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.

WARNING: This is a test site. Data and tools here are under construction, have not been quality reviewed, and are subject to change at any time. For high-quality reviewed annotations on our production server, visit http://genome.ucsc.edu.

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.

We are pleased to announce the release of four tracks derived from dbSNP build 135, available on the human assembly (GRCh37/hg19). dbSNP build 135 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 dbSNP build 132, there are four tracks in this release. One is a track containing all mappings of reference SNPs to the human assembly, labeled "All SNPs (135)". The other three tracks are subsets of this track and show interesting and easily defined subsets of dbSNP:

• Common SNPs (135): uniquely mapped variants that appear in at least 1% of the population
• Flagged SNPs (135): uniquely mapped variants, excluding Common SNPs, that have been flagged by dbSNP as "clinically associated"
• Mult. SNPs (135): variants that have been mapped to more than one genomic location

By default, only the Common SNPs (135) are visible; other tracks must be made visible using the track controls.

You will find the four SNPs (135) tracks on the Human Feb. 2009 (GRCh37/hg19) browser in the "Variation and Repeats" group.

We're happy to announce the release of an updated UCSC Genes track for the GRCh37/hg19 human Genome Browser. This release includes more noncoding transcripts based on data from Rfam and from the tRNA Genes track contributed by the Todd Lowe lab at UCSC.

The new release has 80,922 total transcripts, compared with 77,614 in the previous version. The total number of canonical genes has increased from 27,297 to 31,227. Comparing the new gene set with the previous version:

• 24,804 transcripts did not change between versions.
• 483 transcripts were not carried forward to the new version.
• 46,367 transcripts are "compatible" with those in the previous set, meaning that the two transcripts show consistent splicing. In most cases, the old and new transcripts differ in the lengths of their UTRs.
• 5,960 transcripts overlap with those in the previous set but do not show consistent splicing, i.e., they contain overlapping introns with differing splice sites.

Additionally, several improvements where made to the UCSC Genes build pipeline:

• We developed new genomic alignment protocols for aligning short sequences, facilitating the expansion of the noncoding RNA content.
• We changed the way that gene symbols are assigned to transcripts so that names from curated sources are favored over names coming directly from GenBank mRNA records. This change resolved several confusing naming issues reported to us by users.
• We tracked down and corrected a bug in the pipeline that was causing a number of poor quality protein mappings to displace high quality protein mappings.
• We have started producing two new tables, knownGeneTxMrna and knownGeneTxPep, that contain sequence derived from the genome rather than from the mRNA used for the transcript.

More details about the new UCSC Genes track can be found on the UCSC Genes track description page.

Many thanks to Melissa Cline, Jim Kent, Brian Raney, Mark Diekhans, and Brooke Rhead for their work on this track!

3 January 2012 - Roadmap Epigenomics Now Available through Data Hub at Washington University: We are pleased to announce the release of the Roadmap Epigenomics data on the UCSC Genome Browser through our Data Hub function. Read more.

19 December 2011 - Variant Call Format (VCF) Now Supported in Genome Browser: We are pleased to announce that the UCSC Genome Browser now supports Variant Call Format (VCF). Read more.

==> News Archives

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.