Question: transcription factor binding site
0
gravatar for bioinfo
3.4 years ago by
bioinfo50
research
bioinfo50 wrote:

hi how to retrieve the sequences of the proximal promoter of the genes from the database of transcriptional start site?

genome • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Denise - Open Targets5.0k • written 3.4 years ago by bioinfo50

Which database of transcription start sites are you looking at? Are you looking at single genes or genome-wide? What species is this in? What coding languages do you know?

ADD REPLYlink written 3.4 years ago by Emily_Ensembl19k

I am looking for a set of genes for Homo sapiens in DBTSS (database of transcription start sites).

ADD REPLYlink written 3.4 years ago by bioinfo50
1
gravatar for Denise - Open Targets
3.4 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

This is the URL of their download page. Please note the has not been updated since July 2015. You may want to have a look at the annotation of promoter regions from the Ensembl Regulatory build, which is more updated than DBTSS. If you know Perl you could download the sequence of those promoter regions (check the Ensembl Regulation API tutorial). If you have a couple of genes only, you can download the sequence from the browser itself. See the sequences of all regulatory regions in the HOXB2 gene

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Denise - Open Targets5.0k
1

Release 9.0 Updated (July 9, 2015) Based on UCSC hg38, mm10 Top|

2009 would be old, but the above is the update information from http://dbtss.hgc.jp/

ADD REPLYlink written 3.4 years ago by Michael Dondrup46k

Yes, it was a typo of mine. I meant 2015. I will edit my original post.

ADD REPLYlink written 3.4 years ago by Denise - Open Targets5.0k

For some genes, i have got the type promoter regions three times and the bp length is different for ex: KRT23. Can you please suggest me!!!

ADD REPLYlink written 3.4 years ago by bioinfo50
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