence
An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mini_gene
sequence
mini gene
By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA.
PMID:15992143
http://purl.org/obo/owl/PMID#PMID_15992143
rescue_gene
sequence
rescue gene
A gene that rescues.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
wild_type
sequence
loinc:LA9658-1
http://purl.org/obo/owl/loinc#loinc_LA9658-1
An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Wild_type
http://en.wikipedia.org/wiki/Wild_type
wild type
wild_type_rescue_gene
sequence
A gene that rescues.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
wild type rescue gene
mitochondrial_chromosome
sequence
A chromosome originating in a mitochondria.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
mitochondrial chromosome
chloroplast_chromosome
sequence
chloroplast chromosome
A chromosome originating in a chloroplast.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
chromoplast_chromosome
sequence
chromoplast chromosome
A chromosome originating in a chromoplast.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
cyanelle_chromosome
sequence
A chromosome originating in a cyanelle.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
cyanelle chromosome
leucoplast_chromosome
sequence
leucoplast chromosome
A chromosome with origin in a leucoplast.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
macronuclear_chromosome
sequence
A chromosome originating in a macronucleus.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
macronuclear chromosome
micronuclear_chromosome
sequence
A chromosome originating in a micronucleus.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
micronuclear chromosome
nuclear_chromosome
sequence
A chromosome originating in a nucleus.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
nuclear chromosome
nucleomorphic_chromosome
sequence
A chromosome originating in a nucleomorph.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
nucleomorphic chromosome
chromosome_part
This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
sequence
chromosome part
A region of a chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene_member_region
A manufactured term used to allow the parts of a gene to have an is_a path to the root.
sequence
A region of a gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene member region
promoter_region
This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.
sequence
A region of sequence which is part of a promoter.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript_region
This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
sequence
transcript region
A region of a transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mature_transcript_region
A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
sequence
A region of a mature transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mature transcript region
primary_transcript_region
This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
sequence
primary transcript region
A part of a primary transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mRNA_region
This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
sequence
A region of an mRNA.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
mRNA region
UTR_region
A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
sequence
UTR region
A region of UTR.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
rRNA_primary_transcript_region
To allow transcribed_spacer_region to have a path to the root.
sequence
rRNA primary transcript region
A region of an rRNA primary transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide_region
Added to allow the polypeptide regions to have is_a paths back to the root.
BS:00124
sequence
BS:00331
region or site annotation
positional
site
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
positional polypeptide feature
region
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
SO:GAR
http://purl.org/obo/owl/SO#SO_GAR
repeat_component
A manufactured to group the parts of repeats, to give them an is_a path back to the root.
sequence
repeat component
A region of a repeated sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
spliceosomal_intron_region
A terms added to allow the parts of introns to have is_a paths to the root.
sequence
spliceosomal intron region
A region within an intron.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene_component_region
sequence
gene component region
bacterial_RNApol_promoter_region
This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.
sequence
A region which is part of a bacterial RNA polymerase promoter.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RNApol_II_promoter_region
This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.
sequence
A region of sequence which is a promoter for RNA polymerase II.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RNApol_III_promoter_type_1_region
This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.
sequence
A region of sequence which is a promoter for RNA polymerase III type 1.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RNApol_III_promoter_type_2_region
This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.
sequence
A region of sequence which is a promoter for RNA polymerase III type 2.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tmRNA_region
This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.
sequence
A region of a tmRNA.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
tmRNA region
LTR_component
sequence
long term repeat component
LTR component
three_prime_LTR_component
sequence
three prime LTR component
3' long terminal repeat component
five_prime_LTR_component
sequence
five prime LTR component
5' long term repeat component
CDS_region
sequence
A region of a CDS.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
CDS region
exon_region
sequence
exon region
A region of an exon.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
homologous_region
sequence
URL:http://en.wikipedia.org/wiki/Homology_(biology)
http://en.wikipedia.org/wiki/Homology_(biology)
A region that is homologous to another region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
homologous region
homolog
homologue
paralogous_region
A term to be used in conjunction with the paralogous_to relationship.
sequence
URL:http://en.wikipedia.org/wiki/Paralog#Paralogy
http://en.wikipedia.org/wiki/Paralog#Paralogy
paralogous region
paralogue
paralog
A homologous_region that is paralogous to another region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
orthologous_region
This term should be used in conjunction with the similarity relationships defined in SO.
sequence
ortholog
URL:http://en.wikipedia.org/wiki/Ortholog#Orthology
http://en.wikipedia.org/wiki/Ortholog#Orthology
A homologous_region that is orthologous to another region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
orthologous region
orthologue
conserved
sequence
homologous
sequence
Similarity due to common ancestry.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
orthologous
sequence
An attribute describing a kind of homology where divergence occured after a speciation event.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
paralogous
sequence
An attribute describing a kind of homology where divergence occurred after a duplication event.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
syntenic
sequence
Attribute describing sequence regions occurring in same order on chromosome of different species.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Syntenic
http://en.wikipedia.org/wiki/Syntenic
capped_primary_transcript
sequence
capped primary transcript
A primary transcript that is capped.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
capped_mRNA
sequence
An mRNA that is capped.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
capped mRNA
mRNA_attribute
sequence
An attribute describing an mRNA feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mRNA attribute
exemplar
sequence
An attribute describing a sequence is representative of a class of similar sequences.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
frameshift
sequence
An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Frameshift
http://en.wikipedia.org/wiki/Frameshift
minus_1_frameshift
sequence
A frameshift caused by deleting one base.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
minus 1 frameshift
minus_2_frameshift
sequence
minus 2 frameshift
A frameshift caused by deleting two bases.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
plus_1_frameshift
sequence
plus 1 frameshift
A frameshift caused by inserting one base.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
plus_2_framshift
sequence
plus 2 framshift
A frameshift caused by inserting two bases.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
trans_spliced
sequence
An attribute describing transcript sequence that is created by splicing exons from diferent genes.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
trans-spliced
polyadenylated_mRNA
sequence
An mRNA that is polyadenylated.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
polyadenylated mRNA
trans_spliced_mRNA
sequence
An mRNA that is trans-spliced.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
trans-spliced mRNA
edited_transcript
sequence
A transcript that is edited.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
edited transcript
edited_transcript_by_A_to_I_substitution
sequence
edited transcript by A to I substitution
A transcript that has been edited by A to I substitution.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
bound_by_protein
sequence
An attribute describing a sequence that is bound by a protein.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
bound by protein
bound_by_nucleic_acid
sequence
bound by nucleic acid
An attribute describing a sequence that is bound by a nucleic acid.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
alternatively_spliced
sequence
alternatively spliced
An attribute describing a situation where a gene may encode for more than 1 transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
monocistronic
sequence
An attribute describing a sequence that contains the code for one gene product.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
dicistronic
sequence
An attribute describing a sequence that contains the code for two gene products.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polycistronic
sequence
An attribute describing a sequence that contains the code for more than one gene product.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
recoded
sequence
An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
codon_redefined
sequence
An attribute describing the alteration of codon meaning.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
codon redefined
stop_codon_read_through
sequence
A stop codon redefined to be a new amino acid.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
stop codon read through
stop codon readthrough
stop_codon_redefined_as_pyrrolysine
sequence
A stop codon redefined to be the new amino acid, pyrrolysine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
stop codon redefined as pyrrolysine
stop_codon_redefined_as_selenocysteine
sequence
A stop codon redefined to be the new amino acid, selenocysteine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
stop codon redefined as selenocysteine
recoded_by_translational_bypass
sequence
recoded by translational bypass
Recoded mRNA where a block of nucleotides is not translated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translationally_frameshifted
sequence
translationally frameshifted
Recoding by frameshifting a particular site.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
maternally_imprinted_gene
sequence
maternally imprinted gene
A gene that is maternally_imprinted.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
paternally_imprinted_gene
sequence
A gene that is paternally imprinted.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
paternally imprinted gene
post_translationally_regulated_gene
sequence
A gene that is post translationally regulated.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
post translationally regulated gene
negatively_autoregulated_gene
sequence
A gene that is negatively autoreguated.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
negatively autoregulated gene
positively_autoregulated_gene
sequence
positively autoregulated gene
A gene that is positively autoregulated.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
silenced
sequence
URL:http://en.wikipedia.org/wiki/Silenced
http://en.wikipedia.org/wiki/Silenced
An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
silenced_by_DNA_modification
sequence
silenced by DNA modification
An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
silenced_by_DNA_methylation
sequence
An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
silenced by DNA methylation
translationally_regulated_gene
sequence
A gene that is translationally regulated.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
translationally regulated gene
allelically_excluded_gene
sequence
allelically excluded gene
A gene that is allelically_excluded.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
epigenetically_modified_gene
sequence
epigenetically modified gene
A gene that is epigenetically modified.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nuclear_mitochondrial
sequence
nuclear mitochondrial
An attribute describing a nuclear pseudogene of a mitochndrial gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
processed
sequence
An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
unequally_crossed_over
sequence
An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
unequally crossed over
transgene
sequence
A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
URL:http://en.wikipedia.org/wiki/Transgene
http://en.wikipedia.org/wiki/Transgene
endogenous_retroviral_sequence
sequence
endogenous retroviral sequence
rearranged_at_DNA_level
sequence
An attribute to describe the sequence of a feature, where the DNA is rearranged.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
rearranged at DNA level
status
This term is the hypernym of attributes and should not be annotated to.
sequence
An attribute describing the status of a feature, based on the available evidence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
independently_known
sequence
Attribute to describe a feature that is independently known - not predicted.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
independently known
supported_by_sequence_similarity
sequence
An attribute to describe a feature that has been predicted using sequence similarity techniques.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
supported by sequence similarity
supported_by_domain_match
sequence
An attribute to describe a feature that has been predicted using sequence similarity of a known domain.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
supported by domain match
supported_by_EST_or_cDNA
sequence
An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
supported by EST or cDNA
orphan
sequence
predicted_by_ab_initio_computation
sequence
predicted by ab initio computation
An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
asx_turn
sequence
BS:00203
asx turn
A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
cloned_cDNA_insert
sequence
A clone insert made from cDNA.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
cloned cDNA insert
cloned_genomic_insert
sequence
A clone insert made from genomic DNA.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
cloned genomic insert
engineered_insert
sequence
A clone insert that is engineered.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
engineered insert
edit_operation
sequence
edit operation
insert_U
The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
sequence
An edit to insert a U.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insert U
delete_U
The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
sequence
An edit to delete a uridine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
delete U
substitute_A_to_I
sequence
An edit to substitute an I for an A.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
substitute A to I
insert_C
sequence
insert C
An edit to insert a cytidine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insert_dinucleotide
sequence
An edit to insert a dinucleotide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insert dinucleotide
substitute_C_to_U
sequence
substitute C to U
An edit to substitute an U for a C.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insert_G
sequence
An edit to insert a G.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insert G
insert_GC
The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
sequence
insert GC
An edit to insert a GC dinucleotide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insert_GU
The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
sequence
An edit to insert a GU dinucleotide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insert GU
insert_CU
The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
sequence
An edit to insert a CU dinucleotide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insert CU
insert_AU
The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
sequence
insert AU
An edit to insert a AU dinucleotide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
insert_AA
The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
sequence
insert AA
An edit to insert a AA dinucleotide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
edited_mRNA
sequence
edited mRNA
An mRNA that is edited.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
guide_RNA_region
sequence
guide RNA region
A region of guide RNA.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
anchor_region
sequence
A region of a guide_RNA that base-pairs to a target mRNA.
SO:jk
http://purl.org/obo/owl/SO#SO_jk
anchor region
pre_edited_mRNA
sequence
pre-edited mRNA
intermediate
sequence
An attribute to describe a feature between stages of processing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
miRNA_target_site
sequence
A miRNA target site is a binding site where the molecule is a micro RNA.
FB:cds
http://purl.org/obo/owl/FB#FB_cds
miRNA target site
edited_CDS
sequence
edited CDS
A CDS that is edited.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
sequence
vertebrate immunoglobulin T cell receptor rearranged segment
vertebrate_immune_system_feature
sequence
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
sequence
vertebrate immunoglobulin T cell receptor rearranged gene cluster
vertebrate_immune_system_gene_recombination_signal_feature
sequence
vertebrate immune system gene recombination signal feature
recombinationally_rearranged
sequence
recombinationally rearranged
recombinationally_rearranged_vertebrate_immune_system_gene
sequence
A recombinationally rearranged gene of the vertebrate immune system.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
recombinationally rearranged vertebrate immune system gene
attP_site
sequence
attP site
An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome.
SO:as
http://purl.org/obo/owl/SO#SO_as
attB_site
sequence
attB site
An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.
SO:as
http://purl.org/obo/owl/SO#SO_as
attL_site
sequence
A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site.
SO:as
http://purl.org/obo/owl/SO#SO_as
attBP'
attL site
attR_site
sequence
A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site.
SO:as
http://purl.org/obo/owl/SO#SO_as
attPB'
attR site
integration_excision_site
sequence
A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site.
SO:as
http://purl.org/obo/owl/SO#SO_as
integration excision site
attachment site
resolution_site
sequence
res site
A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles.
SO:as
http://purl.org/obo/owl/SO#SO_as
resolution site
inversion_site
A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
sequence
inversion site
A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
dif_site
sequence
A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase.
SO:as
http://purl.org/obo/owl/SO#SO_as
dif site
attC_site
sequence
An attC site is a sequence required for the integration of a DNA of an integron.
SO:as
http://purl.org/obo/owl/SO#SO_as
attC site
eukaryotic_terminator
sequence
eukaryotic terminator
oriV
sequence
An origin of vegetative replication in plasmids and phages.
SO:as
http://purl.org/obo/owl/SO#SO_as
origin of vegetative replication
oriC
sequence
origin of bacterial chromosome replication
An origin of bacterial chromosome replication.
SO:as
http://purl.org/obo/owl/SO#SO_as
DNA_chromosome
sequence
Structural unit composed of a self-replicating, DNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
DNA chromosome
double_stranded_DNA_chromosome
sequence
double stranded DNA chromosome
Structural unit composed of a self-replicating, double-stranded DNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
single_stranded_DNA_chromosome
sequence
Structural unit composed of a self-replicating, single-stranded DNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
single stranded DNA chromosome
linear_double_stranded_DNA_chromosome
sequence
Structural unit composed of a self-replicating, double-stranded, linear DNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
linear double stranded DNA chromosome
circular_double_stranded_DNA_chromosome
sequence
circular double stranded DNA chromosome
Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
linear_single_stranded_DNA_chromosome
sequence
Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
linear single stranded DNA chromosome
circular_single_stranded_DNA_chromosome
sequence
circular single stranded DNA chromosome
Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
RNA_chromosome
sequence
Structural unit composed of a self-replicating, RNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
RNA chromosome
single_stranded_RNA_chromosome
sequence
Structural unit composed of a self-replicating, single-stranded RNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
single stranded RNA chromosome
linear_single_stranded_RNA_chromosome
sequence
linear single stranded RNA chromosome
Structural unit composed of a self-replicating, single-stranded, linear RNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
linear_double_stranded_RNA_chromosome
sequence
linear double stranded RNA chromosome
Structural unit composed of a self-replicating, double-stranded, linear RNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
double_stranded_RNA_chromosome
sequence
double stranded RNA chromosome
Structural unit composed of a self-replicating, double-stranded RNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
circular_single_stranded_RNA_chromosome
sequence
circular single stranded RNA chromosome
Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
circular_double_stranded_RNA_chromosome
sequence
Structural unit composed of a self-replicating, double-stranded, circular RNA molecule.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
circular double stranded RNA chromosome
sequence_replication_mode
This has been obsoleted as it represents a process. replaced_by: GO:0034961.
sequence
sequence replication mode
rolling_circle
This has been obsoleted as it represents a process. replaced_by: GO:0070581.
sequence
URL:http://en.wikipedia.org/wiki/Rolling_circle
http://en.wikipedia.org/wiki/Rolling_circle
rolling circle
theta_replication
This has been obsoleted as it represents a process. replaced_by: GO:0070582
sequence
theta replication
DNA_replication_mode
This has been obsoleted as it represents a process. replaced_by: GO:0006260.
sequence
DNA replication mode
RNA_replication_mode
This has been obsoleted as it represents a process. replaced_by: GO:0034961.
sequence
RNA replication mode
insertion_sequence
sequence
URL:http://en.wikipedia.org/wiki/Insertion_sequence
http://en.wikipedia.org/wiki/Insertion_sequence
insertion sequence
IS
A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.
SO:as
http://purl.org/obo/owl/SO#SO_as
minicircle_gene
sequence
minicircle gene
cryptic
sequence
A feature_attribute describing a feature that is not manifest under normal conditions.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
anchor_binding_site
Part of an edited transcript only.
sequence
anchor binding site
template_region
sequence
template region
A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
SO:jk
http://purl.org/obo/owl/SO#SO_jk
information region
gRNA_encoding
sequence
gRNA encoding
A non-protein_coding gene that encodes a guide_RNA.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
minicircle
sequence
SO:0000974
minicircle_chromosome
A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs.
PMID:8395055
http://purl.org/obo/owl/PMID#PMID_8395055
URL:http://en.wikipedia.org/wiki/Minicircle
http://en.wikipedia.org/wiki/Minicircle
rho_dependent_bacterial_terminator
sequence
rho dependent bacterial terminator
rho_independent_bacterial_terminator
sequence
rho independent bacterial terminator
strand_attribute
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
sequence
strand attribute
single
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
sequence
double
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
sequence
topology_attribute
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
sequence
topology attribute
linear
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
sequence
two-ended
A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
circular
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
sequence
A quality of a nucleotide polymer that has no terminal nucleotide residues.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
zero-ended
class_II_RNA
sequence
Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
PMID:15333696
http://purl.org/obo/owl/PMID#PMID_15333696
class II RNA
class_I_RNA
Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.
sequence
Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
PMID:15333696
http://purl.org/obo/owl/PMID#PMID_15333696
class I RNA
genomic_DNA
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
genomic DNA
BAC_cloned_genomic_insert
Requested by Andy Schroder - Flybase Harvard, Nov 2006.
sequence
BAC cloned genomic insert
consensus
Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.
sequence
consensus_region
DO not obsolete without considering MGED mapping.
sequence
consensus region
consensus_mRNA
DO not obsolete without considering MGED mapping.
sequence
consensus mRNA
predicted_gene
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
predicted gene
gene_fragment
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
gene fragment
recursive_splice_site
sequence
A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons.
URL:http://www.genetics.org/cgi/content/full/170/2/661
http://www.genetics.org/cgi/content/full/170/2/661
recursive splice site
BAC_end
Requested by Keith Boroevich December, 2006.
sequence
A region of sequence from the end of a BAC clone that may provide a highly specific marker.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
BAC end
BES
BAC end sequence
rRNA_16S
sequence
A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
rRNA 16S
16S rRNA
16S SSU RNA
16S ribosomal RNA
URL:http://en.wikipedia.org/wiki/16S_ribosomal_RNA
http://en.wikipedia.org/wiki/16S_ribosomal_RNA
rRNA_23S
sequence
23S LSU rRNA
23S rRNA
rRNA 23S
A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
23S ribosomal RNA
rRNA_25S
sequence
A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
25S ribosomal RNA
25S rRNA
25S LSU rRNA
rRNA 25S
solo_LTR
Requested by Hadi Quesneville January 2007.
sequence
A recombination product between the 2 LTR of the same element.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
solo LTR
low_complexity
sequence
low complexity
low_complexity_region
sequence
low complexity region
prophage
sequence
A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island".
GOC:jl
http://purl.org/obo/owl/GOC#GOC_jl
URL:http://en.wikipedia.org/wiki/Prophage
http://en.wikipedia.org/wiki/Prophage
cryptic_prophage
This is not cryptic in the same sense as a cryptic gene or cryptic splice site.
sequence
cryptic prophage
URL:http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w
http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w
A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.
GOC:jl
http://purl.org/obo/owl/GOC#GOC_jl
tetraloop
sequence
A base-paired stem with loop of 4 non-hydrogen bonded nucleotides.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Tetraloop
http://en.wikipedia.org/wiki/Tetraloop
DNA_constraint_sequence
sequence
A double-stranded DNA used to control macromolecular structure and function.
DNA constraint sequence
DNA constraint
i_motif
sequence
short intercalated motif
i motif
A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.
PMID:9753739
http://purl.org/obo/owl/PMID#PMID_9753739
PNA_oligo
sequence
URL:http://en.wikipedia.org/wiki/Peptide_nucleic_acid
http://en.wikipedia.org/wiki/Peptide_nucleic_acid
peptide nucleic acid
PNA oligo
Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
DNAzyme
Added by request from Colin Batchelor.
sequence
DNA enzyme
deoxyribozyme
catalytic DNA
A DNA sequence with catalytic activity.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
MNP
sequence
A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.
URL:http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431
http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431
multiple nucleotide polymorphism
intron_domain
Requested by Colin Batchelor, Feb 2007.
sequence
intron domain
wobble_base_pair
sequence
wobble pair
A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C.
PMID:11256617
http://purl.org/obo/owl/PMID#PMID_11256617
wobble base pair
URL:http://en.wikipedia.org/wiki/Wobble_base_pair
http://en.wikipedia.org/wiki/Wobble_base_pair
internal_guide_sequence
sequence
A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
internal guide sequence
IGS
silent_mutation
Added in March 2007 in after meeting with pharmgkb. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc.
sequence
A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
silent mutation
URL:http://en.wikipedia.org/wiki/Silent_mutation
http://en.wikipedia.org/wiki/Silent_mutation
loinc:LA6700-4
http://purl.org/obo/owl/loinc#loinc_LA6700-4
epitope
Requested by Trish Whetzel.
sequence
URL:http://en.wikipedia.org/wiki/Epitope
http://en.wikipedia.org/wiki/Epitope
A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
URL:http://en.wikipedia.org/wiki/Epitope
http://en.wikipedia.org/wiki/Epitope
copy_number_variation
sequence
CNP
CNV
copy number polymorphism
copy number variation
A variation that increases or decreases the copy number of a given region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Copy_number_variation
http://en.wikipedia.org/wiki/Copy_number_variation
sequence_variant_affecting_copy_number
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant affecting copy number
mutation affecting copy number
chromosome_breakpoint
sequence
SO:0001242
aberration_junction
chromosome breakpoint
aberration breakpoint
inversion_breakpoint
sequence
inversion breakpoint
The point within a chromosome where an inversion begins or ends.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
allele
sequence
URL:http://en.wikipedia.org/wiki/Allele
http://en.wikipedia.org/wiki/Allele
allelomorph
An allele is one of a set of coexisting sequence variants of a gene.
SO:immuno_workshop
http://purl.org/obo/owl/SO#SO_immuno_workshop
haplotype
sequence
URL:http://en.wikipedia.org/wiki/Haplotype
http://en.wikipedia.org/wiki/Haplotype
A haplotype is one of a set of coexisting sequence variants of a haplotype block.
SO:immuno_workshop
http://purl.org/obo/owl/SO#SO_immuno_workshop
polymorphic_sequence_variant
sequence
A sequence variant that is segregating in one or more natural populations of a species.
SO:immuno_workshop
http://purl.org/obo/owl/SO#SO_immuno_workshop
polymorphic sequence variant
genome
sequence
A genome is the sum of genetic material within a cell or virion.
SO:immuno_workshop
http://purl.org/obo/owl/SO#SO_immuno_workshop
URL:http://en.wikipedia.org/wiki/Genome
http://en.wikipedia.org/wiki/Genome
genotype
sequence
A genotype is a variant genome, complete or incomplete.
