FTP Download

You can download via a browser from our FTP site, use a script, or even use rsync from the command line.

Globus

For rapid bulk download of files, the Ensembl FTP site is available as an end point in the Globus Online system. In order to access the data you need to sign up for an account with Globus, install the Globus Connect Personal software and setup a personal endpoint to download the data. The Ensembl data is hosted at the EMBL-EBI end point called “Shared EMBL-EBI public endpoint”. Data from the Ensembl FTP site can then be found under the "/gridftp/ensemblorg/pub" directory within the EMBL-EBI public end point.

Custom data sets

If you want to filter or customise your download, please try Biomart, a web-based querying tool.

API Code

If you do not have access to git, you can obtain our latest API code as a gzipped tarball:

Download complete API for this release

Note: the API version needs to be the same as the databases you are accessing, so please use git to obtain a previous version if querying older databases.

Database dumps

Entire databases can be downloaded from our FTP site in a variety of formats. Please be aware that some of these files can run to many gigabytes of data.

Looking for MySQL dumps to install databases locally? See our web installation instructions for full details.

Each directory on https://ftp.ensembl.org contains a README file, explaining the directory structure.

Multi-species data

Database
Comparative genomicsMySQLEMFMAFBEDXMLAncestral Alleles
BioMartMySQL-----
Stable idsMySQL-----

Single species data

Popular species are listed first. You can customise this list via our home page.

