UCSC Genome Bioinformatics
  Querying the Genome Browser

You may browse to the default genome position of an assembly when clicking the "submit" button or you may specify a genome position in a variety of formats.

Valid position queries can include:

  • Chromosome numbers
  • Chromosomal coordinate ranges
  • Gene names
  • Accession numbers
  • An mRNA, EST or STS marker
  • Keywords from the Genbank description of an mRNA

To specify a genome position:

  1. Select the desired clade, genome and assembly
  2. Enter the desired query in the "search term" box (see sample queries below)
  3. Click the "submit" button

Note: A query may have multiple results. If this is the case, a results page will appear listing each result along with the track it is associated with. Once selected, the result will be displayed in the Browser with a highlighted tag, making it easier to identify.

Sample Queries

Below is a list of examples that might be used to query the Genome Browser. Note that not every query listed here will produce a result in every assembly. The list serves only to illustrate the different types of queries that can be performed.
  Query: Genome Browser Response:
  chr7 Displays all of chromosome 7
  chr3:1-1000000 Displays the first million bases of chromosome 3, counting from the p-arm telomere
  chr3:1000000+2000 Displays a region of chromosome 3 that spans 2000 bases, starting with position 1000000
  chrUn_gl000212 Displays all of the unplaced contig gl000212
  chr6_GL285171_random Displays the non-localized contig GL285171
  GL192360 Displays all of scaffold GL192360
  20p13 Displays the region for band p13 on chromosome 20
  374180 Displays the region containing Entrez Gene identifier 374180
  AA205474 Displays the region containing the EST with Genbank accession AA205474 in the BRCA1 cancer gene on chromosome 17
  AC008101 Displays the region containing the clone with Genbank accession AC008101
  AF083811 Displays the region containing the mRNA with Genbank accession number AF083811
  NM_017414 Displays the region containing RefSeq identifier NM_017414
  NP_059110 Displays the region containing protein accession number NP_059110
  PRNP Displays the region containing the HUGO Gene Nomenclature Committee identifier PRNP
Displays the region between genome landmarks, such as the STS markers RH18061 and RH80175, or chromosome
bands 15q11 to 15q13, or SNPs rs1042522 and rs1800370. This syntax may also be used for other range queries,
such as between uniquely determined ESTs, mRNAs, refSeqs, etc.
  pseudogene mRNA Lists transcribed pseudogenes, but not cDNAs
  p53 Lists mRNAs related to the p53 tumor suppressor
  T-cell receptor Lists mRNAs for T-cell receptor genes in Genbank
  breast cancer Lists mRNAs associated with breast cancer
  homeobox caudal Lists mRNAs for caudal homeobox genes
  zinc finger Lists zinc finger mRNAs
  kruppel zinc finger Lists only kruppel-like zinc fingers
  huntington Lists candidate genes associated with Huntington's disease
  zahler Lists mRNAs deposited by a scientist named Zahler
  Evans,J.E. Lists mRNAs deposited by co-author J.E. Evans
  Use this last format for author queries. Although Genbank requires the search format Evans JE, internally it uses the format Evans,J.E.