definition
type: AnnotationProperty

definition_source
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_structure
type: ObjectProperty
inverse of: is structure of

has_region
type: ObjectProperty

results_in
type: ObjectProperty

guided_by
type: ObjectProperty

regulates
type: ObjectProperty

has_participant
type: ObjectProperty

has_role
type: ObjectProperty

adjacent_to
type: ObjectProperty
definition: 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.
definition_source: RO:adjacent_to

derives_from
type: ObjectProperty
definition: 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'.
definition_source: RO:derives_from

has_agent
type: ObjectProperty
range: Material Entity
definition: As for has_participant, but with the additional condition that the component instance is causally active in the relevant process.
definition_source: RO:has_agent

has_part
type: ObjectProperty
inverse of: part_of

part_of
type: ObjectProperty
definition: 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.)
definition_source: RO:part_of

preceded_by
type: ObjectProperty
definition: 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.
definition_source: RO:preceded_by

Reptilia
type: Class
subclass of: Chordata
definition: Cold-blooded, air-breathing VERTEBRATES belonging to the class Reptilia, usually covered with external scales or bony plates.
definition_source: MSH:D012104

Transcription Factor
type: Class
subclass of: Role
definition: A role palyed by a protein that binds to specific DNA sequences, thereby controlling the transcription of genetic information from DNA to mRNA.
definition_source: modified definition from WIkipedia, http://en.wikipedia.org/wiki/Transcription_factor
database_cross_reference: GRO:TranscriptionFactor

Xenacoelomorpha
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

tissues, cell types and enzyme sources
type: Class
subclass of: material anatomical entity
database_cross_reference: BTO:0000000

Plants
type: Class
subclass of: Cellular Organism
definition: 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).
definition_source: NCIThesaurus:Plant

Object
type: Class
subclass of: Material Entity

Immaterial Entity
type: Class
subclass of: Independent Continuant
definition: 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).
definition_source: BFO:0000141

DNA
type: Class
subclass of: Nucleic Acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
definition_source: CHEBI:16991

Nucleic Acid
type: Class
subclass of: Information Biopolymer
definition: 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.
definition_source: CHEBI:33696

RNA
type: Class
subclass of: Nucleic Acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
definition_source: CHEBI:33697
database_cross_reference: RNAO_0000000

Protein
type: Class
subclass of: Information Biopolymer
subclass of: Restriction
  on property: has_role
  some values from: Transcription Factor
definition: A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
definition_source: CHEBI:36080

Cellular Component
type: Class
subclass of: Object
definition: 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.
definition_source: GO:0005575

Chromosome
type: Class
subclass of: Cellular Component
definition: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
definition_source: GO:0005694

Information Content Entity
type: Class
subclass of: Generically Dependent Continuant
subclass of: Restriction
  on property: is about miRNA
  some values from: miRNA
subclass of: Restriction
  on property: is about miRNA target
  some values from: miRNA target gene
definition: A generically dependent continuant that is about some thing.
definition_source: OBI_0000142

Cricetulus griseus
type: Class
subclass of: Mammalia
definition: A species of genus Cricetulus.
has_exact_synonym: Chinese hamster
has_exact_synonym: Cricetulus aureus
has_related_synonym: Cricetulus barabensis griseus
has_related_synonym: Cricetus griseus

Mus musculus
type: Class
subclass of: Mammalia
definition: A species of genus Mus.
has_exact_synonym: House mouse
has_exact_synonym: Mouse
has_related_synonym: Mus muscaris
has_related_synonym: mice C57BL/6xCBA/CaJ hybrid

Rattus norvegicus
type: Class
subclass of: Mammalia
definition: A species of genus Rattus.
has_exact_synonym: Brown rat
has_exact_synonym: Norway rat
has_exact_synonym: Rat
has_exact_synonym: Rattus sp. strain Wistar
has_related_synonym: Gunn rats
has_related_synonym: Rattus norvegicus8
has_related_synonym: Rattus norwegicus
has_related_synonym: Rattus rattiscus

Hemichordata
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Enteropneusta
type: Class
subclass of: Hemichordata
definition: A class of phylum Hemichordata.

Saccoglossus kowalevskii
type: Class
subclass of: Enteropneusta
definition: A species of genus Saccoglossus.
has_related_synonym: Saccoglossus kowalesvskii
has_related_synonym: Saccoglossus kowalevskyi

Virus
type: Class
subclass of: Organism
definition: 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.
definition_source: NCIThesaurus:Virus

Human herpesvirus 1
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_exact_synonym: Herpes simplex virus type 1
has_related_synonym: Herpes simplex virus 1
has_related_synonym: Human Herpesvirus-1
has_related_synonym: Human herpesvirus type 1
has_related_synonym: herpes simplex virus 1 HSV-1
has_related_synonym: herpes simplex virus HSV-1
has_related_synonym: herpes simplex virus type 1 HSV-1
has_related_synonym: herpes simplex virus type 1 HSV1
has_related_synonym: herpes simplex virus type-1 HSV-1

Human herpesvirus 2
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Herpes simplex virus (type 2)
has_related_synonym: Herpes simplex virus 2
has_related_synonym: Herpes simplex virus type 2
has_related_synonym: herpes simplex virus type 2 HSV-2

Bovine herpesvirus 1
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Bovine herpesvirus type 1
has_related_synonym: Bovine herpesvirus-1
has_related_synonym: Bovine rhinotracheitis virus
has_related_synonym: Infectious bovine rhinotracheitis virus
has_related_synonym: bovine herpesvirus 1 BHV 1
has_related_synonym: bovine herpesvirus 1 BHV-1
has_related_synonym: bovine herpesvirus 1 BHV1
has_related_synonym: bovine herpesvirus BHV-1
has_related_synonym: bovine herpesvirus type 1 BHV-1
has_related_synonym: bovine herpesvirus type-1 BHV-1
has_related_synonym: infectious bovine rhinotracheitis virus BHV-1

Macacine herpesvirus 1
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_exact_synonym: Monkey B virus
has_related_synonym: B virus
has_related_synonym: Cercopithecid herpesvirus 1
has_related_synonym: Cercopithecine herpesvirus 1
has_related_synonym: Herpes B virus
has_related_synonym: Herpes virus B
has_related_synonym: Herpesvirus simiae
has_related_synonym: Simian herpes B virus
has_related_synonym: Simian herpes B virus SHBV
has_related_synonym: Simian herpesvirus B

Suid herpesvirus 1
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_exact_synonym: Pseudorabies virus
has_related_synonym: Alphaherpesvirus pseudorabies virus PRV
has_related_synonym: Aujeszky's disease virus
has_related_synonym: Pseudorabies Virus PRV
has_related_synonym: Suid herpesvirus type 1

Human herpesvirus 5
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_exact_synonym: Human cytomegalovirus
has_related_synonym: Human cytomegalovirus HCMV
has_related_synonym: human cytomegalovirus CMV
has_related_synonym: human herpesvirus type 5

Murid herpesvirus 1
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae
has_exact_synonym: Murine cytomegalovirus
has_related_synonym: Mouse cytomegalovirus 1
has_related_synonym: murine cytomegalovirus (MCMV)
has_related_synonym: murine cytomegalovirus MCMV
has_related_synonym: murine herpesvirus 1

Human herpesvirus 4
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_exact_synonym: Epstein-Barr virus
has_related_synonym: Epstein-Barr virus EBV
has_related_synonym: Epstein-Barr-virus EBV
has_related_synonym: Human herpesvirus type 4

Herpesvirus saimiri (strain 11)
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.

Gallid herpesvirus 1
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Avian infectious laryngotracheitis virus
has_related_synonym: Gallid herpesvirus type 1
has_related_synonym: Infectious laryngotracheitis virus
has_related_synonym: Laryngotracheitis virus
has_related_synonym: infectious laryngotracheitis virus ILTV

Gallid herpesvirus 2
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_exact_synonym: Marek disease virus type 1
has_related_synonym: Gallid herpesvirus 1 (serotype 1)
has_related_synonym: Gallid herpesvirus type 2
has_related_synonym: Marek disease virus
has_related_synonym: Marek's disease herpesvirus
has_related_synonym: Marek's disease herpesvirus 1
has_related_synonym: Marek's disease virus
has_related_synonym: Marek's disease virus (MDV)
has_related_synonym: Marek's disease virus MDV
has_related_synonym: Marek's disease virus MDV1
has_related_synonym: Marek's disease virus serotype 1 MDV-1
has_related_synonym: Marek's disease virus type 1
has_related_synonym: Marek's disease virus type 1 MDV1

Anatid herpesvirus 1
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Anatid Herpes virus-1
has_related_synonym: Duck enteritis virus
has_related_synonym: Duck plague virus

BK polyomavirus
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Polyomaviridae.
has_related_synonym: BK virus
has_related_synonym: BK virus BKV
has_related_synonym: Human polyomavirus (type BK)
has_related_synonym: Human polyomavirus BK
has_related_synonym: Human polyomavirus BKV
has_related_synonym: Papovavirus BKV
has_related_synonym: Polyomavirus hominis 1
has_related_synonym: human polyomavirus type BK BKV
has_related_synonym: polyomavirus BK
has_related_synonym: polyomavirus homonis 1

JC polyomavirus
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Polyomaviridae
has_related_synonym: Human polyomavirus (type JC)
has_related_synonym: JC polyomavirus JCV
has_related_synonym: JC virus
has_related_synonym: Polyomavirus hominis 2
has_related_synonym: human polyomavirus JCV
has_related_synonym: polyoma virus JC JCV
has_related_synonym: polyomavirus JC

Simian virus 40
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Polyomaviridae.
has_related_synonym: Polyomavirus maccacae
has_related_synonym: Polyomavirus maccacae 1
has_related_synonym: Rhesus macaque polyomavirus
has_related_synonym: rhesus polyomavirus

Bruguiera cylindrica
type: Class
subclass of: Spermatophyta
definition: A species of genus Bruguiera.
has_related_synonym: Bruguiera cylindrica (L.) Blume

Dengue virus 1
type: Class
subclass of: Dengue virus
has_related_synonym: Dengue virus type 1
has_related_synonym: Type 1 dengue virus
has_related_synonym: dengue type 1 D1 virus
has_related_synonym: dengue virus type 1 DEN1
has_related_synonym: dengue virus type I
has_related_synonym: dengue virus-1 DEN-1
has_related_synonym: type 1 dengue virus DEN-1

Dengue virus 2
type: Class
subclass of: Dengue virus
has_related_synonym: Dengue virus type 2
has_related_synonym: Dengue virus type II
has_related_synonym: dengue 2 virus DEN-2
has_related_synonym: dengue-2 virus
has_related_synonym: dengue-2 virus DEN-2

Dengue Virus 3
type: Class
subclass of: Dengue virus
has_related_synonym: Dengue virus type 3
has_related_synonym: dengue 3 virus

Dengue Virus 4
type: Class
subclass of: Dengue virus
has_related_synonym: Dengue virus type 4
has_related_synonym: dengue type 4 virus DEN4

West Nile Virus
type: Class
subclass of: ssRNA virus
definition: A ssRNA virus of family Flaviviridae.

Human immunodeficiency virus 1
type: Class
subclass of: Retro-transcribing virus
definition: A retro-transcribing virus of family Retroviridae.
has_related_synonym: AIDS virus
has_related_synonym: Human immundeficiency virus type 1
has_related_synonym: Human immunodeficiencey virus type 1
has_related_synonym: Human immunodeficiency virus type 1
has_related_synonym: human immunodeficiency virus 1 HIV-1
has_related_synonym: human immunodeficiency virus HIV-1
has_related_synonym: human immunodeficiency virus type 1 ,HIV-1
has_related_synonym: human immunodeficiency virus type 1 HIV 1
has_related_synonym: human immunodeficiency virus type 1 HIV-1
has_related_synonym: human immunodeficiency virus type 1 HIV1
has_related_synonym: human immunodeficiency virus type 1, HIV-1
has_related_synonym: human immunodeficiency virus type I HIV-1
has_related_synonym: human immunodeficiency virus type-1 HIV-1
has_related_synonym: human immunodeficiency virus-1 HIV-1

Human immunodeficiency virus 2
type: Class
subclass of: Retro-transcribing virus
definition: A retro-transcribing virus of family Retroviridae.
has_related_synonym: AIDS virus
has_related_synonym: HIV type 2
has_related_synonym: Human immunodeficiency virus type 2
has_related_synonym: Human immunodeficiency virus-2
has_related_synonym: human immunodeficiency virus type 2 HIV-2
has_related_synonym: human immunodeficiency virus type 2, HIV-2

Bovine leukemia virus
type: Class
subclass of: Retro-transcribing virus
definition: A retro-transcribing virus of family Retroviridae.
has_related_synonym: bovine leukemia virus BLV
has_related_synonym: bovine leukemia virus, BLV

Dengue virus
type: Class
subclass of: ssRNA virus
definition: A ssRNA virus of family Flaviviridae.

Strigamia maritima
type: Class
subclass of: Chilopoda
definition: A species of genus Strigamia.

Cellular Organism
type: Class
subclass of: Organism

Caenorhabditis brenneri
type: Class
subclass of: Nematoda
definition: A species of genus Caenorhabditis.
has_exact_synonym: Caenorhabditis CB5161
has_exact_synonym: Caenorhabditis n. sp. CB5161
has_exact_synonym: Caenorhabditis sp. 1 CB5161
has_exact_synonym: Caenorhabditis sp. CB5161
has_exact_synonym: Caenorhabditis sp. PB2801

Monodelphis domestica
type: Class
subclass of: Mammalia
definition: A species of genus Monodelphis.
has_exact_synonym: Gray short-tailed opossum
has_related_synonym: Monodelphis domesticus

Brachypodium distachyon
type: Class
subclass of: Spermatophyta
definition: A species of genus Brachypodium.

