UCSC Genome Bioinformatics
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  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 The Description of the annotation database page (no longer maintained) also provides descriptions of selected tables in the database.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
  Human   Horse   Platypus
  Cat   Lamprey   Rat  
  Chicken   Lizard   Rhesus
  Chimpanzee   Marmoset   Stickleback
  Cow   Medaka   Tetraodon
  Dog   Mouse   X. tropicalis
  Fugu   Opossum   Zebra finch
  Guinea pig   Orangutan   Zebrafish

VERTEBRATES - Sequence downloads only
  Armadillo   Rabbit    
  Bushbaby   Shrew    
  Elephant   Tenrec    
  European hedgehog   Tree shrew    

DEUTEROSTOMES
  C. intestinalis
  Lancelet
  S. purpuratus

INSECTS
  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       

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

YEAST
  S. cerevisiae

OTHER DOWNLOADS
  Shared Data (Protein DBs, hgFixed, visiGene)
  LiftOver Files
  ENCODE Files


  Source Downloads
 

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


  Human Genome
  Feb. 2009 (hg19, GRCh37)

Mar. 2006 (hg18)

May 2004 (hg17)

Jul. 2003 (hg16)

Apr. 10, 2003 (hg15)

Archives of older assemblies
Archived hg13 liftOver files
Archived hg12 liftOver files


  Cat Genome
 

Mar. 2006 (felCat3)


  Chicken Genome
 

May 2006 (galGal3)

Feb. 2004 (galGal2)


  Chimpanzee Genome
 

Mar. 2006 (panTro2)

Nov. 2003 (panTro1)


  Cow Genome
 

Oct. 2007 (bosTau4)

Aug. 2006 (bosTau3)

Mar. 2005 (bosTau2)

May 2004 (bosTau1)


  Dog Genome
 

May 2005 (canFam2)

Jul. 2004 (canFam1)


  Fugu Genome
 

Oct. 2004 (fr2)

Aug. 2002 (fr1)


  Guinea Pig Genome
 

Feb. 2008 (cavPor3)

Oct. 2005 (cavPor2) (sequence only)


  Horse Genome
 

Sep. 2007 (equCab2)

Jan. 2007 (equCab1)


  Lamprey Genome
 

Mar. 2007 (petMar1)


  Lancelet Genome
 

Mar. 2006 (braFlo1)


  Lizard Genome
 

Jan. 2007 (anoCar1)


  Marmoset Genome
 

Jun. 2007 (calJac1)


  Medaka Genome
 

Oct. 2005 (oryLat2)


  Mouse Genome
  Jul. 2007 (mm9)

Mar. 2006 (mm8)

Aug. 2005 (mm7)

Mar. 2005 (mm6)

May 2004 (mm5)

Archives of older assemblies
Archived mm4 liftOver files
Archived mm3 liftOver files
Archived mm2 liftOver files


  Opossum Genome
 

Oct. 2006 (monDom5)

  • Multiple Alignments

    Jan. 2006 (monDom4)

    Jun. 2005 (monDom2)

    Oct. 2004 (monDom1)


    •   Orangutan Genome
     

    Jul. 2007 (ponAbe2)


      Platypus Genome
     

    Mar. 2007 (ornAna1)


      Rat Genome
     

    Nov. 2004 (rn4)

    Jun. 2003 (rn3)

    Jan. 2003 (rn2)

    Archives of older assemblies


      Rhesus Genome
     

    Jan. 2006 (rheMac2)

    Archives of older assemblies
    Archived rheMac1 liftOver files

      Stickleback Genome
     

    Feb. 2006 (gasAcu1)


      Tetraodon Genome
     

    Feb. 2004 (tetNig1)


      X. tropicalis Genome
     

    Aug. 2005 (xenTro2)

    Oct. 2004 (xenTro1)


      Zebra Finch Genome
     

    Jul. 2008 (taeGut1)


      Zebrafish Genome
     

    Jul. 2007 (danRer5)

    March 2006 (danRer4)

    May 2005 (danRer3)

    Jun. 2004 (danRer2)

    Archives of older assemblies
    Archived danRer1 liftOver files


      Other 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
     

    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
     

    May 2008 (ce6)

    January 2007 (ce4)

    March 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
     

    June 2008 (sacCer2)

    Oct. 2003 (sacCer1)


      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.