Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Jan;42(Database issue):D764-70.
doi: 10.1093/nar/gkt1168. Epub 2013 Nov 21.

The UCSC Genome Browser Database: 2014 Update

Free PMC article

The UCSC Genome Browser Database: 2014 Update

Donna Karolchik et al. Nucleic Acids Res. .
Free PMC article


The University of California Santa Cruz (UCSC) Genome Browser ( offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser's web-based tools provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation 'tracks' for ∼90 organisms. Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror ( hosted at Bielefeld University in Germany.


Figure 1.
Figure 1.
The haplotype alleles display for the ABO gene, which encodes proteins related to the ABO blood group system. A large portion of the ‘Predicted full sequence’ section is truncated in the upper image for display purposes, and is shown in greater detail in the lower image. The leftmost columns of the top image indicate the frequency of each allele haplotype within the 1000 Genomes sample and the occurrence of homozygosity for each allele. In this instance the haplotype alleles display has been expanded to show the distribution of the haplotypes across the major 1000 Genomes population groups. The ‘Variant Sites’ columns summarize the non-synonymous variant sites that occur in at least 1% of the subject chromosomes, with the value from the reference genome (in this case GRCh37/hg19) indicated at the top of each variant column. In all but one case, the ‘O’ phenotype results from a common insertion (indicated by ‘-’ in the reference) causing a frameshift (indicated by ‘[≫]’) that results in a downstream premature stop codon, thus truncating the protein. Note that although certain haplotyes are more frequently found within one population, the insertion that gives rise to the majority of ‘O’ phenotypes is found across all populations, which may indicate that the insertion predates the most recent migration out of Africa. On the other hand, the haplotype in which the SNP variant introduces a stop codon at the variant site may have arisen in the Americas. The zoomed-in view of the ‘Predicted full sequence’ section in the bottom image shows the reference sequence (top row) and sequences incorporating the common non-synonymous variants. The residues corresponding to the variant sites are highlighted by green vertical bars, the site corresponding to the frameshift-causing insertion is highlighted by a blue bar and changes to the reference amino acid sequence are shown in red.

Similar articles

  • The UCSC Genome Browser database: extensions and updates 2013.
    Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ. Meyer LR, et al. Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9. doi: 10.1093/nar/gks1048. Epub 2012 Nov 15. Nucleic Acids Res. 2013. PMID: 23155063 Free PMC article.
  • The UCSC Genome Browser database: extensions and updates 2011.
    Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, James Kent W. Dreszer TR, et al. Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23. doi: 10.1093/nar/gkr1055. Epub 2011 Nov 15. Nucleic Acids Res. 2012. PMID: 22086951 Free PMC article.
  • The UCSC Genome Browser database: update 2010.
    Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. Rhead B, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9. doi: 10.1093/nar/gkp939. Epub 2009 Nov 11. Nucleic Acids Res. 2010. PMID: 19906737 Free PMC article.
  • UCSC genome browser tutorial.
    Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. Zweig AS, et al. Genomics. 2008 Aug;92(2):75-84. doi: 10.1016/j.ygeno.2008.02.003. Epub 2008 Jun 2. Genomics. 2008. PMID: 18514479 Review.
  • Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.
    Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X; MSeqDR Consortium Participants; MSeqDR Consortium participants: Sherri Bale, Jirair Bedoyan, Doron Behar, Penelope Bonnen, Lisa Brooks, Claudia Calabrese, Sarah Calvo, Patrick Chinnery, John Christodoulou, Deanna Church,; Rosanna Clima, Bruce H. Cohen, Richard G. Cotton, IFM de Coo, Olga Derbenevoa, Johan T. den Dunnen, David Dimmock, Gregory Enns, Giuseppe Gasparre,; Amy Goldstein, Iris Gonzalez, Katrina Gwinn, Sihoun Hahn, Richard H. Haas, Hakon Hakonarson, Michio Hirano, Douglas Kerr, Dong Li, Maria Lvova, Finley Macrae, Donna Maglott, Elizabeth McCormick, Grant Mitchell, Vamsi K. Mootha, Yasushi Okazaki,; Aurora Pujol, Melissa Parisi, Juan Carlos Perin, Eric A. Pierce, Vincent Procaccio, Shamima Rahman, Honey Reddi, Heidi Rehm, Erin Riggs, Richard Rodenburg, Yaffa Rubinstein, Russell Saneto, Mariangela Santorsola, Curt Scharfe,; Claire Sheldon, Eric A. Shoubridge, Domenico Simone, Bert Smeets, Jan A. Smeitink, Christine Stanley, Anu Suomalainen, Mark Tarnopolsky, Isabelle Thiffault, David R. Thorburn, Johan Van Hove, Lynne Wolfe, and Lee-Jun Wong. Falk MJ, et al. Mol Genet Metab. 2015 Mar;114(3):388-96. doi: 10.1016/j.ymgme.2014.11.016. Epub 2014 Dec 4. Mol Genet Metab. 2015. PMID: 25542617 Free PMC article. Review.
See all similar articles

Cited by 394 articles

See all "Cited by" articles


    1. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002;12:996–1006. - PMC - PubMed
    1. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013;41:D64–D69. - PMC - PubMed
    1. NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2013;41:D8–D20. - PMC - PubMed
    1. Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, et al. Ensembl 2013. Nucleic Acids Res. 2013;41:D48–D55. - PMC - PubMed
    1. Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. In: Murphy WJ, editor. Methods in Molecular Biology: Phylogenomics. New York: Springer; 2007. pp. 171–184.

Publication types