SO:immuno_workshop
http://purl.org/obo/owl/SO#SO_immuno_workshop
URL:http://en.wikipedia.org/wiki/Genotype
http://en.wikipedia.org/wiki/Genotype
diplotype
sequence
A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.
SO:immuno_workshop
http://purl.org/obo/owl/SO#SO_immuno_workshop
direction_attribute
sequence
direction attribute
forward
sequence
Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
reverse
sequence
Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mitochondrial_DNA
This terms is used by MO.
sequence
URL:http://en.wikipedia.org/wiki/Mitochondrial_DNA
http://en.wikipedia.org/wiki/Mitochondrial_DNA
mitochondrial DNA
mtDNA
chloroplast_DNA
This term is used by MO.
sequence
chloroplast DNA
mirtron
Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns.
sequence
A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
PMID:17589500
http://purl.org/obo/owl/PMID#PMID_17589500
piRNA
sequence
URL:http://en.wikipedia.org/wiki/PiRNA
http://en.wikipedia.org/wiki/PiRNA
piwi-associated RNA
A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
arginyl_tRNA
sequence
arginyl tRNA
A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mobile_genetic_element
sequence
A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
PMID:14681355
http://purl.org/obo/owl/PMID#PMID_14681355
mobile genetic element
URL:http://en.wikipedia.org/wiki/Mobile_genetic_element
http://en.wikipedia.org/wiki/Mobile_genetic_element
MGE
extrachromosomal_mobile_genetic_element
sequence
An MGE that is not integrated into the host chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
extrachromosomal mobile genetic element
integrated_mobile_genetic_element
sequence
An MGE that is integrated into the host chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
integrated mobile genetic element
integrated_plasmid
sequence
integrated plasmid
A plasmid sequence that is integrated within the host chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
viral_sequence
The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.
sequence
viral sequence
virus sequence
The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
phage_sequence
sequence
The nucleotide sequence of a virus that infects bacteria.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Bacteriophage
http://en.wikipedia.org/wiki/Bacteriophage
phage sequence
phage
bacteriophage
attCtn_site
sequence
An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.
Phigo:at
http://purl.org/obo/owl/Phigo#Phigo_at
attCtn site
nuclear_mt_pseudogene
Definition change requested by Val, 3172757.
sequence
NUMT
nuclear mitochondrial pseudogene
nuclear mt pseudogene
A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
URL:http://en.wikipedia.org/wiki/Numt
http://en.wikipedia.org/wiki/Numt
cointegrated_plasmid
sequence
A MGE region consisting of two fused plasmids resulting from a replicative transposition event.
phigo:at
http://purl.org/obo/owl/phigo#phigo_at
cointegrated plasmid
cointegrated replicon
IRLinv_site
sequence
Component of the inversion site located at the left of a region susceptible to site-specific inversion.
Phigo:at
http://purl.org/obo/owl/Phigo#Phigo_at
IRLinv site
IRRinv_site
sequence
IRRinv site
Component of the inversion site located at the right of a region susceptible to site-specific inversion.
Phigo:at
http://purl.org/obo/owl/Phigo#Phigo_at
inversion_site_part
A term created to allow the parts of an inversion site have an is_a path back to the root.
sequence
inversion site part
A region located within an inversion site.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
defective_conjugative_transposon
sequence
defective conjugative transposon
An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.
Phigo:ariane
http://purl.org/obo/owl/Phigo#Phigo_ariane
repeat_fragment
Requested by Chris Smith, and others at Flybase to help annotate nested repeats.
sequence
A portion of a repeat, interrupted by the insertion of another element.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
repeat fragment
nested_region
sequence
nested_repeat
sequence
nested_transposon
sequence
transposon_fragment
sequence
transposon fragment
A portion of a transposon, interrupted by the insertion of another element.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcriptional_cis_regulatory_region
sequence
A regulatory_region that modulates the transcription of a gene or genes.
SO:regcreative
http://purl.org/obo/owl/SO#SO_regcreative
transcriptional cis regulatory region
splicing_regulatory_region
sequence
splicing regulatory region
A regulatory_region that modulates splicing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
enhanceosome
sequence
promoter_targeting_sequence
sequence
promoter targeting sequence
A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.
SO:regcreative
http://purl.org/obo/owl/SO#SO_regcreative
sequence_alteration
Merged with partially characterized change in nucleotide sequence.
SO:1000004
SO:1000007
sequence
A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence alteration
partially characterised change in DNA sequence
partially_characterised_change_in_DNA_sequence
uncharacterised_change_in_nucleotide_sequence
sequence_variant
sequence
A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence variant
propeptide_cleavage_site
Discrete.
BS:00063
sequence
propeptide cleavage site
The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
propeptide
Range.
sequence
BS:00077
URL:http://en.wikipedia.org/wiki/Propeptide
http://en.wikipedia.org/wiki/Propeptide
Part of a peptide chain which is cleaved off during the formation of the mature protein.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
propep
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
immature_peptide_region
Range.
BS:00129
sequence
An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
immature peptide region
active_peptide
Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.
sequence
BS:00076
Active peptides are proteins which are biologically active, released from a precursor molecule.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
peptide
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
URL:http://en.wikipedia.org/wiki/Peptide
http://en.wikipedia.org/wiki/Peptide
active peptide
compositionally_biased_region_of_peptide
Range.
BS:00068
sequence
compositional bias
compositionally biased
compbias
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
compositionally biased region of peptide
compositionally_biased_region
polypeptide_motif
Range.
BS:00032
sequence
polypeptide motif
A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.).
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
motif
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
polypeptide_repeat
Range.
sequence
BS:00070
A polypeptide_repeat is a single copy of an internal sequence repetition.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
polypeptide repeat
repeat
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
polypeptide_structural_region
Range.
sequence
BS:00337
structural_region
Region of polypeptide with a given structural property.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
polypeptide structural region
membrane_structure
Range.
sequence
BS:00128
Arrangement of the polypeptide with respect to the lipid bilayer.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
membrane structure
extramembrane_polypeptide_region
Range.
BS:00154
sequence
Polypeptide region that is localized outside of a lipid bilayer.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:cb
http://purl.org/obo/owl/SO#SO_cb
topo_dom
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
extramembrane_region
extramembrane
extramembrane polypeptide region
cytoplasmic_polypeptide_region
sequence
BS:00145
Polypeptide region that is localized inside the cytoplasm.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:cb
http://purl.org/obo/owl/SO#SO_cb
inside
cytoplasmic polypeptide region
cytoplasm_location
non_cytoplasmic_polypeptide_region
This could be inside an organelle within the cell.
BS:00144
sequence
non cytoplasmic polypeptide region
outside
non_cytoplasm_location
Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:cb
http://purl.org/obo/owl/SO#SO_cb
intramembrane_polypeptide_region
sequence
BS:00156
Polypeptide region present in the lipid bilayer.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
intramembrane
intramembrane polypeptide region
membrane_peptide_loop
sequence
BS:00155
Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:cb
http://purl.org/obo/owl/SO#SO_cb
membrane_loop
membrane peptide loop
transmembrane_polypeptide_region
BS:00158
sequence
Polypeptide region traversing the lipid bilayer.
UniProt:curator_manual
http://purl.org/obo/owl/UniProt#UniProt_curator_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
transmembrane polypeptide region
transmem
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
transmembrane
polypeptide_secondary_structure
Biosapien term was secondary_structure.
sequence
BS:00003
polypeptide secondary structure
URL:http://en.wikipedia.org/wiki/Secondary_structure
http://en.wikipedia.org/wiki/Secondary_structure
secondary_structure
secondary structure region
A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
secondary structure
2nary structure
polypeptide_structural_motif
BS:0000338
sequence
structural_motif
polypeptide structural motif
Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://en.wikipedia.org/wiki/Structural_motif
http://en.wikipedia.org/wiki/Structural_motif
coiled_coil
Range.
BS:00041
sequence
URL:http://en.wikipedia.org/wiki/Coiled_coil
http://en.wikipedia.org/wiki/Coiled_coil
coiled coil
coiled
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
helix_turn_helix
sequence
BS:00147
helix-turn-helix
HTH
A motif comprising two helices separated by a turn.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
helix turn helix
polypeptide_sequencing_information
Range.
BS:00125
sequence
Incompatibility in the sequence due to some experimental problem.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
sequencing_information
non_adjacent_residues
BS:00182
sequence
non_cons
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
non consecutive
Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them.
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
non_terminal_residue
Discrete.
BS:00072
sequence
non terminal
non_ter
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
The residue at an extremity of the sequence is not the terminal residue.
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
sequence_conflict
Discrete.
BS:00069
sequence
Different sources report differing sequences.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
conflict
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
sequence_uncertainty
sequence
BS:00181
unsure
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
Describes the positions in a sequence where the authors are unsure about the sequence assignment.
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
cross_link
sequence
BS:00178
cross link
crosslink
Posttranslationally formed amino acid bonds.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
disulfide_bond
2 discreet & joined.
BS:00028
sequence
disulphide
disulphide bond
disulfid
disulfide
The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
disulfide bond
post_translationally_modified_region
Discrete.
BS:00052
sequence
URL:http://en.wikipedia.org/wiki/Post_translational_modification
http://en.wikipedia.org/wiki/Post_translational_modification
post_translational_modification
modified residue
mod_res
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein.
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
covalent_binding_site
sequence
BS:00246
covalent binding site
Binding involving a covalent bond.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
non_covalent_binding_site
Discrete.
sequence
BS:00029
non covalent binding site
Binding site for any chemical group (co-enzyme, prosthetic group, etc.).
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
binding
uniprot:curation
http://purl.org/obo/owl/uniprot#uniprot_curation
binding site
polypeptide_metal_contact
Residue is part of a binding site for a metal ion.
BS:00027
sequence
metal_binding
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:cb
http://purl.org/obo/owl/SO#SO_cb
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
protein_protein_contact
BS:00131
sequence
protein_protein_interaction
A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues.
UniProt:Curation_manual
http://purl.org/obo/owl/UniProt#UniProt_Curation_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://en.wikipedia.org/wiki/Protein_protein_interaction
http://en.wikipedia.org/wiki/Protein_protein_interaction
protein protein contact site
protein protein contact
polypeptide_calcium_ion_contact_site
Residue involved in contact with calcium.
BS:00186
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
ca bind
polypeptide calcium ion contact site
Ca_contact_site
polypeptide_cobalt_ion_contact_site
BS:00136
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:cb
http://purl.org/obo/owl/SO#SO_cb
polypeptide cobalt ion contact site
Co_contact_site
polypeptide_copper_ion_contact_site
sequence
BS:00146
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
Cu_contact_site
polypeptide copper ion contact site
polypeptide_iron_ion_contact_site
sequence
BS:00137
Fe_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
polypeptide iron ion contact site
polypeptide_magnesium_ion_contact_site
sequence
BS:00187
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:cb
http://purl.org/obo/owl/SO#SO_cb
polypeptide magnesium ion contact site
Mg_contact_site
polypeptide_manganese_ion_contact_site
BS:00140
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
polypeptide manganese ion contact site
Mn_contact_site
polypeptide_molybdenum_ion_contact_site
sequence
BS:00141
polypeptide molybdenum ion contact site
Mo_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:cb
http://purl.org/obo/owl/SO#SO_cb
polypeptide_nickel_ion_contact_site
BS:00142
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
Ni_contact_site
polypeptide nickel ion contact site
polypeptide_tungsten_ion_contact_site
sequence
BS:00143
W_contact_site
polypeptide tungsten ion contact site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
polypeptide_zinc_ion_contact_site
sequence
BS:00185
Zn_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:cb
http://purl.org/obo/owl/SO#SO_cb
polypeptide zinc ion contact site
catalytic_residue
Discrete.
sequence
BS:00026
act_site
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
Amino acid involved in the activity of an enzyme.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
catalytic residue
active site residue
polypeptide_ligand_contact
BS:00157
sequence
Residues which interact with a ligand.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
protein-ligand interaction
polypeptide ligand contact
asx_motif
sequence
BS:00202
asx motif
A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
beta_bulge
BS:00208
sequence
URL:http://en.wikipedia.org/wiki/Beta_bulge
http://en.wikipedia.org/wiki/Beta_bulge
beta bulge
A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_bulge_loop
sequence
BS:00209
A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
Http://www.ebi.ac.uk/msd-srv/msdmotif/
http://purl.org/obo/owl/Http#Http_//www.ebi.ac.uk/msd-srv/msdmotif/
beta bulge loop
beta_bulge_loop_five
BS:00210
sequence
beta bulge loop five
A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
beta_bulge_loop_six
BS:00211
sequence
beta bulge loop six
A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_strand
Range.
BS:00042
sequence
A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://en.wikipedia.org/wiki/Beta_sheet
http://en.wikipedia.org/wiki/Beta_sheet
strand
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
antiparallel_beta_strand
Range.
BS:0000341
sequence
A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets.
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
antiparallel beta strand
parallel_beta_strand
Range.
BS:00151
sequence
A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets.
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
parallel beta strand
peptide_helix
Range.
BS:00152
sequence
A helix is a secondary_structure conformation where the peptide backbone forms a coil.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
helix
left_handed_peptide_helix
sequence
BS:00222
left handed helix
A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
helix-l
right_handed_peptide_helix
BS:0000339
sequence
right handed helix
helix
A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
alpha_helix
Range.
sequence
BS:00040
helix
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
a-helix
URL:http://en.wikipedia.org/wiki/Alpha_helix
http://en.wikipedia.org/wiki/Alpha_helix
pi_helix
Range.
BS:00153
sequence
URL:http://en.wikipedia.org/wiki/Pi_helix
http://en.wikipedia.org/wiki/Pi_helix
The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
pi helix
three_ten_helix
Range.
sequence
BS:0000340
The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://en.wikipedia.org/wiki/310_helix
http://en.wikipedia.org/wiki/310_helix
three ten helix
3-10 helix
310 helix
3(10) helix
polypeptide_nest_motif
sequence
BS:00223
polypeptide nest motif
nest_motif
A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
nest
polypeptide_nest_left_right_motif
sequence
BS:00224
A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
nest_lr
polypeptide nest left right motif
nest_left_right
polypeptide_nest_right_left_motif
sequence
BS:00225
A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
nest_rl
polypeptide nest right left motif
nest_right_left
schellmann_loop
sequence
BS:00226
A motif of six or seven consecutive residues that contains two H-bonds.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
paperclip loop
schellmann loop
paperclip
schellmann_loop_seven
BS:00228
sequence
schellmann loop seven
seven-residue schellmann loop
Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
schellmann_loop_six
sequence
BS:00227
Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
schellmann loop six
six-residue schellmann loop
serine_threonine_motif
sequence
BS:00229
A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
serine/threonine motif
st_motif
st motif
serine_threonine_staple_motif
BS:00230
sequence
A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
st_staple
serine threonine staple motif
polypeptide_turn_motif
Range.
sequence
BS:00148
A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
turn
asx_turn_left_handed_type_one
BS:00206
sequence
asx turn left handed type one
Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
asx_turn_il
asx_turn_left_handed_type_two
BS:00204
sequence
asx_turn_iil
asx turn left handed type two
Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
asx_turn_right_handed_type_two
sequence
BS:00205
asx turn right handed type two
asx_turn_iir
Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
asx_turn_right_handed_type_one
sequence
BS:00207
Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
asx_turn_ir
asx turn type right handed type one
beta_turn
sequence
BS:00212
beta turn
A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_turn_left_handed_type_one
BS:00215
sequence
type I' turn
beta_turn_il
type I' beta turn
Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
beta turn left handed type one
beta_turn_left_handed_type_two
sequence
BS:00213
Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
type II' beta turn
type II' turn
beta_turn_iil
beta turn left handed type two
beta_turn_right_handed_type_one
BS:00216
sequence
type I beta turn
type I turn
beta turn right handed type one
beta_turn_ir
Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
beta_turn_right_handed_type_two
BS:00214
sequence
type II beta turn
type II turn
beta turn right handed type two
beta_turn_iir
Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
gamma_turn
sequence
BS:00219
gamma turn
Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
gamma_turn_classic
sequence
BS:00220
gamma turn classic
classic gamma turn
Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
gamma_turn_inverse
sequence
BS:00221
gamma turn inverse
Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
serine_threonine_turn
sequence
BS:00231
st_turn
serine/threonine turn
A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
st_turn_left_handed_type_one
BS:00234
sequence
The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
st turn left handed type one
st_turn_il
st_turn_left_handed_type_two
sequence
BS:00232
The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
st turn left handed type two
st_turn_iil
st_turn_right_handed_type_one
BS:00235
sequence
st turn right handed type one
The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
st_turn_ir
st_turn_right_handed_type_two
BS:00233
sequence
st turn right handed type two
The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
st_turn_iir
polypeptide_variation_site
For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
sequence
BS:00336
A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence_variations
natural_variant_site
Discrete.
sequence
BS:00071
Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
variant
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
sequence variation
natural_variant
mutated_variant_site
Discrete.
BS:00036
sequence
mutagen
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
Site which has been experimentally altered.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
mutated_site
mutagenesis
alternate_sequence_site
Discrete.
BS:00073
SO:0001065
sequence
isoform
sequence variation
varsplic
var_seq
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
UniProt:curation_manual
http://purl.org/obo/owl/UniProt#UniProt_curation_manual
alternative_sequence
beta_turn_type_six
sequence
A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
beta turn type six
type VI turn
cis-proline loop
type VI beta turn
beta_turn_type_six_a
sequence
A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.
PMID:2371257
http://purl.org/obo/owl/PMID#PMID_2371257
SO:cb
http://purl.org/obo/owl/SO#SO_cb
beta turn type six a
type VIa beta turn
type VIa turn
beta_turn_type_six_a_one
sequence
beta turn type six a one
type VIa1 beta turn
type VIa1 turn
beta_turn_type_six_a_two
sequence
type VIa2 beta turn
beta turn type six a two
type VIa2 turn
beta_turn_type_six_b
sequence
type VIb turn
beta turn type six b
A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
PMID:2371257
http://purl.org/obo/owl/PMID#PMID_2371257
type VIb beta turn
beta_turn_type_eight
sequence
type VIII beta turn
A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
PMID:2371257
http://purl.org/obo/owl/PMID#PMID_2371257
beta turn type eight
type VIII turn
DRE_motif
This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.
sequence
WATCGATW_motif
A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.
PMID:12537576
http://purl.org/obo/owl/PMID#PMID_12537576
NDM4
DRE motif
DMv4_motif
sequence
DMv4
directional motif v4
DMv4 motif
YGGTCACATR
motif 1 element
promoter motif 1
A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).
PMID:16827941:12537576
http://purl.org/obo/owl/PMID#PMID_16827941:12537576
E_box_motif
sequence
A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).
PMID:12537576:16827941
http://purl.org/obo/owl/PMID#PMID_12537576:16827941
generic E box motif
NDM5
AWCAGCTGWT
E box motif
DMv5_motif
sequence
promoter motif 6
directional motif v5
KTYRGTATWTTT
DMv5 motif
DMv5
A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
PMID:12537576:16827941
http://purl.org/obo/owl/PMID#PMID_12537576:16827941
DMv3_motif
sequence
A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).
PMID:12537576:16827941
http://purl.org/obo/owl/PMID#PMID_12537576:16827941
directional motif v3
DMv3
promoter motif 7
DMv3 motif
KNNCAKCNCTRNY
DMv2_motif
sequence
A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
PMID:12537576:16827941
http://purl.org/obo/owl/PMID#PMID_12537576:16827941
promoter motif 8
directional motif v2
DMv2
MKSYGGCARCGSYSS
DMv2 motif
MTE
sequence
motif ten element
motif_ten_element
A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
PMID:12537576:15231738
http://purl.org/obo/owl/PMID#PMID_12537576:15231738
CSARCSSAACGS
INR1_motif
sequence
directional motif p3
directional promoter motif 3
DMp3
INR1 motif
A promoter motif with consensus sequence TCATTCG.
PMID:16827941
http://purl.org/obo/owl/PMID#PMID_16827941
DPE1_motif
sequence
directional motif 5
A promoter motif with consensus sequence CGGACGT.
PMID:16827941
http://purl.org/obo/owl/PMID#PMID_16827941
DMp5
DPE1 motif
directional promoter motif 5
DMv1_motif
sequence
DMv1
directional promoter motif v1
DMv1 motif
A promoter motif with consensus sequence CARCCCT.
PMID:16827941
http://purl.org/obo/owl/PMID#PMID_16827941
GAGA_motif
sequence
A non directional promoter motif with consensus sequence GAGAGCG.
PMID:16827941
http://purl.org/obo/owl/PMID#PMID_16827941
GAGA
NDM1
GAGA motif
NDM2_motif
sequence
NDM2 motif
non directional promoter motif 2
NDM2
A non directional promoter motif with consensus CGMYGYCR.
PMID:16827941
http://purl.org/obo/owl/PMID#PMID_16827941
NDM3_motif
sequence
NDM3 motif
NDM3
non directional motif 3
A non directional promoter motif with consensus sequence GAAAGCT.
PMID:16827941
http://purl.org/obo/owl/PMID#PMID_16827941
ds_RNA_viral_sequence
sequence
double stranded RNA virus sequence
ds RNA viral sequence
A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polinton
sequence
A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.
PMID:16537396
http://purl.org/obo/owl/PMID#PMID_16537396
maverick element
rRNA_21S
sequence
A component of the large ribosomal subunit in mitochondrial rRNA.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
21S rRNA
rRNA 21S
21S LSU rRNA
21S ribosomal RNA
tRNA_region
sequence
A region of a tRNA.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
tRNA region
anticodon_loop
sequence
anti-codon loop
A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.
ISBN:0716719207
http://purl.org/obo/owl/ISBN#ISBN_0716719207
anticodon loop
anticodon
sequence
A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
URL:http://en.wikipedia.org/wiki/Anticodon
http://en.wikipedia.org/wiki/Anticodon
anti-codon
CCA_tail
sequence
Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.
ISBN:0716719207
http://purl.org/obo/owl/ISBN#ISBN_0716719207
CCA sequence
CCA tail
DHU_loop
sequence
DHU loop
Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
ISBN:071671920
http://purl.org/obo/owl/ISBN#ISBN_071671920
D loop
T_loop
sequence
Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
ISBN:0716719207
http://purl.org/obo/owl/ISBN#ISBN_0716719207
T loop
TpsiC loop
pyrrolysine_tRNA_primary_transcript
sequence
A primary transcript encoding pyrrolysyl tRNA (SO:0000766).
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
pyrrolysine tRNA primary transcript
U3_snoRNA
The definition is most of the old definition for snoRNA (SO:0000275).
sequence
URL:http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3
http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3
U3 snoRNA
U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. 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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012
small nucleolar RNA U3
snoRNA U3
U3 small nucleolar RNA
AU_rich_element
sequence
URL:http://en.wikipedia.org/wiki/AU-rich_element
http://en.wikipedia.org/wiki/AU-rich_element
AU rich element
AU-rich element
A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.
PMID:7892223
http://purl.org/obo/owl/PMID#PMID_7892223
ARE
Bruno_response_element
Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.
sequence
BRE
A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
PMID:10893231
http://purl.org/obo/owl/PMID#PMID_10893231
Bruno response element
iron_responsive_element
sequence
iron responsive element
IRE
URL:http://en.wikipedia.org/wiki/Iron_responsive_element
http://en.wikipedia.org/wiki/Iron_responsive_element
A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.
