promoter search - (Jun/02/2006 )

Hi

I am just wondering how to get a gene's promoter sequence form Genebank or other databases.
Thanks.

CKXX

simple just blast ur gene sequence against the genome of interest and pull out 2000bp upstream of the transcription startsite of ur gene of interest. and do make sure that there is no splice varient for ur gene of interest upstream of what transcript u r looking at. this could be done by blasting ur gene of interest against est of the species of interest.

2000 or 200?

I usually take 2kb. If there is other gene sitting upstream then I will think before including that gene's portion.
It also depends on the model system you are using, for example, if you use human or mouse system then many a times there are regulatory elements of the gene are situated in the intronic region of the upstream gene. If this is known then you should think on how this 'regulatory element' may affect your work. For few systems, such thing doesn't exist, there you can take a part of upstream gene without much hassle.
Should you decide to take a chunk of upstream gene then think about the orientation of the gene as well for the above mentioned reasons.

If its bioinformatics work, then take 2kb. If its wet lab work then think on the points.

Hi,

some times ago I shared the same problem and I decided to use ensEMBL.
http://www.ensembl.org/

After finding your gene of interrest
e.g. GRIP2:
http://www.ensembl.org/Homo_sapiens/genevi...ENSG00000144596
you have to open the corresponding transcript_info link.
http://www.ensembl.org/Homo_sapiens/exonvi...ENST00000273083
http://www.ensembl.org/Homo_sapiens/exonvi...ENST00000383795
Here you have the possibilty to expand the 5' upstream region by using the "Rendering options" -> "Flanking sequence at either end of transcript". If you choose the value 1000 for the "Flanking sequence at either end of transcript" option your result look as followed:
http://www.ensembl.org/Homo_sapiens/exonvi...5&submit=Go
http://www.ensembl.org/Homo_sapiens/exonvi...5&submit=Go

That should solve you problem.

regards Markus

Hi,
my protein binds promoter having a consensus sequence. I want to blast this sequence to obtain information in which gene that protein may bind. Do you know any tool or easy method. (I know, there is a blast option for small sequence in NCBI blast and it is not or it doesn't give what I want)
Thanks,

may be 18 or 20 base