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:1001247
Fiat Object Part
snap:FiatObjectPart
A material entity that is part of an object but is not demarcated by any physical discontinuities.
Flanking 3' Quadraplet Recoding Signal
Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons.
SO:1001281
A phylum of kingdom Animalia.
Porifera
A class of phylum Chordata.
Actinopterygii
Platyhelminthes
A phylum of kingdom Animalia.
A species of genus Sus.
Wild boar
Pig
Swine
Sus scrofa
Sus scrofus
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.
Exemplar mRNA
SO:0000734
Bruguiera gymnorhiza
A species of genus Bruguiera.
Burma mangrove
Bruguiera gymnorhiza (L.) Savigny
Bruguiera gymnorrhizza
Bruguiera gymnorrhiza
SO:0000706
The 3' splice site of the acceptor primary transcript.
Trans Splice Acceptor Site
A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
snap:RealizableEntity
Realizable Entity
SO:0001654
Nucleotide to Protein Binding Site
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA.
pre-miRNA Binding
GO:0070883
Major TSS
SO:0000666
Mobile Intron
An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.
SO:0001002
A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.
rRNA 25S
SO:0000242
The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
Untranslated Region Polycistronic mRNA
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
GO:0005575
Cellular Component
Red-chested mustached tamarin
Saguinus labiatus
A species of genus Saguinus.
A class of phylum Chordata.
Ascidiacea
Coding End
The last base to be translated into protein. It does not include the stop codon.
SO:0000327
A species of genus Medicago.
Medicago truncatula
Barrel medic
Capped mRNA
An mRNA that is capped.
SO:0000862
A species of genus Pongo.
Pongo pygmaeus
Orangutan
Bornean orangutan
Orang-utan
Orang utan
SO:0001176
Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
DHU Loop
SO:0001181
Bruno Response Element
A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
A species of genus Rhipicephalus.
Cattle tick
Southern cattle tick
Boophilus microplus
Rhipicephalus (Boophilus) microplus
Rhipicephalus microplus
SO:0000633
An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
Monocistronic mRNA
SO:0000218
Glycine tRNA Primary Transcript
A primary transcript encoding glycyl tRNA.
A miRNA target site is a binding site where the molecule is a micro RNA.
miRNA Target Site
SO:0000934
Nasonia lonigicornis
Nasonia longicornis
A species of genus Nasonia.
SO:0000225
Proline tRNA Primary Transcript
A primary transcript encoding prolyl tRNA.
mRNA with Minus 1 Frameshift
SO:0000282
An mRNA with a minus 1 frameshift.
SO:0001483
SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
SNV
Naturally occurring macromolecules that harbor biological information in their structures, e.g. proteins, nucleic acids.
Information Biopolymer
GRO:InformationBiopolymer
Trans Splice Site
SO:0001420
Primary transcript region bordering trans-splice junction.
Bombyx mori
A species of genus Bombyx.
Bombyx mori Linnaeus, 1758
Domestic silkworm
Silk moth
Silkworm
A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
Methionyl tRNA
SO:0000266
SO:0000883
Stop Codon Read Through
A stop codon redefined to be a new amino acid.
A species of genus Sarcophilus.
Sarcophilus harrisii
Sarcophilus laniarius
Tasmanian devil
Glutaminyl tRNA
SO:0000259
A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.
A class of phylum Chordata.
Appendicularia
A species of genus Aquilegia.
Aquilegia coerulea
Aquilegia caerulea
RNA Metabolic Process
GO:0016070
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
An mRNA that is trans-spliced.
SO:0000872
Trans Spliced mRNA
A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
SO:0001034
Mirtron
A region within an intron.
SO:0000841
Spliceosomal Intron Region
SO:0000235
Transcription Factor Binding Site
A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex.
Populus balsamifera subsp. trichocarpa (Torr. et A.Gray) Brayshaw
Black cottonwood
Populus trichocarpa Torr. et A.Gray
Western balsam poplar
Populus trichocarpa Torr. & A.Gray
Populus trichocarpa
A species of genus Populus.
Populus balsamifera subsp. trichocarpa
GRO:TranscriptionFactor
Transcription Factor
modified definition from WIkipedia, http://en.wikipedia.org/wiki/Transcription_factor
A role palyed by a protein that binds to specific DNA sequences, thereby controlling the transcription of genetic information from DNA to mRNA.
Dengue virus
A ssRNA virus of family Flaviviridae.
Arachis hypogaea
A species of genus Arachis.
Ground-nut
Goober
Peanut
Arachis hypogea
RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
rRNA
SO:0000252
A region of guide RNA.
Guide RNA Region
SO:0000930
Posttranscriptional Gene Silencing by RNA
GO:0035194
Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation.
SO:0000484
Three Prime Coding Exon Noncoding Region
The sequence of the 3' exon that is not coding.
Red abalone
California red abalone
A species of genus Haliotis.
Haliotis rufescens
The recoding stimulatory signal located downstream of the recoding site.
3' Recoding Site
SO:1001277
A species of genus Salvia.
Clary
Salvia sclarea
Salvia sclarea L.
Dictyostelium discoideum
A species of genus Dictyostelium.
A species of genus Homo.
Homo sapiens
Human
Man
Nucleic Acid Binding
GO:0003676
Interacting selectively and non-covalently with any nucleic acid.
The canonical 3' splice site has the sequence "AG".
SO:0000676
Canonical 3' Splice Site
Taeniopygia guttata
A species of genus Taeniopygia.
Zebra finch
Taenopygia guttata
Poephila guttata
Cerebratulus lacteus
A species of genus Cerebratulus.
Milky ribbon-worm
Milky ribbon worm
Cocoa
Cacao
A species of genus Theobroma.
Theobroma cacao
A class of phylum Mollusca.
Gastropoda
Florida lancelet
A species of genus Branchiostoma.
Amphioxus floridae
Branchiostoma floridea
Branchiostoma floridae
The canonical 5' splice site has the sequence "GT".
Canonical 5' Splice Site
SO:0000677
A dsDNA virus of family Herpesviridae.
herpesvirus of turkey
Meleagrid herpesvirus type 1
herpesvirus of turkeys
turkey herpesvirus HVT
Turkey herpesvirus
Meleagrid herpesvirus 1
The recoding stimulatory signal located upstream of the recoding site.
5' Recoding Site
SO:1001280
Terminal Loop
A contiguous sequence of nucleotide residues that directly links the two halves of an unbroken stem (but does not participate in the stem); this structure is also known as a "hairpin loop". Because a terminal loop may also participate in other inter-base interactions, (a) it is defined relative to a particular unbroken_stem, and (b) it is not implicitly defined as unpaired (or paired). [RNAO:0000098]
RNAO:0000098
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:0000694
SNP
SO:0000195
An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
Coding Exon
A species of genus Drosophila.
Drosophila willistoni
Saccharum sp.
A species of genus Saccharum.
Brugia malayi
A species of genus Brugia.
Agent of lymphatic filariasis
SO:0000275
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.
snoRNA
A primary transcript encoding a tmRNA.
tmRNA Primary Transcript
SO:0000584
An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.
SO:0005843
rRNA Cleavage RNA
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.
5' cis Splice Site
SO:0000163
Citrus reticulata
Citrus poonensis
Tangerine
Mandarin orange
A species of genus Citrus.
Chickens
Bantam
Chicken
A species of genus Gallus.
Gallus gallus domesticus
Gallus domesticus
Gallus gallus
Non-canonical Start Codon
SO:0000680
A start codon that is not the usual AUG sequence.
A species of genus Helianthus.
Helianthus annuus
Common sunflower
Helianthus annus
Helianthus annuus8
An intron which is spliced by the spliceosome.