PMID:8710843
http://purl.org/obo/owl/PMID#PMID_8710843
PMID:3198610
http://purl.org/obo/owl/PMID#PMID_3198610
morpholino_backbone
Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.
sequence
An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
URL:http://en.wikipedia.org/wiki/Morpholino
http://en.wikipedia.org/wiki/Morpholino
morpholino backbone
PNA
Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.
sequence
An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
peptide nucleic acid
enzymatic
Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.
sequence
An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
ribozymic
Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.
sequence
An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
pseudouridylation_guide_snoRNA
Has RNA pseudouridylation guide activity (GO:0030558).
sequence
pseudouridylation guide snoRNA
A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
PMID:12457565
http://purl.org/obo/owl/PMID#PMID_12457565
GOC:mah
http://purl.org/obo/owl/GOC#GOC_mah
LNA
Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.
sequence
An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.
CHEBI:48010
http://purl.org/obo/owl/CHEBI#CHEBI_48010
LNA_oligo
sequence
URL:http://en.wikipedia.org/wiki/Locked_nucleic_acid
http://en.wikipedia.org/wiki/Locked_nucleic_acid
locked nucleic acid
An oligo composed of LNA residues.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
LNA oligo
TNA
Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.
sequence
An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.
CHEBI:48019
http://purl.org/obo/owl/CHEBI#CHEBI_48019
TNA_oligo
sequence
An oligo composed of TNA residues.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
threose nucleic acid
URL:http://en.wikipedia.org/wiki/Threose_nucleic_acid
http://en.wikipedia.org/wiki/Threose_nucleic_acid
TNA oligo
GNA
Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.
sequence
An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.
CHEBI:48015
http://purl.org/obo/owl/CHEBI#CHEBI_48015
GNA_oligo
sequence
glycol nucleic acid
URL:http://en.wikipedia.org/wiki/Glycerol_nucleic_acid
http://en.wikipedia.org/wiki/Glycerol_nucleic_acid
glycerol nucleic acid
An oligo composed of GNA residues.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
GNA oligo
R_GNA
Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.
sequence
R GNA
An attribute describing a GNA sequence in the (R)-GNA enantiomer.
CHEBI:48016
http://purl.org/obo/owl/CHEBI#CHEBI_48016
R_GNA_oligo
sequence
(R)-glycerol nucleic acid
(R)-glycol nucleic acid
R GNA oligo
An oligo composed of (R)-GNA residues.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
S_GNA
Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.
sequence
S GNA
An attribute describing a GNA sequence in the (S)-GNA enantiomer.
CHEBI:48017
http://purl.org/obo/owl/CHEBI#CHEBI_48017
S_GNA_oligo
sequence
S GNA oligo
(S)-glycol nucleic acid
(S)-glycerol nucleic acid
An oligo composed of (S)-GNA residues.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
ds_DNA_viral_sequence
sequence
ds DNA viral sequence
A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
double stranded DNA virus
ss_RNA_viral_sequence
sequence
A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ss RNA viral sequence
single strand RNA virus
negative_sense_ssRNA_viral_sequence
sequence
negative sense single stranded RNA virus
A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
negative sense ssRNA viral sequence
positive_sense_ssRNA_viral_sequence
sequence
positive sense single stranded RNA virus
positive sense ssRNA viral sequence
A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ambisense_ssRNA_viral_sequence
sequence
ambisense ssRNA viral sequence
A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ambisense single stranded RNA virus
RNA_polymerase_promoter
sequence
RNA polymerase promoter
A region (DNA) to which RNA polymerase binds, to begin transcription.
xenbase:jb
http://purl.org/obo/owl/xenbase#xenbase_jb
Phage_RNA_Polymerase_Promoter
sequence
Phage RNA Polymerase Promoter
A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
xenbase:jb
http://purl.org/obo/owl/xenbase#xenbase_jb
SP6_RNA_Polymerase_Promoter
sequence
A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.
xenbase:jb
http://purl.org/obo/owl/xenbase#xenbase_jb
SP6 RNA Polymerase Promoter
T3_RNA_Polymerase_Promoter
sequence
A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.
xenbase:jb
http://purl.org/obo/owl/xenbase#xenbase_jb
T3 RNA Polymerase Promoter
T7_RNA_Polymerase_Promoter
sequence
A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.
xenbase:jb
http://purl.org/obo/owl/xenbase#xenbase_jb
T7 RNA Polymerase Promoter
five_prime_EST
sequence
An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.
URL:http://www.ncbi.nlm.nih.gov/About/primer/est.html
http://www.ncbi.nlm.nih.gov/About/primer/est.html
five prime EST
5' EST
three_prime_EST
sequence
three prime EST
An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).
URL:http://www.ncbi.nlm.nih.gov/About/primer/est.html
http://www.ncbi.nlm.nih.gov/About/primer/est.html
3' EST
translational_frameshift
sequence
ribosomal frameshift
translational frameshift
URL:http://en.wikipedia.org/wiki/Translational_frameshift
http://en.wikipedia.org/wiki/Translational_frameshift
The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
plus_1_translational_frameshift
sequence
plus 1 translational frameshift
plus 1 ribosomal frameshift
The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
plus_2_translational_frameshift
sequence
plus 2 translational frameshift
plus 2 ribosomal frameshift
The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
group_III_intron
GO:0000374.
sequence
URL:http://en.wikipedia.org/wiki/Group_III_intron
http://en.wikipedia.org/wiki/Group_III_intron
group III intron
Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.
PMID:11377794
http://purl.org/obo/owl/PMID#PMID_11377794
noncoding_region_of_exon
An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.
sequence
The maximal intersection of exon and UTR.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
noncoding region of exon
coding_region_of_exon
An exon containing either a start or stop codon will be partially coding and partially non coding.
sequence
coding region of exon
The region of an exon that encodes for protein sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
endonuclease_spliced_intron
sequence
endonuclease spliced intron
An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
protein_coding_gene
sequence
protein coding gene
transgenic_insertion
sequence
An insertion that derives from another organism, via the use of recombinant DNA technology.
SO:bm
http://purl.org/obo/owl/SO#SO_bm
transgenic insertion
retrogene
sequence
silenced_by_RNA_interference
RNA interference is GO:0016246.
sequence
An attribute describing an epigenetic process where a gene is inactivated by RNA interference.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
silenced by RNA interference
silenced_by_histone_modification
Histone modification is GO:0016570.
sequence
silenced by histone modification
An attribute describing an epigenetic process where a gene is inactivated by histone modification.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
silenced_by_histone_methylation
Histone methylation is GO:0016571.
sequence
An attribute describing an epigenetic process where a gene is inactivated by histone methylation.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
silenced by histone methylation
silenced_by_histone_deacetylation
Histone deacetylation is GO:0016573.
sequence
silenced by histone deacetylation
An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
gene_silenced_by_RNA_interference
sequence
RNAi silenced gene
RNA interference silenced gene
gene silenced by RNA interference
A gene that is silenced by RNA interference.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene_silenced_by_histone_modification
sequence
gene silenced by histone modification
A gene that is silenced by histone modification.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene_silenced_by_histone_methylation
sequence
A gene that is silenced by histone methylation.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene silenced by histone methylation
gene_silenced_by_histone_deacetylation
sequence
A gene that is silenced by histone deacetylation.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene silenced by histone deacetylation
dihydrouridine
sequence
D
A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
RNAMOD:051
http://purl.org/obo/owl/RNAMOD#RNAMOD_051
URL:http://en.wikipedia.org/wiki/Dihydrouridine
http://en.wikipedia.org/wiki/Dihydrouridine
pseudouridine
The free molecule is CHEBI:17802.
sequence
A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
RNAMOD:050
http://purl.org/obo/owl/RNAMOD#RNAMOD_050
URL:http://en.wikipedia.org/wiki/Pseudouridine
http://en.wikipedia.org/wiki/Pseudouridine
Y
inosine
The free molecule is CHEBI:17596.
sequence
URL:http://en.wikipedia.org/wiki/Inosine
http://en.wikipedia.org/wiki/Inosine
A modified RNA base in which hypoxanthine is bound to the ribose ring.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
I
RNAMOD:017
seven_methylguanine
The free molecule is CHEBI:2274.
sequence
7-methylguanine
A modified RNA base in which guanine is methylated at the 7- position.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
seven methylguanine
ribothymidine
The free molecule is CHEBI:30832.
sequence
A modified RNA base in which thymine is bound to the ribose ring.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
methylinosine
sequence
A modified RNA base in which methylhypoxanthine is bound to the ribose ring.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
mobile
sequence
URL:http://en.wikipedia.org/wiki/Mobile
http://en.wikipedia.org/wiki/Mobile
An attribute describing a feature that has either intra-genome or intracellular mobility.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
replicon
sequence
A region containing at least one unique origin of replication and a unique termination site.
ISBN:0716719207
http://purl.org/obo/owl/ISBN#ISBN_0716719207
URL:http://en.wikipedia.org/wiki/Replicon_(genetics)
http://en.wikipedia.org/wiki/Replicon_(genetics)
base
sequence
A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Nucleobase
http://en.wikipedia.org/wiki/Nucleobase
amino_acid
Probably in the future this will cross reference to Chebi.
sequence
amino acid
A sequence feature that corresponds to a single amino acid residue in a polypeptide.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
URL:http://en.wikipedia.org/wiki/Amino_acid
http://en.wikipedia.org/wiki/Amino_acid
major_TSS
sequence
major transcription start site
major TSS
minor_TSS
sequence
minor TSS
TSS_region
sequence
The region of a gene from the 5' most TSS to the 3' TSS.
BBOP:nw
http://purl.org/obo/owl/BBOP#BBOP_nw
TSS region
encodes_alternate_transcription_start_sites
sequence
encodes alternate transcription start sites
miRNA_primary_transcript_region
sequence
A part of an miRNA primary_transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
miRNA primary transcript region
pre_miRNA
sequence
The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin sructure.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
pre-miRNA
miRNA_stem
sequence
The stem of the hairpin loop formed by folding of the pre-miRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
miRNA stem
miRNA_loop
sequence
miRNA loop
The loop of the hairpin loop formed by folding of the pre-miRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
synthetic_oligo
sequence
An oligo composed of synthetic nucleotides.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
synthetic oligo
assembly
sequence
URL:http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly
http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly
A region of the genome of known length that is composed by ordering and aligning two or more different regions.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
fragment_assembly
sequence
physical map
A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
fragment assembly
fingerprint_map
sequence
fingerprint map
BACmap
FPCmap
FPC
A fingerprint_map is a physical map composed of restriction fragments.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
restriction map
STS_map
sequence
An STS map is a physical map organized by the unique STS landmarks.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
STS map
RH_map
sequence
A radiation hybrid map is a physical map.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RH map
radiation hybrid map
sonicate_fragment
sequence
sonicate fragment
A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polyploid
sequence
A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Polyploid
http://en.wikipedia.org/wiki/Polyploid
autopolyploid
sequence
A polyploid where the multiple chromosome set was derived from the same organism.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Autopolyploid
http://en.wikipedia.org/wiki/Autopolyploid
allopolyploid
sequence
A polyploid where the multiple chromosome set was derived from a different organism.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Allopolyploid
http://en.wikipedia.org/wiki/Allopolyploid
homing_endonuclease_binding_site
sequence
The binding site (recognition site) of a homing endonuclease. The binding site is typically large.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
homing endonuclease binding site
octamer_motif
Nature. 1986 Oct 16-22;323(6089):640-3.
sequence
A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.
GOC:dh
http://purl.org/obo/owl/GOC#GOC_dh
PMID:3095662
http://purl.org/obo/owl/PMID#PMID_3095662
octamer motif
apicoplast_chromosome
sequence
apicoplast chromosome
A chromosome originating in an apicoplast.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
sequence_collection
sequence
sequence collection
A collection of discontinuous sequences.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
overlapping_feature_set
This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA.
sequence
A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
overlapping feature set
overlapping_EST_set
sequence
A continous experimental result region extending the length of multiple overlapping EST's.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
overlapping EST set
ncRNA_gene
sequence
ncRNA gene
ncRNA gen
non-coding RNA gene
gRNA_gene
sequence
gRNA gene
miRNA_gene
sequence
miRNA gene
scRNA_gene
sequence
scRNA gene
snoRNA_gene
sequence
snoRNA gene
snRNA_gene
sequence
snRNA gene
SRP_RNA_gene
sequence
SRP RNA gene
stRNA_gene
sequence
stRNA gene
tmRNA_gene
sequence
tmRNA gene
tRNA_gene
sequence
tRNA gene
modified_adenosine
sequence
modified adenosine
A modified adenine is an adenine base feature that has been altered.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified_inosine
sequence
A modified inosine is an inosine base feature that has been altered.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified inosine
modified_cytidine
sequence
A modified cytidine is a cytidine base feature which has been altered.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified cytidine
modified_guanosine
sequence
modified guanosine
modified_uridine
sequence
modified uridine
one_methylinosine
sequence
1-methylinosine is a modified insosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
one methylinosine
RNAMOD:018
http://purl.org/obo/owl/RNAMOD#RNAMOD_018
m1I
1-methylinosine
one_two_prime_O_dimethylinosine
sequence
1,2'-O-dimethylinosine is a modified inosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:019
http://purl.org/obo/owl/RNAMOD#RNAMOD_019
1,2'-O-dimethylinosine
m'Im
one two prime O dimethylinosine
two_prime_O_methylinosine
sequence
2'-O-methylinosine is a modified inosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:081
http://purl.org/obo/owl/RNAMOD#RNAMOD_081
two prime O methylinosine
Im
2'-O-methylinosine
three_methylcytidine
sequence
3-methylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
three methylcytidine
3-methylcytidine
m3C
RNAMOD:020
http://purl.org/obo/owl/RNAMOD#RNAMOD_020
five_methylcytidine
sequence
RNAMOD:021
http://purl.org/obo/owl/RNAMOD#RNAMOD_021
5-methylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
m5C
five methylcytidine
5-methylcytidine
two_prime_O_methylcytidine
sequence
2'-O-methylcytidine
2'-O-methylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
Cm
two prime O methylcytidine
RNAMOD:022
http://purl.org/obo/owl/RNAMOD#RNAMOD_022
two_thiocytidine
sequence
s2C
2-thiocytidine
RNAMOD:023
http://purl.org/obo/owl/RNAMOD#RNAMOD_023
2-thiocytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
two thiocytidine
N4_acetylcytidine
sequence
ac4C
N4 acetylcytidine
N4-acetylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N4-acetylcytidine
RNAMOD:024
http://purl.org/obo/owl/RNAMOD#RNAMOD_024
five_formylcytidine
sequence
5-formylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
5-formylcytidine
five formylcytidine
f5C
RNAMOD:025
http://purl.org/obo/owl/RNAMOD#RNAMOD_025
five_two_prime_O_dimethylcytidine
sequence
m5Cm
five two prime O dimethylcytidine
5,2'-O-dimethylcytidine
5,2'-O-dimethylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:026
http://purl.org/obo/owl/RNAMOD#RNAMOD_026
N4_acetyl_2_prime_O_methylcytidine
sequence
ac4Cm
N4-acetyl-2'-O-methylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N4 acetyl 2 prime O methylcytidine
N4-acetyl-2'-O-methylcytidine
RNAMOD:027
http://purl.org/obo/owl/RNAMOD#RNAMOD_027
lysidine
sequence
k2C
URL:http://en.wikipedia.org/wiki/Lysidine
http://en.wikipedia.org/wiki/Lysidine
RNAMOD:028
http://purl.org/obo/owl/RNAMOD#RNAMOD_028
Lysidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N4_methylcytidine
sequence
m4C
N4 methylcytidine
N4-methylcytidine
N4-methylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:082
http://purl.org/obo/owl/RNAMOD#RNAMOD_082
N4_2_prime_O_dimethylcytidine
sequence
m4Cm
N4,2'-O-dimethylcytidine
N4 2 prime O dimethylcytidine
RNAMOD:083
http://purl.org/obo/owl/RNAMOD#RNAMOD_083
N4,2'-O-dimethylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five_hydroxymethylcytidine
sequence
hm5C
RNAMOD:084
http://purl.org/obo/owl/RNAMOD#RNAMOD_084
five hydroxymethylcytidine
5-hydroxymethylcytidine
5-hydroxymethylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five_formyl_two_prime_O_methylcytidine
sequence
five formyl two prime O methylcytidine
5-formyl-2'-O-methylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
f5Cm
5-formyl-2'-O-methylcytidine
RNAMOD:095
http://purl.org/obo/owl/RNAMOD#RNAMOD_095
N4_N4_2_prime_O_trimethylcytidine
sequence
N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N4,N4,2'-O-trimethylcytidine
m42Cm
RNAMOD:107
http://purl.org/obo/owl/RNAMOD#RNAMOD_107
one_methyladenosine
sequence
1_methyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
one methyladenosine
RNAMOD:001
http://purl.org/obo/owl/RNAMOD#RNAMOD_001
1-methyladenosine
m1A
two_methyladenosine
sequence
2_methyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
2-methyladenosine
m2A
two methyladenosine
RNAMOD:002
http://purl.org/obo/owl/RNAMOD#RNAMOD_002
N6_methyladenosine
sequence
N6 methyladenosine
m6A
RNAMOD:003
http://purl.org/obo/owl/RNAMOD#RNAMOD_003
N6-methyladenosine
N6_methyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
two_prime_O_methyladenosine
sequence
Am
2prime_O_methyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
two prime O methyladenosine
RNAMOD:004
http://purl.org/obo/owl/RNAMOD#RNAMOD_004
2'-O-methyladenosine
two_methylthio_N6_methyladenosine
sequence
two methylthio N6 methyladenosine
RNAMOD:005
http://purl.org/obo/owl/RNAMOD#RNAMOD_005
2_methylthio_N6_methyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
ms2m6A
2-methylthio-N6-methyladenosine
N6_isopentenyladenosine
sequence
N6 isopentenyladenosine
N6_isopentenyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
i6A
RNAMOD:006
http://purl.org/obo/owl/RNAMOD#RNAMOD_006
N6-isopentenyladenosine
two_methylthio_N6_isopentenyladenosine
sequence
two methylthio N6 isopentenyladenosine
ms2i6A
2-methylthio-N6-isopentenyladenosine
2_methylthio_N6_isopentenyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:007
http://purl.org/obo/owl/RNAMOD#RNAMOD_007
N6_cis_hydroxyisopentenyl_adenosine
sequence
N6-(cis-hydroxyisopentenyl)adenosine
N6 cis hydroxyisopentenyl adenosine
io6A
RNAMOD:008
http://purl.org/obo/owl/RNAMOD#RNAMOD_008
N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
sequence
RNAMOD:009
http://purl.org/obo/owl/RNAMOD#RNAMOD_009
ms2io6A
2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine
2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
two methylthio N6 cis hydroxyisopentenyl adenosine
N6_glycinylcarbamoyladenosine
sequence
RNAMOD:010
http://purl.org/obo/owl/RNAMOD#RNAMOD_010
N6-glycinylcarbamoyladenosine
N6 glycinylcarbamoyladenosine
g6A
N6_glycinylcarbamoyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N6_threonylcarbamoyladenosine
sequence
RNAMOD:011
http://purl.org/obo/owl/RNAMOD#RNAMOD_011
N6_threonylcarbamoyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
t6A
N6-threonylcarbamoyladenosine
N6 threonylcarbamoyladenosine
two_methylthio_N6_threonyl_carbamoyladenosine
sequence
2-methylthio-N6-threonyl carbamoyladenosine
two methylthio N6 threonyl carbamoyladenosine
ms2t6A
2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:012
http://purl.org/obo/owl/RNAMOD#RNAMOD_012
N6_methyl_N6_threonylcarbamoyladenosine
sequence
N6-methyl-N6-threonylcarbamoyladenosine
N6 methyl N6 threonylcarbamoyladenosine
RNAMOD:013
http://purl.org/obo/owl/RNAMOD#RNAMOD_013
m6t6A
N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N6_hydroxynorvalylcarbamoyladenosine
sequence
N6-hydroxynorvalylcarbamoyladenosine
N6 hydroxynorvalylcarbamoyladenosine
hn6A
N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:014
http://purl.org/obo/owl/RNAMOD#RNAMOD_014
two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
sequence
RNAMOD:015
http://purl.org/obo/owl/RNAMOD#RNAMOD_015
ms2hn6A
2-methylthio-N6-hydroxynorvalyl carbamoyladenosine
2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
two methylthio N6 hydroxynorvalyl carbamoyladenosine
two_prime_O_ribosyladenosine_phosphate
sequence
RNAMOD:016
http://purl.org/obo/owl/RNAMOD#RNAMOD_016
2prime_O_ribosyladenosine_phosphate is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
two prime O ribosyladenosine phosphate
2'-O-ribosyladenosine (phosphate)
Ar(p)
N6_N6_dimethyladenosine
sequence
N6_N6_dimethyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:080
http://purl.org/obo/owl/RNAMOD#RNAMOD_080
N6,N6-dimethyladenosine
m62A
N6_2_prime_O_dimethyladenosine
sequence
m6Am
N6,2'-O-dimethyladenosine
RNAMOD:088
http://purl.org/obo/owl/RNAMOD#RNAMOD_088
N6 2 prime O dimethyladenosine
N6_2prime_O_dimethyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N6_N6_2_prime_O_trimethyladenosine
sequence
N6_N6_2prime_O_trimethyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:089
http://purl.org/obo/owl/RNAMOD#RNAMOD_089
m62Am
N6,N6,2'-O-trimethyladenosine
one_two_prime_O_dimethyladenosine
sequence
RNAMOD:097
http://purl.org/obo/owl/RNAMOD#RNAMOD_097
1,2'-O-dimethyladenosine
m1Am
1,2'-O-dimethyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
one two prime O dimethyladenosine
N6_acetyladenosine
sequence
ac6A
N6_acetyladenosine is a modified adenosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N6 acetyladenosine
N6-acetyladenosine
RNAMOD:102
http://purl.org/obo/owl/RNAMOD#RNAMOD_102
seven_deazaguanosine
sequence
seven deazaguanosine
7-deazaguanosine is a moddified guanosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
7-deazaguanosine
queuosine
sequence
Q
Queuosine is a modified 7-deazoguanosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
URL:http://en.wikipedia.org/wiki/Queuosine
http://en.wikipedia.org/wiki/Queuosine
RNAMOD:043
http://purl.org/obo/owl/RNAMOD#RNAMOD_043
epoxyqueuosine
sequence
RNAMOD:044
http://purl.org/obo/owl/RNAMOD#RNAMOD_044
Epoxyqueuosine is a modified 7-deazoguanosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
eQ
galactosyl_queuosine
sequence
Galactosyl_queuosine is a modified 7-deazoguanosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:045
http://purl.org/obo/owl/RNAMOD#RNAMOD_045
galactosyl queuosine
galactosyl-queuosine
galQ
mannosyl_queuosine
sequence
mannosyl queuosine
mannosyl-queuosine
manQ
RNAMOD:046
http://purl.org/obo/owl/RNAMOD#RNAMOD_046
Mannosyl_queuosine is a modified 7-deazoguanosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
seven_cyano_seven_deazaguanosine
sequence
RNAMOD:047
http://purl.org/obo/owl/RNAMOD#RNAMOD_047
seven cyano seven deazaguanosine
preQ0
7_cyano_7_deazaguanosine is a modified 7-deazoguanosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
