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promoter region of gene

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

gene
• 3,306 views • link
written by bioinfo bioinfo

1 answer

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 ?

• 0 views • link
written by GenoMax GenoMax

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?

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written by bioinfo bioinfo

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

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written by ATpoint ATpoint

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