Spliceosomal Intron
SO:0000662
Lysyl tRNA
A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
SO:0000265
Festuca arundinacea
Schedonorus phoenix
Lolium arundinaceum
Schedonorus arundinaceus
Festuca elatior
Tall fescue
A species of genus Festuca.
A phylum of kingdom Animalia.
Nematoda
Citrus sinensis
Naranja
Navel orange
A species of genus Citrus.
Citrus sinensis (L.) Osbeck
Apfelsine
Sweet orange
Valencia orange
Citrus x sinensis
5' Intron
A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.
SO:0001655
Nucleotide Binding Site
SO:0001215
Coding Region of Exon
The region of an exon that encodes for protein sequence.
The cellular synthesis of RNA on a template of RNA.
GO:0001172
Transcription, RNA-dependent
SO:0000370
A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
Small Regulatory ncRNA
miRNA
Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules 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.
SO:0000276
A species of genus Gossypium.
Arabian cotton
Gossypium herbaceum L.
Gossypium herbaceum
SO:0000836
mRNA Region
A region of an mRNA.
Daphnia pulex
Common water flea
A species of genus Daphnia.
Five Prime Open Reading Frame
Occurent
span:Occurrent
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
SO:0000483
A primary transcript that is never translated into a protein.
Noncoding Primary Transcript
Nematode
A species of genus Caenorhabditis.
Rhabditis elegans
Caenorhabditis elegans
A primary transcript encoding an rRNA cleavage snoRNA.
SO:0000582
rRNA cleavage snoRNA Primary Transcript
Chromosome
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
GO:0005694
U11 snRNA
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.
SO:0000398
Serine tRNA Primary Transcript
A primary transcript encoding seryl tRNA.
SO:0000226
A recoded_mRNA that was modified by an alteration of codon meaning.
SO:1001265
mRNA Recoded by Codon Redefinition
A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
SO:0000147
Exon
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.
Binding Site
SO:0000409
GO:0003677
DNA Binding
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
A species of genus Glycine.
Soybean
Glycine max
Glycine max; cv. Wye
SO:0000647
pri-miRNA
A primary transcript encoding a micro RNA.
SRP 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.
SO:0000590
SO:0001035
piRNA
A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
U5 snRNA
SO:0000395
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.
Small Subunit rRNA
SO:0000650
Ribosomal RNA transcript that structures the small subunit of the ribosome.
SO:0000142
DNA Sequence Secondary Structure
A folded DNA sequence.
RNAO:0000099
Internal Loop
A collection of nucleotide residues that link two given unbroken_stems.
Honey bee
Honeybee
Bee
Apis mellifica
A species of genus Apis.
Apis mellifera
Large Subunit rRNA
SO:0000651
Ribosomal RNA transcript that structures the large subunit of the ribosome.
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.
SO:0000393
U4 snRNA
Arabidopsis lyrata
A species of genus Arabidopsis.
Arabidopsis lyrata (L.) O'Kane & Al-Shehbaz
Lyrate rockcress
Metabolic Process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
GO:0008152
A region of a primary transcript, that is removed via trans splicing.
Outron
SO:0001475
SO:0001171
rRNA 21S
A component of the large ribosomal subunit in mitochondrial rRNA.
SO:0001212
Plus 2 Translational 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.
Strigamia maritima
A species of genus Strigamia.
Ricinus sanguineus
A species of genus Ricinus.
Ricinus comunis
Ricinis communis
Ricinus communis
Castor bean
Ricinus communis L.
Ricinus sanguineus hort. ex Groenl.
Ricimus communis
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.
Recursive Splice Site
SO:0000998
An RNA with catalytic activity.
Ribozyme
SO:0000374
The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
SO:0005837
U14 snoRNA Primary Transcript
SO:0000630
Upstream AUG Codon
A start codon upstream of the ORF.
SO:0000204
A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
Five Prime UTR
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.
SO:0005841
A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
snap:SpecificallyDependentContinuant
Specifically Dependent Continuant
mRNA
SO:0000234
Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
A species of genus Haemonchus.
Barber pole worm
Red stomach worm
Haemonchus contortus
A ssRNA virus of family Flaviviridae.
West Nile Virus
Recoded mRNA
SO:1001261
The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.
A class of phylum Cnidaria.
Hydrozoa
Tobacco hawkmoth
Tobacco hornworm
Tomato hornworm
Hornblower
Carolina sphinx
Manduca sexta
A species of genus Manduca.
Reptilia
MSH:D012104
Cold-blooded, air-breathing VERTEBRATES belonging to the class Reptilia, usually covered with external scales or bony plates.
A species of genus Schistosoma.
Schistosoma mansoni
Shine Dalgarno Sequence
SO:0000552
A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
Plants
Any living organism that typically synthesizes its food from inorganic substances, possesses cellulose cell walls, responds slowly and often permanently to a stimulus, lacks specialized sense organs and nervous system, and has no powers of locomotion. (EPA Terminology Reference System).
NCIThesaurus:Plant
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'.
C/D Box snoRNA
SO:0000593
Mature Transcript
SO:0000233
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.
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.
SO:0000399
U12 snRNA
A CDS that is supported by sequence similarity data.
CDS Supported by Sequence SImilarity Data
SO:1001251
SO:0000479
A transcript that is trans-spliced.
Trans-spliced Transcript
The loop of the hairpin loop formed by folding of the pre-miRNA.
SO:0001246
miRNA Loop
Internal UTR
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:0000241
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:0000001
Region
Helianthus ciliaris
Helianthus ciliaris DC.
Helianthus cilaris
A species of genus Helianthus.
SO:0001419
cis Splice Site
Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
Clip
SO:0000303
Part of the primary transcript that is clipped off during processing.
A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
SO:0000262
Histidyl tRNA
A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
H/ACA Box snoRNA Primary Transcript
SO:0000596
SO:0000214
A primary transcript encoding aspartyl tRNA.
Aspartic acid tRNA Primary Transcript
A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
Protein Binding SIte
SO:0000410
Translational Frameshift
SO:0001210
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.
A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
Pyrrolysyl tRNA
SO:0000766
Echinoidea
A class of phylum Echinodermata.
SO:1001287
Distant 3' Recoding SIgnal
A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon.
Takifugu rubripes (Temminck & Schlegel, 1850)
A species of genus Takifugu.
Tetraodon rubripes
Sphaeroides rubripes
Fugu rubripes
Tiger puffer
Takifugu rubripes
Torafugu
Simian herpes B virus
Herpes virus B
Herpes B virus
Cercopithecid herpesvirus 1
Monkey B virus
Herpesvirus simiae
Simian herpes B virus SHBV
Simian herpesvirus B
A dsDNA virus of family Herpesviridae.
Cercopithecine herpesvirus 1
Macacine herpesvirus 1
B virus
Hippoglossus hippoglossus (Linnaeus, 1758)
Hippoglossus hippoglossus
Atlantic halibut
A species of genus Hippoglossus.
SO:0001877
A non-coding RNA over 200nucleotides in length.
Lnc RNA
A species of genus Oryza.
Oryza sativa
Red rice
Rice
ssRNA virus
Drosophila simulans
A species of genus Drosophila.
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:0001752
SL7 Acceptor Site
A primary transcript encoding a small temporal mRNA.
SO:0000648
stRNA Primary Transcript
Polycistronic Transcript
SO:0000078
A transcript that is polycistronic.
Norway rat
Rat
Rattus norvegicus
Rattus norvegicus8
Rattus rattiscus
Gunn rats
Rattus norwegicus
Rattus sp. strain Wistar
A species of genus Rattus.
Brown rat
A species of genus Manihot.