Turbellaria
type: Class
subclass of: Platyhelminthes
definition: A class of phylum Platyhelminthes.

Pinus densata
type: Class
subclass of: Spermatophyta
definition: A species of genus Pinus.

Acacia auriculiformis
type: Class
subclass of: Spermatophyta
definition: A species of genus Acacia.
has_related_synonym: Acacia auriculiformis A.Cunn. ex Benth.

Aquilegia coerulea
type: Class
subclass of: Spermatophyta
definition: A species of genus Aquilegia.
has_related_synonym: Aquilegia caerulea

Acacia mangium
type: Class
subclass of: Spermatophyta
definition: A species of genus Acacia.
has_related_synonym: Acacia mangium Willd

Lottia gigantea
type: Class
subclass of: Gastropoda
definition: A species of genus Lottia.

Xenoturbella bocki
type: Class
subclass of: Xenacoelomorpha
definition: A species of genus Xenoturbella.

Citrus sinensis
type: Class
subclass of: Spermatophyta
definition: A species of genus Citrus.
has_exact_synonym: Apfelsine
has_exact_synonym: Naranja
has_exact_synonym: Navel orange
has_exact_synonym: Sweet orange
has_exact_synonym: Valencia orange
has_related_synonym: Citrus sinensis (L.) Osbeck
has_related_synonym: Citrus x sinensis

Marsupenaeus japonicus
type: Class
subclass of: Malacostraca
definition: A species of genus Marsupenaeus.
has_related_synonym: Penaeus (Marsupenaeus) japonicus
has_related_synonym: Penaeus (Melicertus) japonicus
has_related_synonym: Penaeus japonicus

Calcarea
type: Class
subclass of: Porifera
definition: A class of phylum Porifera.

Sycon ciliatum
type: Class
subclass of: Calcarea
definition: A species of genus Sycon.
has_related_synonym: Scypha ciliata

Anolis carolinensis
type: Class
subclass of: Reptilia
definition: A species of genus Anolis.
has_exact_synonym: Green anole

Capitella teleta
type: Class
subclass of: Annelida
definition: A species of genus Capitella.
has_related_synonym: Capitella sp. I
has_related_synonym: Capitella sp. I AF-2005
has_related_synonym: Capitella sp. I ECS-2004
has_related_synonym: Capitella sp. I ES-2005
has_related_synonym: Capitella sp. I Grassle & Grassle, 1976
has_related_synonym: Capitella telata

Phaeodactylum tricornutum
type: Class
subclass of: Stramenopiles
definition: A species of genus Phaeodactylum.

Ectocarpus siliculosus
type: Class
subclass of: Stramenopiles
definition: A species of genus Ectocarpus.

Cunninghamia lanceolata
type: Class
subclass of: Spermatophyta
definition: A species of genus Cunninghamia.
has_exact_synonym: China fir
has_related_synonym: Cunninghamia lanceolata (Lamb.) Hook.

Gossypium arboreum
type: Class
subclass of: Spermatophyta
definition: A species of genus Gossypium.
has_exact_synonym: Tree cotton
has_related_synonym: Gossypium arboreum L.

Gossypium raimondii
type: Class
subclass of: Spermatophyta
definition: A species of genus Gossypium.
has_related_synonym: Gossypium raimondii Ulbr.

Vitis vinifera
type: Class
subclass of: Spermatophyta
definition: A species of genus Vitis.
has_exact_synonym: Wine grape
has_related_synonym: Vitis vinifera subsp. vinifera

Appendicularia
type: Class
subclass of: Chordata
definition: A class of phylum Chordata.

Chlorophyta
type: Class
subclass of: Plants
definition: A phylum of Eukaryota.

Chlamydomonas reinhardtii
type: Class
subclass of: Chlorophyta
definition: A species of genus Chlamydomonas.
has_related_synonym: Chlamydomonas reihhardtii
has_related_synonym: Chlamydomonas reinhardtii P.A.Dangeard
has_related_synonym: Chlamydomonas smithii
has_related_synonym: Chlamydomonas smithii R.W.Howshaw & H.Ettl

Takifugu rubripes
type: Class
subclass of: Actinopterygii
definition: A species of genus Takifugu.
has_exact_synonym: Tiger puffer
has_exact_synonym: Torafugu
has_related_synonym: Fugu rubripes
has_related_synonym: Sphaeroides rubripes
has_related_synonym: Takifugu rubripes (Temminck & Schlegel, 1850)
has_related_synonym: Tetraodon rubripes

Caenorhabditis remanei
type: Class
subclass of: Nematoda
definition: A species of genus Caenorhabditis.
has_related_synonym: Caenorhabditis vulgarensis
has_related_synonym: Caenorhabditis vulgariensis
has_related_synonym: Caenorhabditis vulgaris
has_related_synonym: Caenorhabditis vulgaris Baird, Fitch & Emmons, 1994

Bryophyta
type: Class
subclass of: Plants
definition: A phylum of Eukaryota.

Physcomitrella patens
type: Class
subclass of: Bryophyta
definition: A species of genus Physcomitrella.

Tetranychus urticae
type: Class
subclass of: Arachnida
definition: A species of genus Tetranychus.
has_exact_synonym: Red spider mite
has_exact_synonym: Two-spotted spider mite
has_exact_synonym: Twospotted mite
has_related_synonym: Tetranychus urticae Koch, 1836

Lycopodiophyta
type: Class
subclass of: Plants
definition: A division of Eukaryota.

Human herpesvirus 6B
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Human herpesvirus 6 type B

Metazoa
type: Class
subclass of: Cellular Organism
has_related_synonym: Animalia
has_related_synonym: Animals

Picea abies
type: Class
subclass of: Spermatophyta
definition: A species of genus Picea.
has_exact_synonym: Norway spruce
has_related_synonym: Picea abies L., Karst
has_related_synonym: Picea excelsa
has_related_synonym: Pinus abies

Pinus taeda
type: Class
subclass of: Spermatophyta
definition: A species of genus Pinus.
has_exact_synonym: Loblolly pine

Stramenopiles
type: Class
subclass of: Plants
has_exact_synonym: Heterokonts
has_related_synonym: Chromophyta

Murid herpesvirus 4
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_exact_synonym: Murine herpesvirus 68
has_related_synonym: mouse herpesvirus 68
has_related_synonym: mouse herpesvirus strain 68
has_related_synonym: murine gammaherpesvirus 68
has_related_synonym: murine herpesvirus type 68

Gossypium herbaceum
type: Class
subclass of: Spermatophyta
definition: A species of genus Gossypium.
has_exact_synonym: Arabian cotton
has_related_synonym: Gossypium herbaceum L.

Lotus japonicus
type: Class
subclass of: Spermatophyta
definition: A species of genus Lotus.
has_related_synonym: Lotus corniculatus var. japonicus

Glottidia pyramidata
type: Class
subclass of: Brachiopoda
definition: A species of genus Glottidia.
has_related_synonym: Glottidea pyramidata

Heliconius melpomene
type: Class
subclass of: Insecta
definition: A species of genus Heliconius.

Oikopleura dioica
type: Class
subclass of: Appendicularia
definition: A species of genus Oikopleura.

dsDNA virus, no RNA stage
type: Class
subclass of: Virus
definition: A virus having a dsDNA molecule as genetic material. No RNA intermediate molecules are involved during its replication.

Retro-transcribing virus
type: Class
subclass of: Virus
definition: A virus that replicates by the reverse transcription of a RNA or DNA intermediate.

Gossypium hirsutum
type: Class
subclass of: Spermatophyta
definition: A species of genus Gossypium.
has_exact_synonym: American cotton
has_exact_synonym: Cotton
has_exact_synonym: Upland cotton
has_related_synonym: Gossypium hirsutum subsp. mexicanum
has_related_synonym: Gossypium lanceolatum
has_related_synonym: Gossypium purpurascens

Theobroma cacao
type: Class
subclass of: Spermatophyta
definition: A species of genus Theobroma.
has_exact_synonym: Cacao
has_exact_synonym: Cocoa

Carica papaya
type: Class
subclass of: Spermatophyta
definition: A species of genus Carica.
has_exact_synonym: Mamon
has_exact_synonym: Papaya
has_related_synonym: Carica papaya L.
has_related_synonym: Carica payaya

Cucumis melo
type: Class
subclass of: Spermatophyta
definition: A species of genus Cucumis.
has_exact_synonym: Muskmelon
has_exact_synonym: Oriental melon
has_related_synonym: Cucumis melo var. markuwa Markino
has_related_synonym: Cucurbita melo L.

Populus trichocarpa
type: Class
subclass of: Spermatophyta
definition: A species of genus Populus.
has_exact_synonym: Black cottonwood
has_exact_synonym: Western balsam poplar
has_related_synonym: Populus balsamifera subsp. trichocarpa
has_related_synonym: Populus balsamifera subsp. trichocarpa (Torr. et A.Gray) Brayshaw
has_related_synonym: Populus trichocarpa Torr. & A.Gray
has_related_synonym: Populus trichocarpa Torr. et A.Gray

Arabidopsis thaliana
type: Class
subclass of: Spermatophyta
definition: A species of genus Arabidopsis.
has_exact_synonym: Mouse-ear cress
has_exact_synonym: Thale cress
has_exact_synonym: Thale-cress
has_related_synonym: Arabidopsis thaliana (thale cress)
has_related_synonym: Arbisopsis thaliana

Brassica napus
type: Class
subclass of: Spermatophyta
definition: A species of genus Brassica.
has_exact_synonym: Oilseed rape
has_exact_synonym: Rape
has_exact_synonym: Rapeseeds

Meleagrid herpesvirus 1
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_exact_synonym: Turkey herpesvirus
has_related_synonym: Meleagrid herpesvirus type 1
has_related_synonym: herpesvirus of turkey
has_related_synonym: herpesvirus of turkeys
has_related_synonym: turkey herpesvirus HVT

Brassica rapa
type: Class
subclass of: Spermatophyta
definition: A species of genus Brassica.
has_exact_synonym: Field mustard
has_related_synonym: Brassica rapa L.

Brassica oleracea
type: Class
subclass of: Spermatophyta
definition: A species of genus Brassica.
has_related_synonym: Brassica oleracea L.

Human herpesvirus 8
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Human herpesvirus 8 type P
has_related_synonym: Kaposi's sarcoma-associated herpes-like virus
has_related_synonym: Kaposi's sarcoma-associated herpesvirus
has_related_synonym: Kaposi's sarcoma-associated herpesvirus - Human herpesvirus 8
has_related_synonym: Kaposi's sarcoma-associated herpesvirus KSHV
has_related_synonym: Kaposi's sarcoma-associated human herpes virus
has_related_synonym: Karposi's sarcoma-associated herpes-like virus

Malus x domestica
type: Class
subclass of: Spermatophyta
definition: A species of genus Malus.
has_exact_synonym: Apple
has_exact_synonym: Apple tree
has_exact_synonym: Cultivated apple
has_related_synonym: Malus domestica
has_related_synonym: Malus pumila auct.
has_related_synonym: Malus pumila var. domestica
has_related_synonym: Malus sylvestris var. domestica
has_related_synonym: Pyrus malus

Prunus persica
type: Class
subclass of: Spermatophyta
definition: A species of genus Prunus.
has_exact_synonym: peach
has_related_synonym: Amygdalus persica
has_related_synonym: Persica vulgaris
has_related_synonym: Prunus persica var densa

Aegilops tauschii
type: Class
subclass of: Spermatophyta
definition: A species of genus Aegilops.
has_related_synonym: Aegilops squarrosa
has_related_synonym: Aegilops squarrosa auct.
has_related_synonym: Aegilops squarrosa subsp. squarrosa
has_related_synonym: Aegilops tauschii Coss.
has_related_synonym: Aegilops tauschii Cosson
has_related_synonym: Patropyrum tauschii
has_related_synonym: Patropyrum tauschii subsp. tauschii
has_related_synonym: Triticum tauschii

Citrus trifoliata
type: Class
subclass of: Spermatophyta
definition: A species of genus Citrus.
has_exact_synonym: Hardy orange
has_exact_synonym: Trifoliate orange
has_related_synonym: Citrus trifoliatus
has_related_synonym: Poncirus trifoliata
has_related_synonym: Poncirus trifoliate
has_related_synonym: Poncirus trifoliatus

Arachis hypogaea
type: Class
subclass of: Spermatophyta
definition: A species of genus Arachis.
has_exact_synonym: Goober
has_exact_synonym: Ground-nut
has_exact_synonym: Peanut
has_related_synonym: Arachis hypogea

Glycine max
type: Class
subclass of: Spermatophyta
definition: A species of genus Glycine.
has_exact_synonym: Soybean
has_related_synonym: Glycine max; cv. Wye

Glycine soja
type: Class
subclass of: Spermatophyta
definition: A species of genus Glycine.
has_exact_synonym: Wild soybean

Medicago truncatula
type: Class
subclass of: Spermatophyta
definition: A species of genus Medicago.
has_exact_synonym: Barrel medic

Phaseolus vulgaris
type: Class
subclass of: Spermatophyta
definition: A species of genus Phaseolus.
has_exact_synonym: French bean
has_exact_synonym: Kidney bean
has_exact_synonym: String bean

Salvia sclarea
type: Class
subclass of: Spermatophyta
definition: A species of genus Salvia.
has_exact_synonym: Clary
has_related_synonym: Salvia sclarea L.

