Need help on how to find binding sites!!

[chitown82]

Hey,

I am in great need of finding out if a particular protein (TRP-1) has DNA consensus binding sites for the Smad class of proteins (Smad1, 4, 5, 8, etc). Does anyone know how I can find out this information. I don't know enough about ExPASy or SwisProt or the other online tools. Can anyone help!?


Thank you!!!

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[mendel121]

Hey,

I am in great need of finding out if a particular protein (TRP-1) has DNA consensus binding sites for the Smad class of proteins (Smad1, 4, 5, 8, etc). Does anyone know how I can find out this information. I don't know enough about ExPASy or SwisProt or the other online tools. Can anyone help!?


Thank you!!!

Try transfac, if you go to genome.ucsc.edu, go to the genomes linke, then type in TRP-1 (make sure that human is selected under genome), click the first entry that comes up (TRP-185) which takes you to the browser window. CLick the DNA link near the top of the page, and aske for 2,000 or so base pairs upstream, and the copy that sequence into the transfac search engine (link below). It will tell you if there are smad or any other sites.

http://www.gene-regulation.com/pub/databases.html

Also try to google transcription factor binding sites, or something like that, there are lots of sites that will do similar things. Also if you do a pubmed search for the smads (or look at their transfac entries) to find out what their consensus sequence is, you can use Word, or many other programs to search for the sequence as if it were a word. I only say this becomes often the transfac results are a little confusing, but you should start with transfac.

Hope this helps.