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 The Description of the annotation database page (no longer maintained) also provides descriptions of selected tables in the database.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
Guinea pig
Kangaroo rat
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

  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

  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 (hg38, GRCh38)

Feb. 2009 (hg19, GRCh37)

Mar. 2006 (hg18)

May 2004 (hg17)

Jul. 2003 (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 (vicPac2)

July 2008 (vicPac1)

  American alligator Genome

August 2012 (allMis1)

  Armadillo Genome

Dec. 2011 (dasNov3)

  Atlantic cod Genome

May 2010 (gadMor1)

  Baboon Genome

Mar. 2012 (papAnu2)

Nov. 2008 (papHam1)

  Bonobo Genome

May 2012 (panPan1)

  Brown Kiwi Genome

June 2015 (aptMan1)

  Budgerigar Genome

Sep. 2011 (melUnd1)

  Bushbaby Genome

Mar. 2011 (otoGar3)

  Cat Genome

Nov. 2014 (felCat8)

Sep. 2011 (felCat5)

Dec. 2008 (felCat4)

Mar. 2006 (felCat3)

  Chicken Genome

Nov. 2011 (galGal4)

May 2006 (galGal3)

Feb. 2004 (galGal2)

  Chimpanzee Genome

Feb. 2011 (panTro4)

Oct. 2010 (panTro3)

Mar. 2006 (panTro2)

Nov. 2003 (panTro1)

  Chinese hamster Genome

Jul. 2013 (criGri1)

  Coelacanth Genome

Aug. 2011 (latCha1)

  Cow Genome

Jun. 2014 (bosTau8)

Oct. 2011 (bosTau7)

Nov. 2009 (bosTau6)

Apr. 2009 (bosTau5)

Oct. 2007 (bosTau4)

Aug. 2009 (bosTauMd3)

Aug. 2006 (bosTau3)

Mar. 2005 (bosTau2)

May 2004 (bosTau1)

  Crab-eating macaque Genome

Jun. 2013 (macFas5)

  Dog Genome
  Sep. 2011 (canFam3)

May 2005 (canFam2)

Jul. 2004 (canFam1)

  Dolphin Genome

Oct. 2011 (turTru2)

  Elephant Genome

Jul. 2009 (loxAfr3)

May 2005 (loxAfr1)

  Elephant shark Genome

Dec. 2013 (calMil1)

  Ferret Genome

April 2011 (musFur1)

  Fugu Genome

Oct. 2011 (fr3)

Oct. 2004 (fr2)

Aug. 2002 (fr1)

  Gibbon Genome

Oct. 2012 (nomLeu3)

June 2011 (nomLeu2)

Jan. 2010 (nomLeu1)

  Gorilla Genome

Dec 2014 (gorGor4)

May 2010 (gorGor3)

  Guinea Pig Genome

Feb. 2008 (cavPor3)

Oct. 2005 (cavPor2) (sequence only)

  Hedgehog Genome

May 2012 (eriEur2)

June 2006 (eriEur1)

  Horse Genome

Sep. 2007 (equCab2)

Jan. 2007 (equCab1)

  Kangaroo rat Genome

July 2008 (dipOrd1)

  Lamprey Genome

Sep. 2010 (petMar2)

Mar. 2007 (petMar1)

  Lancelet Genome

Mar. 2006 (braFlo1)

  Lizard Genome

May 2010 (anoCar2)

Jan. 2007 (anoCar1)

  Manatee Genome

Oct. 2011 (triMan1)

  Marmoset Genome

Mar. 2009 (calJac3)

Jun. 2007 (calJac1)

  Medaka Genome

Oct. 2005 (oryLat2)

  Medium Ground Finch Genome

Apr. 2012 (geoFor1)

  Megabat Genome

July 2008 (pteVam1)

  Microbat Genome

Jul. 2010 (myoLuc2)

  Minke whale Genome

Oct. 2013 (balAcu1)

  Mouse Genome

Dec. 2011 (mm10)

Jul. 2007 (mm9)

Mar. 2006 (mm8)

Aug. 2005 (mm7)

Mar. 2005 (mm6)

May 2004 (mm5)

Oct. 2003 (mm4)

Feb. 2003 (mm3)

Feb. 2002 (mm2)

Nov. 2001 (mm1)

  Mouse lemur Genome

May 2015 (micMur2)

July 2007 (micMur1)

  Naked mole-rat Genome

Jan. 2012 (hetGla2)

Jul. 2011 (hetGla1)

  Nile tilapia Genome

Jan. 2011 (oreNil2)

  Opossum Genome

Oct. 2006 (monDom5)

  • Multiple Alignments

    Jan. 2006 (monDom4)

    Jun. 2005 (monDom2)

    Oct. 2004 (monDom1)

  •   Orangutan Genome

    Jul. 2007 (ponAbe2)

      Painted turtle Genome

    Dec. 2011 (chrPic1)

      Panda Genome

    Dec. 2009 (ailMel1)

      Pig Genome

    Aug. 2011 (susScr3)

    Nov. 2009 (susScr2)

      Pika Genome

    May 2012 (ochPri3)

    July 2008 (ochPri2)

      Platypus Genome

    Feb. 2007 (ornAna2)

    Mar. 2007 (ornAna1)

      Rabbit Genome

    Apr. 2009 (oryCun2)

