UCSC Genome Bioinformatics
  Sequence and Annotation Downloads

This page contains links to sequence and annotation data downloads for the genome assemblies featured in the UCSC Genome Browser. Table downloads are also available via the Genome Browser FTP server. For quick access to the most recent assembly of each genome, see the current genomes directory. This directory may be useful to individuals with automated scripts that must always reference the most recent assembly.

To view the current descriptions and formats of the tables in the annotation database, use the "describe table schema" button in the Table Browser. The Description of the annotation database page (no longer maintained) also provides descriptions of selected tables in the database.

All tables in the Genome Browser are freely usable for any purpose except as indicated in the README.txt files in the download directories. To view restrictions specific to a particular data set, click on the corresponding download link and review the README text. These data were contributed by many researchers, as listed on the Genome Browser credits page. Please acknowledge the contributor(s) of the data you use.

VERTEBRATES - Complete annotation sets
  American alligator
  Atlantic cod
  Brown kiwi
  Chinese hamster
  Crab-eating macaque
  Elephant shark
Green Monkey
Guinea pig
Kangaroo rat
Malayan flying lemur
Medium ground finch
Minke whale
Mouse lemur
Naked mole-rat
Nile tilapia
Painted turtle
Rock hyrax
Squirrel monkey
Tasmanian devil
Tree shrew
White rhinoceros
X. tropicalis
Zebra finch

VERTEBRATES - Sequence downloads only
  J. Craig Venter
  Data access for non-browser assemblies

  C. intestinalis
  S. purpuratus

  A. gambiae   D. pseudoobscura
  A. mellifera   D. sechellia
  D. ananassae   D. simulans
  D. erecta   D. virilis
  D. grimshawi   D. willistoni
  D. melanogaster   D. yakuba
  D. mojavensis   T. castaneum
  D. persimilis   

  C. brenneri
  C. briggsae
  C. elegans
  C. japonica
  C. remanei
  P. pacificus

  S. cerevisiae
  Sea hare

  Ebola virus

  Access the gbdb Fileserver
  Shared Data (Protein DBs, hgFixed, visiGene)
  LiftOver Files
  ENCODE Project Files (Genome-wide Phase)
  ENCODE Project Files (Pilot Phase)

  Source & Utilities Downloads

The Genome Browser, Blat, and liftOver source are freely downloadable for academic, noncommercial, and personal use. For information on commercial licensing, please see the Genome Browser and Blat licensing requirements.

Genome Browser Mirror
The Genome Browser Mirror is available for installing a local copy of the Genome Browser website onto your web server. We provide precompiled executable binaries for this purpose, so you do not have to compile the whole source code.

Troubleshooting: For slow download speeds, try using UDR (UDT Enabled Rsync), which improves throughput of large data transfers over long distances (64/32-bit also available).

Please review the userApps README for a summary of how to fetch selected directories from the kent source tree, or download userApps.src.tgz, to install all kent utilities.

The utilities directory offers downloads of pre-compiled standalone binaries:

Online Store
The following can be downloaded from our online store:

  • Genome Browser Source Code
  • Genome Browser in a Box (GBiB)
  • LiftOver Program

  Human Genome

Dec. 2013 (GRCh38/hg38)

Feb. 2009 (GRCh37/hg19)

Mar. 2006 (NCBI36/hg18)

May 2004 (NCBI35/hg17)

July 2003 (NCBI34/hg16)

Apr. 10, 2003 (hg15)

Nov. 14, 2002 (hg13):

Jun. 28, 2002 (hg12):

Apr. 5, 2002 (hg11):

Dec. 22, 2001 (hg10):

Aug. 6, 2001 (hg8):

Apr. 1, 2001 (hg7):

Dec. 12, 2000 (hg6):

Oct. 7, 2000 (hg5):

Oct. 7, 2000 preliminary version:

Sep. 5, 2000 (hg4):

June 15, 2000:

May 24, 2000:

Older Human data and documentation:

  Alpaca Genome

Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2)

July 2008 (Broad/vicPac1)

  American alligator Genome

August 2012 (allMis0.2/allMis1)

  Armadillo Genome

Dec. 2011 (Baylor/dasNov3)

  Atlantic cod Genome

May 2010 (Genofisk GadMor_May2010/gadMor1)

  Baboon Genome

Mar. 2012 (Baylor Panu_2.0/papAnu2)

Nov. 2008 (Baylor Pham_1.0/papHam1)

  Bonobo Genome

May 2012 (Max-Planck/panPan1)

  Brown Kiwi Genome

June 2015 (MPI-EVA AptMant0/aptMan1)

  Budgerigar Genome

Sep. 2011 (WUSTL v6.3/melUnd1)

  Bushbaby Genome

Mar. 2011 (Broad/otoGar3)

  Cat Genome

Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)

