How do I know the genomic coordinates for a gene is GRCh37/hg19 or NCBI36/hg18?

[Yu, Jiamei]

I have genomic coordinates for Vysis LSI HER2 is: chr17:37,751,146-37,976,854, genomic coordinates for Abbott 17p is: chr17:52,271-136,647, genomic coordinates for ABsubTel17q is: chr17:80,549,525-80,969,618, how do I know the genomic coordinates for these 3 genes are GRCh37/hg19 or NCBI36/hg18?

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[Luvina Guruvadoo]

Hi Jiamei,

You may search for a gene by using the "search term" box on the Genome Browser Gateway: http://genome.ucsc.edu/cgi-bin/hgGateway. Select the appropriate assembly from the drop-down menu (e.g., hg19), and search for any gene by entering the gene name or position. If I'm not mistaken, the names you provided are probes and not gene names. The first probe is specific to the HER-2 gene. If you search for HER-2 in both hg18 and hg19, the hg19 coordinates aren't exactly those that you list, but they are a lot closer than the hg18 coordinates.

I hope this helps. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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