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to get the sequence of the promoter

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to get the sequence of the promoter

Postby snoopline » Fri May 04, 2007 9:10 am

Hi,

I'd like to analyse the promoter sequence (let's say 1kbp) of a gene using Transfac.
But first, I need the sequence...
Does anyone know how to get the sequence located in the 5' of the first exon on a gene of interest ?

any suggestion very welcome,
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Postby snoopline » Fri May 04, 2007 9:37 pm

Ok I got it
Go on
http://www.dsi.univ-paris5.fr/genatlas
find your gene of interest by filling the form (symbol name or id OMIM).
on the result page click on the gene you are interested about
a page with a lot of information is displayed
In the DNA paragraph you'll find a link :
10 Kb 5' upstream gene genomic sequence study

Just click on it to get the sequence
It's a little bit to long for alibaba2 so cut it and paste it in alibaba2

If others find other solutions, feel free to share.
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Re: to get the sequence of the promoter

Postby Margaret2009 » Tue Sep 22, 2009 12:41 pm

A great site http://www.mybioinfo.info , where you can search your genes using symbol, NCBI RefSeq or words.

And, 5' up-stream 10 kb promoter region is right there for you.
It tells you which strand the gene is on. And 10 kb is in the 5' up-stream for sure. See the number yourself.

This site lists everything, mRNA, protein and genomic sequences in a tabular format. You even can add genes to your gene list and download multiFASTA format of sequences. Neat!
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