SpeciesDNA (FASTA)cDNA (FASTA)CDS (FASTA)ncRNA (FASTA)Protein sequence (FASTA)Annotated sequence (EMBL)Annotated sequence (GenBank)Gene setsOther annotationsWhole databasesVariation (GVF)Variation (VCF)Variation (VEP)Regulation (GFF)Data filesBAM/BigWig
YHuman
Homo sapiens
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEPRegulation (GFF)Regulation data filesBAM/BigWig
YMouse
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEPRegulation (GFF)Regulation data filesBAM/BigWig
YZebrafish
Danio rerio
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Abingdon island giant tortoise
Chelonoidis abingdonii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
African ostrich
Struthio camelus australis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Agassiz's desert tortoise
Gopherus agassizii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Algerian mouse
Mus spretus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Alpaca
Vicugna pacos
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Alpine marmot
Marmota marmota marmota
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Amazon molly
Poecilia formosa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
American beaver
Castor canadensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
American bison
Bison bison bison
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
American black bear
Ursus americanus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
American mink
Neovison vison
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Angola colobus
Colobus angolensis palliatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Arabian camel
Camelus dromedarius
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Arctic ground squirrel
Urocitellus parryii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Argentine black and white tegu
Salvator merianae
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Armadillo
Dasypus novemcinctus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Asian bonytongue
Scleropages formosus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Asiatic black bear
Ursus thibetanus thibetanus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Atlantic cod
Gadus morhua
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Atlantic herring
Clupea harengus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Atlantic salmon
Salmo salar
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Australian saltwater crocodile
Crocodylus porosus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Ballan wrasse
Labrus bergylta
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Barramundi perch
Lates calcarifer
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Beluga whale
Delphinapterus leucas
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Bengalese finch
Lonchura striata domestica
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Bicolor damselfish
Stegastes partitus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Black snub-nosed monkey
Rhinopithecus bieti
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Blind barbel
Sinocyclocheilus anshuiensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Blue tilapia
Oreochromis aureus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Blue tit
Cyanistes caeruleus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Blue whale
Balaenoptera musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Blue-crowned manakin
Lepidothrix coronata
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Blue-ringed sea krait
Laticauda laticaudata
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Blunt-snouted clingfish
Gouania willdenowi
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Bolivian squirrel monkey
Saimiri boliviensis boliviensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Bonobo
Pan paniscus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Brazilian guinea pig
Cavia aperea
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Brown trout
Salmo trutta
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Budgerigar
Melopsittacus undulatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Burrowing owl
Athene cunicularia
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Burton's mouthbrooder
Haplochromis burtoni
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Bushbaby
Otolemur garnettii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
C.intestinalis
Ciona intestinalis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
C.savignyi
Ciona savignyi
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Caenorhabditis elegans (Nematode, N2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
California sea lion
Zalophus californianus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Canada lynx
Lynx canadensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Cat
Felis catus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Central bearded dragon
Pogona vitticeps
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Chacoan peccary
Catagonus wagneri
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Channel bull blenny
Cottoperca gobio
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Channel catfish
Ictalurus punctatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Chicken
Gallus gallus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Chicken (Red Jungle fowl)
Gallus gallus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Chicken (paternal White leghorn layer)
Gallus gallus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Chilean tinamou
Nothoprocta perdicaria
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Chimpanzee
Pan troglodytes
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Chinese hamster CHOK1GS
Cricetulus griseus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Chinese hamster CriGri
Cricetulus griseus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Chinese hamster PICR
Cricetulus griseus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Chinese medaka
Oryzias sinensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Chinese softshell turtle
Pelodiscus sinensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Chinook salmon
Oncorhynchus tshawytscha
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Climbing perch
Anabas testudineus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Clown anemonefish
Amphiprion ocellaris
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Coelacanth
Latimeria chalumnae
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Coho salmon
Oncorhynchus kisutch
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Collared flycatcher
Ficedula albicollis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Common canary
Serinus canaria
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Common carp
Cyprinus carpio carpio
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Common carp german mirror
Cyprinus carpio
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Common carp hebao red
Cyprinus carpio
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Common carp huanghe
Cyprinus carpio
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Common kestrel
Falco tinnunculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Common snapping turtle
Chelydra serpentina
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Common wall lizard
Podarcis muralis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Common wombat
Vombatus ursinus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Coquerel's sifaka
Propithecus coquereli
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Cow
Bos taurus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Crab-eating macaque
Macaca fascicularis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Damara mole rat
Fukomys damarensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Dark-eyed junco
Junco hyemalis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Daurian ground squirrel
Spermophilus dauricus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Degu
Octodon degus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Denticle herring
Denticeps clupeoides
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Dingo
Canis lupus dingo
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Dog
Canis lupus familiaris
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Dog - Basenji
Canis lupus familiaris
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Dog - Boxer
Canis lupus familiaris
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Dog - German Shepherd
Canis lupus familiaris
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Dog - Great Dane
Canis lupus familiaris
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Dolphin
Tursiops truncatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Domestic yak
Bos grunniens
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Donkey
Equus asinus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Drill
Mandrillus leucophaeus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Drosophila melanogaster (Fruit fly)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Duck
Anas platyrhynchos platyrhynchos