Vigna unguiculata
type: Class
subclass of: Spermatophyta
definition: A species of genus Vigna.
has_exact_synonym: Cowpea
has_related_synonym: Phaseolus unguiculatus

Hevea brasiliensis
type: Class
subclass of: Spermatophyta
definition: A species of genus Hevea.
has_exact_synonym: Jebe
has_exact_synonym: Para rubber tree
has_exact_synonym: Rubbertree
has_exact_synonym: Siringa
has_related_synonym: Hevea brasiliensis (Willd. ex A.Juss.) Muell. Arg.

Manihot esculenta
type: Class
subclass of: Spermatophyta
definition: A species of genus Manihot.
has_exact_synonym: Cassava
has_exact_synonym: Manioc
has_exact_synonym: Tapioca
has_exact_synonym: Yuca
has_related_synonym: Manihot esculenta Crantz
has_related_synonym: Manihot esculenta0
has_related_synonym: Manihot utilissima

Ricinus communis
type: Class
subclass of: Spermatophyta
definition: A species of genus Ricinus.
has_exact_synonym: Castor bean
has_related_synonym: Ricimus communis
has_related_synonym: Ricinis communis
has_related_synonym: Ricinus communis L.
has_related_synonym: Ricinus comunis
has_related_synonym: Ricinus sanguineus
has_related_synonym: Ricinus sanguineus hort. ex Groenl.

Bruguiera gymnorhiza
type: Class
subclass of: Spermatophyta
definition: A species of genus Bruguiera.
has_exact_synonym: Burma mangrove
has_related_synonym: Bruguiera gymnorhiza (L.) Savigny
has_related_synonym: Bruguiera gymnorrhiza
has_related_synonym: Bruguiera gymnorrhizza

Helianthus exilis
type: Class
subclass of: Spermatophyta
definition: A species of genus Helianthus.
has_related_synonym: Helianthus exilis A.Gray

Linum usitatissimum
type: Class
subclass of: Spermatophyta
definition: A species of genus Linum.
has_related_synonym: Linum usitatissimum L.

Amphimedon queenslandica
type: Class
subclass of: Demospongiae
definition: A species of genus Amphimedon.
has_related_synonym: Reniera sp. JGI-2005

Panax ginseng
type: Class
subclass of: Spermatophyta
definition: A species of genus Panax.
has_exact_synonym: Chinese ginseng
has_exact_synonym: Korean ginseng
has_exact_synonym: ginseng
has_exact_synonym: hong shen
has_exact_synonym: insam
has_exact_synonym: ninjin
has_exact_synonym: ren seng

Mammalia
type: Class
subclass of: Chordata
definition: A class of phylum Chordata.

Solanum lycopersicum
type: Class
subclass of: Spermatophyta
definition: A species of genus Solanum.
has_exact_synonym: Tomato
has_related_synonym: Lycopersicon esculentum
has_related_synonym: Lycopersicon esculentum Mill.
has_related_synonym: Lycopersicon esculentum var. esculentum
has_related_synonym: Lycopersicon lycopersicum
has_related_synonym: Lycopersicum esculentum
has_related_synonym: Solanum esculentum
has_related_synonym: Solanum esculentum Dunal
has_related_synonym: Solanum lycopersicon
has_related_synonym: Solanum lycopersicum L.

Nicotiana tabacum
type: Class
subclass of: Spermatophyta
definition: A species of genus Nicotiana.
has_exact_synonym: American tobacco
has_exact_synonym: Common tobacco
has_exact_synonym: Tobacco
has_related_synonym: Nicotania tabacum
has_related_synonym: Nicotiana tabacum var. Samsun

Solanum tuberosum
type: Class
subclass of: Spermatophyta
definition: A species of genus Solanum.
has_exact_synonym: Potato
has_related_synonym: Solanum tuberosum subsp. tuberosum

Digitalis purpurea
type: Class
subclass of: Spermatophyta
definition: A species of genus Digitalis.
has_exact_synonym: Common foxglove
has_related_synonym: Digitalis purpurea L.

Helianthus annuus
type: Class
subclass of: Spermatophyta
definition: A species of genus Helianthus.
has_exact_synonym: Common sunflower
has_related_synonym: Helianthus annus
has_related_synonym: Helianthus annuus8

Helianthus tuberosus
type: Class
subclass of: Spermatophyta
definition: A species of genus Helianthus.
has_exact_synonym: Jerusalem artichoke
has_related_synonym: Helianthus tuberosus L.

Helianthus petiolaris
type: Class
subclass of: Spermatophyta
definition: A species of genus Helianthus.
has_related_synonym: Helianthus petiolaris Nutt.

Cynara cardunculus
type: Class
subclass of: Spermatophyta
definition: A species of genus Cynara.
has_exact_synonym: Cardoon
has_exact_synonym: Wild artichoke
has_related_synonym: Cynara cardunculus L.

Leucosolenia complicata
type: Class
subclass of: Calcarea
definition: A species of genus Leucosolenia.

ssRNA virus
type: Class
subclass of: Virus

Dictyostelium discoideum
type: Class
subclass of: Amoebozoa
definition: A species of genus Dictyostelium.

Hordeum vulgare
type: Class
subclass of: Spermatophyta
definition: A species of genus Hordeum.
has_exact_synonym: Barley
has_related_synonym: Hordeum vulgare L.
has_related_synonym: Horedum vulgare

Oryza sativa
type: Class
subclass of: Spermatophyta
definition: A species of genus Oryza.
has_exact_synonym: Red rice
has_exact_synonym: Rice

Nematostella vectensis
type: Class
subclass of: Anthozoa
definition: A species of genus Nematostella.
has_exact_synonym: Starlet sea anemone
has_related_synonym: Nematostella vectensis Stephenson, 1935

Macacine herpesvirus 4
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_exact_synonym: monkey B virus
has_related_synonym: B virus
has_related_synonym: Cercopithecid herpesvirus 1
has_related_synonym: Cercopithecine herpesvirus 1
has_related_synonym: Herpesvirus simiae
has_related_synonym: Simian herpes B virus
has_related_synonym: Simian herpesvirus B
has_related_synonym: herpes B virus
has_related_synonym: herpes virus B
has_related_synonym: simian herpes B virus SHBV

Saccharum officinarum
type: Class
subclass of: Spermatophyta
definition: A species of genus Saccharum.
has_exact_synonym: Noble cane
has_exact_synonym: Sugarcane

Sorghum bicolor
type: Class
subclass of: Spermatophyta
definition: A species of genus Sorghum.
has_exact_synonym: Broomcorn
has_exact_synonym: Milo
has_exact_synonym: Sorghum
has_related_synonym: Sorghum bicolor milo
has_related_synonym: Sorghum saccharatum
has_related_synonym: Sorghum vulgare

Triticum aestivum
type: Class
subclass of: Spermatophyta
definition: A species of genus Triticum.
has_exact_synonym: Bread wheat
has_exact_synonym: Canadian hard winter wheat
has_exact_synonym: Common wheat
has_exact_synonym: Wheat
has_related_synonym: Tricum aestivum
has_related_synonym: Triticum aestivam
has_related_synonym: Triticum aestivum subsp. aestivum
has_related_synonym: Triticum aestivum8
has_related_synonym: Triticum vulgare

Triticum turgidum
type: Class
subclass of: Spermatophyta
definition: A species of genus Triticum.
has_exact_synonym: Cone wheat
has_exact_synonym: English wheat
has_exact_synonym: Poulard wheat
has_exact_synonym: Rivet wheat
has_related_synonym: Triticum aethiopicum
has_related_synonym: Triticum aethiopicum Jakubz.
has_related_synonym: Triticum turgidum L.
has_related_synonym: Triticum turgidum8

Zea mays
type: Class
subclass of: Spermatophyta
definition: A species of genus Zea.
has_exact_synonym: Maize
has_related_synonym: Zea mays mays
has_related_synonym: Zea mays var. japonica

Festuca arundinacea
type: Class
subclass of: Spermatophyta
definition: A species of genus Festuca.
has_exact_synonym: Tall fescue
has_related_synonym: Festuca elatior
has_related_synonym: Lolium arundinaceum
has_related_synonym: Schedonorus arundinaceus
has_related_synonym: Schedonorus phoenix

Bandicoot papillomatosis carcinomatosis virus type 1
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Papillomaviridae.
has_related_synonym: Bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1)

Merkel cell polyomavirus
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Polyomaviridae.

Bandicoot papillomatosis carcinomatosis virus type 2
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Papillomaviridae.

Insecta
type: Class
subclass of: Arthropoda
definition: A class of phylum Arthropoda.

Ciona savignyi
type: Class
subclass of: Ascidiacea
definition: A species of genus Ciona.

Elaeis guineensis
type: Class
subclass of: Spermatophyta
definition: A species of genus Elaeis.
has_exact_synonym: African oil palm
has_related_synonym: Elaeis guineensis Jacq.
has_related_synonym: Elaeis guineensis var. tenera
has_related_synonym: Elaeis guineensis var. tenera (Oil palm)
has_related_synonym: Elaeis guinensi
has_related_synonym: Elaeis gunieensis

Pristionchus pacificus
type: Class
subclass of: Nematoda
definition: A species of genus Pristionchus.

Amoebozoa
type: Class
subclass of: Cellular Organism

Spermatophyta
type: Class
subclass of: Plants
definition: A subset of Embryophytes.

Arabidopsis lyrata
type: Class
subclass of: Spermatophyta
definition: A species of genus Arabidopsis.
has_exact_synonym: Lyrate rockcress
has_related_synonym: Arabidopsis lyrata (L.) O'Kane & Al-Shehbaz

Taeniopygia guttata
type: Class
subclass of: Aves
definition: A species of genus Taeniopygia.
has_exact_synonym: Zebra finch
has_related_synonym: Poephila guttata
has_related_synonym: Taenopygia guttata

Porifera
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Demospongiae
type: Class
subclass of: Porifera
definition: A class of phylum Porifera.

Cnidaria
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Hydrozoa
type: Class
subclass of: Cnidaria
definition: A class of phylum Cnidaria.

Hydra magnipapillata
type: Class
subclass of: Hydrozoa
definition: A species of genus Hydra.

Anthozoa
type: Class
subclass of: Cnidaria
definition: A class of phylum Cnidaria.

Platyhelminthes
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Rhinopithecus bieti
type: Class
subclass of: Mammalia
definition: A species of genus Pygathrix.
has_exact_synonym: Black snub-nosed monkey
has_related_synonym: Pygathrix bieti

Digenea
type: Class
subclass of: Platyhelminthes
definition: A subclass of phylum Platyhelminthes.

Schistosoma japonicum
type: Class
subclass of: Digenea
definition: A species of genus Schistosoma.

Schistosoma mansoni
type: Class
subclass of: Digenea
definition: A species of genus Schistosoma.

Cestoda
type: Class
subclass of: Platyhelminthes
definition: A class of phylum Platyhelminthes.

Echinococcus granulosus
type: Class
subclass of: Cestoda
definition: A species of genus Echinococcus.
has_related_synonym: Echinococcus granulosus (Batsch, 1786)
has_related_synonym: Echinococcus granulosus G1 strain
has_related_synonym: Echinococcus granulosus G2 strain
has_related_synonym: Echinococcus granulosus G3 strain
has_related_synonym: Echinococcus granulosus Tasmanian sheep strain
has_related_synonym: Echinococcus granulosus buffalo strain
has_related_synonym: Echinococcus granulosus s. s.
has_related_synonym: Echinococcus granulosus sensu stricto
has_related_synonym: Echinococcus granulosus sheep strain

Echinococcus multilocularis
type: Class
subclass of: Cestoda
definition: A species of genus Echinococcus.

Nemertea
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Cerebratulus lacteus
type: Class
subclass of: Nemertea
definition: A species of genus Cerebratulus.
has_exact_synonym: Milky ribbon worm
has_exact_synonym: Milky ribbon-worm

Nematoda
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Panagrellus redivivus
type: Class
subclass of: Nematoda
definition: A species of genus Panagrellus.

Caenorhabditis briggsae
type: Class
subclass of: Nematoda
definition: A species of genus Caenorhabditis.

Caenorhabditis elegans
type: Class
subclass of: Nematoda
definition: A species of genus Caenorhabditis.
has_exact_synonym: Nematode
has_related_synonym: Rhabditis elegans

Ascaris suum
type: Class
subclass of: Nematoda
definition: A species of genus Ascaris.
has_exact_synonym: Pig roundworm

Brugia malayi
type: Class
subclass of: Nematoda
definition: A species of genus Brugia.
has_exact_synonym: Agent of lymphatic filariasis

Haemonchus contortus
type: Class
subclass of: Nematoda
definition: A species of genus Haemonchus.
has_exact_synonym: Barber pole worm
has_exact_synonym: Red stomach worm

Annelida
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Mollusca
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Gastropoda
type: Class
subclass of: Mollusca
definition: A class of phylum Mollusca.

Haliotis rufescens
type: Class
subclass of: Gastropoda
definition: A species of genus Haliotis.
has_exact_synonym: California red abalone
has_exact_synonym: Red abalone

Arthropoda
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Branchiopoda
type: Class
subclass of: Arthropoda
definition: A class of phylum Arthropoda.

Daphnia pulex
type: Class
subclass of: Branchiopoda
definition: A species of genus Daphnia.
has_exact_synonym: Common water flea

Malacostraca
type: Class
subclass of: Arthropoda
definition: A class of phylum Arthropoda.

Arachnida
type: Class
subclass of: Arthropoda
definition: A class of phylum Arthropoda.

