What's the difference between 5'RACE and gemome walking? - (Jul/18/2005 )
I know this is a naive question. But I really can't understand at which condition I use 5'RACE and at which condtion I use genome walking. I am going to find the promoter region of a non-coding transcript. I have proved the existance of this transcript, now I want to know the promoter region. At first, I think the only thing I can do is to do 5'RACE. Now I know someone use genome walking to do it. What should I do? Any suggestion is appreciate. 
-seenew-
QUOTE (seenew @ Jul 18 2005, 05:13 AM)
I know this is a naive question. But I really can't understand at which condition I use 5'RACE and at which condtion I use genome walking. I am going to find the promoter region of a non-coding transcript. I have proved the existance of this transcript, now I want to know the promoter region. At first, I think the only thing I can do is to do 5'RACE. Now I know someone use genome walking to do it. What should I do? Any suggestion is appreciate.
Well, you won't find the promoter region using 5'RACE. This is a PCR method used to generate complete cDNA transcripts that contain the entire 5' end (5'RACE) and 3'end (3'RACE). It won't help you get any genomic sequence (where the promoter is located).
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?...hmg.figgrp.2574
I would say inverse PCR is the way to go. Start at the 5'end of your gene and walk to the promotoer region by generating small PCR products to sequence along the way.
Good luck!
LTR
-L_Reiter-