UCSC Genome Bioinformatics
   Home  -   Genomes  -   Blat  -   Tables  -   Gene Sorter  -   PCR  -   Proteome  -   FAQ  -   Help
  Sequence and Annotation Downloads
 

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 The Description of the annotation database page (no longer maintained) also provides descriptions of selected tables in the database.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

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)

  • Full data set
  • Data set by chromosome
  • Annotation database
  • LiftOver files - release pending
  • Pairwise Alignments - release pending
  • Multiple Alignments
    • Multiple alignments of 5 vertebrate genomes with horse - release pending
    • Conservation scores for alignments of 5 vertebrate genomes with horse - release pending

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
 

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
 

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.