Rhesus monkey rhadinovirus H26-95
type: Class
subclass of: dsDNA virus, no RNA stage
definition: A dsDNA virus of family Herpesviridae.
has_related_synonym: Macaca mulatta rhadinovirus 26-95

Gasterosteus aculeatus
type: Class
subclass of: Actinopterygii
definition: A species of genus Gasterosteus.
has_exact_synonym: Three spined stickleback
has_exact_synonym: Three-spined stickleback
has_related_synonym: Gasterosteus aculeatus Linnaeus, 1758

Rhipicephalus microplus
type: Class
subclass of: Arachnida
definition: A species of genus Rhipicephalus.
has_exact_synonym: Cattle tick
has_exact_synonym: Southern cattle tick
has_related_synonym: Boophilus microplus
has_related_synonym: Rhipicephalus (Boophilus) microplus

Ixodes scapularis
type: Class
subclass of: Arachnida
definition: A species of genus Ixodes.
has_exact_synonym: Black-legged tick
has_exact_synonym: Blacklegged tick
has_exact_synonym: Deer tick
has_exact_synonym: Shoulder tick
has_related_synonym: Ixodes dammini

Locusta migratoria
type: Class
subclass of: Insecta
definition: A species of genus Locusta.
has_exact_synonym: Migratory locust

Acyrthosiphon pisum
type: Class
subclass of: Insecta
definition: A species of genus Acyrthosiphon.
has_exact_synonym: Pea aphid
has_related_synonym: Acyrthosiphum pisum

Tribolium castaneum
type: Class
subclass of: Insecta
definition: A species of genus Tribolium.
has_exact_synonym: Red flour beetle
has_exact_synonym: Rust-red flour beetle

Saccharum sp.
type: Class
subclass of: Spermatophyta
definition: A species of genus Saccharum.

Bombyx mori
type: Class
subclass of: Insecta
definition: A species of genus Bombyx.
has_exact_synonym: Domestic silkworm
has_exact_synonym: Silk moth
has_exact_synonym: Silkworm
has_related_synonym: Bombyx mori Linnaeus, 1758

Manduca sexta
type: Class
subclass of: Insecta
definition: A species of genus Manduca.
has_exact_synonym: Carolina sphinx
has_exact_synonym: Hornblower
has_exact_synonym: Tobacco hornworm
has_exact_synonym: Tomato hornworm
has_related_synonym: Tobacco hawkmoth

Aedes aegypti
type: Class
subclass of: Insecta
definition: A species of genus Aedes.
has_exact_synonym: Yellow fever mosquito
has_related_synonym: Stegomyia aegypti

Anopheles gambiae
type: Class
subclass of: Insecta
definition: A species of genus Anopheles.
has_exact_synonym: African malaria mosquito
has_exact_synonym: Anopheles gambiae sensu stricto
has_related_synonym: Anopheles gambia
has_related_synonym: Anopheles gambiae Giles, 1902

Culex quinquefasciatus
type: Class
subclass of: Insecta
definition: A species of genus Culex.
has_exact_synonym: Southern house mosquito
has_related_synonym: Culex pipiens quinquefasciatus
has_related_synonym: Culex pipiens quiquefasciatus
has_related_synonym: Culex quinquifasciatus
has_related_synonym: Culex quinquifasiatus
has_related_synonym: Culex quiquefasciatus

Drosophila ananassae
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.
has_related_synonym: Drosophila annanassae

Drosophila erecta
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.

Drosophila grimshawi
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.
has_related_synonym: Idiomyia grimshawi

Drosophila melanogaster
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.
has_exact_synonym: Fruit fly
has_related_synonym: Drosophila melangaster

Drosophila mojavensis
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.
has_related_synonym: Drosophila mohavensis

Drosophila persimilis
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.

Drosophila pseudoobscura
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.

Drosophila sechellia
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.
has_related_synonym: Drosophila sechellia Tsacas and Bachli, 1981

Drosophila simulans
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.

Drosophila virilis
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.
has_related_synonym: Drosophila irilis
has_related_synonym: Drosophila virilis Sturtevant, 1916

Drosophila yakuba
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.

Drosophila willistoni
type: Class
subclass of: Insecta
definition: A species of genus Drosophila.

Helianthus argophyllus
type: Class
subclass of: Spermatophyta
definition: A species of genus Helianthus.
has_related_synonym: Helianthus argophyllus Torr. & A.Gray

Helianthus ciliaris
type: Class
subclass of: Spermatophyta
definition: A species of genus Helianthus.
has_related_synonym: Helianthus cilaris
has_related_synonym: Helianthus ciliaris DC.

Helianthus paradoxus
type: Class
subclass of: Spermatophyta
definition: A species of genus Helianthus.
has_related_synonym: Helianthus paradoxus Heiser

Capitella sp. 1
type: Class
subclass of: Annelida
definition: A species of genus Capitella.

Nasonia vitripennis
type: Class
subclass of: Insecta
definition: A species of genus Nasonia.
has_exact_synonym: Jewel wasp
has_related_synonym: Nasonia vitripennis (Walker, 1836)

Nasonia giraulti
type: Class
subclass of: Insecta
definition: A species of genus Nasonia.

Nasonia longicornis
type: Class
subclass of: Insecta
definition: A species of genus Nasonia.
has_related_synonym: Nasonia lonigicornis

Apis mellifera
type: Class
subclass of: Insecta
definition: A species of genus Apis.
has_exact_synonym: Bee
has_exact_synonym: Honey bee
has_exact_synonym: Honeybee
has_related_synonym: Apis mellifica

Chilopoda
type: Class
subclass of: Arthropoda
definition: A class of phylum Arthropoda.

Brachiopoda
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Populus euphratica
type: Class
subclass of: Spermatophyta
definition: A species of genus Populus.
has_related_synonym: Popolus euphratica
has_related_synonym: Populus diversifolia

Terebratulina retusa
type: Class
subclass of: Brachiopoda
definition: A species of genus Terebratulina.

Echinodermata
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Echinoidea
type: Class
subclass of: Echinodermata
definition: A class of phylum Echinodermata.

Strongylocentrotus purpuratus
type: Class
subclass of: Echinoidea
definition: A species of genus Strongylocentrotus.
has_exact_synonym: Purple sea urchin
has_exact_synonym: Purple urchin
has_related_synonym: Strongylocentrotus purpuratus (Stimpson, 1857)

Chordata
type: Class
subclass of: Metazoa
definition: A phylum of kingdom Animalia.

Ascidiacea
type: Class
subclass of: Chordata
definition: A class of phylum Chordata.

Ciona intestinalis
type: Class
subclass of: Ascidiacea
definition: A species of genus Ciona.

Branchiostomidae
type: Class
subclass of: Chordata
definition: A class of phylum Chordata.
has_exact_synonym: Leptocardii

Branchiostoma floridae
type: Class
subclass of: Branchiostomidae
definition: A species of genus Branchiostoma.
has_exact_synonym: Florida lancelet
has_related_synonym: Amphioxus floridae
has_related_synonym: Branchiostoma floridea

Branchiostoma belcheri
type: Class
subclass of: Branchiostomidae
definition: A species of genus Branchiostoma.
has_exact_synonym: Belcher's lancelet

Petromyzontidae
type: Class
subclass of: Chordata
definition: A class of phylum Chordata.

Petromyzon marinus
type: Class
subclass of: Petromyzontidae
definition: A species of genus Petromyzon.
has_exact_synonym: Marine lamprey
has_exact_synonym: Sea lamprey

Saguinus labiatus
type: Class
subclass of: Mammalia
definition: A species of genus Saguinus.
has_exact_synonym: Red-chested mustached tamarin

Actinopterygii
type: Class
subclass of: Chordata
definition: A class of phylum Chordata.

Schmidtea mediterranea
type: Class
subclass of: Turbellaria
definition: A species of genus Schmidtea.
has_exact_synonym: Freshwater planarian
has_related_synonym: Dugesia (Schmidtea) mediterranea
has_related_synonym: Dugesia mediterranea

Danio rerio
type: Class
subclass of: Actinopterygii
definition: A species of genus Danio.
has_exact_synonym: Leopard danio
has_exact_synonym: Zebra danio
has_exact_synonym: Zebra fish
has_exact_synonym: Zebrafish
has_related_synonym: Brachidanio rerio
has_related_synonym: Brachydanio rerio
has_related_synonym: Brachydanio rerio frankei
has_related_synonym: Cyprinus rerio
has_related_synonym: Cyprinus rerio Hamilton, 1822
has_related_synonym: Danio frankei
has_related_synonym: Danio rerio (Hamilton, 1822)
has_related_synonym: Danio rerio frankei

Cyprinus carpio
type: Class
subclass of: Actinopterygii
definition: A species of genus Cyprinus.
has_exact_synonym: Carp
has_exact_synonym: Common carp
has_related_synonym: Cyprinus cyprio
has_related_synonym: Cyrpinus carpio

Ictalurus punctatus
type: Class
subclass of: Actinopterygii
definition: A species of genus Ictalurus.
has_exact_synonym: Channel catfish
has_related_synonym: Ictalurus punctatus (Rafinesque, 1818)
has_related_synonym: Silurus punctatus

Oryzias latipes
type: Class
subclass of: Actinopterygii
definition: A species of genus Oryzias.
has_exact_synonym: Japanese medaka
has_exact_synonym: Japanese rice fish
has_exact_synonym: Medaka

Paralichthys olivaceus
type: Class
subclass of: Actinopterygii
definition: A species of genus Paralichthys.
has_exact_synonym: Bastard halibut
has_exact_synonym: False halibut
has_exact_synonym: Japanese flounder
has_exact_synonym: Olive flounder
has_exact_synonym: Paralichthyidae sp. KYJ-2011
has_related_synonym: Hippoglossus olivaceus
has_related_synonym: Paralichthys olivaceous
has_related_synonym: Paralichthys olivaceus (Temminck & Schlegel, 1846)
has_related_synonym: Paralichtys olivaceus

Hippoglossus hippoglossus
type: Class
subclass of: Actinopterygii
definition: A species of genus Hippoglossus.
has_exact_synonym: Atlantic halibut
has_related_synonym: Hippoglossus hippoglossus (Linnaeus, 1758)

Amphibia
type: Class
subclass of: Chordata
definition: A class of phylum Chordata.

Avicennia marina
type: Class
subclass of: Spermatophyta
definition: A species of genus Avicennia.

Xenopus laevis
type: Class
subclass of: Amphibia
definition: A species of genus Xenopus.
has_exact_synonym: African clawed frog
has_exact_synonym: Clawed frog
has_exact_synonym: Common platanna
has_exact_synonym: Platanna
has_related_synonym: Bufo laevis
has_related_synonym: Xenopus laevis (Daudin, 1802)
has_related_synonym: Xenopus leavis

Xenopus (Silurana) tropicalis
type: Class
subclass of: Amphibia
definition: A species of genus Xenopus.
has_exact_synonym: Western clawed frog
has_related_synonym: Silurana tropicalis
has_related_synonym: Xenopus laevis tropicalis
has_related_synonym: Xenopus tropicalis

Citrus reticulata
type: Class
subclass of: Spermatophyta
definition: A species of genus Citrus.
has_exact_synonym: Mandarin orange
has_exact_synonym: Tangerine
has_related_synonym: Citrus poonensis

Citrus clementina
type: Class
subclass of: Spermatophyta
definition: A species of genus Citrus.
has_related_synonym: Citrus clementina hort. ex Tanaka

Aves
type: Class
subclass of: Chordata
definition: A class of phylum Chordata.

Selaginella moellendorffii
type: Class
subclass of: Lycopodiophyta
definition: A species of genus Selaginella.
has_related_synonym: Selaginella moellendorffii Hieron
has_related_synonym: Selaginella moellendorfii

Gallus gallus
type: Class
subclass of: Aves
definition: A species of genus Gallus.
has_exact_synonym: Bantam
has_exact_synonym: Chicken
has_exact_synonym: Chickens
has_related_synonym: Gallus domesticus
has_related_synonym: Gallus gallus domesticus

Ornithorhynchus anatinus
type: Class
subclass of: Mammalia
definition: A species of genus Ornithorhynchus.
has_exact_synonym: Duck-billed platypus
has_exact_synonym: Duckbill platypus
has_exact_synonym: Platypus
has_related_synonym: Ornythorhynchus anatinus

Sarcophilus harrisii
type: Class
subclass of: Mammalia
definition: A species of genus Sarcophilus.
has_exact_synonym: Tasmanian devil
has_related_synonym: Sarcophilus laniarius

Macropus eugenii
type: Class
subclass of: Mammalia
definition: A species of genus Macropus.
has_exact_synonym: Tammar wallaby

Artibeus jamaicensis
type: Class
subclass of: Mammalia
definition: A species of genus Artibeus.
database_cross_reference: GC_ID:1
has_exact_synonym: Jamaican fruit-eating bat

Lemur catta
type: Class
subclass of: Mammalia
definition: A species of genus Lemur.
has_exact_synonym: Ring-tailed lemur

Ateles geoffroyi
type: Class
subclass of: Mammalia
definition: A species of genus Ateles.
has_exact_synonym: Black-handed spider monkey
has_exact_synonym: Central American spider monkey
has_related_synonym: Ateles geoffreyi
has_related_synonym: Ateles jeoffroyi

Lagothrix lagotricha
type: Class
subclass of: Mammalia
definition: A species of genus Lagothrix.
has_exact_synonym: Brown woolly monkey
has_exact_synonym: Common woolly monkey
has_exact_synonym: Humboldt's woolly monkey
has_related_synonym: Lagothrix lagothricha
has_related_synonym: Lagothrix lagotricha lagotricha

Macaca mulatta
type: Class
subclass of: Mammalia
definition: A species of genus Macaca.
has_exact_synonym: Rhesus macaque
has_exact_synonym: Rhesus monkey

Macaca nemestrina
type: Class
subclass of: Mammalia
definition: A species of genus Macaca.
has_exact_synonym: Pig-tailed macaque
has_exact_synonym: Pigtail macaque
has_exact_synonym: Pigtail monkey

