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  About the UCSC Genome Bioinformatics Site

Welcome to the UCSC Genome Browser website. This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to the ENCODE and Neandertal projects.

We encourage you to explore these sequences with our tools. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Blat quickly maps your sequence to the genome. The Table Browser provides convenient access to the underlying database. VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. Genome Graphs allows you to upload and display genome-wide data sets.

The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering (CBSE) at the University of California Santa Cruz (UCSC). If you have feedback or questions concerning the tools or data on this website, feel free to contact us on our public mailing list.


  NewsFollow GenomeBrowser on Twitter

To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the genome-announce mailing list.

20 December 2012 - 28 New Vertebrate Assemblies!

Over the past several weeks, we have released 28 new vertebrate assemblies on the public Genome Browser website, featuring 22 new species and 6 assembly updates. These assemblies were added to support the 60-species Conservation track on the latest mouse assembly (mm10/GRCm38). Several of these species were originally sequenced and assembled for the Mammalian Genome Project (Lindblad-Toh et al., Nature 2011)*.

Primates:

  • Baboon (Papio hamadryas) papHam1 – Pham_1.0 (Nov. 2008) from the Baylor College of Medicine HGSC
  • Bushbaby (Otolemur garnettii) otoGar3 – OtoGar3 (Mar. 2011) from the Broad Institute
  • Chimpanzee (Pan troglodytes) panTro4 – Build 2.1.4 (Feb. 2011) from the Chimpanzee Genome Sequencing Consortium
  • Gibbon (Nomascus leucogenys) nomLeu2 – Nleu1.1 (Jun. 2011) from the Gibbon Genome Sequencing Consortium
  • Mouse lemur (Microcebus murinus) micMur1 – MicMur1.0 (Jul. 2007) from the Broad Institute
  • Rhesus macaque (Macaca mulatta) rheMac3 – CR_1.0 (Oct. 2010) from the Beijing Genomics Institute
  • Squirrel monkey (Saimiri boliviensis) saiBol1 – SaiBol1.0 (Oct. 2011) from the Broad Institute
  • Tarsier (Tarsius syrichta) tarSyr1 – Tarsyr1.0 (Aug. 2008) from WUSTL and the Broad Institute

Other mammals:

  • Alpaca (Vicugna pacos) vicPac1 – VicPac1.0 (Jul. 2008) from the Broad Institute
  • Armadillo (Dasypus novemcinctus) dasNov3 – DasNov3 (Dec. 2011) from the Broad Institute
  • Cat (Felis catus) felCat5 – Felis_catus-6.2 (Sep. 2011) from the International Cat Genome Sequencing Consortium
  • Dolphin (Tursiops truncatus) turTru2 – Ttru_1.4 (Oct. 2011) from the Baylor College of Medicine HGSC
  • Hedgehog (Erinaceus europaeus) eriEur1 – Draft_v1 (Jun. 2006) from the Broad Institute
  • Kangaroo rat (Dipodomys ordii) dipOrd1 – DipOrd1.0 (Jul. 2008) from Baylor College of Medicine HGSC and the Broad Institute
  • Manatee (Trichechus manatus latirostris) triMan1 – TriManLat1.0 (Oct. 2011) from the Broad Institute
  • Megabat (Pteropus vampyrus) pteVam1 – PteVap1.0 (Jul. 2008) from the Broad Institute
  • Naked mole rat (Heterocephalus glaber) hetGla2 – HetGla_female_1.0 (Jan. 2012) from the Broad Institute
  • Pig (Sus scrofa) susScr3 – Sscrofa10.2 (Aug. 2011) from the Swine Genome Sequencing Consortium
  • Pika (Ochotona princeps) ochPri2 – OchPri2 (Jul. 2008) from the Broad Institute
  • Rock hyrax (Procavia capensis) proCap1 – Procap1.0 (Jul. 2008) from the Baylor College of Medicine HGSC
  • Shrew (Sorex araneus) sorAra1 – SorAra1.0 (Jun. 2006) from the Broad Institute
  • Sloth (Choloepus hoffmanni) choHof1 – ChoHof1.0 (Jul. 2008) from the Broad Institute
  • Squirrel (Spermophilus tridecemlineatus) speTri2 – SpeTri2.0 (Nov. 2011) from the Broad Institute
  • Tree shrew (Tupaia belangeri) tupBel1 – Tupbel1.0 (Dec. 2006) from the Broad Institute

Other vertebrates:

  • Atlantic cod (Gadus morhua) gadMor1 – GadMor_May2010 (May 2010) from Genofisk
  • Budgerigar (Melopsittacus undulatus) melUnd1 – v6.3 (Sep. 2011) from WUSTL
  • Coelacanth (Latimeria chalumnae) latCha1 – LatCha1 (Aug. 2011) from the Broad Institute
  • Nile tilapia (Oreochromis niloticus) oreNil2 – OreNil1.1 (Jan. 2011) from the Broad Institute

Our sincere thanks to the many organizations who contributed to the release of these datasets. We'd also like to acknowledge the Genome Browser staff who worked on this release: Hiram Clawson, Chin Li, Brian Raney, Brooke Rhead, Steve Heitner, Pauline Fujita, Luvina Guruvadoo, Greg Roe, and Donna Karolchik. Please see the Genome Browser credits page for complete acknowledgment information and data use restrictions. All datasets may be downloaded from our ftp server or downloads page.

We regret that we don't have the resources to support the many other genomics research communities who would like us to visualize their data in our browser. However, we can provide you with information for setting up your own browser or track hub to display your data, as well as links to other visualization resources on the web that are specific to your genome of interest. Feel free to contact our mail list for more information.

*Lindblad-Toh K et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12;478(7370):476-82.


14 December 2012 - Reduced Coverage During the Holidays

The UCSC campus will be closed for the holidays from December 22, 2012 through January 1, 2013. The Genome Browser will still be available; however, our backup systems will be offline for two days, December 27 and 28. During this time if we experience any issues, associated fixes are likely to be delayed. The help desk will also be minimally staffed during this period. We will be monitoring the mailing lists for urgent messages, but the bulk of the questions will go unanswered until early January.


07 December 2012 - dbSNP 137 Available for hg19: We are pleased to announce the release of four tracks derived from dbSNP build 137, available on the human assembly (GRCh37/hg19). dbSNP build 137 is available at NCBI. The new tracks contain additional annotation data not included in previous dbSNP tracks, with corresponding coloring and filtering options in the Genome Browser. Read more.

27 November 2012 - New UCSC Genes Track Released for Mouse: We're happy to announce the release of a new UCSC Genes track for the GRCm38/mm10 mouse Genome Browser. Read more.

==> News Archives

  Conditions of Use

The sequence and annotation data displayed in the Genome Browser are freely available for any use with the following conditions:

  • Genome sequence data use restrictions are noted within the species sections on the Credits page.
  • Some annotation tracks contributed by external collaborators contain proprietary data that have specific use restrictions. To check for restrictions associated with a particular genome assembly, review the database/README.txt file in the assembly's downloads directory.

The UCSC, Ensembl, and NCBI browser and annotation groups have established a common set of minimum requirements for public display of genome data made available after Spring 2009, described here.

The Genome Browser and Blat software are free for academic, nonprofit, and personal use. A license is required for commercial use. See the Licenses page for more information.

Program-driven use of this software is limited to a maximum of one hit every 15 seconds and no more than 5,000 hits per day.

For assistance with questions or problems regarding the UCSC Genome Browser software, database, genome assemblies, or release cycles, see the FAQ.