Manihot esculenta Crantz
Manihot esculenta0
Manioc
Tapioca
Manihot esculenta
Yuca
Manihot utilissima
Cassava
Echinodermata
A phylum of kingdom Animalia.
A CDS that is part of a transposable element.
Transposable Element CDS
SO:0001869
Pan troglodytes
Chimpansee troglodytes
A species of genus Pan.
Chimpanzee
A species of genus Terebratulina.
Terebratulina retusa
Hydra magnipapillata
A species of genus Hydra.
SO:0000584
tmRNA
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.
SO:0000278
Transcript Bound by Nucleic Acid
A transcript that is bound by a nucleic acid.
SO:0000139
Ribosome Entry Site
Region in mRNA where ribosome assembles.
Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. [SO:0000649]
stRNA
SO:0000649
Retro-transcribing virus
A virus that replicates by the reverse transcription of a RNA or DNA intermediate.
CDS Supported by Domain Match Data
SO:1001249
A CDS that is supported by domain similarity.
Drosophila erecta
A species of genus Drosophila.
A part of a primary transcript.
Primary Transcript Region
SO:0000835
GO:0035198
Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.
miRNA Binding
A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
Cysteinyl tRNA
SO:0000258
Glottidea pyramidata
A species of genus Glottidia.
Glottidia pyramidata
Nicotiana tabacum
Common tobacco
Tobacco
American tobacco
Nicotania tabacum
Nicotiana tabacum var. Samsun
A species of genus Nicotiana.
SO:0000989
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.
Class II RNA
Heliconius melpomene
A species of genus Heliconius.
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:0000145
Recoded Codon
A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA.
Recoding Stimulatory Region
SO:1001268
A contiguous sequence which begins with, and includes, a start codon, and ends with, and includes, a stop codon.
CDS
SO:0000316
A primary transcript encoding glutamyl tRNA.
Glutamine tRNA Primary Transcript
SO:0000217
Locusta migratoria
A species of genus Locusta.
Migratory locust
Phenylalanine tRNA Primary Transcript
SO:0000224
A primary transcript encoding phenylalanyl tRNA.
SO:0001411
Biological Region
A region defined by its disposition to be involved in a biological process.
Regulation of Gene Expression
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
GO:0010468
SO:0000273
Valyl tRNA
A tRNA sequence that has a valine anticodon, and a 3' valine binding region.
Sorghum saccharatum
Sorghum
Sorghum bicolor milo
A species of genus Sorghum.
Broomcorn
Milo
Sorghum bicolor
Sorghum vulgare
Regulation of Metabolic Process
GO:0019222
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
Anopheles gambiae Giles, 1902
Anopheles gambia
Anopheles gambiae
African malaria mosquito
Anopheles gambiae sensu stricto
A species of genus Anopheles.
Macaca nemestrina
Pigtail macaque
Pigtail monkey
Pig-tailed macaque
A species of genus Macaca.
Drosophila melanogaster
Drosophila melangaster
Fruit fly
A species of genus Drosophila.
A binding site that, in the molecule, interacts selectively and non-covalently with DNA.
DNA Binding SIte
SO:0001429
A species of genus Acyrthosiphon.
Acyrthosiphon pisum
Pea aphid
Acyrthosiphum pisum
Processed Transcript
SO:0001503
A transcript for which no open reading frame has been identified and for which no other function has been determined.
A species of genus Aedes.
Stegomyia aegypti
Yellow fever mosquito
Aedes aegypti
A class of phylum Arthropoda.
Malacostraca
The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
SO:0001244
pre-miRNA
dengue type 1 D1 virus
dengue virus-1 DEN-1
Type 1 dengue virus
Dengue virus 1
dengue virus type I
Dengue virus type 1
dengue virus type 1 DEN1
type 1 dengue virus DEN-1
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.
SO:0000386
RNase P RNA
Editing Domain
SO:0000606
Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
Acacia auriculiformis
A species of genus Acacia.
Acacia auriculiformis A.Cunn. ex Benth.
BFO:MaterialEntity
Material Entity
An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
Virus
NCIThesaurus:Virus
An infectious agent which consists of two parts, genetic material and a protein coat. These organisms lack independent metabolism, and they must infect the cells of other types of organisms to reproduce. Most viruses are capable of passing through fine filters that retain bacteria, and are not visible through a light microscope.
Pinus densata
A species of genus Pinus.
RNAO:0000106
Stem Junction
A collection of nucleotide residues consisting of all and only the nucleotide regions that link more than two unbroken stems such that each region links exactly two unbroken stems. This term is defined relative to the particular unbroken_stems involved and, again, does not imply anything about the pairedness/unpairedness of the bases in this region. The degree of a junction is a property (e.g. 3-junction, 4-junction), so the different degrees do not get separate entries in the ontology.
Lagothrix lagotricha
Brown woolly monkey
Common woolly monkey
Humboldt's woolly monkey
Lagothrix lagothricha
Lagothrix lagotricha lagotricha
A species of genus Lagothrix.
Cowpea
Phaseolus unguiculatus
A species of genus Vigna.
Vigna unguiculata
SO:0000407
rRNA 18S
A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.
SO:1001274
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.
SECIS Element
Stop Codon Redefined as Selenocysteine
A stop codon redefined to be the new amino acid, selenocysteine.
SO:0000885
A species of genus Drosophila.
Drosophila yakuba
Echinococcus granulosus sensu stricto
Echinococcus granulosus sheep strain
A species of genus Echinococcus.
Echinococcus granulosus Tasmanian sheep strain
Echinococcus granulosus
Echinococcus granulosus s. s.
Echinococcus granulosus buffalo strain
Echinococcus granulosus (Batsch, 1786)
Echinococcus granulosus G3 strain
Echinococcus granulosus G2 strain
Echinococcus granulosus G1 strain
AIDS virus
human immunodeficiency virus-1 HIV-1
human immunodeficiency virus 1 HIV-1
A retro-transcribing virus of family Retroviridae.
human immunodeficiency virus type 1 HIV-1
Human immundeficiency virus type 1
human immunodeficiency virus type 1 ,HIV-1
human immunodeficiency virus type 1, HIV-1
human immunodeficiency virus type 1 HIV1
Human immunodeficiency virus 1
human immunodeficiency virus HIV-1
human immunodeficiency virus type-1 HIV-1
human immunodeficiency virus type 1 HIV 1
human immunodeficiency virus type I HIV-1
Human immunodeficiencey virus type 1
Human immunodeficiency virus type 1
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
GO:0003723
RNA Binding
herpes simplex virus 1 HSV-1
Human herpesvirus 1
Human herpesvirus type 1
herpes simplex virus type-1 HSV-1
Herpes simplex virus 1
Herpes simplex virus type 1
herpes simplex virus type 1 HSV1
herpes simplex virus type 1 HSV-1
herpes simplex virus HSV-1
A dsDNA virus of family Herpesviridae.
Human Herpesvirus-1
Solanum esculentum
A species of genus Solanum.
Lycopersicon esculentum Mill.
Lycopersicum esculentum
Solanum lycopersicon
Solanum esculentum Dunal
Lycopersicon esculentum var. esculentum
Lycopersicon lycopersicum
Lycopersicon esculentum
Tomato
Solanum lycopersicum L.
Solanum lycopersicum
A paired region made up of two contiguous collections of nucleotides, in which each nucleotide forms a base pair. [RNAO:0000097]
Unbroken Stem
RNAO:0000097
Turbellaria
A class of phylum Platyhelminthes.
Brassica oleracea
Brassica oleracea L.
A species of genus Brassica.
U6atac snRNA
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:0000397
rRNA Large Subunit Primary Transcript
SO:0000325
A primary transcript encoding a large ribosomal subunit RNA.
3'-most region of a precursor transcript that is clipped off during processing.