Symphalangus syndactylus
type: Class
subclass of: Mammalia
definition: A species of genus Symphalangus.
has_exact_synonym: Siamang
has_related_synonym: Hylobates syndactylus

Gorilla gorilla
type: Class
subclass of: Mammalia
definition: A species of genus Gorilla.
has_exact_synonym: Gorilla
has_exact_synonym: Western gorilla

Pan paniscus
type: Class
subclass of: Mammalia
definition: A species of genus Pan.
has_exact_synonym: Bonobo
has_exact_synonym: Pygmy chimpanzee

Pan troglodytes
type: Class
subclass of: Mammalia
definition: A species of genus Pan.
has_exact_synonym: Chimpanzee
has_related_synonym: Chimpansee troglodytes

Pongo pygmaeus
type: Class
subclass of: Mammalia
definition: A species of genus Pongo.
has_exact_synonym: Bornean orangutan
has_exact_synonym: Orang utan
has_exact_synonym: Orang-utan
has_exact_synonym: Orangutan

Homo sapiens
type: Class
subclass of: Mammalia
definition: A species of genus Homo.
has_exact_synonym: Human
has_exact_synonym: Man

Canis lupus familiaris
type: Class
subclass of: Mammalia
definition: A species of genus Canis.
has_exact_synonym: Dog
has_related_synonym: Canis canis
has_related_synonym: Canis domesticus
has_related_synonym: Canis familiaris

Equus caballus
type: Class
subclass of: Mammalia
definition: A species of genus Equus.
has_exact_synonym: Domestic horse
has_exact_synonym: Equine
has_exact_synonym: Horse
has_related_synonym: Equus ferus caballus
has_related_synonym: Equus przewalskii f. caballus
has_related_synonym: Equus przewalskii forma caballus

Sus scrofa
type: Class
subclass of: Mammalia
definition: A species of genus Sus.
has_exact_synonym: Pig
has_exact_synonym: Swine
has_exact_synonym: Wild boar
has_related_synonym: Sus scrofus

Bos taurus
type: Class
subclass of: Mammalia
definition: A species of genus Bos.
has_exact_synonym: Bovine
has_exact_synonym: Cattle
has_exact_synonym: Cow
has_exact_synonym: Domestic cattle
has_exact_synonym: Domestic cow
has_related_synonym: Bos bovis
has_related_synonym: Bos primigenius taurus
has_related_synonym: Bos tauurus

Rehmannia glutinosa
type: Class
subclass of: Spermatophyta
definition: A species of genus Rehmannia.
has_exact_synonym: Chinese foxglove

Ovis aries
type: Class
subclass of: Mammalia
definition: A species of genus Ovis.
has_exact_synonym: Domestic sheep
has_exact_synonym: Lambs
has_exact_synonym: Sheep
has_exact_synonym: Wild sheep
has_related_synonym: Ovis ammon aries
has_related_synonym: Ovis orientalis aries
has_related_synonym: Ovis ovis

Tetraodon nigroviridis
type: Class
subclass of: Actinopterygii
definition: A species of genus Tetraodon.
has_exact_synonym: Spotted green pufferfish
has_related_synonym: Tetraodon nigroviridis Marion de Proce, 1822

Primary Structure of DNA Macromolecule
type: Class
subclass of: sequence feature

Primary Structure of RNA Molecule
type: Class
subclass of: sequence feature

Organism
type: Class
subclass of: Object
definition: 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.
definition_source: OBI:0100026

Disease
type: Class
subclass of: Disposition
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
definition_source: IDO:Disease

Paired Region
type: Class
subclass of: RNA Sequence Secondary Structure
definition: A collection of one or more adjacent nucleotide residues in which at least one residue is part of a base pair.
definition_source: RNAO:0000095

Unpaired Region
type: Class
subclass of: RNA Sequence Secondary Structure
definition: A collection of one or more nucleotides that are not involved in base pairing.
definition_source: RNAO:0000096

Unbroken Stem
type: Class
subclass of: Paired Region
definition: A paired region made up of two contiguous collections of nucleotides, in which each nucleotide forms a base pair. [RNAO:0000097]
definition_source: RNAO:0000097

Terminal Loop
type: Class
subclass of: RNA Sequence Secondary Structure
definition: 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]
definition_source: RNAO:0000098

Internal Loop
type: Class
subclass of: RNA Sequence Secondary Structure
definition: A collection of nucleotide residues that link two given unbroken_stems.
definition_source: RNAO:0000099

Stem Junction
type: Class
subclass of: RNA Sequence Secondary Structure
definition: 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.
definition_source: RNAO:0000106

Strand End
type: Class
subclass of: RNA Sequence Secondary Structure
definition: 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]
definition_source: RNAO:0000107

Collection of Nucleotides Residues
type: Class
subclass of: Collection of Material Entities
definition: A collection of nucleotide residues is a part of a nucleic acid consisting of one or more nucleotides.
definition_source: RNAO:0000108

Collection of Material Entities
type: Class
subclass of: Material Entity

Region
type: Class
subclass of: Monocistronic Transcript
definition: 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.
definition_source: SO:0000001

Interior Coding Exon
type: Class
subclass of: Coding Exon

scRNA Primary Transcript
type: Class
subclass of: Noncoding Primary Transcript
definition: The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote.
definition_source: SO:0000012

scRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: scRNA Primary Transcript
definition: Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.
definition_source: SO:0000013

Riboswitch
type: Class
subclass of: mRNA Region
subclass of: Restriction
  on property: part_of
  some values from: mRNA
definition: 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.
definition_source: SO:0000035

Polycistronic Transcript
type: Class
subclass of: Transcript
definition: A transcript that is polycistronic.
definition_source: SO:0000078

mRNA with Frameshift
type: Class
subclass of: mRNA
definition: An mRNA with a frameshift.
definition_source: SO:0000108

Transcript with Translational Frameshift
type: Class
subclass of: Transcript
definition: A transcript with a translational frameshift.
definition_source: SO:0000118

Protein Coding Primary Transcript
type: Class
subclass of: Primary Transcript
definition: A primary transcript that, at least in part, encodes one or more proteins.
definition_source: SO:0000120

RNA Sequence Secondary Structure
type: Class
subclass of: sequence secondary structure
definition: A folded RNA sequence.
definition_source: SO:0000122

Ribosome Entry Site
type: Class
subclass of: mRNA Region
definition: Region in mRNA where ribosome assembles.
definition_source: SO:0000139

DNA Sequence Secondary Structure
type: Class
subclass of: sequence secondary structure
definition: A folded DNA sequence.
definition_source: SO:0000142

Recoded Codon
type: Class
subclass of: Codon
definition: A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.
definition_source: SO:0000145

Exon
type: Class
subclass of: Transcript Region
definition: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
definition_source: SO:0000147

Splice Site
type: Class
subclass of: Primary Transcript Region
definition: Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
definition_source: SO:0000162

5' cis Splice Site
type: Class
subclass of: cis Splice Site
definition: 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.
definition_source: SO:0000163

3' cis Splice Site
type: Class
subclass of: cis Splice Site
definition: 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.
definition_source: SO:0000164

U2 Intron
type: Class
subclass of: Spliceosomal Intron
definition: A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
definition_source: SO:0000184

Primary Transcript
type: Class
subclass of: Transcript
definition: A transcript that in its initial state requires modification to be functional.
definition_source: SO:0000185

Intron
type: Class
subclass of: Primary Transcript Region
definition: 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.
definition_source: SO:0000188

5' Intron
type: Class
subclass of: Intron

Interior Intron
type: Class
subclass of: Intron

3' Intron
type: Class
subclass of: Intron

Coding Exon
type: Class
subclass of: Exon
definition: An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
definition_source: SO:0000195

Five Prime Coding Exon Coding Region
type: Class
subclass of: Coding Region of Exon
subclass of: Restriction
  on property: part_of
  some values from: Five Prime Coding Exon
definition: The sequence of the five_prime_coding_exon that codes for protein.
definition_source: SO:0000196

Three Prime Coding Exon Coding Region
type: Class
subclass of: Coding Region of Exon
subclass of: Restriction
  on property: part_of
  some values from: Three Prime Coding Exon
definition: The sequence of the three_prime_coding_exon that codes for protein.
definition_source: SO:0000197

Noncoding Exon
type: Class
subclass of: Exon
definition: An exon that does not contain any codons.
definition_source: SO:0000198

Five Prime Coding Exon
type: Class
subclass of: Coding Exon
definition: The 5' most coding exon.
definition_source: SO:0000200

Interior Exon
type: Class
subclass of: Exon
definition: An exon that is bounded by 5' and 3' splice sites.
definition_source: SO:0000201

Three Prime Coding Exon
type: Class
subclass of: Coding Exon
definition: The coding exon that is most 3-prime on a given transcript.
definition_source: SO:0000202

UTR
type: Class
subclass of: mRNA Region
definition: Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
definition_source: SO:0000203

Five Prime UTR
type: Class
subclass of: UTR
definition: A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
definition_source: SO:0000204

Three Prime UTR
type: Class
subclass of: UTR
definition: A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
definition_source: SO:0000205

rRNA Primary Transcript
type: Class
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a ribosomal RNA.
definition_source: SO:0000209

tRNA Primary Transcript
type: Class
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a transfer RNA.
definition_source: SO:0000210

Alanine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding alanyl tRNA.
definition_source: SO:0000211

Arginine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding arginyl tRNA.
definition_source: SO:0000212

Asparagine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding asparaginyl tRNA.
definition_source: SO:0000213

Aspartic acid tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding aspartyl tRNA.
definition_source: SO:0000214

Cysteine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding cysteinyl tRNA.
definition_source: SO:0000215

Glutamic acid tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding glutaminyl tRNA.
definition_source: SO:0000216

Glutamine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding glutamyl tRNA.
definition_source: SO:0000217

Glycine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding glycyl tRNA.
definition_source: SO:0000218

Histidine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding histidyl tRNA.
definition_source: SO:0000219

Isoleucine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding isoleucyl tRNA.
definition_source: SO:0000220

Leucine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding leucyl tRNA.
definition_source: SO:0000221

Lysine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding lysyl tRNA.
definition_source: SO:0000222

Methionine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding methionyl tRNA.
definition_source: SO:0000223

Phenylalanine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding phenylalanyl tRNA.
definition_source: SO:0000224

Proline tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding prolyl tRNA.
definition_source: SO:0000225

Serine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding seryl tRNA.
definition_source: SO:0000226

Threonine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding threonyl tRNA.
definition_source: SO:0000227

Tryptophan tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding tryptophanyl tRNA.
definition_source: SO:0000228

Tyrosine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding tyrosyl tRNA.
definition_source: SO:0000229

Valine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding valyl tRNA.
definition_source: SO:0000230

snRNA Primary Transcript
type: Class
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a small nuclear RNA.
definition_source: SO:0000231

snoRNA Primary Transcript
type: Class
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a small nucleolar mRNA.
definition_source: SO:0000232

Mature Transcript
type: Class
subclass of: Transcript
subclass of: Restriction
  on property: derives_from
  some values from: Primary Transcript
definition: 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.
definition_source: SO:0000233

mRNA
type: Class
subclass of: Mature Transcript
definition: Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
definition_source: SO:0000234

Transcription Factor Binding Site
type: Class
subclass of: Nucleotide to Protein Binding Site
definition: A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex.
definition_source: SO:0000235

Internal UTR
type: Class
subclass of: UTR
definition: A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.
definition_source: SO:0000241

Untranslated Region Polycistronic mRNA
type: Class
subclass of: UTR
definition: The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
definition_source: SO:0000242

Internal Ribosome Entry Site
type: Class
subclass of: Ribosome Entry Site
definition: Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
definition_source: SO:0000243

rRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA Primary Transcript
definition: RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
definition_source: SO:0000252

tRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: tRNA Primary Transcript
definition: Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. 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.
definition_source: SO:0000253

Alanyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Alanine tRNA Primary Transcript
definition: A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
definition_source: SO:0000254

rRNA Small Subunit Primary Transcript
type: Class
subclass of: rRNA Primary Transcript
definition: A primary transcript encoding a small ribosomal subunit RNA.
definition_source: SO:0000255

Asparaginyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Asparagine tRNA Primary Transcript
definition: A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
definition_source: SO:0000256

Aspartyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Aspartic acid tRNA Primary Transcript
definition: A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
definition_source: SO:0000257

Cysteinyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Cysteine tRNA Primary Transcript
definition: A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
definition_source: SO:0000258

Glutaminyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Glutamic acid tRNA Primary Transcript
definition: A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.
definition_source: SO:0000259

Glutamyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Glutamine tRNA Primary Transcript
definition: A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
definition_source: SO:0000260

Glycyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Glycine tRNA Primary Transcript
definition: A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.
definition_source: SO:0000261

Histidyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Histidine tRNA Primary Transcript
definition: A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
definition_source: SO:0000262

Isoleucyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Isoleucine tRNA Primary Transcript
definition: A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.
definition_source: SO:0000263

Leucyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Leucine tRNA Primary Transcript
definition: A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
definition_source: SO:0000264

Lysyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Lysine tRNA Primary Transcript
definition: A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
definition_source: SO:0000265

Methionyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Methionine tRNA Primary Transcript
definition: A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
definition_source: SO:0000266

Phenylalanyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Phenylalanine tRNA Primary Transcript
definition: A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
definition_source: SO:0000267

Prolyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Proline tRNA Primary Transcript
definition: A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
definition_source: SO:0000268

Seryl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Serine tRNA Primary Transcript
definition: A tRNA sequence that has a serine anticodon, and a 3' serine binding region.
definition_source: SO:0000269

Threonyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Threonine tRNA Primary Transcript
definition: A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
definition_source: SO:0000270

Tryptophanyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Tryptophan tRNA Primary Transcript
definition: A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
definition_source: SO:0000271

Tyrosyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Tyrosine tRNA Primary Transcript
definition: A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.
definition_source: SO:0000272

Valyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Valine tRNA Primary Transcript
definition: A tRNA sequence that has a valine anticodon, and a 3' valine binding region.
definition_source: SO:0000273

snRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: snRNA Primary Transcript
definition: A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
definition_source: SO:0000274

snoRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: snoRNA Primary Transcript
definition: 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.
definition_source: SO:0000275

miRNA
type: Class
subclass of: Small Regulatory ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: pri-miRNA
definition: 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.
definition_source: SO:0000276

Transcript Bound by Nucleic Acid
type: Class
subclass of: Transcript
definition: A transcript that is bound by a nucleic acid.
definition_source: SO:0000278

Transcript Bound by Protein
type: Class
subclass of: Transcript
definition: A transcript that is bound by a protein.
definition_source: SO:0000279

mRNA with Minus 1 Frameshift
type: Class
subclass of: mRNA with Frameshift
definition: An mRNA with a minus 1 frameshift.
definition_source: SO:0000282

U12 Intron
type: Class
subclass of: Spliceosomal Intron
definition: A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
definition_source: SO:0000295

Clip
type: Class
subclass of: Primary Transcript Region
definition: Part of the primary transcript that is clipped off during processing.
definition_source: SO:0000303

TSS
type: Class
subclass of: Primary Transcript Region
definition: The first base where RNA polymerase begins to synthesize the RNA transcript.
definition_source: SO:0000315

CDS
type: Class
subclass of: mRNA Region
definition: A contiguous sequence which begins with, and includes, a start codon, and ends with, and includes, a stop codon.
definition_source: SO:0000316

Start Codon
type: Class
subclass of: Codon
definition: First codon to be translated by a ribosome.
definition_source: SO:0000318

Stop Codon
type: Class
subclass of: Codon
definition: In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
definition_source: SO:0000319

Intronic Splice Enhancer
type: Class
subclass of: Spliceosomal Intron Region
definition: Sequences within the intron that modulate splice site selection for some introns.
definition_source: SO:0000320

mRNA with Plus 1 Frameshift
type: Class
subclass of: mRNA with Frameshift
definition: An mRNA with a plus 1 frameshift.
definition_source: SO:0000321

Coding Start
type: Class
subclass of: CDS Region
definition: The first base to be translated into a protein.
definition_source: SO:0000323

rRNA Large Subunit Primary Transcript
type: Class
subclass of: rRNA Primary Transcript
definition: A primary transcript encoding a large ribosomal subunit RNA.
definition_source: SO:0000325

Coding End
type: Class
subclass of: CDS Region
definition: The last base to be translated into protein. It does not include the stop codon.
definition_source: SO:0000327

mRNA with Minus 2 Frameshift
type: Class
subclass of: mRNA with Frameshift
definition: A mRNA with a minus 2 frameshift.
definition_source: SO:0000335

Codon
type: Class
subclass of: CDS Region
definition: 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.
definition_source: SO:0000360

Small Regulatory ncRNA
type: Class
subclass of: ncRNA
definition: A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
definition_source: SO:0000370

Enzymatic RNA
type: Class
subclass of: Transcript
definition: An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
definition_source: SO:0000372

Ribozyme
type: Class
subclass of: Enzymatic RNA
definition: An RNA with catalytic activity.
definition_source: SO:0000374

rRNA 5_8S
type: Class
subclass of: Large Subunit rRNA
definition: 5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.
definition_source: SO:0000375

RNA 6S
type: Class
subclass of: Small Regulatory ncRNA
definition: A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.
definition_source: SO:0000376

CsrB RsmB RNA
type: Class
subclass of: Small Regulatory ncRNA
definition: An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.
definition_source: SO:0000377

DsrA RNA
type: Class
subclass of: Small Regulatory ncRNA
definition: DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.
definition_source: SO:0000378

GcvB RNA
type: Class
subclass of: DsrA RNA
definition: A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
definition_source: SO:0000379

Group IIA Intron
type: Class
subclass of: Group II Intron

Group IIB Intron
type: Class
subclass of: Group II Intron

MicF RNA
type: Class
subclass of: Antisense RNA
definition: A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.
definition_source: SO:0000383

OxyS RNA
type: Class
subclass of: Small Regulatory ncRNA
definition: A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.
definition_source: SO:0000384

RNase MRP RNA
type: Class
subclass of: ncRNA
definition: The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
definition_source: SO:0000385

RNase P RNA
type: Class
subclass of: ncRNA
definition: The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best 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.
definition_source: SO:0000386

RprA RNA
type: Class
subclass of: Small Regulatory ncRNA
definition: Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.
definition_source: SO:0000387

RRE RNA
type: Class
subclass of: Small Regulatory ncRNA
definition: The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.
definition_source: SO:0000388

Spot 42 RNA
type: Class
subclass of: Small Regulatory ncRNA
definition: A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.
definition_source: SO:0000389

Telomerase RNA
type: Class
subclass of: ncRNA
definition: The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
definition_source: SO:0000390

U1 snRNA
type: Class
subclass of: snRNA
definition: U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
definition_source: SO:0000391

U2 snRNA
type: Class
subclass of: snRNA
definition: U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
definition_source: SO:0000392

U4 snRNA
type: Class
subclass of: snRNA
definition: U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
definition_source: SO:0000393

U4atac snRNA
type: Class
subclass of: snRNA
definition: An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA.
definition_source: SO:0000394

U5 snRNA
type: Class
subclass of: snRNA
definition: U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
definition_source: SO:0000395

U6 snRNA
type: Class
subclass of: snRNA
definition: U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
definition_source: SO:0000396

U6atac snRNA
type: Class
subclass of: snRNA
definition: 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.
definition_source: SO:0000397

U11 snRNA
type: Class
subclass of: snRNA
definition: U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
definition_source: SO:0000398

U12 snRNA
type: Class
subclass of: snRNA
definition: The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
definition_source: SO:0000399

U14 snoRNA
type: Class
subclass of: C/D Box snoRNA
subclass of: Restriction
  on property: derives_from
  some values from: U14 snoRNA Primary Transcript
definition: U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
definition_source: SO:0000403

Vault RNA
type: Class
subclass of: ncRNA
definition: 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.
definition_source: SO:0000404

Y RNA
type: Class
subclass of: ncRNA
definition: Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
definition_source: SO:0000405

Twintron
type: Class
subclass of: Intron
definition: An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
definition_source: SO:0000406

rRNA 18S
type: Class
subclass of: Small Subunit rRNA
definition: A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.
definition_source: SO:0000407

Binding Site
type: Class
subclass of: Biological Region
definition: 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.
definition_source: SO:0000409

Protein Binding SIte
type: Class
subclass of: Binding Site
definition: A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
definition_source: SO:0000410

Three Prime Noncoding Exon
type: Class
subclass of: Noncoding Exon
definition: Non-coding exon in the 3' UTR.
definition_source: SO:0000444

Five Prime Noncoding Exon
type: Class
subclass of: Noncoding Exon
definition: Non-coding exon in the 5' UTR.
definition_source: SO:0000445

UTR Intron
type: Class
subclass of: Intron
definition: Intron located in the untranslated region.
definition_source: SO:0000446

5' UTR Intron
type: Class
subclass of: UTR Intron
definition: An intron located in the 5' UTR.
definition_source: SO:0000447

3' UTR Intron
type: Class
subclass of: UTR Intron
definition: An intron located in the 3' UTR.
definition_source: SO:0000448

rasiRNA
type: Class
subclass of: ncRNA
definition: A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
definition_source: SO:0000454

Trans-spliced Transcript
type: Class
subclass of: Transcript
definition: A transcript that is trans-spliced.
definition_source: SO:0000479

Noncoding Primary Transcript
type: Class
subclass of: Primary Transcript
definition: A primary transcript that is never translated into a protein.
definition_source: SO:0000483

Three Prime Coding Exon Noncoding Region
type: Class
subclass of: Noncoding Region of Exon
subclass of: Restriction
  on property: part_of
  some values from: Three Prime Noncoding Exon
definition: The sequence of the 3' exon that is not coding.
definition_source: SO:0000484

Five Prime Coding Exon Noncoding Region
type: Class
subclass of: Noncoding Region of Exon
subclass of: Restriction
  on property: part_of
  some values from: Five Prime Noncoding Exon
definition: The sequence of the 5' exon preceding the start codon.
definition_source: SO:0000486

Shine Dalgarno Sequence
type: Class
subclass of: Ribosome Entry Site
definition: A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
definition_source: SO:0000552

5' Clip
type: Class
subclass of: Clip
definition: 5' most region of a precursor transcript that is clipped off during processing.
definition_source: SO:0000555

3' Clip
type: Class
subclass of: Clip
definition: 3'-most region of a precursor transcript that is clipped off during processing.
definition_source: SO:0000557

Edited Transcript Feature
type: Class
subclass of: Transcript Region
definition: A locatable feature on a transcript that is edited.
definition_source: SO:0000579

Methylation Guide snoRNA Primary Transcript
type: Class
subclass of: snoRNA Primary Transcript
definition: A primary transcript encoding a methylation guide small nucleolar RNA.
definition_source: SO:0000580

rRNA cleavage snoRNA Primary Transcript
type: Class
subclass of: snoRNA Primary Transcript
definition: A primary transcript encoding an rRNA cleavage snoRNA.
definition_source: SO:0000582

Pre-edited Region
type: Class
subclass of: Edited Transcript Feature
definition: The region of a transcript that will be edited.
definition_source: SO:0000583

tmRNA
type: Class
subclass of: Small Regulatory ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: tmRNA Primary Transcript
definition: 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.
definition_source: SO:0000584

tmRNA Primary Transcript
type: Class
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a tmRNA.
definition_source: SO:0000584

Group I Intron
type: Class
subclass of: Autocatalutically Spliced Intron
definition: 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.
definition_source: SO:0000587

Autocatalutically Spliced Intron
type: Class
subclass of: Intron
definition: A self spliced intron.
definition_source: SO:0000588

SRP RNA Primary Transcript
type: Class
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a signal recognition particle RNA.
definition_source: SO:0000589

SRP RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: SRP RNA Primary Transcript
definition: The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
definition_source: SO:0000590

C/D Box snoRNA
type: Class
subclass of: snoRNA
subclass of: Restriction
  on property: derives_from
  some values from: C/D Box snoRNA Primary Transcript
definition: Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.
definition_source: SO:0000593

H/ACA Box snoRNA
type: Class
subclass of: snoRNA
subclass of: Restriction
  on property: derives_from
  some values from: H/ACA Box snoRNA Primary Transcript
definition: Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.
definition_source: SO:0000594

C/D Box snoRNA Primary Transcript
type: Class
subclass of: snoRNA Primary Transcript
definition: A primary transcript encoding a small nucleolar RNA of the box C/D family.
definition_source: SO:0000595

H/ACA Box snoRNA Primary Transcript
type: Class
subclass of: snoRNA Primary Transcript
definition: A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
definition_source: SO:0000596

Guide RNA
type: Class
subclass of: ncRNA
definition: 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.
definition_source: SO:0000602

Group II Intron
type: Class
subclass of: Autocatalutically Spliced Intron
definition: Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
definition_source: SO:0000603

Editing Block
type: Class
subclass of: Edited Transcript Feature
definition: Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
definition_source: SO:0000604

Editing Domain
type: Class
subclass of: Edited Transcript Feature
definition: Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
definition_source: SO:0000606

Unedited Region
type: Class
subclass of: Edited Transcript Feature
definition: The region of an edited transcript that will not be edited.
definition_source: SO:0000607

Branch Site
type: Class
subclass of: Spliceosomal Intron Region
definition: A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
definition_source: SO:0000611

Polypirimidine Tract
type: Class
subclass of: Spliceosomal Intron Region
definition: The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
definition_source: SO:0000612

Transcription End Site
type: Class
subclass of: Primary Transcript Region
definition: The base where transcription ends.
definition_source: SO:0000616

Five Prime Open Reading Frame
type: Class
subclass of: mRNA Region
subclass of: Restriction
  on property: part_of
  some values from: Five Prime UTR

Upstream AUG Codon
type: Class
subclass of: UTR Region
subclass of: Restriction
  on property: part_of
  some values from: UTR
definition: A start codon upstream of the ORF.
definition_source: SO:0000630

Polycistronic Primary Transcript
type: Class
subclass of: Primary Transcript
definition: A primary transcript encoding for more than one gene product.
definition_source: SO:0000631

Monocistronic Primary Transcript
type: Class
subclass of: Monocistronic Transcript
definition: A primary transcript encoding for one gene product.
definition_source: SO:0000632

Monocistronic mRNA
type: Class
subclass of: mRNA
definition: An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
definition_source: SO:0000633

Polycistronic mRNA
type: Class
subclass of: mRNA
definition: An mRNA that encodes multiple proteins from at least two non-overlapping regions.
definition_source: SO:0000634

Mini Exon Donor RNA
type: Class
subclass of: Primary Transcript
definition: A primary transcript that donates the spliced leader to other mRNA.
definition_source: SO:0000635

Spliced Leader RNA
type: Class
subclass of: Primary Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: Mini Exon Donor RNA

Transcribed Spacer Region
type: Class
subclass of: rRNA Primary Transcript Region
definition: Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
definition_source: SO:0000638

Internal Transcribed Spacer Region
type: Class
subclass of: Transcribed Spacer Region
definition: Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
definition_source: SO:0000639

External Transcribed Spacer Region
type: Class
subclass of: Transcribed Spacer Region
definition: Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
definition_source: SO:0000640

