promoter region

[aftabac]

Hi
if we know the cDNA of a gene and we want to find out promoter of that particular gene by bioinformatics, then how we can find that?

aftab

[moleculardude]

Dear Aftabac,
there is the manual way and the bioinformatic way.

The manual way is you get your cDNA sequence and get the nucleotide sequence for the genomic complement of the cDNA.
This is very important as cDNAs do not have promoter regions only genomic DNAs should.

Scan for ATG sites which are in frame with your gene. Your promoter should be upstream 5' of this sequence. This still does not tell you the region your promoter lies in.
To do this, you must do experiments to confirm the activity of the regions upstream of this region / ATG.
You can clone the genomic sequence upstream of your known cDNA sequence and generate deletion constructs using PCR. This should find you the minimal region that is responsible for expression.

The other and more easy way is Bioinformatics. You can do this using Promoter analysis tools. The first step would be to get the genomic sequence of your cDNA. you can do this from Entrez Pubmed Nucleotide search or Blastn.

Next you can use the following Promoter Finding / Start Site Finding Programs:

[Only registered users see links. ]

[Only registered users see links. ]

[Only registered users see links. ]

[Only registered users see links. ] (not associated with McDonald's!)

More [Only registered users see links. ]

I would use several of these and see how they relate.
Best way after is to confirm using deletion constructs mentioned above.

hope this all helps!

[monica]

Again, check BioInfoMan at [Only registered users see links. ]. I remember it has an automatic annotation function which can help you find the promoter region.