SO:0000557
3' Clip
Generically Dependent Continuant
A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time.
snap:GenericallyDependentContinuant
SO:0000665
Monocistronic Transcript
A transcript that is monocistronic.
Pyrrolysine tRNA Primary Transcript
SO:0001178
A primary transcript encoding pyrrolysyl tRNA.
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.
Branch Site
SO:0000611
SO:0000201
An exon that is bounded by 5' and 3' splice sites.
Interior Exon
SO:0001180
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.
An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
Enzymatic RNA
SO:0000372
Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
SO:0000638
Transcribed Spacer Region
SO:0000709
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.
SL2 Acceptor Site
polyomavirus JC
JC virus
Human polyomavirus (type JC)
JC polyomavirus JCV
human polyomavirus JCV
JC polyomavirus
Polyomavirus hominis 2
A dsDNA virus of family Polyomaviridae
polyoma virus JC JCV
SO:0000323
The first base to be translated into a protein.
Coding Start
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.
SO:0000990
Class I RNA
Common wheat
Triticum aestivum8
A species of genus Triticum.
Wheat
Triticum aestivum
Bread wheat
Triticum vulgare
Tricum aestivum
Triticum aestivum subsp. aestivum
Canadian hard winter wheat
Triticum aestivam
Noncoding Region of Exon
The maximal intersection of exon and UTR.
SO:0001214
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.
SO:0000387
RprA RNA
Oikopleura dioica
A species of genus Oikopleura.
Protein Coding Primary Transcript
SO:0000120
A primary transcript that, at least in part, encodes one or more proteins.
RNA 6S
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.
SO:0000376
Ring-tailed lemur
A species of genus Lemur.
Lemur catta
Insecta
A class of phylum Arthropoda.
Field mustard
A species of genus Brassica.
Brassica rapa
Brassica rapa L.
SO:0000447
5' UTR Intron
An intron located in the 5' UTR.
A species of genus Vitis.
Vitis vinifera subsp. vinifera
Wine grape
Vitis vinifera
Glycine soja
Wild soybean
A species of genus Glycine.
SO:0000392
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.
U2 snRNA
SO:0000851
CDS Region
A region of a CDS.
SO:0000232
snoRNA Primary Transcript
A primary transcript encoding a small nucleolar mRNA.
Mollusca
A phylum of kingdom Animalia.
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.
SO:0000405
Amoebozoa
A species of genus Drosophila.
Drosophila mohavensis
Drosophila mojavensis
Minor TSS
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GO:0005488]
GO:0005488
Binding
A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
Function
snap:Function
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:0001016
Internal Guide Sequence
tmRNA Region
A region of a tmRNA.
SO:0000847
A dsDNA virus of family Herpesviridae.
Human herpesvirus 5
Human cytomegalovirus HCMV
human cytomegalovirus CMV
human herpesvirus type 5
Human cytomegalovirus
Polycistronic mRNA
SO:0000634
An mRNA that encodes multiple proteins from at least two non-overlapping regions.
Internal Shine Dalgarno Sequence
SO:1001260
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:0000770
tmRNA Acceptor Piece
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.
Anthozoa
A class of phylum Cnidaria.
rRNA 28S
SO:0000653
A component of the large ribosomal subunit.
rRNA 16S
A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
SO:0001000
Culex quinquifasciatus
Culex quinquefasciatus
Southern house mosquito
Culex quiquefasciatus
Culex pipiens quinquefasciatus
Culex quinquifasiatus
A species of genus Culex.
Culex pipiens quiquefasciatus
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.
tmRNA Coding Piece
SO:0000769
Ectocarpus siliculosus
A species of genus Ectocarpus.
A primary transcript encoding a signal recognition particle RNA.
SO:0000589
SRP RNA Primary Transcript
Bandicoot papillomatosis carcinomatosis virus type 2
A dsDNA virus of family Papillomaviridae.
SO:0000388
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.
CsrB RsmB RNA
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.
SO:0000377
A region of a transcript.
Transcript Region
SO:0000833
Simian virus 40
Polyomavirus maccacae 1
Rhesus macaque polyomavirus
Polyomavirus maccacae
rhesus polyomavirus
A dsDNA virus of family Polyomaviridae.
3' Stem-loop Structure
A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region.
SO:1001279
SO:0000270
A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
Threonyl tRNA
Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA.
SO:0001904
Antisense lncRNA
SO:0000254
A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
Alanyl tRNA
A class of phylum Chordata.
Amphibia
A species of genus Gossypium.
Gossypium arboreum L.
Gossypium arboreum
Tree cotton
Annelida
A phylum of kingdom Animalia.
Cultivated apple
Pyrus malus
Malus pumila auct.
Malus x domestica
Apple
Malus sylvestris var. domestica
Apple tree
A species of genus Malus.
Malus domestica
Malus pumila var. domestica
Pseudorabies Virus PRV
Suid herpesvirus type 1
Aujeszky's disease virus
Alphaherpesvirus pseudorabies virus PRV
Pseudorabies virus
A dsDNA virus of family Herpesviridae.
Suid herpesvirus 1
GO:0050789
Regulation of Biological Process
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
A species of genus Helianthus.
Helianthus petiolaris Nutt.
Helianthus petiolaris
Duck-billed platypus
Duckbill platypus
Platypus
A species of genus Ornithorhynchus.
Ornythorhynchus anatinus
Ornithorhynchus anatinus
Interior Intron
pre-edited mRNA
SO:0000861
Capped Primary Transcript
A primary transcript that is capped.
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:0001751
Kaposi's sarcoma-associated herpesvirus
Karposi's sarcoma-associated herpes-like virus
A dsDNA virus of family Herpesviridae.
Human herpesvirus 8
Human herpesvirus 8 type P
Kaposi's sarcoma-associated herpesvirus - Human herpesvirus 8
Kaposi's sarcoma-associated herpesvirus KSHV
Kaposi's sarcoma-associated human herpes virus
Kaposi's sarcoma-associated herpes-like virus
SO:0000639
Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
Internal Transcribed Spacer Region
SO:0000229
Tyrosine tRNA Primary Transcript
A primary transcript encoding tyrosyl tRNA.
A transcript that is bound by a protein.
SO:0000279
Transcript Bound by Protein
U2 Intron
SO:0000184
A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
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.
SO:0000383
MicF RNA
A dsDNA virus of family Herpesviridae.
Macaca mulatta rhadinovirus 26-95
Rhesus monkey rhadinovirus H26-95
Aegilops tauschii
Aegilops tauschii Coss.
Aegilops tauschii Cosson
Triticum tauschii
A species of genus Aegilops.
Aegilops squarrosa subsp. squarrosa
Aegilops squarrosa
Patropyrum tauschii subsp. tauschii
Patropyrum tauschii
Aegilops squarrosa auct.
Murine herpesvirus 68
A dsDNA virus of family Herpesviridae.
Murid herpesvirus 4
mouse herpesvirus 68
murine gammaherpesvirus 68
murine herpesvirus type 68
mouse herpesvirus strain 68
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.
SL11 Acceptor Site
SO:0001756
Cryptic Splice SIte
SO:0001533
A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.
Cynara cardunculus L.
Cardoon
Wild artichoke
Cynara cardunculus
A species of genus Cynara.
A species of genus Helianthus.
Helianthus exilis
Helianthus exilis A.Gray
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:0000644
Animals
Animalia
Metazoa
A collection of one or more adjacent nucleotide residues in which at least one residue is part of a base pair.
RNAO:0000095
Paired Region
SO:0000264
Leucyl tRNA
A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
Pseudouridylation Guide snoRNA
SO:0001187
Dengue virus type 3
dengue 3 virus
Dengue Virus 3
A species of genus Drosophila.