7-cyano-7-deazaguanosine
seven_aminomethyl_seven_deazaguanosine
sequence
preQ1
seven aminomethyl seven deazaguanosine
7-aminomethyl-7-deazaguanosine
7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:048
http://purl.org/obo/owl/RNAMOD#RNAMOD_048
archaeosine
sequence
G+
Archaeosine is a modified 7-deazoguanosine.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:049
http://purl.org/obo/owl/RNAMOD#RNAMOD_049
one_methylguanosine
sequence
1_methylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
m1G
1-methylguanosine
one methylguanosine
RNAMOD:029
http://purl.org/obo/owl/RNAMOD#RNAMOD_029
N2_methylguanosine
sequence
N2 methylguanosine
N2-methylguanosine
m2G
RNAMOD:030
http://purl.org/obo/owl/RNAMOD#RNAMOD_030
N2_methylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
seven_methylguanosine
sequence
m7G
seven methylguanosine
RNAMOD:031
http://purl.org/obo/owl/RNAMOD#RNAMOD_031
7_methylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
7-methylguanosine
two_prime_O_methylguanosine
sequence
RNAMOD:032
http://purl.org/obo/owl/RNAMOD#RNAMOD_032
2'-O-methylguanosine
Gm
two prime O methylguanosine
2prime_O_methylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N2_N2_dimethylguanosine
sequence
N2_N2_dimethylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:033
http://purl.org/obo/owl/RNAMOD#RNAMOD_033
m22G
N2,N2-dimethylguanosine
N2_2_prime_O_dimethylguanosine
sequence
m2Gm
N2,2'-O-dimethylguanosine
N2 2 prime O dimethylguanosine
N2_2prime_O_dimethylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:034
http://purl.org/obo/owl/RNAMOD#RNAMOD_034
N2_N2_2_prime_O_trimethylguanosine
sequence
N2,N2,2'-O-trimethylguanosine
m22Gmv
N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:035
http://purl.org/obo/owl/RNAMOD#RNAMOD_035
two_prime_O_ribosylguanosine_phosphate
sequence
2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
two prime O ribosylguanosine phosphate
Gr(p)
RNAMOD:036
http://purl.org/obo/owl/RNAMOD#RNAMOD_036
2'-O-ribosylguanosine (phosphate)
wybutosine
sequence
yW
Wybutosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:037
http://purl.org/obo/owl/RNAMOD#RNAMOD_037
peroxywybutosine
sequence
RNAMOD:038
http://purl.org/obo/owl/RNAMOD#RNAMOD_038
Peroxywybutosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
o2yW
hydroxywybutosine
sequence
Hydroxywybutosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
OHyW
RNAMOD:039
http://purl.org/obo/owl/RNAMOD#RNAMOD_039
undermodified_hydroxywybutosine
sequence
undermodified hydroxywybutosine
Undermodified_hydroxywybutosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
OHyW*
RNAMOD:040
http://purl.org/obo/owl/RNAMOD#RNAMOD_040
wyosine
sequence
RNAMOD:041
http://purl.org/obo/owl/RNAMOD#RNAMOD_041
IMG
Wyosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
methylwyosine
sequence
RNAMOD:042
http://purl.org/obo/owl/RNAMOD#RNAMOD_042
Methylwyosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
mimG
N2_7_dimethylguanosine
sequence
N2,7-dimethylguanosine
m2,7G
N2 7 dimethylguanosine
RNAMOD:090
http://purl.org/obo/owl/RNAMOD#RNAMOD_090
N2_7_dimethylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N2_N2_7_trimethylguanosine
sequence
m2,2,7G
N2,N2,7-trimethylguanosine
RNAMOD:091
http://purl.org/obo/owl/RNAMOD#RNAMOD_091
N2_N2_7_trimethylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
one_two_prime_O_dimethylguanosine
sequence
1_2prime_O_dimethylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:096
http://purl.org/obo/owl/RNAMOD#RNAMOD_096
m1Gm
one two prime O dimethylguanosine
1,2'-O-dimethylguanosine
four_demethylwyosine
sequence
4-demethylwyosine
4_demethylwyosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
imG-14
four demethylwyosine
RNAMOD:100
http://purl.org/obo/owl/RNAMOD#RNAMOD_100
isowyosine
sequence
RNAMOD:101
http://purl.org/obo/owl/RNAMOD#RNAMOD_101
Isowyosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
imG2
N2_7_2prirme_O_trimethylguanosine
sequence
N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
N2 7 2prirme O trimethylguanosine
m2,7Gm
RNAMOD:106
http://purl.org/obo/owl/RNAMOD#RNAMOD_106
N2,7,2'-O-trimethylguanosine
five_methyluridine
sequence
five methyluridine
m5U
5-methyluridine
5_methyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
URL:http://en.wikipedia.org/wiki/5-methyluridine
http://en.wikipedia.org/wiki/5-methyluridine
RNAMOD:052
http://purl.org/obo/owl/RNAMOD#RNAMOD_052
two_prime_O_methyluridine
sequence
2prime_O_methyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:053
http://purl.org/obo/owl/RNAMOD#RNAMOD_053
Um
2'-O-methyluridine
two prime O methyluridine
five_two_prime_O_dimethyluridine
sequence
5_2_prime_O_dimethyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:054
http://purl.org/obo/owl/RNAMOD#RNAMOD_054
m5Um
five two prime O dimethyluridine
5,2'-O-dimethyluridine
one_methylpseudouridine
sequence
RNAMOD:055
http://purl.org/obo/owl/RNAMOD#RNAMOD_055
1-methylpseudouridine
1_methylpseudouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
one methylpseudouridine
m1Y
two_prime_O_methylpseudouridine
sequence
two prime O methylpseudouridine
Ym
2prime_O_methylpseudouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:056
http://purl.org/obo/owl/RNAMOD#RNAMOD_056
2'-O-methylpseudouridine
two_thiouridine
sequence
two thiouridine
2_thiouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:057
http://purl.org/obo/owl/RNAMOD#RNAMOD_057
s2U
2-thiouridine
four_thiouridine
sequence
4_thiouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
4-thiouridine
s4U
four thiouridine
RNAMOD:058
http://purl.org/obo/owl/RNAMOD#RNAMOD_058
five_methyl_2_thiouridine
sequence
five methyl 2 thiouridine
m5s2U
5-methyl-2-thiouridine
5_methyl_2_thiouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:059
http://purl.org/obo/owl/RNAMOD#RNAMOD_059
two_thio_two_prime_O_methyluridine
sequence
two thio two prime O methyluridine
RNAMOD:060
http://purl.org/obo/owl/RNAMOD#RNAMOD_060
2-thio-2'-O-methyluridine
s2Um
2_thio_2prime_O_methyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
three_three_amino_three_carboxypropyl_uridine
sequence
RNAMOD:061
http://purl.org/obo/owl/RNAMOD#RNAMOD_061
3-(3-amino-3-carboxypropyl)uridine
acp3U
3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five_hydroxyuridine
sequence
5-hydroxyuridine
RNAMOD:060
http://purl.org/obo/owl/RNAMOD#RNAMOD_060
5_hydroxyuridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five hydroxyuridine
ho5U
five_methoxyuridine
sequence
5_methoxyuridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:063
http://purl.org/obo/owl/RNAMOD#RNAMOD_063
5-methoxyuridine
five methoxyuridine
mo5U
uridine_five_oxyacetic_acid
sequence
cmo5U
Uridine_5_oxyacetic_acid is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:064
http://purl.org/obo/owl/RNAMOD#RNAMOD_064
uridine 5-oxyacetic acid
uridine five oxyacetic acid
uridine_five_oxyacetic_acid_methyl_ester
sequence
Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
uridine five oxyacetic acid methyl ester
RNAMOD:065
http://purl.org/obo/owl/RNAMOD#RNAMOD_065
mcmo5U
uridine 5-oxyacetic acid methyl ester
five_carboxyhydroxymethyl_uridine
sequence
five carboxyhydroxymethyl uridine
5_carboxyhydroxymethyl_uridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:066
http://purl.org/obo/owl/RNAMOD#RNAMOD_066
5-(carboxyhydroxymethyl)uridine
chm5U
five_carboxyhydroxymethyl_uridine_methyl_ester
sequence
5-(carboxyhydroxymethyl)uridine methyl ester
5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:067
http://purl.org/obo/owl/RNAMOD#RNAMOD_067
mchm5U
five carboxyhydroxymethyl uridine methyl ester
five_methoxycarbonylmethyluridine
sequence
RNAMOD:068
http://purl.org/obo/owl/RNAMOD#RNAMOD_068
Five_methoxycarbonylmethyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five methoxycarbonylmethyluridine
5-methoxycarbonylmethyluridine
mcm5U
five_methoxycarbonylmethyl_two_prime_O_methyluridine
sequence
mcm5Um
five methoxycarbonylmethyl two prime O methyluridine
5-methoxycarbonylmethyl-2'-O-methyluridine
RNAMOD:069
http://purl.org/obo/owl/RNAMOD#RNAMOD_069
Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five_methoxycarbonylmethyl_two_thiouridine
sequence
5-methoxycarbonylmethyl-2-thiouridine
mcm5s2U
5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:070
http://purl.org/obo/owl/RNAMOD#RNAMOD_070
five methoxycarbonylmethyl two thiouridine
five_aminomethyl_two_thiouridine
sequence
RNAMOD:071
http://purl.org/obo/owl/RNAMOD#RNAMOD_071
5_aminomethyl_2_thiouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
5-aminomethyl-2-thiouridine
nm5s2U
five aminomethyl two thiouridine
five_methylaminomethyluridine
sequence
5-methylaminomethyluridine
five methylaminomethyluridine
mnm5U
RNAMOD:072
http://purl.org/obo/owl/RNAMOD#RNAMOD_072
5_methylaminomethyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five_methylaminomethyl_two_thiouridine
sequence
RNAMOD:073
http://purl.org/obo/owl/RNAMOD#RNAMOD_073
5-methylaminomethyl-2-thiouridine
five methylaminomethyl two thiouridine
mnm5s2U
5_methylaminomethyl_2_thiouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five_methylaminomethyl_two_selenouridine
sequence
mnm5se2U
five methylaminomethyl two selenouridine
5_methylaminomethyl_2_selenouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
5-methylaminomethyl-2-selenouridine
RNAMOD:074
http://purl.org/obo/owl/RNAMOD#RNAMOD_074
five_carbamoylmethyluridine
sequence
5-carbamoylmethyluridine
5_carbamoylmethyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
ncm5U
RNAMOD:075
http://purl.org/obo/owl/RNAMOD#RNAMOD_075
five carbamoylmethyluridine
five_carbamoylmethyl_two_prime_O_methyluridine
sequence
5-carbamoylmethyl-2'-O-methyluridine
RNAMOD:076
http://purl.org/obo/owl/RNAMOD#RNAMOD_076
5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
ncm5Um
five carbamoylmethyl two prime O methyluridine
five_carboxymethylaminomethyluridine
sequence
RNAMOD:077
http://purl.org/obo/owl/RNAMOD#RNAMOD_077
five carboxymethylaminomethyluridine
5_carboxymethylaminomethyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
cmnm5U
5-carboxymethylaminomethyluridine
five_carboxymethylaminomethyl_two_prime_O_methyluridine
sequence
five carboxymethylaminomethyl two prime O methyluridine
RNAMOD:078
http://purl.org/obo/owl/RNAMOD#RNAMOD_078
5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
cmnm5Um
5-carboxymethylaminomethyl- 2'-O-methyluridine
five_carboxymethylaminomethyl_two_thiouridine
sequence
RNAMOD:079
http://purl.org/obo/owl/RNAMOD#RNAMOD_079
five carboxymethylaminomethyl two thiouridine
5-carboxymethylaminomethyl-2-thiouridine
cmnm5s2U
5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
three_methyluridine
sequence
RNAMOD:085
http://purl.org/obo/owl/RNAMOD#RNAMOD_085
m3U
three methyluridine
3-methyluridine
3_methyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
sequence
1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine
m1acp3Y
1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:086
http://purl.org/obo/owl/RNAMOD#RNAMOD_086
five_carboxymethyluridine
sequence
5_carboxymethyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:087
http://purl.org/obo/owl/RNAMOD#RNAMOD_087
5-carboxymethyluridine
cm5U
five carboxymethyluridine
three_two_prime_O_dimethyluridine
sequence
3_2prime_O_dimethyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
three two prime O dimethyluridine
m3Um
RNAMOD:092
http://purl.org/obo/owl/RNAMOD#RNAMOD_092
3,2'-O-dimethyluridine
five_methyldihydrouridine
sequence
m5D
five methyldihydrouridine
5-methyldihydrouridine
RNAMOD:093
http://purl.org/obo/owl/RNAMOD#RNAMOD_093
5_methyldihydrouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
three_methylpseudouridine
sequence
3_methylpseudouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
m3Y
3-methylpseudouridine
RNAMOD:094
http://purl.org/obo/owl/RNAMOD#RNAMOD_094
three methylpseudouridine
five_taurinomethyluridine
sequence
5_taurinomethyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:098
http://purl.org/obo/owl/RNAMOD#RNAMOD_098
5-taurinomethyluridine
five taurinomethyluridine
tm5U
five_taurinomethyl_two_thiouridine
sequence
tm5s2U
5_taurinomethyl_2_thiouridineis a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five taurinomethyl two thiouridine
RNAMOD:099
http://purl.org/obo/owl/RNAMOD#RNAMOD_099
5-taurinomethyl-2-thiouridine
five_isopentenylaminomethyl_uridine
sequence
inm5U
RNAMOD:103
http://purl.org/obo/owl/RNAMOD#RNAMOD_103
5_isopentenylaminomethyl_uridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five isopentenylaminomethyl uridine
5-(isopentenylaminomethyl)uridine
five_isopentenylaminomethyl_two_thiouridine
sequence
RNAMOD:104
http://purl.org/obo/owl/RNAMOD#RNAMOD_104
inm5s2U
5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
five isopentenylaminomethyl two thiouridine
5-(isopentenylaminomethyl)- 2-thiouridine
five_isopentenylaminomethyl_two_prime_O_methyluridine
sequence
5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature.
URL:http://library.med.utah.edu/RNAmods/
http://library.med.utah.edu/RNAmods/
RNAMOD:105
http://purl.org/obo/owl/RNAMOD#RNAMOD_105
inm5Um
five isopentenylaminomethyl two prime O methyluridine
5-(isopentenylaminomethyl)- 2'-O-methyluridine
histone_binding_site
sequence
histone binding site
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
CDS_fragment
sequence
incomplete CDS
CDS fragment
modified_amino_acid_feature
sequence
A post translationally modified amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified amino acid feature
modified_glycine
sequence
modified glycine
A post translationally modified glycine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ModGly
MOD:00908
http://purl.org/obo/owl/MOD#MOD_00908
modified_L_alanine
sequence
A post translationally modified alanine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
MOD:00901
http://purl.org/obo/owl/MOD#MOD_00901
modified L-alanine
modified L alanine
ModAla
modified_L_asparagine
sequence
MOD:00903
http://purl.org/obo/owl/MOD#MOD_00903
A post translationally modified asparagine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ModAsn
modified L-asparagine
modified L asparagine
modified_L_aspartic_acid
sequence
MOD:00904
http://purl.org/obo/owl/MOD#MOD_00904
A post translationally modified aspartic acid amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ModAsp
modified L aspartic acid
modified L-aspartic acid
modified_L_cysteine
sequence
modified L-cysteine
MOD:00905
http://purl.org/obo/owl/MOD#MOD_00905
modified L cysteine
ModCys
A post translationally modified cysteine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified_L_glutamic_acid
sequence
MOD:00906
http://purl.org/obo/owl/MOD#MOD_00906
modified L glutamic acid
ModGlu
modified L-glutamic acid
modified_L_threonine
sequence
A post translationally modified threonine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
MOD:00917
http://purl.org/obo/owl/MOD#MOD_00917
modified L threonine
modified L-threonine
ModThr
modified_L_tryptophan
sequence
ModTrp
MOD:00918
http://purl.org/obo/owl/MOD#MOD_00918
modified L tryptophan
modified L-tryptophan
A post translationally modified tryptophan amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified_L_glutamine
sequence
ModGln
A post translationally modified glutamine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
MOD:00907
http://purl.org/obo/owl/MOD#MOD_00907
modified L glutamine
modified L-glutamine
modified_L_methionine
sequence
MOD:00913
http://purl.org/obo/owl/MOD#MOD_00913
modified L-methionine
ModMet
A post translationally modified methionine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified L methionine
modified_L_isoleucine
sequence
ModIle
MOD:00910
http://purl.org/obo/owl/MOD#MOD_00910
modified L isoleucine
modified L-isoleucine
A post translationally modified isoleucine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified_L_phenylalanine
sequence
A post translationally modified phenylalanine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ModPhe
modified L-phenylalanine
modified L phenylalanine
MOD:00914
http://purl.org/obo/owl/MOD#MOD_00914
modified_L_histidine
sequence
A post translationally modified histidie amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
MOD:00909
http://purl.org/obo/owl/MOD#MOD_00909
modified L-histidine
modified L histidine
ModHis
modified_L_serine
sequence
MosSer
modified L-serine
modified L serine
MOD:00916
http://purl.org/obo/owl/MOD#MOD_00916
A post translationally modified serine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified_L_lysine
sequence
A post translationally modified lysine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified L-lysine
ModLys
modified L lysine
MOD:00912
http://purl.org/obo/owl/MOD#MOD_00912
modified_L_leucine
sequence
ModLeu
modified L-leucine
modified L leucine
A post translationally modified leucine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
MOD:00911
http://purl.org/obo/owl/MOD#MOD_00911
modified_L_selenocysteine
sequence
modified L selenocysteine
modified L-selenocysteine
MOD:01158
http://purl.org/obo/owl/MOD#MOD_01158
A post translationally modified selenocysteine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
modified_L_valine
sequence
ModVal
A post translationally modified valine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
MOD:00920
http://purl.org/obo/owl/MOD#MOD_00920
modified L-valine
modified L valine
modified_L_proline
sequence
A post translationally modified proline amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ModPro
MOD:00915
http://purl.org/obo/owl/MOD#MOD_00915
modified L proline
modified L-proline
modified_L_tyrosine
sequence
modified L tyrosine
MOD:00919
http://purl.org/obo/owl/MOD#MOD_00919
A post translationally modified tyrosine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ModTry
modified L-tyrosine
modified_L_arginine
sequence
modified L-arginine
ModArg
modified L arginine
MOD:00902
http://purl.org/obo/owl/MOD#MOD_00902
A post translationally modified arginine amino acid feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
peptidyl
sequence
An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cleaved_for_gpi_anchor_region
sequence
cleaved for gpi anchor region
The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor.
EBI:rh
http://purl.org/obo/owl/EBI#EBI_rh
biomaterial_region
sequence
biomaterial region
A region which is intended for use in an experiment.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
experimental_feature
sequence
A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
analysis feature
experimental_output_artefact
experimental output artefact
biological_region
sequence
biological region
A region defined by its disposition to be involved in a biological process.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
topologically_defined_region
sequence
topologically defined region
A region that is defined according to its relations with other regions within the same sequence.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
translocation_breakpoint
sequence
translocation breakpoint
The point within a chromosome where a translocation begins or ends.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
insertion_breakpoint
sequence
The point within a chromosome where a insertion begins or ends.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
insertion breakpoint
deletion_breakpoint
sequence
deletion breakpoint
The point within a chromosome where a deletion begins or ends.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
five_prime_flanking_region
sequence
A flanking region located five prime of a specific region.
SO:chado
http://purl.org/obo/owl/SO#SO_chado
five prime flanking region
5' flanking region
three_prime_flanking_region
sequence
A flanking region located three prime of a specific region.
SO:chado
http://purl.org/obo/owl/SO#SO_chado
three prime flanking region
3' flanking region
transcribed_fragment
Term requested by the MODencode group.
sequence
transfrag
An experimental region, defined by a tiling array experiment to be transcribed at some level.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcribed fragment
cis_splice_site
sequence
cis splice site
Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
trans_splice_site
sequence
trans splice site
Primary transcript region bordering trans-splice junction.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
splice_junction
sequence
The boundary between an intron and an exon.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
splice junction
splice boundary
conformational_switch
MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999.
sequence
A region of a polypeptide, involved in the transition from one conformational state to another.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide conformational switch
dye_terminator_read
sequence
dye terminator read
A read produced by the dye terminator method of sequencing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
pyrosequenced_read
An example is a read produced by Roche 454 technology.
sequence
A read produced by pyrosequencing technology.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
pyorsequenced read
ligation_based_read
An example of this kind of read is one produced by ABI SOLiD.
sequence
A read produced by ligation based sequencing technologies.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ligation based read
polymerase_synthesis_read
An example is a read produced by Illumina technology.
sequence
polymerase synthesis read
A read produced by the polymerase based sequence by synthesis method.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cis_regulatory_frameshift_element
sequence
A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence.
RFAM:jd
http://purl.org/obo/owl/RFAM#RFAM_jd
cis regulatory frameshift element
expressed_sequence_assembly
From tracker [ 2372385 ] expressed_sequence_assembly.
sequence
expressed sequence assembly
A sequence assembly derived from expressed sequences.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
DNA_binding_site
sequence
DNA binding site
A binding site that, in the molecule, interacts selectively and non-covalently with DNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cryptic_gene
sequence
A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cryptic gene
sequence_variant_affecting_polyadenylation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant affecting polyadenylation
mutation affecting polyadenylation
three_prime_RACE_clone
sequence
3' RACE clone
A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host.
modENCODE:nlw
http://purl.org/obo/owl/modENCODE#modENCODE_nlw
cassette_pseudogene
Requested by the Trypanosome community.
sequence
A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cassette type psedogene
cassette pseudogene
alanine
A place holder for a cross product with chebi.
sequence
A
Ala
valine
A place holder for a cross product with chebi.
sequence
Val
V
leucine
A place holder for a cross product with chebi.
sequence
Leu
L
isoleucine
A place holder for a cross product with chebi.
sequence
I
Ile
proline
A place holder for a cross product with chebi.
sequence
Pro
P
tryptophan
A place holder for a cross product with chebi.
sequence
Trp
W
phenylalanine
A place holder for a cross product with chebi.
sequence
Phe
F
methionine
A place holder for a cross product with chebi.
sequence
M
Met
glycine
A place holder for a cross product with chebi.
sequence
Gly
G
serine
A place holder for a cross product with chebi.
sequence
S
Ser
threonine
A place holder for a cross product with chebi.
sequence
Thr
T
tyrosine
A place holder for a cross product with chebi.
sequence
Tyr
Y
cysteine
A place holder for a cross product with chebi.
sequence
Cys
C
glutamine
A place holder for a cross product with chebi.
sequence
Q
Gln
asparagine
A place holder for a cross product with chebi.
sequence
Asn
N
lysine
A place holder for a cross product with chebi.
sequence
K
Lys
arginine
A place holder for a cross product with chebi.
sequence
Arg
R
histidine
A place holder for a cross product with chebi.
sequence
His
H
aspartic_acid
A place holder for a cross product with chebi.
sequence
Asp
aspartic acid
D
glutamic_acid
A place holder for a cross product with chebi.
sequence
E
Glu
glutamic acid
selenocysteine
A place holder for a cross product with chebi.
sequence
U
Sec
pyrrolysine
A place holder for a cross product with chebi.
sequence
O
Pyl
transcribed_cluster
This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
sequence
A region defined by a set of transcribed sequences from the same gene or expressed pseudogene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcribed cluster
unigene cluster
unigene_cluster
This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
sequence
unigene cluster
A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
CRISPR
sequence
Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences.
