how to get characterized basal promoter regions - NOT predicted ones!! (Aug/31/2005 )
please somebody help me as i am facing lot of problems in getting the basal/functional promoter regions of certain eukaryotic genes.
What i am doing is:
1) searching ncbi be giving "gene name+ promoter" , if any hits are there then checking manually in the refrences given that whether the promoter region had been characterized or not?
2) followed by doing pubmed search..
3) if i don't get any hits then does that surely mean that the promoter of that gene is not yet characterized?? which to me is a little dicey...
Please can somebody tell me how to go about it ie getting functional promoter regions for eukaryotic genes??
Also i intend to clone these promoters.
As I said before the NCBI search is very stupid when coming to promoter search. You can first obtain the predicted 5' flanking sequence from ensembl and then do a blast search against nr database at NCBI and hopefully you will fish out the characterized promoter sequence if there is any.
i am sorry pcrman....but your way of getting functionally characterized promoters doesn't help much. through ensembl even after getting predicted 5' flanking sequence from nowhere you can get the exact promoter region information not even after 5' sequence blast in nr.
Please tell any other way if possible ??
The method I said is just for retrieving promoter sequence from GenBank in case you couldn't get it using NCBI search tool. If there is no functionally characterized promoters deposited in GenBank, the only way to get it is to clone and do a reporter gene analysis by yourself. At most times especially for methylation study there is no such need to do so because there is no much exception to the rule that a promoter sequence lies immediately upstream the transcripted sequence. If there is a CpG island there, the chance is even higher that it is a true promoter.