How can I find the location of promoter of a gene?

Question

[karthik]

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

Answer 1

[EagleEye]

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