Sep. 2011 (ICGSC Felis_catus 6.2/felCat5)

Dec. 2008 (NHGRI/GTB V17/felCat4)

Mar. 2006 (Broad/felCat3)

  Chicken Genome

Dec. 2015 (Gallus_gallus-5.0/galGal5)

Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4)

May 2006 (WUGSC 2.1/galGal3)

Feb. 2004 (WUGSC 1.0/galGal2)

  Chimpanzee Genome

May. 2016 (Pan_tro 3.0/panTro5)

Feb. 2011 (CSAC 2.1.4/panTro4)

Oct. 2010 (CGSC 2.1.3/panTro3)

Mar. 2006 (CGSC 2.1/panTro2 )

Nov. 2003 (CGSC 1.1/panTro1)

  Chinese hamster Genome

Jul. 2013 (C_griseus_v1.0/criGri1)

  Coelacanth Genome

Aug. 2011 (LatCha1/latCha1)

  Cow Genome

Jun. 2014 (UMD_3.1.1/bosTau8)

Oct. 2011 (Btau_4.6.1/bosTau7)

Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)

Apr. 2009 (bosTau5)/bosTau5)

Oct. 2007 (Baylor 4.0/bosTau4)

Aug. 2009 (bosTauMd3)/bosTauMd3)

Aug. 2006 (Baylor 3.1/bosTau3)

Mar. 2005 (Baylor 2.0/bosTau2)

May 2004 (bosTau1/bosTau1)

  Crab-eating macaque Genome

Jun. 2013 (Macaca_fascicularis_5.0/macFas5)

  Dog Genome
  Sep. 2011 (Broad CanFam3.1/canFam3)

May 2005 (Broad/canFam2)

Jul. 2004 (Broad/canFam1)

  Dolphin Genome

Oct. 2011 (Baylor Ttru_1.4/turTru2)

  Elephant Genome

Jul. 2009 (Broad/loxAfr3)

May 2005 (loxAfr1/loxAfr1)

  Elephant shark Genome

Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1)

  Ferret Genome

April 2011 (MusPutFur1.0/musFur1)

  Fugu Genome

Oct. 2011 (FUGU5/fr3/fr3)

Oct. 2004 (JGI V4.0/fr2)

Aug. 2002 (fugu/fr1)

  Gibbon Genome

Oct. 2012 (Nleu_3.0/nomLeu3)

June 2011 (GGSC Nleu1.1/nomLeu2)

Jan. 2010 (GGSC Nleu1.0/nomLeu1)

  Gorilla Genome

Mar. 2016 (GMSRT3/gorGor5)

Dec 2014 (gorGor4.1/gorGor4)

May 2010 (gorGor3.1/gorGor3)

  Green Monkey Genome

Mar 2014 (Chlorocebus_sabeus 1.1/chlSab2)

  Guinea Pig Genome

Feb. 2008 (Broad/cavPor3)

Oct. 2005 (cavPor2) (sequence only)

  Hedgehog Genome

May 2012 (EriEur2.0/eriEur2)

June 2006 (Broad/eriEur1)

  Horse Genome

Sep. 2007 (Broad/equCab2)

Jan. 2007 (Broad/equCab1)

  Kangaroo rat Genome

July 2008 (Broad/dipOrd1)

  Lamprey Genome

Sep. 2010 (WUGSC 7.0/petMar2)

Mar. 2007 (WUGSC 3.0/petMar1)

  Lancelet Genome

Mar. 2006 (JGI 1.0/braFlo1)

  Lizard Genome

May 2010 (Broad AnoCar2.0/anoCar2)

Jan. 2007 (Broad/anoCar1)

  Malayan flying lemur Genome

June 2014 (G_variegatus-3.0.2/galVar1)

  Manatee Genome

Oct. 2011 (Broad v1.0/triMan1)

  Marmoset Genome

Mar. 2009 (WUGSC 3.2/calJac3)

Jun. 2007 (WUGSC 2.0.2/calJac1)

  Medaka Genome

Oct. 2005 (NIG/UT MEDAKA1/oryLat2)

  Medium Ground Finch Genome

Apr. 2012 (GeoFor_1.0/geoFor1)

  Megabat Genome

July 2008 (Broad/pteVam1)

  Microbat Genome

Jul. 2010 (Myoluc2.0/myoLuc2)

  Minke whale Genome

Oct. 2013 (KORDI BalAcu1.0/balAcu1)

  Mouse Genome

Dec. 2011 (GRCm38/mm10)

Jul. 2007 (NCBI37/mm9)

Mar. 2006 (NCBI36/mm8)

Aug. 2005 (NCBI35/mm7)

Mar. 2005 (mm6/mm6)

May 2004 (mm5/mm5)

Oct. 2003 (mm4/mm4)

Feb. 2003 (mm3/mm3)

