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