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Eastern brown snake
Pseudonaja textilis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Eastern buzzard
Buteo japonicus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Eastern happy
Astatotilapia calliptera
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Eastern spot-billed duck
Anas zonorhyncha
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Electric eel
Electrophorus electricus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Elephant
Loxodonta africana
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Elephant shark
Callorhinchus milii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Emu
Dromaius novaehollandiae
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Eurasian eagle-owl
Bubo bubo
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Eurasian red squirrel
Sciurus vulgaris
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Eurasian sparrowhawk
Accipiter nisus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
European seabass
Dicentrarchus labrax
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Ferret
Mustela putorius furo
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Fugu
Takifugu rubripes
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Gelada
Theropithecus gelada
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Giant panda
Ailuropoda melanoleuca
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Gibbon
Nomascus leucogenys
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Gilthead seabream
Sparus aurata
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Goat
Capra hircus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Goat (black bengal)
Capra hircus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Golden Hamster
Mesocricetus auratus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Golden eagle
Aquila chrysaetos chrysaetos
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Golden pheasant
Chrysolophus pictus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Golden snub-nosed monkey
Rhinopithecus roxellana
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Golden-collared manakin
Manacus vitellinus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Golden-line barbel
Sinocyclocheilus grahami
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Goldfish
Carassius auratus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Goodes thornscrub tortoise
Gopherus evgoodei
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Gorilla
Gorilla gorilla gorilla
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Gouldian finch
Erythrura gouldiae
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Great Tit
Parus major
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Great spotted kiwi
Apteryx haastii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Greater amberjack
Seriola dumerili
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Greater bamboo lemur
Prolemur simus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Greater horseshoe bat
Rhinolophus ferrumequinum
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Green anole
Anolis carolinensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Guinea Pig
Cavia porcellus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Guppy
Poecilia reticulata
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Hagfish
Eptatretus burgeri
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Hedgehog
Erinaceus europaeus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Helmeted guineafowl
Numida meleagris
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Horned golden-line barbel
Sinocyclocheilus rhinocerous
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Horse
Equus caballus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Huchen
Hucho hucho
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Hybrid - Bos Indicus
Bos indicus x Bos taurus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Hybrid - Bos Taurus
Bos indicus x Bos taurus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Hyrax
Procavia capensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Indian cobra
Naja naja
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Indian glassy fish
Parambassis ranga
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Indian medaka
Oryzias melastigma
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Indian peafowl
Pavo cristatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Japanese medaka HNI
Oryzias latipes
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Japanese medaka HSOK
Oryzias latipes
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Japanese medaka HdrR
Oryzias latipes
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Japanese quail
Coturnix japonica
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Javanese ricefish
Oryzias javanicus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Jewelled blenny
Salarias fasciatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Kakapo
Strigops habroptila
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Kangaroo rat
Dipodomys ordii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Koala
Phascolarctos cinereus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Komodo dragon
Varanus komodoensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Lamprey
Petromyzon marinus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Large yellow croaker
Larimichthys crocea
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Leishan spiny toad
Leptobrachium leishanense
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Leopard
Panthera pardus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Lesser Egyptian jerboa
Jaculus jaculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Lesser hedgehog tenrec
Echinops telfairi
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Lion
Panthera leo
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Little spotted kiwi
Apteryx owenii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Live sharksucker
Echeneis naucrates
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Long-tailed chinchilla
Chinchilla lanigera
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Lumpfish
Cyclopterus lumpus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Lyretail cichlid
Neolamprologus brichardi
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Ma's night monkey
Aotus nancymaae
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Macaque
Macaca mulatta
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Mainland tiger snake
Notechis scutatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Makobe Island cichlid
Pundamilia nyererei
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Mallard
Anas platyrhynchos
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Mangrove rivulus
Kryptolebias marmoratus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Medium ground-finch
Geospiza fortis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Meerkat
Suricata suricatta
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Megabat
Pteropus vampyrus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mexican tetra
Astyanax mexicanus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Microbat
Myotis lucifugus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Midas cichlid
Amphilophus citrinellus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mongolian gerbil
Meriones unguiculatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Monterrey platyfish
Xiphophorus couchianus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse 129S1/SvImJ
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse A/J
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse AKR/J
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse BALB/cJ
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse C3H/HeJ
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse C57BL/6NJ
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse CAST/EiJ
Mus musculus castaneus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse CBA/J
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse DBA/2J
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse FVB/NJ
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse LP/J
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse Lemur
Microcebus murinus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Mouse NOD/ShiLtJ
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse NZO/HlLtJ
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse PWK/PhJ
Mus musculus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mouse WSB/EiJ
Mus musculus domesticus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Mummichog
Fundulus heteroclitus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Muscovy Duck (domestic type)
Cairina moschata domestica
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Naked mole-rat female
Heterocephalus glaber
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Naked mole-rat male
Heterocephalus glaber
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Narwhal
Monodon monoceros
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
New Caledonian crow
Corvus moneduloides