Drosophila persimilis
Elaeis guineensis var. tenera (Oil palm)
Elaeis gunieensis
A species of genus Elaeis.
African oil palm
Elaeis guinensi
Elaeis guineensis
Elaeis guineensis var. tenera
Elaeis guineensis Jacq.
Consensus mRNA
SO:0000222
A primary transcript encoding lysyl tRNA.
Lysine tRNA Primary Transcript
SO:0000274
snRNA
A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
Kozak Sequence
SO:0001647
Riboswitch
SO:0000035
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.
Gene Expression
GO:0010467
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
SO:0000834
A region of a mature transcript.
Mature Transcript Region
miRNA Primary Transcript Region
SO:0001243
A part of an miRNA primary_transcript.
A short ncRNA that is transcribed from an enhancer. May have a regulatory function.
SO:0001870
Enhancer RNA
Drosophila virilis
Drosophila irilis
Drosophila virilis Sturtevant, 1916
A species of genus Drosophila.
SO:0000655
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.
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
IDO:Disease
Disease
A species of genus Rehmannia.
Chinese foxglove
Rehmannia glutinosa
A species of genus Gossypium.
Gossypium raimondii
Gossypium raimondii Ulbr.
A primary transcript encoding a tasiRNA.
tasiRNA Primary Transcript
SO:0001801
A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
Quality
snap:Quality
A dsDNA virus of family Herpesviridae.
Epstein-Barr virus EBV
Human herpesvirus type 4
Epstein-Barr-virus EBV
Human herpesvirus 4
Epstein-Barr virus
A transcript that has been edited by A to I substitution.
Edited Transcript by A to I Substitution
SO:0000874
Helianthus paradoxus Heiser
A species of genus Helianthus.
Helianthus paradoxus
A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
Aspartyl tRNA
SO:0000257
SO:0000255
A primary transcript encoding a small ribosomal subunit RNA.
rRNA Small Subunit Primary Transcript
3' Intron
An mRNA that is polyadenylated.
Polyadenylated mRNA
SO:0000871
Japanese flounder
Bastard halibut
A species of genus Paralichthys.
Paralichtys olivaceus
Paralichthyidae sp. KYJ-2011
Hippoglossus olivaceus
Olive flounder
Paralichthys olivaceus
False halibut
Paralichthys olivaceus (Temminck & Schlegel, 1846)
Paralichthys olivaceous
Five Prime Coding Exon Noncoding Region
SO:0000486
The sequence of the 5' exon preceding the start codon.
A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
SO:0000978
Template Region
A primary transcript encoding methionyl tRNA.
SO:0000223
Methionine tRNA Primary Transcript
Anolis carolinensis
Green anole
A species of genus Anolis.
A species of genus Zea.
Maize
Zea mays var. japonica
Zea mays mays
Zea mays
Disposition
snap:Disposition
A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
Gasterosteus aculeatus Linnaeus, 1758
A species of genus Gasterosteus.
Three-spined stickleback
Three spined stickleback
Gasterosteus aculeatus
Pig roundworm
A species of genus Ascaris.
Ascaris suum
Chordata
A phylum of kingdom Animalia.
French bean
Kidney bean
String bean
A species of genus Phaseolus.
Phaseolus vulgaris
Valine tRNA Primary Transcript
A primary transcript encoding valyl tRNA.
SO:0000230
The region of an edited transcript that will not be edited.
SO:0000607
Unedited Region
RNAO:0000096
A collection of one or more nucleotides that are not involved in base pairing.
Unpaired Region
Dengue virus 2
Dengue virus type 2
dengue 2 virus DEN-2
dengue-2 virus
dengue-2 virus DEN-2
Dengue virus type II
Sheep
Ovis ammon aries
Ovis aries
A species of genus Ovis.
Ovis ovis
Ovis orientalis aries
Lambs
Wild sheep
Domestic sheep
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.
U3 snoRNA
SO:0001179
CHEBI:16991
DNA
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
A primary transcript encoding glutaminyl tRNA.
SO:0000216
Glutamic acid tRNA Primary Transcript
A primary transcript encoding a small nucleolar RNA of the box C/D family.
C/D Box snoRNA Primary Transcript
SO:0000595
Merkel cell polyomavirus
A dsDNA virus of family Polyomaviridae.
Mamon
Papaya
Carica papaya
Carica papaya L.
Carica payaya
A species of genus Carica.
The sequence of nucleotide residues along an RNA chain.
RNA Sequence
NCI Thesaurus:RNA_Sequence
NCIThesaurus:DNA_Sequence
Physcomitrella patens
A species of genus Physcomitrella.
A class of phylum Arthropoda.
Arachnida
Transcript
SO:0000673
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
SO:0000185
Primary Transcript
A transcript that in its initial state requires modification to be functional.
BFO:0000141
Immaterial Entity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth).
Hylobates syndactylus
Symphalangus syndactylus
A species of genus Symphalangus.
Siamang
A class of phylum Chordata.
Petromyzontidae
The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers.
GO:0032774
RNA Biosynthetic Process
A stop codon signal for a UAA stop codon redefinition.
UAA Stop Codon Signal
SO:1001283
A species of genus Picea.
Picea excelsa
Pinus abies
Picea abies L., Karst
Picea abies
Norway spruce
A class of phylum Porifera.
Demospongiae
Tetranychus urticae Koch, 1836
Red spider mite
Twospotted mite
Two-spotted spider mite
A species of genus Tetranychus.
Tetranychus urticae
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.
U14 snoRNA
SO:0000403
SO:0000444
Non-coding exon in the 3' UTR.
Three Prime Noncoding Exon
A species of genus Echinococcus.
Echinococcus multilocularis
SL1 Acceptor Site
A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.
SO:0000708
Dicistronic mRNA
An mRNA that has the quality dicistronic.
SO:0000716
A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
Glutamyl tRNA
SO:0000260
SO:0000212
Arginine tRNA Primary Transcript
A primary transcript encoding arginyl tRNA.
A subclass of phylum Platyhelminthes.
Digenea
Intron Domain
Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
Posttranscriptional Regulation of Gene Expression
GO:0010608
A species of genus Caenorhabditis.
Caenorhabditis vulgaris Baird, Fitch & Emmons, 1994
Caenorhabditis vulgariensis
Caenorhabditis vulgaris
Caenorhabditis vulgarensis
Caenorhabditis remanei
Non-canonical 5' Splice SIte
SO:0000679
A 5' splice site which does not have the sequence "GT".
DNA Sequence
NCI Thesaurus:DNA_Sequence
NCIThesaurus:DNA_Sequence
The sequence of nucleotide residues along a DNA chain.
bovine herpesvirus type 1 BHV-1
bovine herpesvirus 1 BHV 1
bovine herpesvirus type-1 BHV-1
bovine herpesvirus 1 BHV-1
bovine herpesvirus BHV-1
Bovine herpesvirus 1
Bovine herpesvirus type 1
Bovine rhinotracheitis virus
infectious bovine rhinotracheitis virus BHV-1
Infectious bovine rhinotracheitis virus
bovine herpesvirus 1 BHV1
Bovine herpesvirus-1
A dsDNA virus of family Herpesviridae.
SO:1001282
UAG Stop Codon Signal
A stop codon signal for a UAG stop codon redefinition.
SO:0000929
Edited mRNA
An mRNA that is edited.
U6 snRNA
SO:0000396
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.
SO:0000604
Editing Block
Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
Herpes simplex virus (type 2)
Herpes simplex virus 2
Herpes simplex virus type 2
herpes simplex virus type 2 HSV-2
A dsDNA virus of family Herpesviridae.
Human herpesvirus 2
A class of phylum Chordata.
