Science Forums Biology Forum Molecular Biology Forum Physics Chemistry Forum

Science Forums Biology Forum Molecular Biology Forum Physics Chemistry Forum (http://www.molecularstation.com/forum/)
-   Bioinformatics (http://www.molecularstation.com/forum/bioinformatics/)
-   -   promoter region (http://www.molecularstation.com/forum/bioinformatics/180-promoter-region.html)

aftabac 07-13-2006 11:37 AM

promoter region
 
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 07-13-2006 04:52 PM

Re: promoter region
 
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 and activated users can see links. Click Here To Register...]

[Only registered and activated users can see links. Click Here To Register...]

[Only registered and activated users can see links. Click Here To Register...]

[Only registered and activated users can see links. Click Here To Register...] (not associated with McDonald's!)

More [Only registered and activated users can see links. Click Here To Register...]

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 08-13-2006 04:56 AM

Re: promoter region
 
Again, check BioInfoMan at [Only registered and activated users can see links. Click Here To Register...]. I remember it has an automatic annotation function which can help you find the promoter region.

bioinfo_bio 01-28-2012 09:52 AM

Re: promoter region
 
Hi...

I download the nucleotide of my gene . my gene is of Plant (Wheat) and i want to find the promoter region of it. How can we determine the promoter region of my gene. Please reply

Mzebra 02-13-2012 02:58 PM

Re: promoter region
 
how about if we do not know the cDNA of a gene...

is searching for transposable elements key??? anyone here carried out such research?


All times are GMT. The time now is 04:08 PM.

Powered by vBulletin® Version 3.8.4
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.
Copyright 2005 - 2012 Molecular Station | All Rights Reserved

Page generated in 0.09454 seconds with 11 queries