Question: promoter region of gene
0
gravatar for bioinfo
9 months 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 • 524 views
ADD COMMENTlink written 9 months ago by bioinfo50
0
gravatar for genomax
9 months ago by
genomax58k
United States
genomax58k 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 9 months ago • written 9 months ago by genomax58k

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 9 months ago by bioinfo50

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

ADD REPLYlink written 9 months ago by ATpoint9.3k
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