Question: Get gene promoter coordinates
1
gravatar for manu
7 weeks ago by
manu20
manu20 wrote:

Hello everyone, I'm trying to find a way to get the coordinates of the promoter region of a gene (if possible, of a list of genes). So let's suppose that i have the gene BRCA2 and I know that for genome version hg38 this gene has coordinates Chr13: 32,315,086-32,400,268. Now what i would like to get is the the start and end coordinate of the promoter region. Is there a way to get such info? I've already tried with biomart-ensembl (but i managed to get only the promoter sequence and not the coordinates) and plus i can do it only one gene at a time and, since i have a long list, that would take too long. Moreover, I tried in R with the function promoter() but it doesn't return results for all the genes in the list, but only for some of them.

Do you know any way to get these coordinates? Any additional info is very appreciated! Thank you

coordinates hg38 promoter gene • 176 views
ADD COMMENTlink written 7 weeks ago by manu20

The promoter is right upstream of the gene start coordinate (TSS to be precise), people often use something like 200-500bp upstream as a proxy, isn't that sufficient for your purpose?

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by ATpoint44k

Hi! Yes either 500bp or 2k bp are ok. Do you know how to get the coordinates?

ADD REPLYlink written 7 weeks ago by manu20

From which package is the promoter() function? The FANTOM project surveyed enhancer and promoter regions genome-wide - perhaps you can use their data: https://fantom.gsc.riken.jp/5/

ADD REPLYlink written 7 weeks ago by Kevin Blighe69k
1

Hi Kevin, the function prom promoter() is from the package GenomicFeatures.

ADD REPLYlink written 7 weeks ago by manu20
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