promoter region of gene

Question

[bioinfo]

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

Answer 1

[GenoMax]

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 ?

[bioinfo]

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?

[ATpoint]

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