Branchiostomidae
Leptocardii
A species of genus Helianthus.
Helianthus argophyllus Torr. & A.Gray
Helianthus argophyllus
UTR
Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
SO:0000203
Aves
A class of phylum Chordata.
SO:0000935
Edited CDS
A CDS that is edited.
Digitalis purpurea
Common foxglove
A species of genus Digitalis.
Digitalis purpurea L.
A species of genus Xenoturbella.
Xenoturbella bocki
Spermatophyta
A subset of Embryophytes.
Group IIA Intron
SO:0001749
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.
GO:0090304
Nucleic Acid Metabolic Process
Any cellular metabolic process involving nucleic acids.
Methylation Guide snoRNA Primary Transcript
SO:0000580
A primary transcript encoding a methylation guide small nucleolar RNA.
An mRNA with a plus 1 frameshift.
mRNA with Plus 1 Frameshift
SO:0000321
Transcription, DNA-dependent
GO:0006351
The cellular synthesis of RNA on a template of DNA.
Domestic cow
Cattle
Domestic cattle
Bos bovis
Bos primigenius taurus
A species of genus Bos.
Bos tauurus
Bovine
Cow
Bos taurus
Anchor Binding Site
SO:0000335
A mRNA with a minus 2 frameshift.
mRNA with Minus 2 Frameshift
The first base where RNA polymerase begins to synthesize the RNA transcript.
TSS
SO:0000315
A phylum of kingdom Animalia.
Nemertea
H/ACA Box snoRNA
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.
SO:0000594
SO:0001001
rRNA 23S
A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.
SO:0000645
The reverse complement of the primary transcript.
Antisense Primary Transcript
SO:0000202
The coding exon that is most 3-prime on a given transcript.
Three Prime Coding Exon
SO:0001173
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.
Anticodon Loop
GO:0065007
Biological Regulation
Any process that modulates the frequency, rate or extent of any biological process, quality or function.
Intronic lncRNA
SO:0001903
A lnc_RNA totally contained within an intron.
Monodelphis domestica
Gray short-tailed opossum
A species of genus Monodelphis.
Monodelphis domesticus
A phylum of kingdom Animalia.
Hemichordata
A species of genus Lotus.
Lotus japonicus
Lotus corniculatus var. japonicus
RNAO_0000000
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
CHEBI:33697
RNA
The inactivation of gene expression by a posttranscriptional mechanism.
GO:0016441
Posttranscriptional Gene Silencing
Xenacoelomorpha
A phylum of kingdom Animalia.
SO:0000209
A primary transcript encoding a ribosomal RNA.
rRNA Primary Transcript
CDS Independently Known
A CDS with the evidence status of being independently known.
SO:1001246
Telomerase RNA
SO:0000390
The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
SO:0000652
rRNA 5S
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.
SO:0001748
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.
SL3 Acceptor Site
3' cis 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:0000164
polyomavirus BK
Papovavirus BKV
A dsDNA virus of family Polyomaviridae.
human polyomavirus type BK BKV
polyomavirus homonis 1
Human polyomavirus BKV
Human polyomavirus BK
BK virus
BK virus BKV
Polyomavirus hominis 1
BK polyomavirus
Human polyomavirus (type BK)
A species of genus Drosophila.
Drosophila ananassae
Drosophila annanassae
Loblolly pine
Pinus taeda
A species of genus Pinus.
HIV type 2
human immunodeficiency virus type 2 HIV-2
Human immunodeficiency virus-2
AIDS virus
A retro-transcribing virus of family Retroviridae.
Human immunodeficiency virus type 2
human immunodeficiency virus type 2, HIV-2
Human immunodeficiency virus 2
Collection of Material Entities
A dsDNA virus of family Herpesviridae.
Gallid herpesvirus type 2
Marek's disease virus MDV1
Gallid herpesvirus 1 (serotype 1)
Marek's disease virus
Marek disease virus
Marek's disease herpesvirus
Marek's disease herpesvirus 1
Marek's disease virus type 1 MDV1
Marek's disease virus type 1
Marek disease virus type 1
Marek's disease virus (MDV)
Marek's disease virus MDV
Marek's disease virus serotype 1 MDV-1
Gallid herpesvirus 2
Guide RNA
SO:0000602
A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail) with a stretch of mature edited mRNA.
SO:0000406
Twintron
An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote.
SO:0000012
scRNA Primary Transcript
Start Codon
SO:0000318
First codon to be translated by a ribosome.
Interacting selectively and non-covalently with a primary microRNA (pri-miRNA) transcript, an RNA molecule that is processed into a short hairpin-shaped structure called a pre-miRNA and finally into a functional miRNA. Both double-stranded and single-stranded regions of a pri-miRNA are required for binding.
pri-miRNA Binding
GO:0070878
Cestoda
A class of phylum Platyhelminthes.
Alternatively Spliced Transcript
SO:1001187
A transcript that is alternatively spliced.
Isoleucyl tRNA
SO:0000263
A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.
Tribolium castaneum
A species of genus Tribolium.
Red flour beetle
Rust-red flour beetle
Gallid herpesvirus 1
Avian infectious laryngotracheitis virus
Infectious laryngotracheitis virus
Gallid herpesvirus type 1
Laryngotracheitis virus
infectious laryngotracheitis virus ILTV
A dsDNA virus of family Herpesviridae.
SO:0000253
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.
A folded RNA sequence.
SO:0000122
RNA Sequence Secondary Structure
SO:0000243
Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
Internal Ribosome Entry Site
SO:0000635
Mini Exon Donor RNA
A primary transcript that donates the spliced leader to other mRNA.
Citrus clementina
Citrus clementina hort. ex Tanaka
A species of genus Citrus.
Nasonia vitripennis (Walker, 1836)
Nasonia vitripennis
A species of genus Nasonia.
Jewel wasp
A species of genus Phaeodactylum.
Phaeodactylum tricornutum
OBI:0100026
Organism
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
SO:0001211
Plus 1 Translational 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.
A region of a guide_RNA that base-pairs to a target mRNA.
Anchor Region
SO:0000931
A transcript that is edited.
Edited Transcript
SO:0000873
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GO:0008150
Biological Process
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
snap:Role
Role
A species of genus Macropus.
Macropus eugenii
Tammar wallaby
SL10 Acceptor Site
SO:0001755
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:0000013
Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.
scRNA
A non-canonical start codon with 4 base pairs.
4bp Start Codon
SO:1001269
Equine
Equus przewalskii f. caballus
Equus caballus
Equus przewalskii forma caballus
Domestic horse
A species of genus Equus.
Equus ferus caballus
Horse
A collection of nucleotide residues is a part of a nucleic acid consisting of one or more nucleotides.
Collection of Nucleotides Residues
RNAO:0000108
Hevea brasiliensis
Jebe
Rubbertree
Para rubber tree
Siringa
Hevea brasiliensis (Willd. ex A.Juss.) Muell. Arg.
A species of genus Hevea.
SO:0001174
A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
Anticodon
span:Process
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
Process
SO:0000268
A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
Prolyl tRNA
SO:1001273
CTG Start Codon
A non-canonical start codon of sequence CTG.
Bruguiera cylindrica
Bruguiera cylindrica (L.) Blume
A species of genus Bruguiera.
A primary transcript encoding leucyl tRNA.
Leucine tRNA Primary Transcript
SO:0000221
Object
Schmidtea mediterranea
Freshwater planarian
A species of genus Schmidtea.
Dugesia (Schmidtea) mediterranea
Dugesia mediterranea
Endonuclease Spliced Intron
SO:0001216
An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
Group IIB Intron
Group I Intron
SO:0000587
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.
An exon that is the only exon in a gene.