Feb. 2002 (mm2/mm2)

Nov. 2001 (mm1/mm1)

  Mouse lemur Genome

May 2015 (Mouse lemur/micMur2)

July 2007 (Broad/micMur1)

  Naked mole-rat Genome

Jan. 2012 (Broad HetGla_female_1.0/hetGla2)

Jul. 2011 (HetGla_1.0/hetGla1)

  Nile tilapia Genome

Jan. 2011 (Nile tilapia/oreNil2)

  Opossum Genome

Oct. 2006 (Broad/monDom5)

  • Multiple Alignments

    Jan. 2006 (Broad/monDom4)

    Jun. 2005 (Broad/monDom2)

    Oct. 2004 (Broad prelim/monDom1)

  •   Orangutan Genome

    Jul. 2007 (WUGSC 2.0.2/ponAbe2)

      Painted turtle Genome

    Dec. 2011 (v3.0.1/chrPic1)

      Panda Genome

    Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)

      Pig Genome

    Aug. 2011 (SGSC Sscrofa10.2/susScr3)

    Nov. 2009 (SGSC Sscrofa9.2/susScr2)

      Pika Genome

    May 2012 (OchPri3.0/ochPri3)

    July 2008 (Broad/ochPri2)

      Platypus Genome

    Feb. 2007 (ASM227v2/ornAna2)

    Mar. 2007 (WUGSC 5.0.1/ornAna1)

      Rabbit Genome

    Apr. 2009 (Broad/oryCun2)

    May 2005 (oryCun1/oryCun1)

      Rat Genome

    Jul. 2014 (RGSC 6.0/rn6)

    Mar. 2012 (RGSC 5.0/rn5)

    Nov. 2004 (Baylor 3.4/rn4)

    Jun. 2003 (Baylor 3.1/rn3)

    Jan. 2003 (rn2/rn2)

    Nov. 2002 (rn1/rn1)

      Rhesus Genome

    Nov. 2015 (BCM Mmul_8.0.1/rheMac8)

    Oct. 2010 (BGI CR_1.0/rheMac3)

    Jan. 2006 (MGSC Merged 1.0/rheMac2)

    Jan. 2005 (Mmul_0.1/rheMac1)

      Rock hyrax Genome

    July 2008 (Broad/proCap1)

      Sheep Genome

    Aug. 2012 (ISGC Oar_v3.1/oviAri3)

    Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)

      Shrew Genome

    Aug. 2008 ((Broad/sorAra2)

    June 2006 (Broad/sorAra1)

      Sloth Genome

    July 2008 (Broad/choHof1)

      Squirrel Genome

    Nov. 2011 (Broad/speTri2)

      Squirrel monkey Genome

    Oct. 2011 (Broad/saiBol1)

      Stickleback Genome

    Feb. 2006 (Broad/gasAcu1)

  • Multiple Alignments

  •   Tarsier Genome

    Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)

    Aug. 2008 (Broad/tarSyr1)

      Tasmanian devil Genome

    Feb. 2011 (WTSI Devil_ref v7.0/sarHar1)

      Tenrec Genome

    Nov. 2012 (Broad/echTel2)

    July 2005 (Broad/echTel1)

      Tetraodon Genome

    Mar. 2010 (Genoscope 8.0/tetNig2)

    Feb. 2004 (Genoscope 7/tetNig1)

      Tree shrew Genome

    Dec. 2006 (Broad/tupBel1)

      Turkey Genome

    Dec. 2009 (TGC Turkey_2.01/melGal1)

      Wallaby Genome

    Sep. 2009 (TWGS Meug_1.1/macEug2)

      White rhinoceros Genome

    May 2012 (CerSimSim1.0/cerSim1)

      X. tropicalis Genome

    Sep. 2012 (JGI 7.0/xenTro7)

    Nov. 2009 (JGI 4.2/xenTro3)

    Aug. 2005 (JGI 4.1/xenTro2)

    Oct. 2004 (JGI 3.0/xenTro1)

      Zebra Finch Genome

    Feb. 2013 (taeGut2/taeGut2)

    Jul. 2008 (WUGSC 3.2.4/taeGut1)

      Zebrafish Genome

    Sep. 2014 (GRCz10/danRer10)

    Jul. 2010 (Zv9/danRer7)

    Dec. 2008 (Zv8/danRer6)

    Jul. 2007 (Zv7/danRer5)

    Mar. 2006 (Zv6/danRer4)

    May 2005 (Zv5/danRer3)

    Jun. 2004 (danRer2/danRer2)

    Nov. 2003 (danRer1/danRer1)

      Vertebrates (sequence only)

      C. intestinalis Genome

    Mar. 2005 (JGI 2.1/ci2)

    Dec. 2002 (JGI 1.0/ci1)