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Nile tilapia
Oreochromis niloticus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Northern American deer mouse
Peromyscus maniculatus bairdii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Northern pike
Esox lucius
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Northern spotted owl
Strix occidentalis caurina
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Ocean sunfish
Mola mola
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Okarito brown kiwi
Apteryx rowi
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Olive baboon
Papio anubis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Opossum
Monodelphis domestica
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Orange clownfish
Amphiprion percula
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Orbiculate cardinalfish
Sphaeramia orbicularis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Oriental scops-owl
Otus sunia
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pachon cavefish
Astyanax mexicanus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Painted turtle
Chrysemys picta bellii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Panamanian white-faced capuchin
Cebus imitator
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Paramormyrops kingsleyaeFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Periophthalmus magnuspinnatusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Pig
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Pig - Bamei
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig - Berkshire
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig - Hampshire
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig - Jinhua
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig - Landrace
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig - Largewhite
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig - Meishan
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig - Pietrain
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig - Rongchang
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig - Tibetan
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig - Wuzhishan
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig USMARC
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pig-tailed macaque
Macaca nemestrina
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pika
Ochotona princeps
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Pike-perch
Sander lucioperca
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pinecone soldierfish
Myripristis murdjan
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Pink-footed goose
Anser brachyrhynchus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Platyfish
Xiphophorus maculatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Platypus
Ornithorhynchus anatinus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Polar bear
Ursus maritimus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Prairie vole
Microtus ochrogaster
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Rabbit
Oryctolagus cuniculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Rainbow trout
Oncorhynchus mykiss
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Rat
Rattus norvegicus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Rat - SHR/Utx RGD_8142385
Rattus norvegicus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Rat - SHRSP/BbbUtx
Rattus norvegicus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Rat - WKY/Bbb RGD_1581635
Rattus norvegicus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Red fox
Vulpes vulpes
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Red-bellied piranha
Pygocentrus nattereri
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Reedfish
Erpetoichthys calabaricus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Ring-necked pheasant
Phasianus colchicus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Round goby
Neogobius melanostomus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Ruff
Calidris pugnax
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Rufous-capped babbler
Cyanoderma ruficeps
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Ryukyu mouse
Mus caroli
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Saccharomyces cerevisiae
Saccharomyces cerevisiae S288c
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP---
Sailfin molly
Poecilia latipinna
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Sheep
Ovis aries
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Sheep (texel)
Ovis aries
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP--BAM/BigWig
Sheepshead minnow
Cyprinodon variegatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Shortfin molly
Poecilia mexicana
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Shrew
Sorex araneus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Shrew mouse
Mus pahari
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Siamese fighting fish
Betta splendens
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Siberian musk deer
Moschus moschiferus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Silver-eye
Zosterops lateralis melanops
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Sloth
Choloepus hoffmanni
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Small tree finch
Camarhynchus parvulus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Sooty mangabey
Cercocebus atys
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Sperm whale
Physeter catodon
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Spiny chromis
Acanthochromis polyacanthus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Spoon-billed sandpiper
Calidris pygmaea
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Spotted gar
Lepisosteus oculatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Squirrel
Ictidomys tridecemlineatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Steppe mouse
Mus spicilegus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Stickleback
Gasterosteus aculeatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Sumatran orangutan
Pongo abelii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Superb fairywren
Malurus cyaneus samueli
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Swainson's thrush
Catharus ustulatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Swamp eel
Monopterus albus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Swan goose
Anser cygnoides
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Tarsier
Carlito syrichta
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Tasmanian devil
Sarcophilus harrisii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Tetraodon
Tetraodon nigroviridis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQLGVFVCFVEP---
Three-toed box turtle
Terrapene carolina triunguis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Tiger
Panthera tigris altaica
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Tiger tail seahorse
Hippocampus comes
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Tongue sole
Cynoglossus semilaevis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Tree Shrew
Tupaia belangeri
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
Tropical clawed frog
Xenopus tropicalis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Tuatara
Sphenodon punctatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Turbot
Scophthalmus maximus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Turkey
Meleagris gallopavo
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Turquoise killifish
Nothobranchius furzeri
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Ugandan red Colobus
Piliocolobus tephrosceles
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Upper Galilee mountains blind mole rat
Nannospalax galili
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Vaquita
Phocoena sinus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Vervet-AGM
Chlorocebus sabaeus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Wallaby
Notamacropus eugenii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP---
West African mud turtle
Pelusios castaneus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Western mosquitofish
Gambusia affinis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
White-throated sparrow
Zonotrichia albicollis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
White-tufted-ear marmoset
Callithrix jacchus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Wild yak
Bos mutus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Yarkand deer
Cervus hanglu yarkandensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Yellow-billed parrot
Amazona collaria
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Yellowtail amberjack
Seriola lalandi dorsalis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Zebra finch
Taeniopygia guttata
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Zebra mbuna
Maylandia zebra
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig
Zig-zag eel
Mastacembelus armatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV JSONMySQL--VEP--BAM/BigWig