Exon of Single Exon Gene
SO:0005845
SO:0000404
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.
SO:0000228
Tryptophan tRNA Primary Transcript
A primary transcript encoding tryptophanyl tRNA.
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.
SO:0000378
Dengue Virus 4
Dengue virus type 4
dengue type 4 virus DEN4
Human herpesvirus 6B
Human herpesvirus 6 type B
A dsDNA virus of family Herpesviridae.
Saccharum officinarum
A species of genus Saccharum.
Sugarcane
Noble cane
3' Repeat Recoding Signal
SO:1001286
A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.
SO:0005857
Selenocysteinyl tRNA
A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.
SO:0000210
tRNA Primary Transcript
A primary transcript encoding a transfer RNA.
SL12 Acceptor Site
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:0001757
A species of genus Ixodes.
Ixodes scapularis
Ixodes dammini
Shoulder tick
Blacklegged tick
Black-legged tick
Deer tick
SO:0000446
Intron located in the untranslated region.
UTR Intron
Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
Gene Silencing by miRNA
GO:0035195
A class of phylum Chordata.
Mammalia
CDS Predicted
A CDS that is predicted.
SO:1001254
A species of genus Cricetulus.
Cricetulus barabensis griseus
Cricetus griseus
Cricetulus aureus
Chinese hamster
Cricetulus griseus
Translation
GO:0006412
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome.
Protein
CHEBI:36080
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
A stop codon redefined to be the new amino acid, pyrrolysine.
Stop Codon Redefined as Pyrrolysine
SO:0000884
Caenorhabditis briggsae
A species of genus Caenorhabditis.
SO:0000616
Transcription End Site
The base where transcription ends.
mRNA with Plus 2 Frameshift
An mRNA with a plus 2 frameshift.
SO:0000329
Monocistronic Primary Transcript
A primary transcript encoding for one gene product.
SO:0000632
Brachypodium distachyon
A species of genus Brachypodium.
A species of genus Amphimedon.
Amphimedon queenslandica
Reniera sp. JGI-2005
An intron located in the 3' UTR.
SO:0000448
3' UTR Intron
Lycopodiophyta
A division of Eukaryota.
Five Prime Noncoding Exon
Non-coding exon in the 5' UTR.
SO:0000445
A species of genus Cucumis.
Cucumis melo
Cucurbita melo L.
Cucumis melo var. markuwa Markino
Oriental melon
Muskmelon
Sea lamprey
Marine lamprey
Petromyzon marinus
A species of genus Petromyzon.
A primary transcript encoding threonyl tRNA.
SO:0000227
Threonine tRNA Primary Transcript
UGA Stop Codon Signal
A stop codon signal for a UGA stop codon redefinition.
SO:1001285
A transcript with a translational frameshift.
SO:0000118
Transcript with Translational Frameshift
External Transcribed Spacer Region
Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
SO:0000640
The region of a transcript that will be edited.
Pre-edited Region
SO:0000583
A phylum of Eukaryota.
Chlorophyta
A region of an rRNA primary transcript.
rRNA Primary Transcript Region
SO:0000838
Enteropneusta
A class of phylum Hemichordata.
A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.
SO:0000681
Aberrant Processed Transcript
SO:0001463
A multiexonic non-coding RNA transcribed by RNA polymerase II.
Linc RNA
Polypirimidine Tract
The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
SO:0000612
The 5' five prime splice site region of the donor RNA.
Trans Splice Donor Site
SO:0000707
SO:0000261
A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.
Glycyl tRNA
Exon Region
A region of an exon.
SO:0000852
Stop Codon
SO:0000319
In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
snap:DependentContinuant
Dependent Continuant
A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.
A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
Asparaginyl tRNA
SO:0000256
Spotted green pufferfish
Tetraodon nigroviridis Marion de Proce, 1822
Tetraodon nigroviridis
A species of genus Tetraodon.
A primary transcript encoding a small nuclear RNA.
snRNA Primary Transcript
SO:0000231
Archaeal Intron
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.
SO:1001271
SO:0000555
5' most region of a precursor transcript that is clipped off during processing.
5' Clip
Tyrosyl tRNA
SO:0000272
A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
GO:0003674
Molecular Function
Cysteine tRNA Primary Transcript
SO:0000215
A primary transcript encoding cysteinyl tRNA.
A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding.
SO:1001288
Stop Codon Signal
Spliced Leader RNA
SO:0001750
SL5 Acceptor Site
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:0000579
Edited Transcript Feature
A locatable feature on a transcript that is edited.
The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
Protein Metabolic Process
GO:0019538
Polycistronic Primary Transcript
A primary transcript encoding for more than one gene product.
SO:0000631
Jerusalem artichoke
Helianthus tuberosus
A species of genus Helianthus.
Helianthus tuberosus L.
Cellular Organism
A species of genus Nasonia.
Nasonia giraulti
CDS Fragment
SO:0000162
Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
Splice Site
Gorilla
Western gorilla
A species of genus Gorilla.
Gorilla gorilla
Brachiopoda
A phylum of kingdom Animalia.
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.
OxyS RNA
SO:0000384
Selaginella moellendorffii
A species of genus Selaginella.
Selaginella moellendorfii
Selaginella moellendorffii Hieron
Non-canonical 3' Splice Site
A 3' splice site that does not have the sequence "AG".
SO:0000678
A species of genus Chlamydomonas.
Chlamydomonas reinhardtii
Chlamydomonas smithii R.W.Howshaw & H.Ettl
Chlamydomonas smithii
Chlamydomonas reinhardtii P.A.Dangeard
Chlamydomonas reihhardtii
Xenopus (Silurana) tropicalis
Western clawed frog
A species of genus Xenopus.
Xenopus tropicalis
Xenopus laevis tropicalis
Silurana tropicalis
Five Prime Coding Exon
The 5' most coding exon.
SO:0000200
Upland cotton
Gossypium hirsutum subsp. mexicanum
Gossypium lanceolatum
Gossypium purpurascens
American cotton
A species of genus Gossypium.
Cotton
Gossypium hirsutum
Nucleic Acid
CHEBI:33696
A macromolecule made up of nucleotide units and hydrolyzable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
A retro-transcribing virus of family Retroviridae.
bovine leukemia virus BLV
bovine leukemia virus, BLV
Bovine leukemia virus
Histidine tRNA Primary Transcript
SO:0000219
A primary transcript encoding histidyl tRNA.
A species of genus Pan.
Pygmy chimpanzee
Bonobo
Pan paniscus
Continuant
snap:Continuant
An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
Chilopoda
A class of phylum Arthropoda.
A phylum of Eukaryota.
Bryophyta
Drosophila pseudoobscura
A species of genus Drosophila.
SO:0001172
A region of a tRNA.
tRNA Region
Autocatalutically Spliced Intron
A self spliced intron.
SO:0000588
A phylum of kingdom Animalia.
Cnidaria
Interior Coding Exon
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.
SO:0000188
Intron
SO:0001800
The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene.
tasiRNA
A primary transcript encoding alanyl tRNA.
Alanine tRNA Primary Transcript
SO:0000211
Barley
Hordeum vulgare
A species of genus Hordeum.
Hordeum vulgare L.
Horedum vulgare
A species of genus Capitella.
Capitella sp. 1
A class of phylum Arthropoda.
Branchiopoda
Tryptophanyl tRNA
A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
SO:0000271
SO:1001197
Dicistronic Primary Transcript
A primary transcript that has the quality dicistronic.
A species of genus Pristionchus.
Pristionchus pacificus
U1 snRNA
SO:0000391
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.
A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.
mRNA Recoded by Translation Bypass
SO:1001264
Cyprinus cyprio
Cyrpinus carpio
Cyprinus carpio
Common carp
Carp
A species of genus Cyprinus.
