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From the Genomes page, you can jump to the default position of an assembly by clicking the "Go" button or you can specify a particular genome position in a variety of formats. These same formats are valid in the search bar above the main Genome Browser track display.
Valid position queries can include:
To specify a genome position:
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.
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_GL000213v1||Displays all of the unplaced contig GL000213v1|
|chr3_GL000221v1_random||Displays the unlocalized contig GL000221v1|
|chr1_KN196472v1_fix||Displays all of patch fix KN196472v1|
|20p13||Displays the region for band p13 on chromosome 20|
|GTATGTAGCCACGGAGCACCATTACCTGTCACCATTACCTGAATGGCTA||Displays the first best match to this DNA sequence, e.g. chr21:33034835-33034883 for hg19|
|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 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 NM_000310.4 and NM_012090.5. This syntax may also be used for other range queries,
such as between uniquely determined ESTs, mRNAs, refSeqs, SNPS, etc.
|Displays the region containing HGVS term|
|chr1 0 1000||When entered without ":" and "-", uses 0-based, half-open coordinates (like custom tracks and internal table coordinates), so displays chr1:1-1000|
|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..