RFAM:jd
http://purl.org/obo/owl/RFAM#RFAM_jd
http:en.wikipedia.org/wiki/CRISPR
http://purl.org/obo/owl/http#http_en.wikipedia.org/wiki/CRISPR
CRISPR element
Clustered_Regularly_Interspaced_Short_Palindromic_Repeat
insulator_binding_site
See tracker ID 2060908.
sequence
insulator binding site
A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
enhancer_binding_site
sequence
A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
enhancer binding site
contig_collection
See tracker ID: 2138359.
sequence
contig collection
A collection of contigs.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
lincRNA
sequence
long intergenic non-coding RNA
large intervening non-coding RNA
A multiexonic non-coding RNA transcribed by RNA polymerase II.
PMID:19182780
http://purl.org/obo/owl/PMID#PMID_19182780
SO:ke
http://purl.org/obo/owl/SO#SO_ke
UST
sequence
UTR sequence tag
An EST spanning part or all of the untranslated regions of a protein-coding transcript.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
three_prime_UST
sequence
A UST located in the 3'UTR of a protein-coding transcript.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
3' UST
five_prime_UST
sequence
An UST located in the 5'UTR of a protein-coding transcript.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
5' UST
RST
sequence
RACE sequence tag
A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
three_prime_RST
sequence
3' RST
A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
five_prime_RST
sequence
5' RST
A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
UST_match
sequence
A match against an UST sequence.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
UST match
RST_match
sequence
A match against an RST sequence.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
RST match
primer_match
sequence
A nucleotide match to a primer sequence.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
primer match
miRNA_antiguide
sequence
miRNA antiguide
miRNA star
A region of the pri miRNA that basepairs with the guide to form the hairpin.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
miRNA passenger strand
trans_splice_junction
sequence
The boundary between the spliced leader and the first exon of the mRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
trans-splice junction
outron
sequence
A region of a primary transcript, that is removed via trans splicing.
PMID:16401417
http://purl.org/obo/owl/PMID#PMID_16401417
SO:ke
http://purl.org/obo/owl/SO#SO_ke
natural_plasmid
sequence
A plasmid that occurs naturally.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
natural plasmid
gene_trap_construct
sequence
gene trap construct
A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker.
ZFIN:dh
http://purl.org/obo/owl/ZFIN#ZFIN_dh
promoter_trap_construct
sequence
A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.
ZFIN:dh
http://purl.org/obo/owl/ZFIN#ZFIN_dh
promoter trap construct
enhancer_trap_construct
sequence
enhancer trap construct
An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic.
ZFIN:dh
http://purl.org/obo/owl/ZFIN#ZFIN_dh
PAC_end
sequence
A region of sequence from the end of a PAC clone that may provide a highly specific marker.
ZFIN:mh
http://purl.org/obo/owl/ZFIN#ZFIN_mh
PAC end
RAPD
sequence
RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers.
ZFIN:mh
http://purl.org/obo/owl/ZFIN#ZFIN_mh
Random Amplification Polymorphic DNA
shadow_enhancer
sequence
shadow enhancer
SNV
sequence
SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
SO:bm
http://purl.org/obo/owl/SO#SO_bm
single nucleotide variant
X_element_combinatorial_repeat
X element combinatorial repeats contain Tbf1p binding sites,nand possible functions include a role in telomerase-independent telomerenmaintenance via recombination or as a barrier against transcriptionalnsilencing. These are usually present as a combination of one or more ofnseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
sequence
An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element.
URL:http://www.yeastgenome.org/help/glossary.html
http://www.yeastgenome.org/help/glossary.html
X element combinatorial repeat
Y_prime_element
This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
sequence
Y' element
A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies.
http:http://www.yeastgenome.org/help/glossary.html
http://purl.org/obo/owl/http#http_http://www.yeastgenome.org/help/glossary.html
standard_draft
sequence
The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete.
DOI:10.1126
http://purl.org/obo/owl/DOI#DOI_10.1126
standard draft
high_quality_draft
sequence
The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome.
DOI:10.1126
http://purl.org/obo/owl/DOI#DOI_10.1126
high quality draft
improved_high_quality_draft
sequence
The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution.
DOI:10.1126
http://purl.org/obo/owl/DOI#DOI_10.1126
improved high quality draft
annotation_directed_improved_draft
sequence
annotation directed improvement
The status of a whole genome sequence,where annotation, and verification of coding regions has occurred.
DOI:10.1126
http://purl.org/obo/owl/DOI#DOI_10.1126
noncontiguous_finished
sequence
non contiguous finished
The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions.
DOI:10.1126
http://purl.org/obo/owl/DOI#DOI_10.1126
finished_genome
sequence
finished genome
finished
The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.
DOI:10.1126
http://purl.org/obo/owl/DOI#DOI_10.1126
intronic_regulatory_region
sequence
intronic regulatory region
A regulatory region that is part of an intron.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
centromere_DNA_Element_I
This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
sequence
Centromere DNA Element I
A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p).
PMID:11222754
http://purl.org/obo/owl/PMID#PMID_11222754
CDEI
centromere_DNA_Element_II
This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
sequence
CDEII
centromere DNA Element II
A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.
PMID:11222754
http://purl.org/obo/owl/PMID#PMID_11222754
centromere_DNA_Element_III
This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
sequence
A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex.
PMID:11222754
http://purl.org/obo/owl/PMID#PMID_11222754
CDEIII
centromere DNA Element III
telomeric_repeat
The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739.
sequence
telomeric repeat
The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.
PMID:8720065
http://purl.org/obo/owl/PMID#PMID_8720065
X_element
Possible functions include roles in chromosomal segregation,nmaintenance of chromosome stability, recombinational sequestering, or as anbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
sequence
The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.
URL:http://www.yeastgenome.org/help/glossary.html#xelemcoresequence
http://www.yeastgenome.org/help/glossary.html#xelemcoresequence
X element
YAC_end
sequence
A region of sequence from the end of a YAC clone that may provide a highly specific marker.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
YAC end
whole_genome_sequence_status
This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms.
sequence
The status of whole genome sequence.
DOI:10.1126
http://purl.org/obo/owl/DOI#DOI_10.1126
whole genome sequence status
heritable_phenotypic_marker
sequence
phenotypic marker
heritable phenotypic marker
A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.
JAX:hdene
http://purl.org/obo/owl/JAX#JAX_hdene
peptide_collection
Term requested via tracker ID: 2910829.
sequence
A collection of peptide sequences.
BBOP:nlw
http://purl.org/obo/owl/BBOP#BBOP_nlw
peptide set
peptide collection
high_identity_region
Requested by tracker ID: 2902685.
sequence
An experimental feature with high sequence identity to another sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
high identity region
processed_transcript
Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.
sequence
A transcript for which no open reading frame has been identified and for which no other function has been determined.
MGI:hdeen
http://purl.org/obo/owl/MGI#MGI_hdeen
processed transcript
assortment_derived_variation
sequence
A chromosome variation derived from an event during meiosis.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
assortment derived variation
reference_genome
sequence
A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
reference genome
variant_genome
sequence
variant genome
A collection of sequences (often chromosomes) of an individual.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
variant_collection
sequence
variant collection
A collection of one or more sequences of an individual.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
alteration_attribute
sequence
alteration attribute
chromosomal_variation_attribute
sequence
chromosomal variation attribute
intrachromosomal
sequence
interchromosomal
sequence
insertion_attribute
sequence
insertion attribute
A quality of a chromosomal insertion,.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tandem
sequence
direct
sequence
A quality of an insertion where the insert is not in a cytologically inverted orientation.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inverted
sequence
A quality of an insertion where the insert is in a cytologically inverted orientation.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
free
sequence
The quality of a duplication where the new region exists independently of the original.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inversion_attribute
sequence
inversion attribute
pericentric
sequence
paracentric
sequence
translocaton_attribute
sequence
translocation attribute
reciprocal
sequence
insertional
sequence
duplication_attribute
sequence
duplication attribute
chromosomally_aberrant_genome
sequence
chromosomally aberrant genome
assembly_error_correction
sequence
assembly error correction
A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
base_call_error_correction
sequence
base call error correction
A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
peptide_localization_signal
sequence
A region of peptide sequence used to target the polypeptide molecule to a specific organelle.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
peptide localization signal
localization signal
nuclear_localization_signal
sequence
URL:http://en.wikipedia.org/wiki/Nuclear_localization_signal
http://en.wikipedia.org/wiki/Nuclear_localization_signal
A polypeptide region that targets a polypeptide to the nucleus.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
NLS
endosomal_localization_signal
sequence
endosomal localization signal
A polypeptide region that targets a polypeptide to the endosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
lysosomal_localization_signal
sequence
A polypeptide region that targets a polypeptide to the lysosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
lysosomal localization signal
nuclear_export_signal
sequence
NES
nuclear export signal
URL:http://en.wikipedia.org/wiki/Nuclear_export_signal
http://en.wikipedia.org/wiki/Nuclear_export_signal
A polypeptide region that targets a polypeptide to he cytoplasm.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
recombination_signal_sequence
sequence
A region recognized by a recombinase.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
recombination signal sequence
URL:http://en.wikipedia.org/wiki/Recombination_Signal_Sequences
http://en.wikipedia.org/wiki/Recombination_Signal_Sequences
cryptic_splice_site
sequence
cryptic splice signal
cryptic splice site
A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nuclear_rim_localization_signal
sequence
PMID:16027110
http://purl.org/obo/owl/PMID#PMID_16027110
nuclear rim localization signal
A polypeptide region that targets a polypeptide to the nuclear rim.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
p_element
sequence
A P_element is a DNA transposon responsible for hybrid dysgenesis.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
P element
functional_variant
sequence
A sequence variant in which the function of a gene product is altered with respect to a reference.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
functional variant
structural_variant
sequence
structural variant
A sequence variant that changes one or more sequence features.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript_function_variant
sequence
transcript function variant
A sequence variant which alters the functioning of a transcript with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translational_product_function_variant
sequence
A sequence variant that affects the functioning of a translational product with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translational product variant
level_of_transcript_variant
sequence
A sequence variant which alters the level of a transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
level of transcript variant
decreased_transcript_level_variant
sequence
decreased transcript level
A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
increased_transcript_level_variant
sequence
A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
increased transcript level variant
transcript_processing_variant
sequence
transcript processing variant
A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
editing_variant
sequence
editing variant
A transcript processing variant whereby the process of editing is disrupted with respect to the reference.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polyadenylation_variant
sequence
A sequence variant that changes polyadenylation with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polyadenylation variant
transcript_stability_variant
sequence
A variant that changes the stability of a transcript with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript stability variant
decreased_transcript_stability_variant
sequence
decrease transcript stability variant
A sequence variant that decreases transcript stability with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
increased_transcript_stability_variant
sequence
increased transcript stability variant
A sequence variant that increases transcript stability with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcription_variant
sequence
transcription variant
A variant that changes alters the transcription of a transcript with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
rate_of_transcription_variant
sequence
rate of transcription variant
A sequence variant that changes the rate of transcription with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
increased_transcription_rate_variant
sequence
A sequence variant that increases the rate of transcription with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
increased transcription rate variant
decreased_transcription_rate_variant
sequence
decreased transcription rate variant
A sequence variant that decreases the rate of transcription with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translational_product_level_variant
sequence
A functional variant that changes the translational product level with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translational product level variant
polypeptide_function_variant
sequence
A sequence variant which changes polypeptide functioning with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide function variant
decreased_translational_product_level
sequence
decrease translational product level
A sequence variant which decreases the translational product level with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
increased_translational_product_level
sequence
A sequence variant which increases the translational product level with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
increase translational product level
polypeptide_gain_of_function_variant
sequence
A sequence variant which causes gain of polypeptide function with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide gain of function variant
polypeptide_localization_variant
sequence
polypeptide localization variant
A sequence variant which changes the localization of a polypeptide with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide_loss_of_function_variant
sequence
polypeptide loss of function variant
A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inactive_ligand_binding_site
sequence
inactive ligand binding site
A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide_partial_loss_of_function
sequence
polypeptide partial loss of function
A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide_post_translational_processing_variant
sequence
A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide post translational processing variant
copy_number_change
sequence
A sequence variant where copies of a feature (CNV) are either increased or decreased.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
copy number change
gene_variant
sequence
gene structure variant
A sequence variant where the structure of the gene is changed.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene_fusion
sequence
A sequence variant whereby a two genes have become joined.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene fusion
regulatory_region_variant
EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.
sequence
A sequence variant located within a regulatory region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
regulatory region variant
regulatory_region_
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
stop_retained_variant
sequence
A sequence variant where at least one base in the terminator codon is changed, but the terminator remains.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
stop retained variant
splicing_variant
sequence
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
splicing variant
A sequence variant that changes the process of splicing.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cryptic_splice_site_variant
sequence
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
cryptic splice site activation
A sequence variant causing a new (functional) splice site.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
cryptic_splice_acceptor
sequence
cryptic splice acceptor
A sequence variant whereby a new splice site is created due to the activation of a new acceptor.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cryptic_splice_donor
sequence
cryptic splice donor
A sequence variant whereby a new splice site is created due to the activation of a new donor.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
exon_loss
sequence
A sequence variant whereby an exon is lost from the transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
exon loss
intron_gain
sequence
A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
intron gain
splice_acceptor_variant
sequence
splice acceptor variant
A splice variant that changes the 2 base region at the 3' end of an intron.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
splice_donor_variant
sequence
A splice variant that changes the2 base region at the 5' end of an intron.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
splice donor variant
transcript_variant
sequence
A sequence variant that changes the structure of the transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript variant
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
complex_transcript_variant
EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
sequence
complex transcript variant
A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
complext change in transcript
complex_indel
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
stop_lost
EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.
sequence
A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
stop lost
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
stop codon lost
transcript_sequence_variant
sequence
transcript sequence variant
coding_sequence_variant
sequence
SO:0001581
coding sequence variant
coding variant
codon variant
codon_variant
A sequence variant that changes the coding sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
initiator_codon_variant
sequence
loinc:LA6695-6
http://purl.org/obo/owl/loinc#loinc_LA6695-6
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
initiatior codon variant
initiator codon change
A codon variant that changes at least one base of the first codon of a transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
missense_variant
EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution.
SO:0001783
SO:0001584
sequence
non synonymous variant
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
loinc:LA6698-0
http://purl.org/obo/owl/loinc#loinc_LA6698-0
URL:http://en.wikipedia.org/wiki/Missense_mutation
http://en.wikipedia.org/wiki/Missense_mutation
non synonymous codon
missense codon
missense
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
EBI:gr
http://purl.org/obo/owl/EBI#EBI_gr
non_synonymous_coding
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
conservative_missense_variant
sequence
neutral missense codon
quiet missense codon
A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
conservative missense variant
conservative missense codon
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
non_conservative_missense_variant
sequence
A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
non conservative missense codon
non conservative missense variant
stop_gained
EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
sequence
A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nonsense
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
nonsense codon
stop gained
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
stop codon gained
loinc:LA6699-8
http://purl.org/obo/owl/loinc#loinc_LA6699-8
frameshift_variant
EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
sequence
frameshift variant
A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
frameshift_
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
loinc:LA6694-9
http://purl.org/obo/owl/loinc#loinc_LA6694-9
frameshift_coding
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
terminator_codon_variant
The terminal codon may be the terminator, or in an incomplete transcript the last available codon.
sequence
SO:0001625
terminator codon variant
terminal_codon_variant
A sequence variant whereby at least one of the bases in the terminator codon is changed.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
loinc:LA6700-2
http://purl.org/obo/owl/loinc#loinc_LA6700-2
terminal codon variant
frame_restoring_variant
sequence
A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
frame restoring variant
minus_1_frameshift_variant
sequence
-1 frameshift variant
A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead.
URL:http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535
http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535
minus 1 frameshift variant
minus_2_frameshift_variant
sequence
-2 frameshift variant
minus 2 frameshift variant
plus_1_frameshift_variant
sequence
+1 frameshift variant
plus 1 frameshift variant
A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward.
URL:http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535
http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535
plus_2_frameshift_variant
sequence
plus 2 frameshift variant
+2 frameshift variant
transcript_secondary_structure_variant
sequence
A sequence variant within a transcript that changes the secondary structure of the RNA product.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript secondary structure variant
compensatory_transcript_secondary_structure_variant
sequence
A secondary structure variant that compensate for the change made by a previous variant.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
compensatory transcript secondary structure variant
translational_product_structure_variant
sequence
translational product structure variant
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
A sequence variant within the transcript that changes the structure of the translational product.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
3D_polypeptide_structure_variant
sequence
3D polypeptide structure variant
A sequence variant that changes the resulting polypeptide structure.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
complex_3D_structural_variant
sequence
A sequence variant that changes the resulting polypeptide structure.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
complex 3D structural variant
conformational_change_variant
sequence
conformational change variant
A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
complex_change_of_translational_product_variant
sequence
complex change of translational product variant
polypeptide_sequence_variant
sequence
A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide sequence variant
amino_acid_deletion
sequence
A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
amino acid deletion
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
amino_acid_insertion
sequence
A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
amino acid insertion
amino_acid_substitution
sequence
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
amino acid substitution
conservative_amino_acid_substitution
sequence
conservative amino acid substitution
A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
non_conservative_amino_acid_substitution
sequence
non conservative amino acid substitution
A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
elongated_polypeptide
sequence
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
elongated polypeptide
A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
elongated_polypeptide_C_terminal
sequence
A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
elongated polypeptide C terminal
elongated_polypeptide_N_terminal
sequence
elongated polypeptide N terminal
A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
elongated_in_frame_polypeptide_C_terminal
sequence
elongated in frame polypeptide C terminal
A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
elongated_out_of_frame_polypeptide_C_terminal
sequence
elongated polypeptide out of frame C terminal
A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
elongated_in_frame_polypeptide_N_terminal_elongation
sequence
A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
elongated in frame polypeptide N terminal
elongated_out_of_frame_polypeptide_N_terminal
sequence
A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
elongated out of frame N terminal
polypeptide_fusion
sequence
A sequence variant that causes a fusion of two polypeptide sequences.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide fusion
polypeptide_truncation
sequence
polypeptide truncation
A sequence variant of the CD that causes a truncation of the resulting polypeptide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
inactive_catalytic_site
sequence
inactive catalytic site
A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nc_transcript_variant
Within non-coding gene - Located within a gene that does not code for a protein.
sequence
within_non_coding_gene
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
non coding transcript variant
nc transcript variant
A transcript variant of a non coding RNA gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mature_miRNA_variant
EBI term: Within mature miRNA - Located within a microRNA.
sequence
within_mature_miRNA
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
mature miRNA variant
A transcript variant located with the sequence of the mature miRNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
NMD_transcript_variant
sequence
NMD_transcript
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
NMD transcript variant
A variant in a transcript that is the target of NMD.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
UTR_variant
sequence
UTR_
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
UTR variant
A transcript variant that is located within the UTR.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
5_prime_UTR_variant
EBI term: 5prime UTR variations - In 5prime UTR (untranslated region).
sequence
untranslated-5
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
five prime UTR variant
5'UTR variant
5PRIME_UTR
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
A UTR variant of the 5' UTR.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
3_prime_UTR_variant
EBI term 3prime UTR variations - In 3prime UTR.
sequence
three prime UTR variant
3PRIME_UTR
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
untranslated-3
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
3'UTR variant
A UTR variant of the 3' UTR.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
incomplete_terminal_codon_variant
EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.
sequence
incomplete terminal codon variant
A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
partial_codon
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
intron_variant
EBI term: Intronic variations - In intron.
sequence
A transcript variant occurring within an intron.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
intron_
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
intron variant
intronic
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
intergenic_variant
EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript.
sequence
intergenic variant
intergenic
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
A sequence variant located in the intergenic region, between genes.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
splice_site_variant
EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger.
sequence
splice site variant
essential_splice_site
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript.
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
splice_region_variant
EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.
sequence
splice region variant
splice_region_variant
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
upstream_gene_variant
Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
sequence
upstream gene variant
A sequence variant located 5' of a gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
downstream_gene_variant
Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
sequence
downstream gene variant
A sequence variant located 3' of a gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
5KB_downstream_variant
EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
sequence
within 5KB downstream
A sequence variant located within 5 KB of the end of a gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
5KB downstream variant
downstream
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
500B_downstream_variant
sequence
500B downstream variant
A sequence variant located within a half KB of the end of a gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
near-gene-3
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
5KB_upstream_variant
EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
sequence
5kb upstream variant
upstream
URL:http://ensembl.org/info/docs/variation/index.html
http://ensembl.org/info/docs/variation/index.html
A sequence variant located within 5KB 5' of a gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
2KB_upstream_variant
sequence
near-gene-5
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
2KB upstream variant
A sequence variant located within 2KB 5' of a gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
rRNA_gene
sequence
A gene that encodes for ribosomal RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
rRNA gene
piRNA_gene
sequence
A gene that encodes for an piwi associated RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
piRNA gene
RNase_P_RNA_gene
sequence
A gene that encodes an RNase P RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
RNase P RNA gene
RNase_MRP_RNA_gene
sequence
RNase MRP RNA gene
A gene that encodes a RNase_MRP_RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
lincRNA_gene
sequence
lincRNA gene
A gene that encodes large intervening non-coding RNA.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mathematically_defined_repeat
Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.).
sequence
mathematically defined repeat
A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness.
SO:jestill
http://purl.org/obo/owl/SO#SO_jestill
telomerase_RNA_gene
sequence
TERC
A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
http:http://en.wikipedia.org/wiki/Telomerase_RNA_component
http://purl.org/obo/owl/http#http_http://en.wikipedia.org/wiki/Telomerase_RNA_component
Telomerase RNA component
telomerase RNA gene
targeting_vector
sequence
targeting vector
An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications.
PMID:10354467
http://purl.org/obo/owl/PMID#PMID_10354467
MGD:tm
http://purl.org/obo/owl/MGD#MGD_tm
genetic_marker
sequence
genetic marker
A measurable sequence feature that varies within a population.
SO:db
http://purl.org/obo/owl/SO#SO_db
DArT_marker
sequence
A genetic marker, discovered using Diversity Arrays Technology (DArT) technology.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
DArT marker
kozak_sequence
sequence
URL:http://en.wikipedia.org/wiki/Kozak_consensus_sequence
http://en.wikipedia.org/wiki/Kozak_consensus_sequence
A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
kozak sequence
kozak consensus
kozak consensus sequence
nested_transposon
sequence
A transposon that is disrupted by the insertion of another element.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nested transposon
nested_repeat
sequence
nested repeat
A repeat that is disrupted by the insertion of another element.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inframe_variant
sequence
A sequence variant which does not cause a disruption of the translational reading frame.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inframe variant
cds-indel
retinoic_acid_responsive_element
sequence
A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.
PMID:19917671
http://purl.org/obo/owl/PMID#PMID_19917671
PMID:11327309
http://purl.org/obo/owl/PMID#PMID_11327309
retinoic acid responsive element
RARE
nucleotide_to_protein_binding_site
sequence
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nucleotide to protein binding site
nucleotide_binding_site
See GO:0000166 : nucleotide binding.
sequence
A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
nucleotide binding site
metal_binding_site
See GO:0046872 : metal ion binding.
sequence
A binding site that, in the molecule, interacts selectively and non-covalently with metal ions.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
metal binding site
ligand_binding_site
sequence
ligand binding site
A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
nested_tandem_repeat
Tracker ID: 3052459.
sequence
NTR
nested tandem repeat
An NTR is a nested repeat of two distinct tandem motifs interspersed with each other.