    May 2005 (oryCun1)

      Rat Genome

    Jul. 2014 (rn6)

    Mar. 2012 (rn5)

    Nov. 2004 (rn4)

    Jun. 2003 (rn3)

    Jan. 2003 (rn2)

    Nov. 2002 (rn1)

      Rhesus Genome

    Nov. 2015 (rheMac8)

    Oct. 2010 (rheMac3)

    Jan. 2006 (rheMac2)

    Jan. 2005 (rheMac1)

      Rock hyrax Genome

    July 2008 (proCap1)

      Sheep Genome

    Aug. 2012 (oviAri3)

    Feb. 2010 (oviAri1)

      Shrew Genome

    Aug. 2008 (sorAra2)

    June 2006 (sorAra1)

      Sloth Genome

    July 2008 (choHof1)

      Squirrel Genome

    Nov. 2011 (speTri2)

      Squirrel monkey Genome

    Oct. 2011 (saiBol1)

      Stickleback Genome

    Feb. 2006 (gasAcu1)

  • Multiple Alignments

  •   Tarsier Genome

    Sep. 2013 (tarSyr2)

    Aug. 2008 (tarSyr1)

      Tasmanian devil Genome

    Feb. 2011 (sarHar1)

      Tenrec Genome

    Nov. 2012 (echTel2)

    July 2005 (echTel1)

      Tetraodon Genome

    Mar. 2010 (tetNig2)

    Feb. 2004 (tetNig1)

      Tree shrew Genome

    Dec. 2006 (tupBel1)

      Turkey Genome

    Dec. 2009 (melGal1)

      Wallaby Genome

    Sep. 2009 (macEug2)

      White rhinoceros Genome

    May 2012 (cerSim1)

      X. tropicalis Genome

    Sep. 2012 (xenTro7)

    Nov. 2009 (xenTro3)

    Aug. 2005 (xenTro2)

    Oct. 2004 (xenTro1)

      Zebra Finch Genome

    Feb. 2013 (taeGut2)

    Jul. 2008 (taeGut1)

      Zebrafish Genome

    Sep. 2014 (danRer10)

    Jul. 2010 (danRer7)

    Dec. 2008 (danRer6)

    Jul. 2007 (danRer5)

    Mar. 2006 (danRer4)

    May 2005 (danRer3)

    Jun. 2004 (danRer2)

    Nov. 2003 (danRer1)

      Vertebrates (sequence only)

      C. intestinalis Genome

    Mar. 2005 (ci2)

    Dec. 2002 (ci1)

      S. purpuratus Genome

    Sep. 2006 (strPur2)

    Apr. 2005 (strPur1)

      A. gambiae Genome

    Feb. 2003 (anoGam1)

      A. mellifera Genome

    May 2005 (apiMel3)

    Jan. 2005 (apiMel2)

    Jul. 2004 (apiMel1)

      D. ananassae Genome

    Feb. 2006 (droAna3)

    Aug. 2005 (droAna2)

    Jul. 2004 (droAna1)

      D. erecta Genome

    Feb. 2006 (droEre2)

    Aug. 2005 (droEre1)

      D. grimshawi Genome

    Feb. 2006 (droGri2)

    Aug. 2005 (droGri1)

      D. melanogaster Genome

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

    Apr. 2006 (dm3)

    Apr. 2004 (dm2)

    Jan. 2003 (dm1)

      D. mojavensis Genome

    Feb. 2006 (droMoj3)

    Aug. 2005 (droMoj2)

    Aug. 2004 (droMoj1)

      D. persimilis Genome

    Oct. 2005 (droPer1)

      D. pseudoobscura Genome

    Feb. 2006 (dp4)

    Nov. 2004 (dp3)

    Aug. 2003 (dp2)

      D. sechellia Genome

    Oct. 2005 (droSec1)

      D. simulans Genome

    Apr. 2005 (droSim1)

      D. virilis Genome

    Feb. 2006 (droVir3)

    Aug. 2005 (droVir2)

    Jul. 2004 (droVir1)

      D. willistoni Genome

    Feb. 2006 (droWil1)

      D. yakuba Genome

    Nov. 2005 (droYak2)

    Apr. 2004 (droYak1)

      T. castaneum Genome

    Sep. 2005 (triCas2)

      C. brenneri Genome

    Feb. 2008 (caePb2)

    Jul. 2007 (caePb1)

      C. briggsae Genome

    Jan. 2007 (cb3)

    Jul. 2002 (cb1)

      C. elegans Genome

    Feb. 2013 (ce11)

    Oct. 2010 (ce10)

    May 2008 (ce6)

    Jan. 2007 (ce4)

    Mar. 2004 (ce2)

    May 2003 (ce1)

      C. japonica Genome

    Mar. 2008 (caeJap1)

      C. remanei Genome

    May 2007 (caeRem3)

    Mar. 2006 (caeRem2)

      P. pacificus Genome

    Feb. 2007 (priPac1)

      Yeast (S. cerevisiae) Genome

    Apr. 2011 (sacCer3)

    Jun. 2008 (sacCer2)

    Oct. 2003 (sacCer1)

      Sea Hare (Aplysia californica) Genome

    Sep. 2008 (aplCal1)

      Denisova Genome

      Ebola Virus Genome

    June 2014 (eboVir3)

      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.