Need help on finding out DNA binding sites

[chitown82]

Hey,

I'm posting this here with the hopes that someone who has done research can help me out.

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/databases. Can anyone help?!?


Thank you!!!

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[EvoDevo]

Your question is a little out of whack. You asked whether a protein has DNA binding sites for Smad class proteins. I assume that what you meant to ask was, "Does the TRP-1 gene region (promoter, gene region) contain any Smad class protein consensus sequences/sites?"

(IIRC, Smads are a class of transcription factors or co-factors that operate in the TGF-Beta family..yep, here's a figure:

)

Anyway, unless that information has been published before (and I did a quick pubmed search for "TRP-1 and Smad" - no matches), the best way to do this is to:

1. find the TRP-1 gene regulatory sequence and copy it.
2. Go to one of several websites (I like Transfac) and plug your sequence in.
3. See if any Smad consensus sequences pop up.

Good luck!

 

[chitown82]

Your question is a little out of whack. You asked whether a protein has DNA binding sites for Smad class proteins. I assume that what you meant to ask was, "Does the TRP-1 gene region (promoter, gene region) contain any Smad class protein consensus sequences/sites?"

(IIRC, Smads are a class of transcription factors or co-factors that operate in the TGF-Beta family..yep, here's a figure:

)

Anyway, unless that information has been published before (and I did a quick pubmed search for "TRP-1 and Smad" - no matches), the best way to do this is to:

1. find the TRP-1 gene regulatory sequence and copy it.
2. Go to one of several websites (I like Transfac) and plug your sequence in.
3. See if any Smad consensus sequences pop up.

Good luck!

Hey there,
Thanks for your response - I was freaking out and I just realized my question made little sense. I am, in fact, looking to see whether the TRP-1 gene has Smad consensus sequences. I will try the link you posted. Thank you so much!

 

[EvoDevo]

No prob