Tips - how to find a promoter sequence - (Jun/08/2005 )

hi

we can find promoter in a simple way .
take the mRNA of the gene of interest and take the first 60 or more basepairs and blast it with the whole genome of the organism .
the hit having plus plus and 100 % similarity , click on the hit .
in this way either the gene map or the genbank flat file will come .
from the map we can see where there is 100% blast hit ..take some 1500 bp before it and some bp after that .
in the flat file u can take also same bp as in the blast hit the sbjct is shown from where it has 100% similarity .so u take some 1500 bp before that and some base pairs after that.
than take that seq and align with the portions of mRNA that u had taken in clustalW .take the regions before the alignment . as the regions are before the TSS it is the promoter region.
cheers

Yes, sometimes promoter search is a pain. Since not every promoter has been experimentally characterized and thus has a promoter sequence in the GenBank database. Even there is a promoter sequence for a particular gene deposited by researchers, the NCBI entrez search tool is TOO stupid to return it to you. In this case you can follow ruchita_sweet's method to fish it out. NCBI should ask Google to do the job and should also annotate promoter sequences as they have done with refseq.

EZRetrieve ( http://siriusb.umdnj.edu:18080/EZRetrieve/index.jsp ) can do the job. also check Adnan's page:
http://arep.med.harvard.edu/labgc/adnan/hsmmupstream/

One thing I want to point out is that for human, promoter can be 20 kb upstream, most people take 4kb upstream to be safe, some take 2kb + downstream 100 bp. When dealing with individual genes should be cautious, large scale is ok.