SO:AF
http://purl.org/obo/owl/SO#SO_AF
promoter_element
sequence
promoter element
core_promoter_element
sequence
core promoter element
general transcription factor binding site
RNA_polymerase_II_TATA_box
sequence
A TATA box core promoter of a gene transcribed by RNA polymerase II.
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
RNA polymerase II TATA box
RNA_polymerase_III_TATA_box
sequence
RNA polymerase III TATA box
A TATA box core promoter of a gene transcribed by RNA polymerase III.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
BREd_motif
sequence
BREd
BREd motif
A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G).
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
DCE
sequence
downstream core element
A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII.
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
DCE_SI
sequence
A sub element of the DCE core promoter element, with consensus sequence CTTC.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
DCE SI
DCE_SII
sequence
A sub element of the DCE core promoter element with consensus sequence CTGT.
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
SO:ke
http://purl.org/obo/owl/SO#SO_ke
DCE SII
DCE_SIII
sequence
A sub element of the DCE core promoter element with consensus sequence AGC.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
DCE SIII
proximal_promoter_element
sequence
specific transcription factor binding site
proximal promoter element
RNApol_II_core_promoter
sequence
RNApol II core promoter
The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
PMID:16858867
http://purl.org/obo/owl/PMID#PMID_16858867
distal_promoter_element
sequence
distal promoter element
bacterial_RNApol_promoter_sigma_70
sequence
bacterial RNA polymerase promoter sigma 70
bacterial_RNApol_promoter_sigma54
sequence
bacterial RNA polymerase promoter sigma54
minus_12_signal
sequence
minus 12 signal
A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.
PMID:18331472
http://purl.org/obo/owl/PMID#PMID_18331472
minus_24_signal
sequence
minus 24 signal
A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.
PMID:18331472
http://purl.org/obo/owl/PMID#PMID_18331472
A_box_type_1
The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
sequence
An A box within an RNA polymerase III type 1 promoter.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
A box type 1
A_box_type_2
The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
sequence
An A box within an RNA polymerase III type 2 promoter.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
A box type 2
intermediate_element
sequence
IE
A core promoter region of RNA polymerase III type 1 promoters.
PMID:12381659
http://purl.org/obo/owl/PMID#PMID_12381659
intermediate element
regulatory_promoter_element
sequence
A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region.
PMID:12381659
http://purl.org/obo/owl/PMID#PMID_12381659
regulatory promoter element
transcription_regulatory_region
sequence
transcription regulatory region
A regulatory region that is involved in the control of the process of transcription.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translation_regulatory_region
sequence
A regulatory region that is involved in the control of the process of translation.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
translation regulatory region
recombination_regulatory_region
sequence
A regulatory region that is involved in the control of the process of recombination.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
recombination regulatory region
replication_regulatory_region
sequence
A regulatory region that is involved in the control of the process of nucleotide replication.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
replication regulatory region
sequence_motif
sequence
A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
URL:http://en.wikipedia.org/wiki/Sequence_motif
http://en.wikipedia.org/wiki/Sequence_motif
URL:http://en.wikipedia.org/wiki/Sequence_motif
http://en.wikipedia.org/wiki/Sequence_motif
sequence motif
experimental_feature_attribute
sequence
An attribute of an experimentally derived feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
experimental feature attribute
score
sequence
The score of an experimentally derived feature such as a p-value.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
quality_value
sequence
An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
quality value
restriction_enzyme_recognition_site
sequence
The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
restriction enzyme recognition site
restriction endonuclease recognition site
restriction_enzyme_cleavage_junction
sequence
restriction enzyme cleavage junction
The boundary at which a restriction enzyme breaks the nucleotide sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
five_prime_restriction_enzyme_junction
sequence
5' restriction enzyme junction
The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
three_prime_restriction_enzyme_junction
sequence
3' restriction enzyme junction
blunt_end_restriction_enzyme_cleavage_site
sequence
blunt end restriction enzyme cleavage site
sticky_end_restriction_enzyme_cleavage_site
sequence
sticky end restriction enzyme cleavage site
blunt_end_restriction_enzyme_cleavage_junction
sequence
A restriction enzyme cleavage site where both strands are cut at the same position.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
blunt end restriction enzyme cleavage site
single_strand_restriction_enzyme_cleavage_site
sequence
single strand restriction enzyme cleavage site
A restriction enzyme cleavage site whereby only one strand is cut.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
restriction_enzyme_single_strand_overhang
sequence
sticky end
single strand overhang
A terminal region of DNA sequence where the end of the region is not blunt ended.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
experimentally_defined_binding_region
sequence
experimentally defined binding region
A region that has been implicated in binding although the exact coordinates of binding may be unknown.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ChIP_seq_region
sequence
ChIP seq region
A region of sequence identified by CHiP seq technology to contain a protein binding site.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
ASPE_primer
sequence
"A primer containing an SNV at the 3' end for accurate genotyping.
URL:http://www.ncbi.nlm.nih.gov/pubmed/11252801
http://www.ncbi.nlm.nih.gov/pubmed/11252801
ASPE primer
allele specific primer extension primer
dCAPS_primer
sequence
A primer with one or more mis-matches to the DNA template corresponding to a position within a restriction enzyme recognition site.
URL:http://www.ncbi.nlm.nih.gov/pubmed/9628033
http://www.ncbi.nlm.nih.gov/pubmed/9628033
derived cleaved amplified polymorphic primer
dCAPS primer
histone_modification
sequence
histone modification
histone modification site
Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation.
http:en.wikipedia.org/wiki/Histone
http://purl.org/obo/owl/http#http_en.wikipedia.org/wiki/Histone
histone_methylation_site
sequence
histone methylation
histone methylation site
A histone modification site where the modification is the methylation of the residue.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
histone_acetylation_site
sequence
histone acetylatoin site
A histone modification where the modification is the acylation of the residue.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
histone acetylation
H3K9_acetylation_site
sequence
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H3K9 acetylation site
H3K9Ac
H3K14_acetylation_site
sequence
H3K14 acetylation site
A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H3K14Ac
H3K4_monomethylation_site
sequence
H3K4me1
H3K4 mono-methylation site
A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H3K4_trimethylation
sequence
A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H3K4 tri-methylation
H3K4me3
H3K9_trimethylation_site
sequence
H3K9 tri-methylation site
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H3K9Me3
H3K27_monomethylation_site
sequence
H2K27Me1
H2K27 mono-methylation site
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H3K27_trimethylation_site
sequence
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H3K27Me3
H3K27 tri-methylation site
H3K79_monomethylation_site
sequence
H3K79me1
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H3K79 mono-methylation site
H3K79_dimethylation_site
sequence
H3K79Me2
H3K79 di-methylation site
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H3K79_trimethylation_site
sequence
H3K79 tri-methylation site
H3K79Me3
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H4K20_monomethylation_site
sequence
H4K20Me1
H4K20 mono-methylation site
A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H34histone protein is mono-methylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
H2BK5_monomethylation_site
sequence
H2BK5 mono-methylation site
A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated.
URL:http://en.wikipedia.org/wiki/Histone
http://en.wikipedia.org/wiki/Histone
ISRE
Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term.
sequence
An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.
URL:http://genesdev.cshlp.org/content/2/4/383.abstrac
http://genesdev.cshlp.org/content/2/4/383.abstrac
interferon stimulated response element
histone_ubiqitination_site
sequence
histone ubiquitination site
A histone modification site where ubiquitin may be added.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H2B_ubiquitination_site
sequence
A histone modification site on H2B where ubiquitin may be added.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H2BUbiq
H3K18_acetylation_site
sequence
A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K18Ac
H3K18 acetylation site
H3K23_acylation_site
sequence
A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K23 acylation site
H3K23Ac
epigenetically_modified_region
sequence
epigenetically modified region
A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.
URL:http://en.wikipedia.org/wiki/Epigenetics
http://en.wikipedia.org/wiki/Epigenetics
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K27_acylation_site
sequence
H3K27 acylation site
H3K27Ac
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K36_monomethylation_site
sequence
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K36<Me1
H3K36 mono-methylation site
H3K36_dimethylation_site
sequence
H3K36 di-methylation site
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K36Me2
H3K36_trimethylation_site
sequence
H3K36 tri-methylation site
H3K36Me3
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K4_dimethylation_site
sequence
H3K4 di-methylation site
A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K4Me2
H3K27_dimethylation_site
sequence
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K27Me2
H3K27 di-methylation site
H3K9_monomethylation_site
sequence
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K9 mono-methylation site
H3K9Me1
H3K9_dimethylation_site
sequence
H3K9 di-methylation site
H3K9Me2
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H4K16_acylation_site
sequence
H4K16Ac
H4K16 acylation_site
A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H4K5_acylation_site
sequence
H4K5 acylation site
H4K5Ac
A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H4K8_acylation_site
sequence
H4K8 acylation site
H4K8Ac
A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated.
SO:KE
http://purl.org/obo/owl/SO#SO_KE
H3K27_methylation_site
sequence
H3K27 methylation site
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K36_methylation_site
sequence
H3K36 methylation site
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K4_methylation_site
sequence
A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K4 methylation site
H3K79_methylation_site
sequence
H3K79 methylation site
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K9_methylation_site
sequence
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H3K9 methylation site
histone_acylation_region
sequence
histone acylation region
A histone modification, whereby the histone protein is acylated at multiple sites in a region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H4K_acylation_region
sequence
A region of the H4 histone whereby multiple lysines are acylated.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
H4K acylation region
H4KAc
gene_with_non_canonical_start_codon
Requested by flybase, Dec 2010.
sequence
gene with non canonical start codon
A gene with a start codon other than AUG.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
gene_with_start_codon_CUG
Requested by flybase, Dec 2010.
sequence
A gene with a translational start codon of CUG.
SO:mc
http://purl.org/obo/owl/SO#SO_mc
gene with start codon CUG
pseudogenic_gene_segment
sequence
pseudogenic gene segment
A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.
SO:hd
http://purl.org/obo/owl/SO#SO_hd
copy_number_gain
sequence
A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gain
URL:http://www.ncbi.nlm.nih.gov/dbvar/
http://www.ncbi.nlm.nih.gov/dbvar/
copy number gain
copy_number_loss
sequence
A sequence alteration whereby the copy number of a given region is less than the reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
loss
URL:http://www.ncbi.nlm.nih.gov/dbvar/
http://www.ncbi.nlm.nih.gov/dbvar/
copy number loss
UPD
sequence
UPD
URL:http://www.ncbi.nlm.nih.gov/dbvar/
http://www.ncbi.nlm.nih.gov/dbvar/
uniparental disomy
http:http://en.wikipedia.org/wiki/Uniparental_disomy
http://purl.org/obo/owl/http#http_http://en.wikipedia.org/wiki/Uniparental_disomy
Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent.
SO:BM
http://purl.org/obo/owl/SO#SO_BM
maternal_uniparental_disomy
sequence
Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father.
SO:bm
http://purl.org/obo/owl/SO#SO_bm
maternal uniparental disomy
paternal_uniparental_disomy
sequence
Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother.
SO:bm
http://purl.org/obo/owl/SO#SO_bm
paternal uniparental disomy
open_chromatin_region
Requested by John Calley 3125900.
sequence
open chromatin region
A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA.
SO:cb
http://purl.org/obo/owl/SO#SO_cb
SL3_acceptor_site
sequence
A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL3 acceptor site
SL4_acceptor_site
sequence
SL4 acceptor site
A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL5_acceptor_site
sequence
A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL5 acceptor site
SL6_acceptor_site
sequence
SL6 acceptor site
A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL7_acceptor_site
sequence
SL37 acceptor site
A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL8_acceptor_site
sequence
A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL8 acceptor site
SL9_acceptor_site
sequence
A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL9 acceptor site
SL10_acceptor_site
sequence
SL10 acceptor site
A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL11_acceptor_site
sequence
A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL11 acceptor site
SL12_acceptor_site
sequence
A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
http://purl.org/obo/owl/SO#SO_nlw
SL12 acceptor site
duplicated_pseudogene
sequence
duplicated pseudogene
A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence.
URL:http://en.wikipedia.org/wiki/Pseudogene
http://en.wikipedia.org/wiki/Pseudogene
unitary_pseudogene
This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates.
sequence
unitary pseudogene
disabled gene
A pseudogene, deactivated from original state by mutation, fixed in a population.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Pseudogene
http://en.wikipedia.org/wiki/Pseudogene
non_processed_pseudogene
sequence
A pseudogene that arose from a means other than retrotransposition.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
non processed pseudogene
variant_quality
sequence
A dependent entity that inheres in a bearer, a sequence variant.
PMID:17597783
http://purl.org/obo/owl/PMID#PMID_17597783
SO:ke
http://purl.org/obo/owl/SO#SO_ke
variant quality
variant_origin
sequence
A quality inhering in a variant by virtue of its origin.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
PMID:17597783
http://purl.org/obo/owl/PMID#PMID_17597783
variant origin
variant_frequency
sequence
A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.
PMID:17597783
http://purl.org/obo/owl/PMID#PMID_17597783
SO:ke
http://purl.org/obo/owl/SO#SO_ke
variant frequency
unique_variant
sequence
A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
unique variant
rare_variant
sequence
rare variant
polymorphic_variant
sequence
polymorphic variant
common_variant
sequence
common variant
fixed_variant
sequence
fixed variant
variant_phenotype
sequence
A quality inhering in a variant by virtue of its phenotype.
PMID:17597783
http://purl.org/obo/owl/PMID#PMID_17597783
SO:ke
http://purl.org/obo/owl/SO#SO_ke
variant phenotype
benign_variant
sequence
benign variant
disease_associated_variant
sequence
disease associated variant
disease_causing_variant
sequence
disease causing variant
lethal_variant
sequence
lethal variant
quantitative_variant
sequence
quantitative variant
maternal_variant
sequence
maternal variant
paternal_variant
sequence
paternal variant
somatic_variant
sequence
somatic variant
germline_variant
sequence
germline variant
pedigree_specific_variant
sequence
pedigree specific variant
population_specific_variant
sequence
population specific variant
de_novo_variant
sequence
de novo variant
TF_binding_site_variant
sequence
A sequence variant located within a transcription factor binding site.
EBI:fc
http://purl.org/obo/owl/EBI#EBI_fc
TF binding site variant
complex_structural_alteration
sequence
complex
URL:http://www.ncbi.nlm.nih.gov/dbvar/
http://www.ncbi.nlm.nih.gov/dbvar/
A structural sequence alteration or rearrangement encompassing one or more genome fragments.
NCBI:th
http://purl.org/obo/owl/NCBI#NCBI_th
SO:ke
http://purl.org/obo/owl/SO#SO_ke
structural_alteration
sequence
structural alteration
loss_of_heterozygosity
sequence
loss of heterozygosity
LOH
A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
splice_donor_5th_base_variant
sequence
splice donor 5th base variant
A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript.
EBI:gr
http://purl.org/obo/owl/EBI#EBI_gr
U_box
sequence
An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription.
PMID:9649446
http://purl.org/obo/owl/PMID#PMID_9649446
PMID:11577982
http://purl.org/obo/owl/PMID#PMID_11577982
PMID:10556309
http://purl.org/obo/owl/PMID#PMID_10556309
U-box
mating_type_region
sequence
mating type region
A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
URL:http://en.wikipedia.org/wiki/Mating-type_region
http://en.wikipedia.org/wiki/Mating-type_region
paired_end_fragment
sequence
paired end fragment
An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
exon_variant
sequence
exon variant
A sequence variant that changes exon sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
non_coding_exon_variant
sequence
A sequence variant that changes non-coding exon sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
clone_end
sequence
A read from an end of the clone sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
clone end
point_centromere
sequence
point centromere
A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae.
SO:vw
http://purl.org/obo/owl/SO#SO_vw
PMID:7502067
http://purl.org/obo/owl/PMID#PMID_7502067
regional_centromere
sequence
regional centromere
A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions.
SO:vw
http://purl.org/obo/owl/SO#SO_vw
PMID:7502067
http://purl.org/obo/owl/PMID#PMID_7502067
regional_centromere_central_core
sequence
regional centromere central core
A conserved region within the central region of a modular centromere, where the kinetochore is formed.
SO:vw
http://purl.org/obo/owl/SO#SO_vw
centromeric_repeat
sequence
A repeat region found within the modular centromere.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
centromeric repeat
regional_centromere_inner_repeat_region
sequence
The inner inverted repeat region of a modular centromere and part of the entral core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm.
SO:vw
http://purl.org/obo/owl/SO#SO_vw
lmr1R
regional centromere inner repeat region
lmr repeat
lmr1L
regional_centromere_outer_repeat_region
sequence
The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms.
SO:vw
http://purl.org/obo/owl/SO#SO_vw
regional centromere outer repeat region
tasiRNA
sequence
trans acting small interfering RNA
The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene.
PMID:16145017
http://purl.org/obo/owl/PMID#PMID_16145017
tasiRNA_primary_transcript
sequence
A primary transcript encoding a tasiRNA.
PMID:16145017
http://purl.org/obo/owl/PMID#PMID_16145017
tasiRNA primary transcript
increased_polyadenylation_variant
Term requested by M. Dumontier, June 1 2011.
sequence
increased polyadenylation variant
A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
decreased_polyadenylation_variant
Term requested by M. Dumontier, June 1 2011.
sequence
decreased polyadenylation variant
A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
DDB_box
Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence.
sequence
DDB box
DDB-box
A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases.
PMID:19818632
http://purl.org/obo/owl/PMID#PMID_19818632
PMID:18794354
http://purl.org/obo/owl/PMID#PMID_18794354
destruction_box
sequence
destruction box
D-box
A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN.
PMID:1842691
http://purl.org/obo/owl/PMID#PMID_1842691
PMID:12208841
http://purl.org/obo/owl/PMID#PMID_12208841
ER_retention_signal
sequence
endoplasmic reticulum retention signal
ER retention signal
A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL.
PMID:2077689
http://purl.org/obo/owl/PMID#PMID_2077689
doi:10.1093/jxb/50.331.157
http://purl.org/obo/owl/doi#doi_10.1093/jxb/50.331.157
KEN_box
sequence
KEN box
A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN.
PMID:10733526
http://purl.org/obo/owl/PMID#PMID_10733526
PMID:1220884
http://purl.org/obo/owl/PMID#PMID_1220884
PMID:18426916
http://purl.org/obo/owl/PMID#PMID_18426916
mitochondrial_targeting_signal
sequence
mitochondrial targeting signal
MTS
A polypeptide region that targets a polypeptide to the mitochondrion.
PomBase:mah
http://purl.org/obo/owl/PomBase#PomBase_mah
mitochondrial signal sequence
signal_anchor
sequence
signal anchor
uncleaved signal peptide
A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane.
URL:http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php
http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php
PIP_box
sequence
PIP box
A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains.
PMID:9631646
http://purl.org/obo/owl/PMID#PMID_9631646
phosphorylation_site
sequence
phosphorylation site
A post-translationally modified region in which residues of the protein are modified by phosphorylation.
PomBase:mah
http://purl.org/obo/owl/PomBase#PomBase_mah
transmembrane_helix
sequence
transmembrane helix
A region that traverses the lipid bilayer and adopts a helical secondary structure.
PomBase:mah
http://purl.org/obo/owl/PomBase#PomBase_mah
vacuolar_sorting_signal
sequence
vacuolar sorting signal
A polypeptide region that targets a polypeptide to the vacuole.
PomBase:mah
http://purl.org/obo/owl/PomBase#PomBase_mah
coding_variant_quality
sequence
coding variant quality
synonymous
sequence
non_synonymous
sequence
non synonymous
inframe
sequence
An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
protein_altering_variant
sequence
A sequence_variant which is predicted to change the protein encoded in the coding sequence.
EBI:gr
http://purl.org/obo/owl/EBI#EBI_gr
protein altering variant
synonymous_variant
EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).nThis term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term.
SO:0001588
sequence
synonymous codon
A sequence variant where there is no resulting change to the encoded amino acid.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
synonymous_codon
synonymous_coding
coding-synon
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
http://purl.org/obo/owl/ftp#ftp_//ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
URL:http://en.wikipedia.org/wiki/Synonymous_mutation
http://en.wikipedia.org/wiki/Synonymous_mutation
URL:http://en.wikipedia.org/wiki/Silent_mutation
http://en.wikipedia.org/wiki/Silent_mutation
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
silent mutation
silent_mutation
silent substitution
inframe_indel
sequence
inframe change in CDS length
inframe indel
A coding sequence variant where the change does not alter the frame of the transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inframe_insertion
sequence
SO:0001651
inframe codon gain
An inframe non synonymous variant that inserts bases into in the coding sequence.
EBI:gr
http://purl.org/obo/owl/EBI#EBI_gr
inframe_codon_gain
inframe increase in CDS length
inframe insertion
inframe_deletion
sequence
SO:0001652
inframe_codon_loss
inframe decrease in CDS length
An inframe non synonymous variant that deletes bases from the coding sequence.
EBI:gr
http://purl.org/obo/owl/EBI#EBI_gr
inframe deletion
inframe codon loss
conservative_inframe_insertion
sequence
conservative inframe insertion
conservative increase in CDS length
An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons.
EBI:gr
http://purl.org/obo/owl/EBI#EBI_gr
disruptive_inframe_insertion
sequence
An inframe_increase_in_cds_length that inserts one or more codons into the coding sequence within an existing codon.
EBI:gr
http://purl.org/obo/owl/EBI#EBI_gr
disruptive inframe insertion
disruptive increase in CDS length
conservative_inframe_deletion
sequence
conservative decrease in CDS length
conservative inframe deletion
An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons.
EBI:gr
http://purl.org/obo/owl/EBI#EBI_gr
disruptive_inframe_deletion
sequence
disruptive decrease in CDS length
disruptive inframe deletion
An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon.
EBI:gr
http://purl.org/obo/owl/EBI#EBI_gr
mRNA_read
Requested by Bayer Cropscience June, 2011.
sequence
A sequencer read of an mRNA substrate.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mRNA read
genomic_DNA_read
sequence
A sequencer read of a genomic DNA substrate.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
genomic DNA read
mRNA_contig
Requested by Bayer Cropscience June, 2011.
sequence
mRNA contig
A contig composed of mRNA_reads.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
AFLP_fragment
Requested by Bayer Cropscience June, 2011.
sequence
A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments.
GMOD:ea
http://purl.org/obo/owl/GMOD#GMOD_ea
AFLP
AFLP fragment
AFLP-PCR
URL:http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism
http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism
amplified fragment length polymorphism
amplified fragment length polymorphism PCR
protein_hmm_match
sequence
A match to a protein HMM such as pfam.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
protein hmm match
immunoglobulin_region
sequence
immunoglobulin region
A region of immunoglobulin sequence, either constant or variable.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
V_region
sequence
V region
The variable region of an immunoglobulin polypeptide sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
C_region
sequence
C region
The constant region of an immunoglobulin polypeptide sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
N_region
sequence
N-region
Extra nucleotides inserted between rearranged immunoglobulin segments.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
S_region
sequence
The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
S region
mobile_element_insertion
Requested by the ebi.
sequence
A kind of insertion where the inserted sequence is a mobile element.
