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. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