      S. purpuratus Genome

    Sep. 2006 (Baylor 2.1/strPur2)

    Apr. 2005 (Baylor 1.1/strPur1)

      A. gambiae Genome

    Feb. 2003 (IAGEC MOZ2/anoGam1)

      A. mellifera Genome

    May 2005 (Baylor HGSC Amel_3.0/apiMel3)

    Jan. 2005 (Baylor 2.0/apiMel2)

    Jul. 2004 (Baylor 1.2/apiMel1)

      D. ananassae Genome

    Feb. 2006 (droAna3/droAna3)

    Aug. 2005 (Agencourt prelim/droAna2)

    Jul. 2004 (TIGR/droAna1 )

      D. erecta Genome

    Feb. 2006 (droEre2/droEre2)

    Aug. 2005 (Agencourt prelim/droEre1)

      D. grimshawi Genome

    Feb. 2006 (droGri2/droGri2)

    Aug. 2005 (Agencourt prelim/droGri1)

      D. melanogaster Genome

    Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)

    Apr. 2006 (BDGP R5/dm3)

    Apr. 2004 (BDGP R4/dm2)

    Jan. 2003 (BDGP R3/dm1)

      D. mojavensis Genome

    Feb. 2006 (droMoj3)

    Aug. 2005 (Agencourt prelim/droMoj2)

    Aug. 2004 (Agencourt prelim/droMoj1)

      D. persimilis Genome

    Oct. 2005 (Broad/droPer1)

      D. pseudoobscura Genome

    Feb. 2006 (dp4)

    Nov. 2004 (FlyBase 1.03/dp3)

    Aug. 2003 (Baylor freeze1/dp2)

      D. sechellia Genome

    Oct. 2005 (Broad/droSec1)

      D. simulans Genome

    Apr. 2005 (WUGSC mosaic 1.0/droSim1)

      D. virilis Genome

    Feb. 2006 (droVir3)

    Aug. 2005 (Agencourt prelim/droVir2)

    July 2004 (Agencourt prelim/droVir1)

      D. willistoni Genome

    Feb. 2006 (droWil1)

      D. yakuba Genome

    Nov. 2005 (WUGSC 7.1/droYak2)

    Apr. 2004 (WUGSC 1.0/droYak1)

      T. castaneum Genome

    Sep. 2005 (triCas2)

      C. brenneri Genome

    Feb. 2008 (WUGSC 6.0.1/caePb2)

    Jan. 2007 (WUGSC 4.0/caePb1)

      C. briggsae Genome

    Jan. 2007 (WUGSC 1.0/cb3)

    July 2002 (WormBase cb25.agp8/cb1)

      C. elegans Genome

    Feb. 2013 (WBcel235/ce11)

    Oct. 2010 (WS220/ce10)

    May 2008 (WS190/ce6)

    Jan. 2007 (WS170/ce4)

    Mar. 2004 (WS120/ce2)

    May 2003 (ce1)

      C. japonica Genome

    Mar. 2008 (WUGSC 3.0.2/caeJap1)

      C. remanei Genome

    May 2007 (WUGSC 15.0.1/caeRem3)

    Mar. 2006 (WUGSC 1.0/caeRem2)

      P. pacificus Genome

    Feb. 2007 (WUGSC 5.0/priPac1)

      Yeast (S. cerevisiae) Genome

    Apr. 2011 (SacCer_Apr2011/sacCer3)

    June 2008 (SGD/sacCer2)

    Oct. 2003 (SGD/sacCer1)

      Sea Hare (Aplysia californica) Genome

    Sept. 2008 (Broad 2.0/aplCal1)

      Denisova Genome

      Ebola Virus Genome

    June 2014 (G3683/KM034562.1/eboVir3)

      Data Access through the gbdb Fileserver

    • The /gbdb fileserver holds all files referenced by the genome browser tables. Some files in the browser are hosted in binary files such as a bigBed file that can be downloaded from our download server from the /gbdb location.
      • Examples for the hg38 database are the crispr.bb and crisprDetails.tab files for the CRISPR track which can be found here.
      • Individual regions or the whole genome annotation from such binary files can be obtained using tools like bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here.
      • The bigBedToBed tool can also be used to obtain only features within a given range,
        e.g. bigBedToBed http://hgdownload.cse.ucsc.edu/gbdb/hg38/crispr/crispr.bb -chrom=chr21 -start=25000000 -end=30000000 stdout

    • Sequence files for assembly sequences used in alignment tracks, such as in the 100-species conservation track are also found in the /gbdb location.

      Data Shared by Multiple Assemblies

      LiftOver Files (over.chain)

    The liftOver links have been moved to the corresponding assembly sections (for example, the link for the mm5-to-mm6 over.chain file is now located in the mm5 downloads section). The liftOver source download link is now located in the source downloads section.