This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project.

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.

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 June 2006 - Genome Browser Released for Baylor v3.4 Rat Assembly

The UCSC Genome Bioinformatics group has released a Genome Browser for the v3.4 rat (Rattus norvegicus) genome. This assembly--UCSC version rn4, November 2004--was produced by the Atlas group at Baylor Human Genome Sequencing Center (HGSC) as part of the Rat Genome Sequencing Consortium.

The sequence was assembled using a hybrid approach that combines the clone-by-clone and whole genome shotgun methods. The assembly is a minor update to version 3.3 that spliced in 54.6 Mb finished BAC sequences; the overall statistics are unchanged from releases 3.0 to 3.4.

The 3.x assemblies reflect several sequence additions and software improvements over the previous 2.x assemblies, including the sequencing of over 1100 new BACs to cover gaps, an improved marker set from the Medical College of Wisconsin, a new FPC map from the BC Cancer Agency Genome Sciences Centre, and improved linking of bactigs. For detailed information and statistics about the 3.x assemblies, see the Baylor HGSC Rat Genome Project web page.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data are made available with specific conditions for use.

We'd like to thank the Rat Genome Sequencing Consortium and the Baylor HGSC for providing this assembly. We'd also like to acknowledge the UCSC team who produced the rn4 Genome Browser: Angie Hinrichs, Fan Hsu, Brooke Rhead, Archana Thakkapallayil, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik. The rn4 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

25 May 2006 - Zv6 Zebrafish Browser Released: The latest zebrafish assembly -- Zv6 (UCSC version danRer4, March 2006) -- is now available in the UCSC Genome Browser. Read more.

10 May 2006 - NCBI Mouse Build 36 Released in Genome Browser: The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 36, is now available in the UCSC Genome Browser. Read more.

The sequence and annotation data displayed in the Genome Browser are freely available for academic, nonprofit, and personal 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 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.

• Description of the annotation database
• Data organization and format
• Terminology

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