A species of genus Ciona.
Ciona intestinalis
Splice Region
A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
SO:0001902
CCA Tail
SO:0001175
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.
A species of genus Schistosoma.
Schistosoma japonicum
SO:0000385
RNase MRP RNA
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.
SO:0001213
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.
U4atac snRNA
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:0000394
Codon
SO:0000360
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.
rasiRNA
A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
SO:0000454
A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.
Independent Continuant
snap:IndependentContinuant
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.
SO:0000375
Gene
SO:0000704
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.
A sequence_region bounded at one end by the 5' or 3' end of the molecule, and at the other by an unbroken_stem. [RNAO:0000107]
Strand End
RNAO:0000107
Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
SO:0001177
T Loop
A phylum of kingdom Animalia.
Arthropoda
House mouse
Mouse
mice C57BL/6xCBA/CaJ hybrid
Mus muscaris
A species of genus Mus.
Mus musculus
A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
Arginyl tRNA
SO:0001036
Acacia mangium
Acacia mangium Willd
A species of genus Acacia.
Cyprinus rerio Hamilton, 1822
Brachydanio rerio
Zebra danio
Brachidanio rerio
Zebrafish
Danio rerio frankei
Brachydanio rerio frankei
Cyprinus rerio
A species of genus Danio.
Danio rerio
Leopard danio
Danio frankei
Zebra fish
Danio rerio (Hamilton, 1822)
SO:0000198
Noncoding Exon
An exon that does not contain any codons.
A species of genus Lottia.
Lottia gigantea
SO:0005856
Selenocysteine tRNA Primary Transcript
A primary transcript encoding seryl tRNA.
Poncirus trifoliate
Citrus trifoliatus
A species of genus Citrus.
Poncirus trifoliatus
Trifoliate orange
Citrus trifoliata
Hardy orange
Poncirus trifoliata
SO:0001754
SL9 Acceptor Site
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.
A CDS that is supported by similarity to EST or cDNA data.
SO:1001259
CDS Supported by EST or cDNA Data
A species of genus Pygathrix.
Black snub-nosed monkey
Pygathrix bieti
Rhinopithecus bieti
A species of genus Nematostella.
Nematostella vectensis Stephenson, 1935
Nematostella vectensis
Starlet sea anemone
SO:0000379
A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
GcvB RNA
SO:0000205
Three Prime UTR
A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
Ateles geoffroyi
Ateles jeoffroyi
Ateles geoffreyi
A species of genus Ateles.
Black-handed spider monkey
Central American spider monkey
A species of genus Drosophila.
Drosophila grimshawi
Idiomyia grimshawi
dsDNA virus, no RNA stage
A virus having a dsDNA molecule as genetic material. No RNA intermediate molecules are involved during its replication.
A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
SO:0000267
Phenylalanyl tRNA
A species of genus Solanum.
Solanum tuberosum subsp. tuberosum
Solanum tuberosum
Potato
Mouse cytomegalovirus 1
murine cytomegalovirus MCMV
murine herpesvirus 1
murine cytomegalovirus (MCMV)
Murid herpesvirus 1
A dsDNA virus of family Herpesviridae
Murine cytomegalovirus
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.
SO:0000603
Purple sea urchin
Purple urchin
A species of genus Strongylocentrotus.
Strongylocentrotus purpuratus (Stimpson, 1857)
Strongylocentrotus purpuratus
Marsupenaeus japonicus
A species of genus Marsupenaeus.
Penaeus japonicus
Penaeus (Marsupenaeus) japonicus
Penaeus (Melicertus) japonicus
A region of the pri miRNA that basepairs with the guide to form the hairpin.
SO:0001473
miRNA Antiguide
Capitella sp. I ES-2005
A species of genus Capitella.
Capitella telata
Capitella sp. I AF-2005
Capitella sp. I ECS-2004
Capitella sp. I
Capitella teleta
Capitella sp. I Grassle & Grassle, 1976
Rape
Oilseed rape
Rapeseeds
Brassica napus
A species of genus Brassica.
SO:0000108
An mRNA with a frameshift.
mRNA with Frameshift
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
Molecular Entity
http://en.wikipedia.org/wiki/Molecular_entity
A primary transcript encoding isoleucyl tRNA.
Isoleucine tRNA Primary Transcript
SO:0000220
tRNA Intron
SO:1001272
An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.
A species of genus Triticum.
English wheat
Triticum aethiopicum
Triticum turgidum8
Triticum turgidum L.
Cone wheat
Poulard wheat
Triticum aethiopicum Jakubz.
Rivet wheat
Triticum turgidum
A primary transcript encoding asparaginyl tRNA.
Asparagine tRNA Primary Transcript
SO:0000213
SO:0000389
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.
Spot 42 RNA
A species of genus Arabidopsis.
Mouse-ear cress
Thale cress
Thale-cress
Arabidopsis thaliana
Arbisopsis thaliana
Arabidopsis thaliana (thale cress)
The stem of the hairpin loop formed by folding of the pre-miRNA.
SO:0001245
miRNA Stem
SO:0000646
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.
siRNA
A dsDNA virus of family Papillomaviridae.
Bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1)
Bandicoot papillomatosis carcinomatosis virus type 1
A species of genus Populus.
Populus diversifolia
Popolus euphratica
Populus euphratica
Heterokonts
Stramenopiles
Chromophyta
A species of genus Saccoglossus.
Saccoglossus kowalevskyi
Saccoglossus kowalesvskii
Saccoglossus kowalevskii
A species of genus Oryzias.
Japanese rice fish
Japanese medaka
Medaka
Oryzias latipes
Sequences within the intron that modulate splice site selection for some introns.
SO:0000320
Intronic Splice Enhancer
SL8 Acceptor Site
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:0001753
A species of genus Ciona.
Ciona savignyi
SO:0001182
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.
Cercopithecine herpesvirus 1
Herpesvirus simiae
Simian herpesvirus B
monkey B virus
herpes B virus
Cercopithecid herpesvirus 1
herpes virus B
Simian herpes B virus
simian herpes B virus SHBV
B virus
A dsDNA virus of family Herpesviridae.
Macacine herpesvirus 4
A region of UTR.
UTR Region
SO:0000837
Drosophila sechellia
Drosophila sechellia Tsacas and Bachli, 1981
A species of genus Drosophila.
SO:0000269
Seryl tRNA
A tRNA sequence that has a serine anticodon, and a 3' serine binding region.
Macaca mulatta
Rhesus monkey
Rhesus macaque
A species of genus Macaca.
Five Prime Coding Exon Coding Region
The sequence of the five_prime_coding_exon that codes for protein.
SO:0000196
Dog
Canis lupus familiaris
A species of genus Canis.
Canis domesticus
Canis canis
Canis familiaris
Clawed frog
Bufo laevis
Xenopus leavis
Xenopus laevis
African clawed frog
Platanna
A species of genus Xenopus.
Common platanna
Xenopus laevis (Daudin, 1802)
SO:0000295
U12 Intron
A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
Herpesvirus saimiri (strain 11)
A dsDNA virus of family Herpesviridae.
The sequence of the three_prime_coding_exon that codes for protein.
Three Prime Coding Exon Coding Region
SO:0000197
has_region
regulates
Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
RO:derives_from
derives_from
guided_by
has_part
C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity.
adjacent_to
RO:adjacent_to
RO:preceded_by
P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
preceded_by
For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
part_of
RO:part_of
results_in
has_role
has_participant
As for has_participant, but with the additional condition that the component instance is causally active in the relevant process.
has_agent
RO:has_agent
has_structure
definition_source
definition
database_cross_reference
has_related_synonym
has_exact_synonym