Antisense RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: Antisense Primary Transcript
definition: Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
definition_source: SO:0000644

Antisense Primary Transcript
type: Class
subclass of: Primary Transcript
definition: The reverse complement of the primary transcript.
definition_source: SO:0000645

siRNA
type: Class
subclass of: ncRNA
definition: 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.
definition_source: SO:0000646

pri-miRNA
type: Class
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a micro RNA.
definition_source: SO:0000647

stRNA Primary Transcript
type: Class
subclass of: pri-miRNA
definition: A primary transcript encoding a small temporal mRNA.
definition_source: SO:0000648

stRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: stRNA Primary Transcript
definition: Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. [SO:0000649]
definition_source: SO:0000649

Small Subunit rRNA
type: Class
subclass of: rRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA Small Subunit Primary Transcript
definition: Ribosomal RNA transcript that structures the small subunit of the ribosome.
definition_source: SO:0000650

Large Subunit rRNA
type: Class
subclass of: rRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA Large Subunit Primary Transcript
definition: Ribosomal RNA transcript that structures the large subunit of the ribosome.
definition_source: SO:0000651

rRNA 5S
type: Class
subclass of: Large Subunit rRNA
definition: 5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription.
definition_source: SO:0000652

rRNA 28S
type: Class
subclass of: Large Subunit rRNA
definition: A component of the large ribosomal subunit.
definition_source: SO:0000653

ncRNA
type: Class
subclass of: Mature Transcript
definition: 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.
definition_source: SO:0000655

Spliceosomal Intron
type: Class
subclass of: Intron
definition: An intron which is spliced by the spliceosome.
definition_source: SO:0000662

Monocistronic Transcript
type: Class
subclass of: Transcript
definition: A transcript that is monocistronic.
definition_source: SO:0000665

Mobile Intron
type: Class
subclass of: Intron
definition: An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.
definition_source: SO:0000666

Transcript
type: Class
subclass of: RNA
definition: An RNA synthesized on a DNA or RNA template by an RNA polymerase.
definition_source: SO:0000673

Canonical 3' Splice Site
type: Class
subclass of: 3' cis Splice Site
definition: The canonical 3' splice site has the sequence "AG".
definition_source: SO:0000676

Canonical 5' Splice Site
type: Class
subclass of: 5' cis Splice Site
definition: The canonical 5' splice site has the sequence "GT".
definition_source: SO:0000677

Non-canonical 3' Splice Site
type: Class
subclass of: 3' cis Splice Site
definition: A 3' splice site that does not have the sequence "AG".
definition_source: SO:0000678

Non-canonical 5' Splice SIte
type: Class
subclass of: 5' cis Splice Site
definition: A 5' splice site which does not have the sequence "GT".
definition_source: SO:0000679

Non-canonical Start Codon
type: Class
subclass of: Start Codon
definition: A start codon that is not the usual AUG sequence.
definition_source: SO:0000680

Aberrant Processed Transcript
type: Class
subclass of: Transcript
definition: A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.
definition_source: SO:0000681

SNP
type: Class
subclass of: SNV
definition: 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.
definition_source: SO:0000694

Gene
type: Class
subclass of: Biological Region
definition: 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.
definition_source: SO:0000704

Trans Splice Acceptor Site
type: Class
subclass of: Trans Splice Site
definition: The 3' splice site of the acceptor primary transcript.
definition_source: SO:0000706

Trans Splice Donor Site
type: Class
subclass of: Trans Splice Site
definition: The 5' five prime splice site region of the donor RNA.
definition_source: SO:0000707

SL1 Acceptor Site
type: Class
subclass of: Trans Splice Acceptor Site
definition: A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.
definition_source: SO:0000708

SL2 Acceptor Site
type: Class
subclass of: Trans Splice Acceptor Site
definition: 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.
definition_source: SO:0000709

Dicistronic mRNA
type: Class
subclass of: Polycistronic mRNA
definition: An mRNA that has the quality dicistronic.
definition_source: SO:0000716

Exemplar mRNA
type: Class
subclass of: mRNA
definition: An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.
definition_source: SO:0000734

Pyrrolysyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Pyrrolysine tRNA Primary Transcript
definition: A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
definition_source: SO:0000766

tmRNA Coding Piece
type: Class
subclass of: tmRNA Region
definition: The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
definition_source: SO:0000769

tmRNA Acceptor Piece
type: Class
subclass of: tmRNA Region
definition: The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
definition_source: SO:0000770

Transcript Region
type: Class
subclass of: Biological Region
subclass of: Restriction
  on property: part_of
  some values from: Transcript
definition: A region of a transcript.
definition_source: SO:0000833

Mature Transcript Region
type: Class
subclass of: Transcript Region
definition: A region of a mature transcript.
definition_source: SO:0000834

Primary Transcript Region
type: Class
subclass of: Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: Primary Transcript
definition: A part of a primary transcript.
definition_source: SO:0000835

mRNA Region
type: Class
subclass of: Mature Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: mRNA
definition: A region of an mRNA.
definition_source: SO:0000836

UTR Region
type: Class
subclass of: mRNA Region
definition: A region of UTR.
definition_source: SO:0000837

rRNA Primary Transcript Region
type: Class
subclass of: Primary Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: rRNA Primary Transcript
definition: A region of an rRNA primary transcript.
definition_source: SO:0000838

Spliceosomal Intron Region
type: Class
subclass of: Primary Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: Spliceosomal Intron
definition: A region within an intron.
definition_source: SO:0000841

tmRNA Region
type: Class
subclass of: Mature Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: tmRNA
definition: A region of a tmRNA.
definition_source: SO:0000847

CDS Region
type: Class
subclass of: mRNA Region
subclass of: Restriction
  on property: part_of
  some values from: CDS
definition: A region of a CDS.
definition_source: SO:0000851

Exon Region
type: Class
subclass of: Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: Exon
definition: A region of an exon.
definition_source: SO:0000852

Capped Primary Transcript
type: Class
subclass of: Primary Transcript
definition: A primary transcript that is capped.
definition_source: SO:0000861

Capped mRNA
type: Class
subclass of: mRNA
definition: An mRNA that is capped.
definition_source: SO:0000862

Polyadenylated mRNA
type: Class
subclass of: mRNA
definition: An mRNA that is polyadenylated.
definition_source: SO:0000871

Trans Spliced mRNA
type: Class
subclass of: mRNA
subclass of: Restriction
  on property: adjacent_to
  some values from: Spliced Leader RNA
definition: An mRNA that is trans-spliced.
definition_source: SO:0000872

Edited Transcript
type: Class
subclass of: Transcript
subclass of: Restriction
  on property: guided_by
  some values from: Guide RNA
subclass of: Restriction
  on property: has_part
  some values from: Anchor Binding Site
definition: A transcript that is edited.
definition_source: SO:0000873

Edited Transcript by A to I Substitution
type: Class
subclass of: Edited Transcript
definition: A transcript that has been edited by A to I substitution.
definition_source: SO:0000874

Stop Codon Read Through
type: Class
subclass of: Recoded Codon
definition: A stop codon redefined to be a new amino acid.
definition_source: SO:0000883

Stop Codon Redefined as Pyrrolysine
type: Class
subclass of: Stop Codon Read Through
definition: A stop codon redefined to be the new amino acid, pyrrolysine.
definition_source: SO:0000884

Stop Codon Redefined as Selenocysteine
type: Class
subclass of: Stop Codon Read Through
definition: A stop codon redefined to be the new amino acid, selenocysteine.
definition_source: SO:0000885

Edited mRNA
type: Class
subclass of: mRNA
definition: An mRNA that is edited.
definition_source: SO:0000929

Guide RNA Region
type: Class
subclass of: Mature Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: Guide RNA
definition: A region of guide RNA.
definition_source: SO:0000930

Anchor Region
type: Class
subclass of: Guide RNA Region
definition: A region of a guide_RNA that base-pairs to a target mRNA.
definition_source: SO:0000931

pre-edited mRNA
type: Class
subclass of: Protein Coding Primary Transcript

miRNA Target Site
type: Class
subclass of: Nucleotide Binding Site
definition: A miRNA target site is a binding site where the molecule is a micro RNA.
definition_source: SO:0000934

Edited CDS
type: Class
subclass of: CDS
definition: A CDS that is edited.
definition_source: SO:0000935

Anchor Binding Site
type: Class
subclass of: Transcript Region

Template Region
type: Class
subclass of: Guide RNA Region
definition: A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
definition_source: SO:0000978

Class II RNA
type: Class
subclass of: ncRNA
definition: 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.
definition_source: SO:0000989

Class I RNA
type: Class
subclass of: ncRNA
definition: 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.
definition_source: SO:0000990

Consensus mRNA
type: Class
subclass of: mRNA

Recursive Splice Site
type: Class
subclass of: cis Splice Site
definition: 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.
definition_source: SO:0000998

rRNA 16S
type: Class
subclass of: Small Subunit rRNA
definition: A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
definition_source: SO:0001000

rRNA 23S
type: Class
subclass of: Large Subunit rRNA
definition: A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.
definition_source: SO:0001001

rRNA 25S
type: Class
subclass of: Large Subunit rRNA
definition: A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.
definition_source: SO:0001002

Intron Domain
type: Class
subclass of: Primary Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: Intron

Internal Guide Sequence
type: Class
subclass of: Intron Domain
subclass of: Restriction
  on property: part_of
  some values from: Group I Intron
definition: 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.
definition_source: SO:0001016

Mirtron
type: Class
subclass of: Intron Domain
definition: A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
definition_source: SO:0001034

piRNA
type: Class
subclass of: ncRNA
definition: A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
definition_source: SO:0001035

Arginyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Arginine tRNA Primary Transcript
definition: A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
definition_source: SO:0001036

rRNA 21S
type: Class
subclass of: Large Subunit rRNA
definition: A component of the large ribosomal subunit in mitochondrial rRNA.
definition_source: SO:0001171

tRNA Region
type: Class
subclass of: Mature Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: tRNA
definition: A region of a tRNA.
definition_source: SO:0001172

Anticodon Loop
type: Class
subclass of: tRNA Region
definition: 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.
definition_source: SO:0001173

Anticodon
type: Class
subclass of: tRNA Region
subclass of: Restriction
  on property: part_of
  some values from: Anticodon Loop
definition: A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
definition_source: SO:0001174

CCA Tail
type: Class
subclass of: tRNA Region
definition: 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.
definition_source: SO:0001175

DHU Loop
type: Class
subclass of: tRNA Region
definition: Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
definition_source: SO:0001176

T Loop
type: Class
subclass of: tRNA Region
definition: Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
definition_source: SO:0001177

Pyrrolysine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding pyrrolysyl tRNA.
definition_source: SO:0001178

U3 snoRNA
type: Class
subclass of: C/D Box snoRNA
definition: 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.
definition_source: SO:0001179

AU Rich Element
type: Class
subclass of: UTR Region
subclass of: Restriction
  on property: part_of
  some values from: Three Prime UTR
definition: 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.
definition_source: SO:0001180

Bruno Response Element
type: Class
subclass of: UTR Region
subclass of: Restriction
  on property: part_of
  some values from: Three Prime UTR
definition: A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
definition_source: SO:0001181

Iron Responsive Element
type: Class
subclass of: UTR Region
subclass of: Restriction
  on property: part_of
  some values from: UTR
definition: 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.
definition_source: SO:0001182

Pseudouridylation Guide snoRNA
type: Class
subclass of: H/ACA Box snoRNA
definition: A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
definition_source: SO:0001187

Translational Frameshift
type: Class
subclass of: mRNA Region
definition: 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.
definition_source: SO:0001210

Plus 1 Translational Frameshift
type: Class
subclass of: Translational Frameshift
definition: 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.
definition_source: SO:0001211

Plus 2 Translational Frameshift
type: Class
subclass of: Translational Frameshift
definition: 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.
definition_source: SO:0001212

Group III Intron
type: Class
subclass of: Autocatalutically Spliced Intron
definition: 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.
definition_source: SO:0001213

Noncoding Region of Exon
type: Class
subclass of: Exon Region
definition: The maximal intersection of exon and UTR.
definition_source: SO:0001214

Coding Region of Exon
type: Class
subclass of: Exon Region
definition: The region of an exon that encodes for protein sequence.
definition_source: SO:0001215

Endonuclease Spliced Intron
type: Class
subclass of: Intron
definition: An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
definition_source: SO:0001216

Major TSS
type: Class
subclass of: TSS

Minor TSS
type: Class
subclass of: TSS

miRNA Primary Transcript Region
type: Class
subclass of: Primary Transcript Region
definition: A part of an miRNA primary_transcript.
definition_source: SO:0001243

pre-miRNA
type: Class
subclass of: miRNA Primary Transcript Region
subclass of: Restriction
  on property: has_region
  some values from: Unbroken Stem
subclass of: Restriction
  on property: has_region
  some values from: Internal Loop
subclass of: Restriction
  on property: part_of
  some values from: pri-miRNA
definition: The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
definition_source: SO:0001244

miRNA Stem
type: Class
subclass of: miRNA Primary Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: pre-miRNA
definition: The stem of the hairpin loop formed by folding of the pre-miRNA.
definition_source: SO:0001245

miRNA Loop
type: Class
subclass of: miRNA Primary Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: pre-miRNA
definition: The loop of the hairpin loop formed by folding of the pre-miRNA.
definition_source: SO:0001246

CDS Fragment
type: Class
subclass of: CDS

Biological Region
type: Class
subclass of: Region
definition: A region defined by its disposition to be involved in a biological process.
definition_source: SO:0001411

cis Splice Site
type: Class
subclass of: Splice Site
definition: Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
definition_source: SO:0001419

