Question: promoter region of gene
0
gravatar for bioinfo
11 days ago by
bioinfo50
research
bioinfo50 wrote:

Hi How to download the defined promoter region (−1500/+500 around TSS) of genes and miRNAs from the UCSC Table Browser?

gene • 109 views
ADD COMMENTlink written 11 days ago by bioinfo50
0
gravatar for GenoMax
11 days ago by
GenoMax42k
United States
GenoMax42k wrote:

https://genome.ucsc.edu/FAQ/FAQdownloads.html#download18

You will need to use the Table Browser method mentioned since even though the "bigZips" folder is supposed to contain files for the upstream sequences they are not there in GRCh38.

@Giovanni's answer here may also be helpful: How to get promoter coordinates of hg19 from UCSC genome browser ?

ADD COMMENTlink modified 11 days ago • written 11 days ago by GenoMax42k

Thanks for the response. One more query, i have entered one gene to check the promoter sequence in UCSC genome browser, say for eg, EGFR and i got different promoter sequence for different transcript variant. So which one to take?

ADD REPLYlink written 11 days ago by bioinfo50

The one that fits your scientific question :-D No one here should know better than you.

ADD REPLYlink written 11 days ago by ATpoint3.0k
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