EBI:dvga
http://purl.org/obo/owl/EBI#EBI_dvga
mobile element insertion
novel_sequence_insertion
Requested by the NCBI.
sequence
novel sequence insertion
An insertion the sequence of which cannot be mapped to the reference genome.
NCBI:th
http://purl.org/obo/owl/NCBI#NCBI_th
CSL_response_element
sequence
CSL response element
A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors.
PMID:19101542
http://purl.org/obo/owl/PMID#PMID_19101542
GATA_box
sequence
GATA element
GATA box
A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G).
PMID:8321208
http://purl.org/obo/owl/PMID#PMID_8321208
polymorphic_pseudogene
This terms is used by ensembl and vega.
sequence
Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
JAX:hd
http://purl.org/obo/owl/JAX#JAX_hd
polymorphic psuedogene
AP_1_binding_site
sequence
AP-1 binding site
A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors.
PMID:1899230
http://purl.org/obo/owl/PMID#PMID_1899230
PMID:3034432
http://purl.org/obo/owl/PMID#PMID_3034432
PMID:3125983
http://purl.org/obo/owl/PMID#PMID_3125983
CRE
sequence
cyclic AMP response element
A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors.
PMID:11483355
http://purl.org/obo/owl/PMID#PMID_11483355
PMID:11483993
http://purl.org/obo/owl/PMID#PMID_11483993
ATF/CRE site
PMID:11483993
http://purl.org/obo/owl/PMID#PMID_11483993
CuRE
sequence
copper-response element
A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast).
PMID:9188496
http://purl.org/obo/owl/PMID#PMID_9188496
PMID:9211922
http://purl.org/obo/owl/PMID#PMID_9211922
PMID:10593913
http://purl.org/obo/owl/PMID#PMID_10593913
DRE
sequence
DNA damage response element
A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis.
PMID:11073995
http://purl.org/obo/owl/PMID#PMID_11073995
PMID:8668127
http://purl.org/obo/owl/PMID#PMID_8668127
FLEX_element
sequence
FLEX element
A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain.
PMID:14871934
http://purl.org/obo/owl/PMID#PMID_14871934
PMID:10747048
http://purl.org/obo/owl/PMID#PMID_10747048
forkhead_motif
sequence
A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain.
PMID:15195092
http://purl.org/obo/owl/PMID#PMID_15195092
forkhead motif
homol_D_box
sequence
A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence.
PMID:7501449
http://purl.org/obo/owl/PMID#PMID_7501449
PMID:8458332
http://purl.org/obo/owl/PMID#PMID_8458332
homol D box
homol_E_box
sequence
A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence.
PMID:7501449
http://purl.org/obo/owl/PMID#PMID_7501449
homol E box
HSE
sequence
heat shock element
A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF.
PMID:17347150
http://purl.org/obo/owl/PMID#PMID_17347150
PMID:8689565
http://purl.org/obo/owl/PMID#PMID_8689565
iron_repressed_GATA_element
The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes.
sequence
iron repressed GATA element
IDP (GATA)
A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron.
PMID:17211681
http://purl.org/obo/owl/PMID#PMID_17211681
PMID:11956219
http://purl.org/obo/owl/PMID#PMID_11956219
mating_type_M_box
Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF.
sequence
A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc.
PMID:9233811
http://purl.org/obo/owl/PMID#PMID_9233811
mating type M-box
androgen_response_element
sequence
A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen.
PMID:21796522
http://purl.org/obo/owl/PMID#PMID_21796522
androgen response element
ARE
smFISH_probe
sequence
smFISH probe
A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment.
PMID:18806792
http://purl.org/obo/owl/PMID#PMID_18806792
single molecule fish probe
MCB
sequence
A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle.
PMID:16285853
http://purl.org/obo/owl/PMID#PMID_16285853
MluI cell cycle box
CCAAT_motif
sequence
A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels.
PMID:16963626
http://purl.org/obo/owl/PMID#PMID_16963626
CCAAT motif
Ace2_UAS
sequence
A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2.
PMID:16678171
http://purl.org/obo/owl/PMID#PMID_16678171
Ace2 upstream activating sequence
TR_box
sequence
TR box
A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis.
PMID:1657709
http://purl.org/obo/owl/PMID#PMID_1657709
STREP_motif
sequence
A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2.
PMID:11739717
http://purl.org/obo/owl/PMID#PMID_11739717
stress-starvation response element of Schizosaccharomyces pombe
STREP motif
rDNA_intergenic_spacer_element
sequence
rDIS
A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1).
PMID:9016645
http://purl.org/obo/owl/PMID#PMID_9016645
sterol_regulatory_element
sequence
SRE
GO:mah
http://purl.org/obo/owl/GO#GO_mah
A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs.
GO:mah
http://purl.org/obo/owl/GO#GO_mah
PMID:16537923
http://purl.org/obo/owl/PMID#PMID_16537923
PMID:11111080
http://purl.org/obo/owl/PMID#PMID_11111080
GT_dinucleotide_repeat
paper:PMID:16043634.
sequence
A dinucleotide repeat region composed of GT repeating elements.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
d(GT)n
GTT_trinucleotide_repeat
sequence
d(GTT)
A trinucleotide repeat region composed of GTT repeating elements.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
Sap1_recognition_motif
sequence
Sap1 recognitions site
A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats.
PMID:7651412
http://purl.org/obo/owl/PMID#PMID_7651412
PMID:16166653
http://purl.org/obo/owl/PMID#PMID_16166653
CDRE_motif
sequence
An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA.
PMID:16928959
http://purl.org/obo/owl/PMID#PMID_16928959
calcineurin-dependent response element
PMID:16928959
http://purl.org/obo/owl/PMID#PMID_16928959
CDRE motif
BAC_read_contig
Requested by Bayer Cropscience December, 2011.
sequence
A contig of BAC reads.
GMOD:ea
http://purl.org/obo/owl/GMOD#GMOD_ea
BAC read contig
candidate_gene
Requested by Bayer Cropscience December, 2011.
sequence
A gene suspected of being involved in the expression of a trait.
GMOD:ea
http://purl.org/obo/owl/GMOD#GMOD_ea
candidate gene
target gene
positional_candidate_gene
Requested by Bayer Cropscience December, 2011.
sequence
A candidate gene whose association with a trait is based on the gene's location on a chromosome.
GMOD:ea
http://purl.org/obo/owl/GMOD#GMOD_ea
positional target gene
positional candidate gene
functional_candidate_gene
Requested by Bayer Cropscience December, 2011.
sequence
functional target gene
functional candidate gene
A candidate gene whose function has something in common biologically with the trait under investigation.
GMOD:ea
http://purl.org/obo/owl/GMOD#GMOD_ea
enhancerRNA
sequence
eRNA
A short ncRNA that is transcribed from an enhancer. May have a regulatory function.
SO:cjm
http://purl.org/obo/owl/SO#SO_cjm
doi:10.1038/465173a
http://purl.org/obo/owl/doi#doi_10.1038/465173a
PCB
sequence
A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle.
PMID:12411492
http://purl.org/obo/owl/PMID#PMID_12411492
GO:mah
http://purl.org/obo/owl/GO#GO_mah
rearrangement_breakpoint
NCBI definition: An orphan rearrangement between chromosomal location observed in isolation.
sequence
A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome.
PMID:18564416
http://purl.org/obo/owl/PMID#PMID_18564416
NCBI:th
http://purl.org/obo/owl/NCBI#NCBI_th
rearrangement breakpoint
interchromosomal_breakpoint
sequence
A rearrangement breakpoint between two different chromosomes.
NCBI:th
http://purl.org/obo/owl/NCBI#NCBI_th
interchromosomal breakpoint
intrachromosomal_breakpoint
sequence
intrachromosomal breakpoint
A rearrangement breakpoint within the same chromosome.
NCBI:th
http://purl.org/obo/owl/NCBI#NCBI_th
unassigned_supercontig
comment: Requested by Bayer Cropscience January, 2012.
sequence
unassigned supercontig
A supercontig that is not been assigned to any ultracontig during a genome assembly project.
GMOD:ea
http://purl.org/obo/owl/GMOD#GMOD_ea
unassigned scaffold
partial_genomic_sequence_assembly
comment: Requested by Bayer Cropscience January, 2012.
sequence
sequence assembly with N-gaps
partial genomic sequence assembly
A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's.
GMOD:ea
http://purl.org/obo/owl/GMOD#GMOD_ea
pseudomolecule
lnc_RNA
sequence
A non-coding RNA over 200nucleotides in length.
HGNC:mw
http://purl.org/obo/owl/HGNC#HGNC_mw
long non-coding RNA
feature_variant
Created in conjunction with the EBI.
sequence
feature alteration
A sequence variant that falls entirely or partially within a genomic feature.
EBI:fc
http://purl.org/obo/owl/EBI#EBI_fc
SO:ke
http://purl.org/obo/owl/SO#SO_ke
feature_ablation
Created in conjunction with the EBI.
sequence
feature ablation
A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
feature_amplification
Created in conjunction with the EBI.
sequence
feature amplification
A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
feature_translocation
Created in conjunction with the EBI.
sequence
feature translocation
A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
feature_fusion
Created in conjunction with the EBI.
sequence
feature fusion
A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript_translocation
Created in conjunction with the EBI.
sequence
A feature translocation where the region contains a transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript translocation
regulatory_region_translocation
Created in conjunction with the EBI.
sequence
A feature translocation where the region contains a regulatory region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
regulatory region translocation
TFBS_translocation
Created in conjunction with the EBI.
sequence
A feature translocation where the region contains a transcription factor binding site.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcription factor binding site translocation
TFBS binding site translocation
transcript_fusion
Created in conjunction with the EBI.
sequence
A feature fusion where the deletion brings together transcript regions.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript fusion
regulatory_region_fusion
Created in conjunction with the EBI.
sequence
regulatory region fusion
A feature fusion where the deletion brings together regulatory regions.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
TFBS_fusion
Created in conjunction with the EBI.
sequence
A fusion where the deletion brings together transcription factor binding sites.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcription factor binding site fusion
TFBS fusion
transcript_amplification
Created in conjunction with the EBI.
sequence
transcript amplification
A feature amplification of a region containing a transcript.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript_regulatory_region_fusion
Created in conjunction with the EBI.
sequence
A feature fusion where the deletion brings together a regulatory region and a transcript region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript regulatory region fusion
regulatory_region_amplification
Created in conjunction with the EBI.
sequence
A feature amplification of a region containing a regulatory region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
regulatory region amplification
TFBS_amplification
Created in conjunction with the EBI.
sequence
A feature amplification of a region containing a transcription factor binding site.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcription factor binding site amplification
TFBS amplification
transcript_ablation
Created in conjunction with the EBI.
sequence
A feature ablation whereby the deleted region includes a transcript feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcript ablation
regulatory_region_ablation
Created in conjunction with the EBI.
sequence
regulatory region ablation
A feature ablation whereby the deleted region includes a regulatory region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
TFBS_ablation
Created in conjunction with the EBI.
sequence
A feature ablation whereby the deleted region includes a transcription factor binding site.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transcription factor binding site ablation
TFBS ablation
transposable_element_CDS
sequence
transposable element CDS
A CDS that is part of a transposable element.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transposable_element_pseudogene
sequence
transposable element pseudogene
A pseudogene contained within a transposable element.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
dg_repeat
For the S. pombe project - requested by Val Wood.
sequence
dg repeat
A repeat region which is part of the regional centromere outer repeat region.
PMID:16407326
http://purl.org/obo/owl/PMID#PMID_16407326
SO:vw
http://purl.org/obo/owl/SO#SO_vw
dh_repeat
For the S. pombe project - requested by Val Wood.
sequence
A repeat region which is part of the regional centromere outer repeat region.
PMID:16407326
http://purl.org/obo/owl/PMID#PMID_16407326
SO:vw
http://purl.org/obo/owl/SO#SO_vw
dh repeat
m26_site
sequence
A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components.
PMID:15448137
http://purl.org/obo/owl/PMID#PMID_15448137
m26 site
AACCCT_box
sequence
AACCCT box
A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site.
PMID:4092687
http://purl.org/obo/owl/PMID#PMID_4092687
PMID:17452352
http://purl.org/obo/owl/PMID#PMID_17452352
splice_region
sequence
A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
SO:bm
http://purl.org/obo/owl/SO#SO_bm
splice region
intronic_lncRNA
sequence
intronic lncRNA
A lnc_RNA totally contained within an intron.
PMID:19071207
http://purl.org/obo/owl/PMID#PMID_19071207
SO:ke
http://purl.org/obo/owl/SO#SO_ke
antisense_lncRNA
sequence
natural antisense transcript
antisense lncRNA
Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA.
PMID:19638999
http://purl.org/obo/owl/PMID#PMID_19638999
regional_centromere_outer_repeat_transcript
sequence
regional centromere outer repeat region transcript
A transcript that is transcribed from the outer repeat region of a regional centromere.
PomBase:mah
http://purl.org/obo/owl/PomBase#PomBase_mah
centromere outer repeat transcript
regional_centromere_outer_repeat_region_transcript
feature_truncation
sequence
feature truncation
A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
feature_elongation
sequence
A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
feature elongation
internal_feature_elongation
sequence
internal feature elongation
A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
frameshift_elongation
sequence
A frameshift variant that causes the translational reading frame to be extended relative to the reference feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
frameshift elongation
frameshift_truncation
sequence
A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
frameshft truncation
copy_number_increase
sequence
A sequence variant where copies of a feature are increased relative to the reference.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
copy number increase
copy_number_decrease
sequence
A sequence variant where copies of a feature are decreased relative to the reference.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
regulatory_region
sequence
A region of sequence that is involved in the control of a biological process.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
regulatory region
URL:http://en.wikipedia.org/wiki/Regulatory_region
http://en.wikipedia.org/wiki/Regulatory_region
U14_snoRNA_primary_transcript
sequence
4.5S snRNA primary transcript
U14 snoRNA primary transcript
The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
PMID:2251119
http://purl.org/obo/owl/PMID#PMID_2251119
methylation_guide_snoRNA
Has RNA 2'-O-ribose methylation guide activity (GO:0030561).
sequence
methylation guide snoRNA
A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.
PMID:12457565
http://purl.org/obo/owl/PMID#PMID_12457565
GOC:mah
http://purl.org/obo/owl/GOC#GOC_mah
rRNA_cleavage_RNA
sequence
rRNA cleavage RNA
An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.
GOC:kgc
http://purl.org/obo/owl/GOC#GOC_kgc
exon_of_single_exon_gene
sequence
singleton exon
An exon that is the only exon in a gene.
RSC:cb
http://purl.org/obo/owl/RSC#RSC_cb
exon of single exon gene
single_exon
cassette_array_member
sequence
cassette array member
gene_cassette_member
sequence
gene cassette member
gene_subarray_member
sequence
gene subarray member
primer_binding_site
sequence
primer binding site
URL:http://en.wikipedia.org/wiki/Primer_binding_site
http://en.wikipedia.org/wiki/Primer_binding_site
Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.
URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
gene_array
This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
sequence
gene array
An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
gene_subarray
This would include, for example, a cluster of genes encoding different histones.
sequence
gene subarray
A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
gene_cassette
This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid.
sequence
A gene that can be substituted for a related gene at a different site in the genome.
SGD:se
http://purl.org/obo/owl/SGD#SGD_se
URL:http://en.wikipedia.org/wiki/Gene_cassette
http://en.wikipedia.org/wiki/Gene_cassette
gene cassette
gene_cassette_array
This would include, for example, the arrays of non-functional VSG genes of Trypanosomes.
sequence
gene cassette array
An array of non-functional genes whose members, when captured by recombination form functional genes.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
gene_group
sequence
A collection of related genes.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
gene group
selenocysteine_tRNA_primary_transcript
sequence
A primary transcript encoding seryl tRNA (SO:000269).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
selenocysteine tRNA primary transcript
selenocysteinyl_tRNA
sequence
A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
selenocysteinyl-transfer RNA
selenocysteinyl tRNA
selenocysteinyl-transfer ribonucleic acid
syntenic_region
sequence
A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.
URL:http://www.informatics.jax.org/silverbook/glossary.shtml
http://www.informatics.jax.org/silverbook/glossary.shtml
syntenic region
biochemical_region_of_peptide
Range.
sequence
A region of a peptide that is involved in a biochemical function.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
biochemical_region
biochemical motif
biochemical region of peptide
molecular_contact_region
Range.
sequence
A region that is involved a contact with another molecule.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
molecular contact region
intrinsically_unstructured_polypeptide_region
sequence
intrinsically unstructured polypeptide region
A region of polypeptide chain with high conformational flexibility.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
disordered region
catmat_left_handed_three
sequence
catmat-3l
A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
catmat_left_handed_four
sequence
catmat-4l
A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
catmat_right_handed_three
sequence
catmat-3r
A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
catmat_right_handed_four
sequence
A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
catmat-4r
alpha_beta_motif
sequence
A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.
URL:http://www.ebi.ac.uk/msd-srv/msdmotif/
http://www.ebi.ac.uk/msd-srv/msdmotif/
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
alpha beta motif
lipoprotein_signal_peptide
sequence
prokaryotic membrane lipoprotein lipid attachment site
lipoprotein signal peptide
A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
no_output
sequence
An experimental region wherean analysis has been run and not produced any annotation.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
no output
cleaved_peptide_region
Range.
sequence
cleaved peptide region
The cleaved_peptide_regon is the a region of peptide sequence that is cleaved during maturation.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
peptide_coil
sequence
random coil
peptide coil
coil
Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds).
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
hydrophobic_region_of_peptide
Range.
sequence
hydrophobicity
hydrophobic region of peptide
hydropathic
hydrophobic_region
Hydrophobic regions are regions with a low affinity for water.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
n_terminal_region
sequence
N-region
The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa).
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
c_terminal_region
sequence
The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa).
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
C-region
central_hydrophobic_region_of_signal_peptide
sequence
central_hydrophobic_region
H-region
The central, hydrophobic region of the signal peptide (approx 7-15 aa).
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
central hydrophobic region of signal peptide
polypeptide_conserved_motif
sequence
motif
A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
polypeptide_binding_motif
sequence
polypeptide binding motif
binding
uniprot:feature_type
http://purl.org/obo/owl/uniprot#uniprot_feature_type
A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
polypeptide_catalytic_motif
sequence
A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
catalytic_motif
polypeptide catalytic motif
polypeptide_DNA_contact
sequence
polypeptide DNA contact
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
SO:ke
http://purl.org/obo/owl/SO#SO_ke
polypeptide_conserved_region
sequence
polypeptide conserved region
A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.
EBIBS:GAR
http://purl.org/obo/owl/EBIBS#EBIBS_GAR
substitution
sequence
A sequence alteration where the length of the change in the variant is the same as that of the reference.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
loinc:LA6690-7
http://purl.org/obo/owl/loinc#loinc_LA6690-7
complex_substitution
sequence
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.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
complex substitution
point_mutation
sequence
A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.
SO:immuno_workshop
http://purl.org/obo/owl/SO#SO_immuno_workshop
URL:http://en.wikipedia.org/wiki/Point_mutation
http://en.wikipedia.org/wiki/Point_mutation
point mutation
transition
sequence
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.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
pyrimidine_transition
sequence
pyrimidine transition
A substitution of a pyrimidine, C or T, for another pyrimidine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
C_to_T_transition
sequence
C to T transition
A transition of a cytidine to a thymine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
C_to_T_transition_at_pCpG_site
sequence
C to T transition at pCpG site
The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
T_to_C_transition
sequence
T to C transition
purine_transition
sequence
A substitution of a purine, A or G, for another purine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
purine transition
A_to_G_transition
sequence
A transition of an adenine to a guanine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
A to G transition
G_to_A_transition
sequence
G to A transition
A transition of a guanine to an adenine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
transversion
sequence
URL:http://en.wikipedia.org/wiki/Transversion
http://en.wikipedia.org/wiki/Transversion
Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
pyrimidine_to_purine_transversion
sequence
Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
pyrimidine to purine transversion
C_to_A_transversion
sequence
A transversion from cytidine to adenine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
C to A transversion
C_to_G_transversion
sequence
C to G transversion
T_to_A_transversion
sequence
T to A transversion
A transversion from T to A.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
T_to_G_transversion
sequence
T to G transversion
A transversion from T to G.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
purine_to_pyrimidine_transversion
sequence
purine to pyrimidine transversion
Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
A_to_C_transversion
sequence
A to C transversion
A transversion from adenine to cytidine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
A_to_T_transversion
sequence
A transversion from adenine to thymine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
A to T transversion
G_to_C_transversion
sequence
A transversion from guanine to cytidine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
G to C transversion
G_to_T_transversion
sequence
A transversion from guanine to thymine.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
G to T transversion
intrachromosomal_mutation
sequence
A chromosomal structure variation within a single chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
intrachromosomal mutation
chromosomal_deletion
sequence
(bacteria)&Dgr;
(Drosophila)Df
(fungi)D
URL:http://en.wikipedia.org/wiki/Chromosomal_deletion
http://en.wikipedia.org/wiki/Chromosomal_deletion
chromosomal deletion
deficiency
An incomplete chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
chromosomal_inversion
sequence
URL:http://en.wikipedia.org/wiki/Chromosomal_inversion
http://en.wikipedia.org/wiki/Chromosomal_inversion
(fungi)In
(bacteria)IN
(Drosophila)In
An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
chromosomal inversion
interchromosomal_mutation
sequence
interchromosomal mutation
A chromosomal structure variation whereby more than one chromosome is involved.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
indel
Indels can have a different number of bases than the corresponding reference sequence.
sequence
URL:http://en.wikipedia.org/wiki/Indel
http://en.wikipedia.org/wiki/Indel
A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.
http:http://www.hgvs.org/mutnomen/recs-DNA.html#indel
http://purl.org/obo/owl/http#http_http://www.hgvs.org/mutnomen/recs-DNA.html#indel
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
loinc:LA9659-9
http://purl.org/obo/owl/loinc#loinc_LA9659-9
duplication
sequence
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.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
loinc:LA6686-5
http://purl.org/obo/owl/loinc#loinc_LA6686-5
nucleotide duplication
nucleotide_duplication
inversion
sequence
A continuous nucleotide sequence is inverted in the same position.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
loinc:LA6689-9
http://purl.org/obo/owl/loinc#loinc_LA6689-9
inversion
URL:http://www.ncbi.nlm.nih.gov/dbvar/
http://www.ncbi.nlm.nih.gov/dbvar/
chromosomal_duplication
sequence
(fungi)Dp
URL:http://en.wikipedia.org/wiki/Chromosomal_duplication
http://en.wikipedia.org/wiki/Chromosomal_duplication
chromosomal duplication
(Drosophila)Dp
An extra chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
intrachromosomal_duplication
sequence
A duplication that occurred within a chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
intrachromosomal duplication
direct_tandem_duplication
sequence
A tandem duplication where the individual regions are in the same orientation.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
direct tandem duplication
inverted_tandem_duplication
sequence
mirror duplication
A tandem duplication where the individual regions are not in the same orientation.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inverted tandem duplication
intrachromosomal_transposition
sequence
intrachromosomal transposition
(Drosophila)Tp
A chromosome structure variation whereby a transposition occurred within a chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
compound_chromosome
sequence
compound chromosome
A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
Robertsonian_fusion
sequence
A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere.