Trans Splice Site
type: Class
subclass of: Splice Site
definition: Primary transcript region bordering trans-splice junction.
definition_source: SO:0001420

DNA Binding SIte
type: Class
subclass of: Nucleotide Binding Site
definition: A binding site that, in the molecule, interacts selectively and non-covalently with DNA.
definition_source: SO:0001429

Linc RNA
type: Class
subclass of: Lnc RNA
definition: A multiexonic non-coding RNA transcribed by RNA polymerase II.
definition_source: SO:0001463

miRNA Antiguide
type: Class
subclass of: miRNA Primary Transcript Region
definition: A region of the pri miRNA that basepairs with the guide to form the hairpin.
definition_source: SO:0001473

Outron
type: Class
subclass of: Primary Transcript Region
definition: A region of a primary transcript, that is removed via trans splicing.
definition_source: SO:0001475

SNV
type: Class
subclass of: Biological Region
definition: SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
definition_source: SO:0001483

Processed Transcript
type: Class
subclass of: Transcript
definition: A transcript for which no open reading frame has been identified and for which no other function has been determined.
definition_source: SO:0001503

Cryptic Splice SIte
type: Class
subclass of: Splice Site
definition: A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.
definition_source: SO:0001533

Kozak Sequence
type: Class
subclass of: Ribosome Entry Site
definition: A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
definition_source: SO:0001647

Nucleotide to Protein Binding Site
type: Class
subclass of: Protein Binding SIte
definition: A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
definition_source: SO:0001654

Nucleotide Binding Site
type: Class
subclass of: Binding Site
definition: A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.
definition_source: SO:0001655

SL3 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: 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.
definition_source: SO:0001748

SL4 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: 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.
definition_source: SO:0001749

SL5 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: 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.
definition_source: SO:0001750

SL6 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: 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.
definition_source: SO:0001751

SL7 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: 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.
definition_source: SO:0001752

SL8 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: 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.
definition_source: SO:0001753

SL9 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: 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.
definition_source: SO:0001754

SL10 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: 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.
definition_source: SO:0001755

SL11 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: 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.
definition_source: SO:0001756

SL12 Acceptor Site
type: Class
subclass of: SL2 Acceptor Site
definition: 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.
definition_source: SO:0001757

tasiRNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: tasiRNA Primary Transcript
definition: The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene.
definition_source: SO:0001800

tasiRNA Primary Transcript
type: Class
subclass of: Noncoding Primary Transcript
definition: A primary transcript encoding a tasiRNA.
definition_source: SO:0001801

Transposable Element CDS
type: Class
subclass of: CDS
definition: A CDS that is part of a transposable element.
definition_source: SO:0001869

Enhancer RNA
type: Class
subclass of: ncRNA
definition: A short ncRNA that is transcribed from an enhancer. May have a regulatory function.
definition_source: SO:0001870

Lnc RNA
type: Class
subclass of: ncRNA
definition: A non-coding RNA over 200nucleotides in length.
definition_source: SO:0001877

Splice Region
type: Class
subclass of: Primary Transcript Region
subclass of: Restriction
  on property: part_of
  some values from: Primary Transcript
definition: A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
definition_source: SO:0001902

Intronic lncRNA
type: Class
subclass of: Lnc RNA
definition: A lnc_RNA totally contained within an intron.
definition_source: SO:0001903

Antisense lncRNA
type: Class
subclass of: Lnc RNA
definition: Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA.
definition_source: SO:0001904

U14 snoRNA Primary Transcript
type: Class
subclass of: snoRNA Primary Transcript
definition: The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
definition_source: SO:0005837

Methylation Guide snoRNA
type: Class
subclass of: C/D Box snoRNA
subclass of: Restriction
  on property: derives_from
  some values from: Methylation Guide snoRNA Primary Transcript
definition: 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.
definition_source: SO:0005841

rRNA Cleavage RNA
type: Class
subclass of: ncRNA
subclass of: Restriction
  on property: derives_from
  some values from: rRNA cleavage snoRNA Primary Transcript
definition: An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.
definition_source: SO:0005843

Exon of Single Exon Gene
type: Class
subclass of: Exon
definition: An exon that is the only exon in a gene.
definition_source: SO:0005845

Selenocysteine tRNA Primary Transcript
type: Class
subclass of: tRNA Primary Transcript
definition: A primary transcript encoding seryl tRNA.
definition_source: SO:0005856

Selenocysteinyl tRNA
type: Class
subclass of: tRNA
subclass of: Restriction
  on property: derives_from
  some values from: Selenocysteine tRNA Primary Transcript
definition: A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.
definition_source: SO:0005857

Alternatively Spliced Transcript
type: Class
subclass of: Transcript
definition: A transcript that is alternatively spliced.
definition_source: SO:1001187

Dicistronic Primary Transcript
type: Class
subclass of: Polycistronic Primary Transcript
definition: A primary transcript that has the quality dicistronic.
definition_source: SO:1001197

3' Recoding Site
type: Class
subclass of: Recoding Stimulatory Region
definition: The recoding stimulatory signal located downstream of the recoding site.
definition_source: SO:1001277

CDS Independently Known
type: Class
subclass of: CDS
definition: A CDS with the evidence status of being independently known.
definition_source: SO:1001246

Orphan CDS
type: Class
subclass of: CDS Predicted
definition: A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.
definition_source: SO:1001247

CDS Supported by Domain Match Data
type: Class
subclass of: CDS Supported by Sequence SImilarity Data
definition: A CDS that is supported by domain similarity.
definition_source: SO:1001249

CDS Supported by Sequence SImilarity Data
type: Class
subclass of: CDS Predicted
definition: A CDS that is supported by sequence similarity data.
definition_source: SO:1001251

CDS Predicted
type: Class
subclass of: CDS
definition: A CDS that is predicted.
definition_source: SO:1001254

CDS Supported by EST or cDNA Data
type: Class
subclass of: CDS Supported by Sequence SImilarity Data
definition: A CDS that is supported by similarity to EST or cDNA data.
definition_source: SO:1001259

Internal Shine Dalgarno Sequence
type: Class
subclass of: Internal Ribosome Entry Site
subclass of: Recoding Stimulatory Region
definition: 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.
definition_source: SO:1001260

Recoded mRNA
type: Class
subclass of: mRNA
definition: The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.
definition_source: SO:1001261

mRNA Recoded by Translation Bypass
type: Class
subclass of: Recoded mRNA
definition: A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.
definition_source: SO:1001264

mRNA Recoded by Codon Redefinition
type: Class
subclass of: Recoded mRNA
definition: A recoded_mRNA that was modified by an alteration of codon meaning.
definition_source: SO:1001265

Recoding Stimulatory Region
type: Class
subclass of: mRNA Region
definition: A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA.
definition_source: SO:1001268

4bp Start Codon
type: Class
subclass of: Non-canonical Start Codon
definition: A non-canonical start codon with 4 base pairs.
definition_source: SO:1001269

Archaeal Intron
type: Class
subclass of: Endonuclease Spliced Intron
definition: 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.
definition_source: SO:1001271

tRNA Intron
type: Class
subclass of: Endonuclease Spliced Intron
definition: An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.
definition_source: SO:1001272

CTG Start Codon
type: Class
subclass of: Non-canonical Start Codon
definition: A non-canonical start codon of sequence CTG.
definition_source: SO:1001273

SECIS Element
type: Class
subclass of: Recoding Stimulatory Region
definition: The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes.
definition_source: SO:1001274

3' Stem-loop Structure
type: Class
subclass of: 3' Recoding Site
definition: A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region.
definition_source: SO:1001279

5' Recoding Site
type: Class
subclass of: Recoding Stimulatory Region
definition: The recoding stimulatory signal located upstream of the recoding site.
definition_source: SO:1001280

Flanking 3' Quadraplet Recoding Signal
type: Class
subclass of: 3' Recoding Site
definition: Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons.
definition_source: SO:1001281

UAG Stop Codon Signal
type: Class
subclass of: Stop Codon Signal
definition: A stop codon signal for a UAG stop codon redefinition.
definition_source: SO:1001282

UAA Stop Codon Signal
type: Class
subclass of: Stop Codon Signal
definition: A stop codon signal for a UAA stop codon redefinition.
definition_source: SO:1001283

UGA Stop Codon Signal
type: Class
subclass of: Stop Codon Signal
definition: A stop codon signal for a UGA stop codon redefinition.
definition_source: SO:1001285

3' Repeat Recoding Signal
type: Class
subclass of: 3' Recoding Site
definition: A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.
definition_source: SO:1001286

Distant 3' Recoding SIgnal
type: Class
subclass of: 3' Recoding Site
definition: A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon.
definition_source: SO:1001287

Stop Codon Signal
type: Class
subclass of: Recoding Stimulatory Region
definition: A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding.
definition_source: SO:1001288

mRNA with Plus 2 Frameshift
type: Class
subclass of: mRNA with Frameshift
definition: An mRNA with a plus 2 frameshift.
definition_source: SO:0000329

Molecular Function
type: Class
subclass of: Function
definition: 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.
definition_source: GO:0003674

Nucleic Acid Binding
type: Class
subclass of: Binding
definition: Interacting selectively and non-covalently with any nucleic acid.
definition_source: GO:0003676

DNA Binding
type: Class
subclass of: Nucleic Acid Binding
definition: Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
definition_source: GO:0003677

RNA Binding
type: Class
subclass of: Nucleic Acid Binding
definition: Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
definition_source: GO:0003723

Binding
type: Class
subclass of: Molecular Function
definition: The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GO:0005488]
definition_source: GO:0005488

miRNA Binding
type: Class
subclass of: RNA Binding
subclass of: Restriction
  on property: has_participant
  some values from: mRNA
subclass of: Restriction
  on property: has_agent
  some values from: miRNA
definition: 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.
definition_source: GO:0035198

pri-miRNA Binding
type: Class
subclass of: RNA Binding
subclass of: Restriction
  on property: has_agent
  some values from: pri-miRNA
definition: 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.
definition_source: GO:0070878

pre-miRNA Binding
type: Class
subclass of: RNA Binding
subclass of: Restriction
  on property: has_agent
  some values from: pre-miRNA
definition: Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA.
definition_source: GO:0070883

Information Biopolymer
type: Class
subclass of: Molecular Entity
definition: Naturally occurring macromolecules that harbor biological information in their structures, e.g. proteins, nucleic acids.
definition_source: GRO:InformationBiopolymer

Molecular Entity
type: Class
subclass of: Object
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
definition_source: http://en.wikipedia.org/wiki/Molecular_entity

Continuant
type: Class
definition: 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.
definition_source: snap:Continuant

Dependent Continuant
type: Class
subclass of: Continuant
definition: 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.
definition_source: snap:DependentContinuant

Disposition
type: Class
subclass of: Realizable Entity
definition: 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.
definition_source: snap:Disposition

Fiat Object Part
type: Class
subclass of: Material Entity
definition: A material entity that is part of an object but is not demarcated by any physical discontinuities.
definition_source: snap:FiatObjectPart

Function
type: Class
subclass of: Realizable Entity
definition: 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.
definition_source: snap:Function

Generically Dependent Continuant
type: Class
subclass of: Dependent Continuant
definition: 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.
definition_source: snap:GenericallyDependentContinuant

Independent Continuant
type: Class
subclass of: Continuant
definition: 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.
definition_source: snap:IndependentContinuant

Material Entity
type: Class
subclass of: Independent Continuant
definition: 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.
definition_source: BFO:MaterialEntity

Quality
type: Class
subclass of: Specifically Dependent Continuant
definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
definition_source: snap:Quality

Realizable Entity
type: Class
subclass of: Specifically Dependent Continuant
definition: 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.
definition_source: snap:RealizableEntity

Role
type: Class
subclass of: Realizable Entity
definition: 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.
definition_source: snap:Role

Specifically Dependent Continuant
type: Class
subclass of: Dependent Continuant
definition: 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.
definition_source: snap:SpecificallyDependentContinuant

Occurent
type: Class
definition: An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
definition_source: span:Occurrent

Process
type: Class
subclass of: Occurent
definition: A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
definition_source: span:Process

Identification of novel genes coding for small expressed RNAs
type: NamedIndividual
type: Restriction
  on property: has ID
  some values from: PubMed id
has ID: PMID:11679670
comment: Lagos-Quintana, M., Rauhut, R., Lendeckel, W., & Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. Science, 294(5543), 853-858.

MIRLET7A1 location
type: NamedIndividual
type: chromosome part
comment: 9q22.3

NC 000009.12
type: NamedIndividual
type: DNA
type: Primary Structure of DNA Macromolecule
definition: 1 tgggatgagg tagtaggttg tatagtttta gggtcacacc caccactggg agataactat 61 acaatctact gtctttccta

hsa-let-7a-1 NCBI GENE ID
type: NamedIndividual
type: gene id in NCBI gene
has ID: hsa-let-7a-1
definition: 406881

hsa-let-7a-1 location
type: NamedIndividual
type: chromosome part
part_of: Homo sapiens
part_of: Kidney
definition: chr9:94175957-94176036 (+)

hsa-let-7a-1 sequence
type: NamedIndividual
type: Primary Structure of RNA Molecule
sequence of: hsa-let-7a-1
definition: u gu uuagggucacaccca a uggga gag aguagguuguauaguu cc c ||||| ||| |||||||||||||||| || auccu uuc ucaucuaacauaucaa gg u - ug -----------uaga g

hsa-let-7a-5p mirBase ID
type: NamedIndividual
type: miRNA ID in miRBase
definition: MIMAT0000062

hsa-let-7a-5p sequence
type: NamedIndividual
type: Primary Structure of RNA Molecule
sequence of: hsa-let-7a-5p
definition: 5' - ugagguaguagguuguauaguu - 3'