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Ensembl stable IDs

Ensembl annotation uses a system of stable IDs that have prefixes based on the species scientific name plus the feature type, followed by a series of digits and a version e.g. ENSG00000139618.1. The version may be omitted.

Feature Stable ID prefixes

E exon
FM Ensembl protein family
G gene
GT gene tree
P protein
R regulatory feature
T transcript

Ensembl Gene Stable IDs

All genes, transcripts, translations (proteins) and exons (referred to here as 'entities') are assigned stable identifiers. When annotating a species for the first time, these identifiers are auto-generated. For subsequent new gene annotations for a species, the entity identifiers are mapped between re-annotation processes using a combination of location based mappings and those generated by Exonerate so that equivalent genes for a species can be linked between releases. The process performs exon based mapping and deriving subsequent identifier mappings based upon these findings. Further details about our methods is available from Ruffier M. et al. 2016.

Ensembl Stable ID Versioning

When reassigning stable identifiers between reannotation we can optionally choose to increment the version number assigned with a stable identifier. We do so to indicate an underlying change in the entity. The rules for incrementing the version depends on the entity in question and detailed below:

  • Genes: increments when the set of transcripts linked to a gene changes
  • Transcripts: increments when there is a change in a transcript's splicing pattern, chromsome location or a sequence change in the cDNA
  • Proteins: increments when there is a sequence change in the peptide sequence
  • Exons: increments when there is a sequence change in the exon genomic sequence

Stable identifier versions do not increment when there are changes to the annotation linked to an entity.

