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.

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

18 April 2011 - dbSNP 132 Available for hg19

We are pleased to announce the release of four tracks derived from dbSNP build 132, available on the human assembly (GRCh37/hg19). dbSNP build 132 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.

As for prior builds of dbSNP, there is a track that contains all mappings of reference SNPs to the human assembly; it is now labeled "All SNPs (132)". Three new tracks have been added to show interesting and easily defined subsets of dbSNP:

• Common SNPs (132): uniquely mapped variants that appear in at least 1% of the population
• Flagged SNPs (132): uniquely mapped variants, excluding Common SNPs, that have been flagged by dbSNP as "clinically associated"
• Mult. SNPs (132): variants that have been mapped to more than one genomic location

By default, only the Common SNPs (132) are visible; other tracks must be made visible using the track controls.

The counts of distinct reference SNPs and their mappings to hg19 differ greatly among the tracks:

* The Common and Flagged tracks have more mappings than SNPs due to the alternate haplotype sequences and the pseudoautosomal regions on X and Y. SNPs are considered uniquely mapped if they map only once to a haploid reference genome. These regions add non-haploid sequence to the reference genome; therefore, multiple mappings involving these regions are still considered unique.

You will find the four SNPs (132) tracks on the Human Feb. 2009 (GRCh37/hg19) browser in the "Variation and Repeats" group.

Many thanks to dbSNP at NCBI for the data, and to Mary-Claire King at the University of Washington for helpful comments that motivated us to enhance our dbSNP annotations. The tracks were produced at UCSC by Angie Hinrichs, Brooke Rhead, Bob Kuhn, and Jim Kent.

18 April 2011 - Sheep Browser Released

We are happy to announce a Genome Browser for the initial release of sheep (Ovis aries) genome. The Feb. 2010 Ovis aries draft assembly (NCBI project 10709, GCA_000005525.1) was produced by the International Sheep Genomics Consortium (ISGC) sequencing center. The mitochondrial genome was sequenced by Justus-Liebig-University.

There are 27 chromosomes: chr1 - chr26, chrX, plus the mitochondrial sequence chrM from genbank accession NC_001941, for a total sequence length of 2,860,512,983 bases. There are 1,659,241,706 'N' bases in gaps, leaving 1,201,271,277 ACGT bases.

The genome has been sequenced using 454 FLX sequencing to 3X coverage (DNA derived from six female sheep each sequenced with 0.5X coverage). Contigs were assembled based on alignment to the bovine genome and ordered into ovine chromosomes using BAC-end sequences and the virtual sheep genome.

We'd like to thank the International Sheep Genomics Consortium (ISGC) sequencing center and Justus-Liebig-University for providing this assembly. We'd also like to acknowledge the UCSC team who worked on this release: Chin Li, Greg Roe, and Luvina Guruvadoo. The sheep browser annotation tracks were generated by UCSC and collaborators worldwide.

04 March 2011 - The Meaning of Red: Consensus on color scheme for CNVs: Consensus was reached on color standards to represent CNV loss (red) and gain (blue) in genomics databases by DGV, NCBI, DECIPHER, UCSC and ISCA during the 1st annual ISCA Scientific Conference. Read more

01 March 2011 - Updated Chimpanzee Browser Released: We are happy to announce the release of a Genome Browser for the latest release of the chimpanzee (Pan troglodytes) genome. Read more

19 January 2011 - Browser Released for Zebrafish Zv9 Assembly: The most recent zebrafish assembly -- Zv9 (UCSC version danRer7, Jul. 2010) -- is now available in the UCSC Genome Browser. Read more

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.