Question: promoter region of gene
0
gravatar for bioinfo
2.4 years ago by
bioinfo60
research
bioinfo60 wrote:

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

gene • 1.4k views
ADD COMMENTlink written 2.4 years ago by bioinfo60
0
gravatar for genomax
2.4 years ago by
genomax85k
United States
genomax85k 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 2.4 years ago • written 2.4 years ago by genomax85k

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 2.4 years ago by bioinfo60

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

ADD REPLYlink written 2.4 years ago by ATpoint36k
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