Species prefixes

PrefixSpecies name
ENSECAEquus caballus (Horse)
ENSCLAChinchilla lanigera (Long-tailed chinchilla)
ENSODEOctodon degus (Degu)
ENSOCUOryctolagus cuniculus (Rabbit)
MGP_LPJ_Mus musculus (Mouse LP/J)
ENSSHASarcophilus harrisii (Tasmanian devil)
ENSDNODasypus novemcinctus (Armadillo)
ENSMEUNotamacropus eugenii (Wallaby)
ENSMMUMacaca mulatta (Macaque)
ENSCSAChlorocebus sabaeus (Vervet-AGM)
ENSCGRCricetulus griseus (Chinese hamster CHOK1GS)
ENSETEEchinops telfairi (Lesser hedgehog tenrec)
ENSSTOIctidomys tridecemlineatus (Squirrel)
ENSSARSorex araneus (Shrew)
ENSLAFLoxodonta africana (Elephant)
ENSMOCMicrotus ochrogaster (Prairie vole)
ENSCAPCavia aperea (Brazilian guinea pig)
ENSTTRTursiops truncatus (Dolphin)
ENSSCESaccharomyces cerevisiae (Saccharomyces cerevisiae)
ENSDARDanio rerio (Zebrafish)
ENSMAUMesocricetus auratus (Golden Hamster)
ENSFCAFelis catus (Cat)
MGP_DBA2J_Mus musculus (Mouse DBA/2J)
ENSRNORattus norvegicus (Rat)
ENSMLUMyotis lucifugus (Microbat)
ENSJJAJaculus jaculus (Lesser Egyptian jerboa)
ENSPCAProcavia capensis (Hyrax)
ENSMUSMus musculus (Mouse)
FBDrosophila melanogaster (Fruitfly)
MGP_AKRJ_Mus musculus (Mouse AKR/J)
ENSVPAVicugna pacos (Alpaca)
ENSAMXAstyanax mexicanus (Cave fish)
ENSGGOGorilla gorilla gorilla (Gorilla)
ENSOPROchotona princeps (Pika)
ENSPANPapio anubis (Olive baboon)
MGP_NODShiLtJ_Mus musculus (Mouse NOD/ShiLtJ)
ENSONIOreochromis niloticus (Tilapia)
ENSBTABos taurus (Cow)
ENSMPUMustela putorius furo (Ferret)
MGP_PWKPhJ_Mus musculus musculus (Mouse PWK/PhJ)
ENSHGLFHeterocephalus glaber (Naked mole-rat female)
ENSCINCiona intestinalis
ENSCPOCavia porcellus (Guinea Pig)
ENSPEMPeromyscus maniculatus bairdii (Northern American deer mouse)
ENSCJACallithrix jacchus (Marmoset)
ENSHGLMHeterocephalus glaber (Naked mole-rat male)
ENSCELCaenorhabditis elegans (Caenorhabditis elegans)
ENSMODMonodelphis domestica (Opossum)
ENSOAROvis aries (Sheep)
ENSTNITetraodon nigroviridis (Tetraodon)
ENSPTRPan troglodytes (Chimpanzee)
ENSPPYPongo abelii (Orangutan)
ENSCGRCricetulus griseus (Chinese hamster CriGri)
ENSHomo sapiens (Human)
ENSOANOrnithorhynchus anatinus (Platypus)
MGP_AJ_Mus musculus (Mouse A/J)
ENSFALFicedula albicollis (Flycatcher)
ENSAMEAiluropoda melanoleuca (Panda)
MGP_NZOHlLtJ_Mus musculus (Mouse NZO/HlLtJ)
ENSGALGallus gallus (Chicken)
ENSGACGasterosteus aculeatus (Stickleback)
MGP_C3HHeJ_Mus musculus (Mouse C3H/HeJ)
ENSTSYCarlito syrichta (Tarsier)
ENSLOCLepisosteus oculatus (Spotted gar)
ENSTGUTaeniopygia guttata (Zebra Finch)
ENSPMAPetromyzon marinus (Lamprey)
ENSTBETupaia belangeri (Tree Shrew)
ENSLACLatimeria chalumnae (Coelacanth)
MGP_CAROLIEiJ_Mus caroli (Ryukyu mouse)
MGP_C57BL6NJ_Mus musculus (Mouse C57BL/6NJ)
MGP_CBAJ_Mus musculus (Mouse CBA/J)
ENSNGANannospalax galili (Upper Galilee mountains blind mole rat)
MGP_CASTEiJ_Mus musculus castaneus (Mouse CAST/EiJ)
ENSMGAMeleagris gallopavo (Turkey)
ENSCSAVCiona savignyi
ENSDORDipodomys ordii (Kangaroo rat)
ENSACAAnolis carolinensis (Anole lizard)
ENSAPLAnas platyrhynchos (Duck)
ENSNLENomascus leucogenys (Gibbon)
ENSCAFCanis lupus familiaris (Dog)
ENSXMAXiphophorus maculatus (Platyfish)
ENSEEUErinaceus europaeus (Hedgehog)
MGP_129S1SvImJ_Mus musculus (Mouse 129S1/SvImJ)
ENSGMOGadus morhua (Cod)
ENSXETXenopus tropicalis (Xenopus)
ENSTRUTakifugu rubripes (Fugu)
MGP_FVBNJ_Mus musculus (Mouse FVB/NJ)
MGP_PahariEiJ_Mus pahari (Shrew mouse)
ENSPVAPteropus vampyrus (Megabat)
ENSPFOPoecilia formosa (Amazon molly)
ENSPSIPelodiscus sinensis (Chinese softshell turtle)
MGP_WSBEiJ_Mus musculus domesticus (Mouse WSB/EiJ)
ENSCHOCholoepus hoffmanni (Sloth)
ENSMICMicrocebus murinus (Mouse Lemur)
ENSORLOryzias latipes (Medaka)
MGP_SPRETEiJ_Mus spretus (Algerian mouse)
ENSSSCSus scrofa (Pig)
MGP_BALBcJ_Mus musculus (Mouse BALB/cJ)
ENSFDAFukomys damarensis (Damara mole rat)
ENSOGAOtolemur garnettii (Bushbaby)