To facilitate storage and download all databases are GNU Zip (gzip, *.gz) compressed.

About the data

The following types of data dumps are available on the FTP site.

FASTA
FASTA sequence databases of Ensembl gene, transcript and protein model predictions. Since the FASTA format does not permit sequence annotation, these database files are mainly intended for use with local sequence similarity search algorithms. Each directory has a README file with a detailed description of the header line format and the file naming conventions.
DNA
Masked and unmasked genome sequences associated with the assembly (contigs, chromosomes etc.).
The header line in an FASTA dump files containing DNA sequence consists of the following attributes : coord_system:version:name:start:end:strand This coordinate-system string is used in the Ensembl API to retrieve slices with the SliceAdaptor.
CDS
Coding sequences for Ensembl or ab initio predicted genes.
cDNA
cDNA sequences for Ensembl or ab initio predicted genes.
Peptides
Protein sequences for Ensembl or ab initio predicted genes.
RNA
Non-coding RNA gene predictions.
Annotated sequence
Flat files allow more extensive sequence annotation by means of feature tables and contain thus the genome sequence as annotated by the automated Ensembl genome annotation pipeline. Each nucleotide sequence record in a flat file represents a 1Mb slice of the genome sequence. Flat files are broken into chunks of 1000 sequence records for easier downloading.
EMBL
Ensembl database dumps in EMBL nucleotide sequence database format
GenBank
Ensembl database dumps in GenBank nucleotide sequence database format
MySQL
All Ensembl MySQL databases are available in text format as are the SQL table definition files. These can be imported into any SQL database for a local installation of a mirror site. Generally, the FTP directory tree contains one directory per database. For more information about these databases and their Application Programming Interfaces (or APIs) see the API section.
GTF
Gene sets for each species. These files include annotations of both coding and non-coding genes. This file format is described here.
GFF3
GFF3 provides access to all annotated transcripts which make up an Ensembl gene set. This file format is described here.
EMF flatfile dumps (comparative data)

Alignments of resequencing data are available for several species as Ensembl Multi Format (EMF) flatfile dumps. The accompanying README file describes the file format.

Also, the same format is used to dump whole-genome multiple alignments as well as gene-based multiple alignments and phylogentic trees used to infer Ensembl orthologues and paralogues. These files are available in the ensembl_compara database which will be found in the mysql directory.

MAF (comparative data)

MAF files are provided for all pairwise alignments containing human (GRCh38), and all multiple alignments. The MAF file format is described here.

GVF (variation data)
GVF (Genome Variation Format) is a simple tab-delimited format derived from GFF3 for variation positions across the genome. There are GVF files for different types of variation data (e.g. somatic variants, structural variants etc). For more information see the "README" files in the GVF directory.
VCF (variation data)
VCF (Variant Call Format) is a text file format containing meta-information lines, a header line, and then data lines each containing information about a position in the genome. This file format can also contain genotype information on samples for each position. More details about the format and its specifications are available here.
VEP (variation data)
Compressed text files (called "cache files") used by the Variant Effect Predictor tool. More information about these files is available here.
BED format files (comparative data)

Constrained elements calculated using GERP are available in BED format. For more information see the accompanying README file.

BED format is a simple line-based format. The first 3 mandatory columns are:

  • chromosome name (may start with 'chr' for compliance with UCSC)
  • start position. This is a 0-based position
  • end position.

More information on the BED file format...

Tarball

The entire Ensembl API is gzipped and concatenated into a single TAR file. This is updated daily.