Question: How can I find the location of promoter of a gene?
2
gravatar for karthik
4.4 years ago by
karthik60
United States
karthik60 wrote:

Hello, I am trying to find the promoter of a mouse gene Thy1 on the UCSC mm9 genome? I am quite new to bioinformatics so I do not know how exactly to go about finding the location of the promoter. I understand that I have to look up a "TATA" motif upstream, but there does not seem to be an obvious location. 

Any help on how to do this would be appreciated. I am using IGV to visualize RNA seq data and I am interested in finding whether the reads that map to my gene of interest (Thy1 in this case) primarily map to the promoter/transcription start site or whether they map across the different exons of the transcript. 

Karthik

igv promoter gene • 3.4k views
ADD COMMENTlink modified 4.4 years ago by EagleEye6.2k • written 4.4 years ago by karthik60
2
gravatar for EagleEye
4.4 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

You can use UCSC table to download the promoters and VISTA enhancer regions.

http://bioinformatics.kandurilab.org/biostars/promoter_ucsc.png

http://bioinformatics.kandurilab.org/biostars/vista_enhancer_ucsc.png

 

ADD COMMENTlink written 4.4 years ago by EagleEye6.2k
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