Hello Rekha, The data you are looking at in the Table Browser is for the RefSeq track (which shows a start position of chr17:41,196,311) and the data you are viewing in the main Browser (from your attached image) is for the UCSC genes track (which shows a start position of chr17:41,196,312). Gene tracks often differ slightly so this is as expected.
To find RefSeq entries for BRCA1 go to the main gateway page (http://genome.ucsc.edu/cgi-bin/hgGateway) and type in "BRCA1" in the position/search box and hit submit. This should bring up a list of related records for the UCSC Genes and RefSeq Genes data sets (as well as others) and you can select the most appropriate entry for your research. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 1/10/12 10:04 PM, Rekha Saini wrote: > Hi Vanessa, > > Thank you for the reply. > > In the Genome Browser, I directly typed 'BRCA1' in the gene search box and > clicked on jump button. > It gave 'chr17:41,196,313-41,277,500' in the position/search box. > > Attached is the file showing the obtained result. > > Thanks and Regards, > Rekha Saini > > -----Original Message----- > From: Vanessa Kirkup Swing [mailto:[email protected]] > Sent: Wednesday, January 11, 2012 4:56 AM > To: Rekha Saini > Cc: [email protected] > Subject: Re: [Genome] Genomic location for the human gene BRCA1 > > Hi Reka, > > Could you tell us the steps in which you got the Genome Browser > Coordinates listed below? > > UCSC Genome Browser:chr17:41,196,313-41,277,500 > > This will help us reproduce the issue you are seeing. Thanks! > > Please reply to: [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ---------- Forwarded message ---------- > From: Vanessa Kirkup Swing<[email protected]> > Date: Tue, Jan 10, 2012 at 2:21 PM > Subject: Re: [Genome] Genomic location for the human gene BRCA1 > To: Rekha Saini<[email protected]> > Cc: "[email protected]"<[email protected]> > > > Hi Reka, > > The example for BRCA1 that you gave appears to be this refSeq ID: NM_007300 > > In the table browser results for hg19: > #geneName name chrom strand txStart txEnd > BRCA1 NM_007300 chr17 - 41196311 41277500 > > Here is the gene details page for this refSeq ID: > > http://genome.ucsc.edu/cgi-bin/hgc?db=hg19&o=41196311&t=41277500&g=refGene&i=NM_007300 > > Scroll down to: "mRNA/Genomic Alignments" > > BROWSER | SIZE IDENTITY CHROMOSOME STRAND START END > QUERY START END TOTAL > ----------------------------------------------------------------------------------------------------- > browser | 7270 100.0% 17 - 41196312 41277500 > NM_007300 1 7270 7287 > > > The start coordinates differ by 1 (41196311 vs. 41196312). The 0-based > vs. 1-based reason applies to this case and is documented here: > > http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 > > > Hopefully this clarifies the issue for you. If you have further > questions, please email the list: [email protected]. > > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > > ---------- Forwarded message ---------- > From: Rekha Saini<[email protected]> > Date: Tue, Jan 10, 2012 at 4:25 AM > Subject: [Genome] Genomic location for the human gene BRCA1 > To: "[email protected]"<[email protected]> > > > Hi, > > I'm interested in the genomic location of 'BRCA1' human gene. > > When I searched it from UCSC table browser selecting refFlat table, > the transcript retrieved lies on Chr17 with transcript start as > 41196311. > And when I used UCSC Genome Browser for the same gene, chromosome > start retrieved is 41196313. > > To be more specific, following are the coordinates obtained: > UCSC table browser :chr17:41196311-41277500 > UCSC Genome Browser:chr17:41,196,313-41,277,500 > > Even if we consider the start coordinates associated with table > browser to be 0-based and assume that the Genome Browser converts it > to 1-based, then also the results are not consistent. > > Could you please help us to understand how the UCSC Genome Browser > process it and which one is the correct genomic location for the gene > 'BRCA1' ? > > Thanks& Regards, > Rekha Saini > > DISCLAIMER > ========== > This e-mail may contain privileged and confidential information which > is the property of Persistent Systems Ltd. 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