URL:http://en.wikipedia.org/wiki/Robertsonian_translocation
http://en.wikipedia.org/wiki/Robertsonian_translocation
URL:http://en.wikipedia.org/wiki/Robertsonian_fusion
http://en.wikipedia.org/wiki/Robertsonian_fusion
centric-fusion translocations
Robertsonian fusion
whole-arm translocations
chromosomal_translocation
sequence
(fungi)T
(Drosophila)T
An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
chromosomal translocation
URL:http://en.wikipedia.org/wiki/Chromosomal_translocation
http://en.wikipedia.org/wiki/Chromosomal_translocation
ring_chromosome
sequence
(fungi)C
(Drosophila)R
ring chromosome
A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome.
URL:http://en.wikipedia.org/wiki/Ring_chromosome
http://en.wikipedia.org/wiki/Ring_chromosome
URL:http://en.wikipedia.org/wiki/Ring_chromosome
http://en.wikipedia.org/wiki/Ring_chromosome
pericentric_inversion
sequence
pericentric inversion
A chromosomal inversion that includes the centromere.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
paracentric_inversion
sequence
A chromosomal inversion that does not include the centromere.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
paracentric inversion
reciprocal_chromosomal_translocation
sequence
A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
reciprocal chromosomal translocation
sequence_variation_affecting_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000177
sequence
SO:1000179
Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation causing uncharacterised change in transcript
mutation causing partially characterised change in transcript
sequence_variant_causing_partially_characterised_change_in_transcript
sequence_variant_causing_uncharacterised_change_in_transcript
sequence variant causing uncharacterised change in transcript
sequence variation affecting transcript
sequence variant causing partially characterised change in transcript
mutation affecting transcript
sequence_variant_causing_no_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term.
sequence
No effect on the state of the RNA.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence variant causing no change in transcript
mutation causing no change in transcript
sequence_variation_affecting_coding_sequence
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
Any of the amino acid coding triplets of a gene are affected by the DNA mutation.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation affecting coding sequence
sequence variation affecting coding sequence
sequence_variant_causing_initiator_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing initiator codon change in transcript
The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence variant causing initiator codon change in transcript
sequence_variant_causing_amino_acid_coding_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing amino acid coding codon change in transcript
The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutaton causing amino acid coding codon change in transcript
sequence_variant_causing_synonymous_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing synonymous codon change in transcript
mutation causing synonymous codon change in transcript
The changed codon has the same translation product as the original codon.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_non_synonymous_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
non-synonymous codon change in transcript
sequence variant causing non synonymous codon change in transcript
mutation causing non synonymous codon change in transcript
A DNA point mutation that causes a substitution of an amino acid by an other.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_missense_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing missense codon change in transcript
sequence variant causing missense codon change in transcript
The nucleotide change in the codon leads to a new codon coding for a new amino acid.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_conservative_missense_codon_change_in_transcript
The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
sequence
mutation causing conservative missense codon change in transcript
The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence variant causing conservative missense codon change in transcript
sequence_variant_causing_nonconservative_missense_codon_change_in_transcript
The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
sequence
The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation causing nonconservative missense codon change in transcript
sequence variant causing nonconservative missense codon change in transcript
sequence_variant_causing_nonsense_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
The nucleotide change in the codon triplet creates a terminator codon.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence variant causing nonsense codon change in transcript
mutation causing nonsense codon change in transcript
sequence_variant_causing_terminator_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing terminator codon change in transcript
The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence variant causing terminator codon change in transcript
sequence_variation_affecting_reading_frame
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
An umbrella term for terms describing an effect of a sequence variation on the frame of translation.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence variation affecting reading frame
mutation affecting reading frame
frameshift_sequence_variation
sequence
frameshift sequence variation
out of frame mutation
URL:http://en.wikipedia.org/wiki/Frameshift_mutation
http://en.wikipedia.org/wiki/Frameshift_mutation
frameshift mutation
A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence_variant_causing_plus_1_frameshift_mutation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing plus 1 frameshift mutation
plus 1 frameshift mutation
A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence_variant_causing_minus_1_frameshift
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing minus 1 frameshift
A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
minus 1 frameshift mutation
sequence_variant_causing_plus_2_frameshift
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
plus 2 frameshift mutation
A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence variant causing plus 2 frameshift
sequence_variant_causing_minus_2_frameshift
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
minus 2 frameshift mutation
sequence variant causing minus 2 frameshift
A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence_variant_affecting_transcript_processing
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant affecting transcript processing
mutation affecting transcript processing
Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_affecting_splicing
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation affecting splicing
sequence variant affecting splicing
A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_affecting_splice_donor
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation affecting splice donor
splice donor mutation
A sequence_variant_effect that changes the splice donor sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence variant affecting splice donor
sequence_variant_affecting_splice_acceptor
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
splice acceptor mutation
A sequence_variant_effect that changes the splice acceptor sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mutation affecting splicing
sequence variant affecting splice acceptor
sequence_variant_causing_cryptic_splice_activation
A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration.
sequence
cryptic splice activator sequence variant
mutation causing cryptic splice activator
sequence variant causing cryptic splice activator
A sequence variant causing a new (functional) splice site.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_affecting_editing
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
Sequence variant affects the editing of the transcript.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation affecting editing
sequence variant affecting editing
sequence_variant_affecting_transcription
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant affecting transcription
Mutation affects the process of transcription, its initiation, progression or termination.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation affecting transcription
sequence_variant_decreasing_rate_of_transcription
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
A sequence variation that decreases the rate a which transcription of the sequence occurs.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mutation decreasing rate of transcription
sequence variation decreasing rate of transcription
sequence_variation_affecting_transcript_sequence
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation affecting transcript sequence
sequence variation affecting transcript sequence
sequence_variant_increasing_rate_of_transcription
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variation increasing rate of transcription
mutation increasing rate of transcription
sequence_variant_affecting_rate_of_transcription
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation affecting rate of transcription
A mutation that alters the rate a which transcription of the sequence occurs.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence variant affecting rate of transcription
sequence variant_affecting_transcript_stability
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
Sequence variant affects the stability of the transcript.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation affecting transcript stability
sequence variant affecting transcript stability
sequence_variant_increasing_transcript_stability
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation increasing transcript stability
sequence variant increasing transcript stability
Sequence variant increases the stability (half-life) of the transcript.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_decreasing_transcript_stability
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant decreasing transcript stability
Sequence variant decreases the stability (half-life) of the transcript.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation decreasing transcript stability
sequence_variation_affecting_level_of_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variation affecting level of transcript
mutation affecting level of transcript
A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence_variation_decreasing_level_of_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence variation decreasing level of transcript
mutation decreasing level of transcript
sequence_variation_increasing_level_of_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variation increasing level of transcript
A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
mutation increasing level of transcript
sequence_variant_affecting_translational_product
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000091
SO:1000090
sequence
A sequence variant causing a change in primary translation product of a transcript.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation causing partially characterised change of translational product
mutation affecting translational product
sequence variant causing partially characterised change of translational product
sequence variant affecting translational product
sequence_variant_causing_partially_characterised_change_of_translational_product
sequence variant causing uncharacterised change of translational product
sequence_variant_causing_uncharacterised_change_of_translational_product
mutation causing uncharacterised change of translational product
sequence_variant_causing_no_change_of_translational_product
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term.
sequence
mutation causing no change of translational product
The sequence variant at RNA level does not lead to any change in polypeptide.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence variant causing no change of translational product
sequence_variant_causing_complex_change_of_translational_product
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence variant causing complex change of translational product
mutation causing complex change of translational product
sequence_variant_causing_amino_acid_substitution
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing amino acid substitution
The replacement of a single amino acid by another.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation causing amino acid substitution
sequence_variant_causing_conservative_amino_acid_substitution
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing conservative amino acid substitution
sequence variant causing conservative amino acid substitution
sequence_variant_causing_nonconservative_amino_acid_substitution
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing nonconservative amino acid substitution
sequence variant causing nonconservative amino acid substitution
sequence_variant_causing_amino_acid_insertion
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing amino acid insertion
mutation causing amino acid insertion
The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_amino_acid_deletion
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation causing amino acid deletion
sequence variant causing amino acid deletion
sequence_variant_causing_polypeptide_truncation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing polypeptide truncation
sequence variant causing polypeptide truncation
The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062).
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_polypeptide_elongation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
The extension of the translational product at either (or both) the N-terminus and/or the C-terminus.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence variant causing polypeptide elongation
mutation causing polypeptide elongation
mutation_causing_polypeptide_N_terminal_elongation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
polypeptide N-terminal elongation
.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation causing polypeptide N terminal elongation
mutation_causing_polypeptide_C_terminal_elongation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing polypeptide C terminal elongation
polypeptide C-terminal elongation
.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_affecting_level_of_translational_product
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation affecting level of translational product
sequence variant affecting level of translational product
sequence_variant_decreasing_level_of_translation_product
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutationdecreasing level of translation product
sequence variant decreasing level of translation product
sequence_variant_increasing_level_of_translation_product
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant increasing level of translation product
mutationt increasing level of translation product
sequence_variant_affecting_polypeptide_amino_acid_sequence
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant affecting polypeptide amino acid sequence
mutation affecting polypeptide amino acid sequence
mutation_causing_inframe_polypeptide_N_terminal_elongation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing inframe polypeptide N terminal elongation
inframe polypeptide N-terminal elongation
mutation_causing_out_of_frame_polypeptide_N_terminal_elongation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing out of frame polypeptide N terminal elongation
out of frame polypeptide N-terminal elongation
mutaton_causing_inframe_polypeptide_C_terminal_elongation
sequence
inframe_polypeptide C-terminal elongation
mutaton causing inframe polypeptide C terminal elongation
mutation_causing_out_of_frame_polypeptide_C_terminal_elongation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
out of frame polypeptide C-terminal elongation
mutation causing out of frame polypeptide C terminal elongation
frame_restoring_sequence_variant
sequence
A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
frame restoring sequence variant
frame restoring mutation
sequence_variant_affecting_3D_structure_of_polypeptide
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000113
SO:1000114
sequence
mutation affecting 3D structure of polypeptide
mutation causing partially characterised 3D structural change
A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence_variant_causing_uncharacterised_3D_structural_change
mutation causing uncharacterised 3D structural change
sequence variant causing uncharacterised 3D structural change
sequence_variant_causing_partially_characterised_3D_structural_change
sequence variant affecting 3D-structure of polypeptide
sequence variant causing partially characterised 3D structural change
sequence variant affecting 3D structure of polypeptide
sequence_variant_causing_no_3D_structural_change
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term.
sequence
mutation causing no 3D structural change
sequence variant causing no 3D structural change
sequence_variant_causing_complex_3D_structural_change
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing complex 3D structural change
mutation causing complex 3D structural change
sequence_variant_causing_conformational_change
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing conformational change
mutation causing conformational change
sequence_variant_affecting_polypeptide_function
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant affecting polypeptide function
mutation affecting polypeptide function
sequence_variant_causing_loss_of_function_of_polypeptide
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing loss of function of polypeptide
sequence variant causing loss of function of polypeptide
loss of function of polypeptide
sequence_variant_causing_inactive_ligand_binding_site
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing inactive ligand binding site
sequence variant causing inactive ligand binding site
sequence_variant_causing_inactive_catalytic_site
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing inactive catalytic site
mutation causing inactive catalytic site
sequence_variant_causing_polypeptide_localization_change
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing polypeptide localization change
sequence variant causing polypeptide localization change
sequence_variant_causing_polypeptide_post_translational_processing_change
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing polypeptide post translational processing change
sequence variant causing polypeptide post translational processing change
polypeptide post-translational processing affected
polypeptide_post_translational_processing_affected
sequence
polypeptide_post-translational_processing_affected
sequence_variant_causing_partial_loss_of_function_of_polypeptide
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing partial loss of function of polypeptide
partial loss of function of polypeptide
sequence variant causing partial loss of function of polypeptide
sequence_variant_causing_gain_of_function_of_polypeptide
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing gain of function of polypeptide
gain of function of polypeptide
sequence variant causing gain of function of polypeptide
sequence_variant_affecting_transcript_secondary_structure
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence variant affecting transcript secondary structure
mutation affecting transcript secondary structure
sequence_variant_causing_compensatory_transcript_secondary_structure_mutation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing compensatory transcript secondary structure mutation
mutation causing compensatory transcript secondary structure mutation
sequence_variant_effect
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.nUpdated after discussion with Peter Taschner - Feb 09.
sequence
sequence variant effect
The effect of a change in nucleotide sequence.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence_variant_causing_polypeptide_fusion
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing polypeptide fusion
mutation causing polypeptide fusion
autosynaptic_chromosome
sequence
(Drosophila)A
An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome.
PMID:6804304
http://purl.org/obo/owl/PMID#PMID_6804304
autosynaptic chromosome
homo_compound_chromosome
sequence
homo compound chromosome
homo-compound chromosome
A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
hetero_compound_chromosome
sequence
A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
SO:ke
http://purl.org/obo/owl/SO#SO_ke
hetero-compound chromosome
hetero compound chromosome
chromosome_fission
sequence
A chromosome that occurred by the division of a larger chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
chromosome fission
dexstrosynaptic_chromosome
sequence
An autosynaptic chromosome carrying the two right (D = dextro) telomeres.
FB:manual
http://purl.org/obo/owl/FB#FB_manual
dexstrosynaptic chromosome
laevosynaptic_chromosome
sequence
LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres.
FB:manual
http://purl.org/obo/owl/FB#FB_manual
laevosynaptic chromosome
free_duplication
sequence
free duplication
A chromosome structure variation whereby the duplicated sequences are carried as a free centric element.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
free_ring_duplication
sequence
free ring duplication
(Drosophila)R
A ring chromosome which is a copy of another chromosome.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
complex_chromosomal_mutation
sequence
complex chromosomal mutation
A chromosome structure variant with 4 or more breakpoints.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
SO:ke
http://purl.org/obo/owl/SO#SO_ke
deficient_translocation
sequence
(Drosophila)Df
(Drosophila)DfT
A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
deficient translocation
inversion_cum_translocation
sequence
inversion cum translocation
A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
(Drosophila)T
(Drosophila)InT
bipartite_duplication
sequence
(Drosophila)bDp
An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
bipartite duplication
cyclic_translocation
sequence
cyclic translocation
A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
bipartite_inversion
sequence
bipartite inversion
A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed).
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
(Drosophila)bIn
uninverted_insertional_duplication
sequence
(Drosophila)eDp
uninverted insertional duplication
An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
inverted_insertional_duplication
sequence
(Drosophila)iDp
inverted insertional duplication
An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
insertional_duplication
sequence
A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication).
SO:ke
http://purl.org/obo/owl/SO#SO_ke
(Drosophila)Dpp
insertional duplication
interchromosomal_transposition
sequence
(Drosophila)Tp
interchromosomal transposition
A chromosome structure variation whereby a transposition occurred between chromosomes.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
inverted_interchromosomal_transposition
sequence
inverted interchromosomal transposition
(Drosophila)iTp
An interchromosomal transposition whereby 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 segment.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
uninverted_interchromosomal_transposition
sequence
uninverted interchromosomal transposition
An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
(Drosophila)eTp
inverted_intrachromosomal_transposition
sequence
inverted intrachromosomal transposition
(Drosophila)iTp
An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
uninverted_intrachromosomal_transposition
sequence
uninverted intrachromosomal transposition
(Drosophila)eTp
An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
unoriented_insertional_duplication
Flag - unknown in the definition.
sequence
unoriented insertional duplication
(Drosophila)uDp
An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
unoriented_interchromosomal_transposition
FLAG - term describes an unknown.
sequence
(Drosophila)uTp
unorientated interchromosomal transposition
An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
unoriented_intrachromosomal_transposition
FLAG - definition describes an unknown.
sequence
An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
(Drosophila)uTp
unorientated intrachromosomal transposition
uncharacterised_chromosomal_mutation
sequence
uncharacterised chromosomal mutation
deficient_inversion
sequence
(Drosophila)DfIn
deficient inversion
(Drosophila)Df
A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted.
FB:reference_manual
http://purl.org/obo/owl/FB#FB_reference_manual
SO:ke
http://purl.org/obo/owl/SO#SO_ke
tandem_duplication
sequence
tandem duplication
A duplication consisting of 2 identical adjacent regions.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
erverted
URL:http://www.ncbi.nlm.nih.gov/dbvar/
http://www.ncbi.nlm.nih.gov/dbvar/
partially_characterised_chromosomal_mutation
sequence
partially characterised chromosomal mutation
sequence_variant_affecting_gene_structure
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
A sequence_variant_effect that changes the gene structure.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence variant affecting gene structure
mutation affecting gene structure
sequence_variant_causing_gene_fusion
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
mutation causing gene fusion
sequence variant causing gene fusion
A sequence_variant_effect that changes the gene structure by causing a fusion to another gene.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
chromosome_number_variation
sequence
chromosome number variation
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
chromosome_structure_variation
sequence
chromosome structure variation
sequence_variant_causes_exon_loss
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
A sequence variant affecting splicing and causes an exon loss.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
sequence variant causes exon loss
mutation causes exon loss
sequence_variant_causes_intron_gain
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072).
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://purl.org/obo/owl/EBI#EBI_www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence variant causes intron gain
mutation causes intron gain
sequence_variant_causing_cryptic_splice_donor_activation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing cryptic splice donor activation
sequence_variant_causing_cryptic_splice_acceptor_activation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
sequence
sequence variant causing cryptic splice acceptor activation
alternatively_spliced_transcript
sequence
alternatively spliced transcript
A transcript that is alternatively spliced.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
encodes_1_polypeptide
sequence
A gene that is alternately spliced, but encodes only one polypeptide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
encodes 1 polypeptide
encodes_greater_than_1_polypeptide
sequence
A gene that is alternately spliced, and encodes more than one polypeptide.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
encodes greater than 1 polypeptide
encodes_different_polypeptides_different_stop
sequence
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
encodes different polypeptides different stop
encodes_overlapping_peptides_different_start
sequence
encodes overlapping peptides different start
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
encodes_disjoint_polypeptides
sequence
encodes disjoint polypeptides
A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
encodes_overlapping_polypeptides_different_start_and_stop
sequence
encodes overlapping polypeptides different start and stop
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping
sequence
encodes_overlapping_peptides
sequence
encodes overlapping peptides
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
cryptogene
sequence
A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
dicistronic_primary_transcript
sequence
A primary transcript that has the quality dicistronic.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
dicistronic primary transcript
member_of_regulon
sequence
member of regulon
alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
sequence
alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping
CDS_independently_known
sequence
A CDS with the evidence status of being independently known.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
CDS independently known
orphan_CDS
sequence
orphan CDS
A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
CDS_supported_by_domain_match_data
sequence
A CDS that is supported by domain similarity.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
CDS supported by domain match data
CDS_supported_by_sequence_similarity_data
sequence
A CDS that is supported by sequence similarity data.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
CDS supported by sequence similarity data
CDS_predicted
sequence
A CDS that is predicted.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
CDS predicted
status_of_coding_sequence
sequence
CDS_supported_by_EST_or_cDNA_data
sequence
CDS supported by EST or cDNA data
A CDS that is supported by similarity to EST or cDNA data.
SO:xp
http://purl.org/obo/owl/SO#SO_xp
internal_Shine_Dalgarno_sequence
sequence
A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
PMID:12519954
http://purl.org/obo/owl/PMID#PMID_12519954
internal Shine Dalgarno sequence
internal Shine-Dalgarno sequence
recoded_mRNA
sequence
recoded mRNA
The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract
minus_1_translationally_frameshifted
sequence
minus 1 translationally frameshifted
An attribute describing a translational frameshift of -1.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
plus_1_translationally_frameshifted
sequence
An attribute describing a translational frameshift of +1.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
plus 1 translationally frameshifted
mRNA_recoded_by_translational_bypass
sequence
A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract
mRNA recoded by translational bypass
mRNA_recoded_by_codon_redefinition
sequence
A recoded_mRNA that was modified by an alteration of codon meaning.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
mRNA recoded by codon redefinition
stop_codon_redefinition_as_selenocysteine
sequence
stop_codon_readthrough
sequence
recoding_stimulatory_region
sequence
recoding stimulatory signal
recoding stimulatory region
A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA.
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract
four_bp_start_codon
sequence
A non-canonical start codon with 4 base pairs.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
4bp start codon
four bp start codon
stop_codon_redefinition_as_pyrrolysine
sequence
archaeal_intron
Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism.
sequence
An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease.
PMID:9301331
http://purl.org/obo/owl/PMID#PMID_9301331
SO:ma
http://purl.org/obo/owl/SO#SO_ma
archaeal intron
tRNA_intron
Could be a cross product with Gene ontology, GO:0006388.
sequence
tRNA intron
An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
pre-tRNA intron
CTG_start_codon
sequence
A non-canonical start codon of sequence CTG.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
CTG start codon
SECIS_element
sequence
SECIS element
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.
URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031
URL:http://en.wikipedia.org/wiki/SECIS_element
http://en.wikipedia.org/wiki/SECIS_element
retron
sequence
Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes.
SO:ma
http://purl.org/obo/owl/SO#SO_ma
three_prime_recoding_site
sequence
three prime recoding site
The recoding stimulatory signal located downstream of the recoding site.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
three_prime_stem_loop_structure
sequence
A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region.
PMID:12519954
http://purl.org/obo/owl/PMID#PMID_12519954
SO:ke
http://purl.org/obo/owl/SO#SO_ke
three prime stem loop structure
five_prime_recoding_site
sequence
The recoding stimulatory signal located upstream of the recoding site.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
five prime recoding site
flanking_three_prime_quadruplet_recoding_signal
sequence
Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
PMID:12519954
http://purl.org/obo/owl/PMID#PMID_12519954
flanking three prime quadruplet recoding signal
UAG_stop_codon_signal
sequence
UAG stop codon signal
A stop codon signal for a UAG stop codon redefinition.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
UAA_stop_codon_signal
sequence
UAA stop codon signal
A stop codon signal for a UAA stop codon redefinition.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
regulon
sequence
URL:http://en.wikipedia.org/wiki/Regulon
http://en.wikipedia.org/wiki/Regulon
A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal.
ISBN:0198506732
http://purl.org/obo/owl/ISBN#ISBN_0198506732
UGA_stop_codon_signal
sequence
UGA stop codon signal
A stop codon signal for a UGA stop codon redefinition.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
three_prime_repeat_recoding_signal
sequence
A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.
PMID:12519954
http://purl.org/obo/owl/PMID#PMID_12519954
SO:ke
http://purl.org/obo/owl/SO#SO_ke
three prime repeat recoding signal
distant_three_prime_recoding_signal
sequence
distant three prime recoding signal
A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon.
URL:http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract
stop_codon_signal
This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal.
sequence
A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding.
PMID:12519954
http://purl.org/obo/owl/PMID#PMID_12519954
SO:ke
http://purl.org/obo/owl/SO#SO_ke
stop codon signal
databank_entry
sequence
databank entry
accession
The sequence referred to by an entry in a databank such as Genbank or SwissProt.
SO:ke
http://purl.org/obo/owl/SO#SO_ke
gene_segment
Requested by tracker 2021594, July 2008, by Alex.
sequence
A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.
GOC:add
http://purl.org/obo/owl/GOC#GOC_add
gene segment
database of genomic structural variation
SO feature annotation
biosapiens protein feature ontology