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