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Question: Hg19 Promoters .Bed File
4
gravatar for Jneary1978
9.7 years ago by
Jneary1978 • 60
San Antonio
Jneary1978 • 60 wrote:

Is there already a pre-defined downloadable list of all predicted promoters in the human genome? Preferably a .bed file? I'm not having a lot of luck finding anything.

If not, can you suggest resources to obtain this info?

Thanks!

bed promoter hg • 7.1k views
ADD COMMENT • link •
modified 9.7 years ago by Casey Bergman ♦ 18k • written 9.7 years ago by Jneary1978 • 60
2
gravatar for Casey Bergman
9.7 years ago by
Casey Bergman ♦ 18k
Athens, GA, USA
Casey Bergman ♦ 18k wrote:

If you define X kb upstream of a gene to be a promoter, you can get this using the UCSC table browser as follows:
ADD COMMENT • link modified 23 months ago by Kevin Blighe ♦ 69k • written 9.7 years ago by Casey Bergman ♦ 18k
1

There's also the Ensembl annotation data - this contains more information on transcripts and exon boundaries too.

But to my knowledge, there's no definitive definition of promoter X being 2kb in length, and promoter Y being 1.5kb. We just have to make a judgment on what's an appropriate size.

ADD REPLY • link modified 16 months ago by _r_am ♦ 32k • written 9.7 years ago by Rob • 140

Thank you much!

ADD REPLY • link written 9.7 years ago by Jneary1978 • 60
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