How to find the promotor region of a given gene by using IGV

Question

[iibrams07]

I am trying to look at the promotor of a gene of interest (e.g. VEGF, mouse mm9) by using IGV. I dont know how to get it. The manual did not help me much. I guess that for a well annotated gene one should find without much difficulty the gene regulatory elements such as promotors. In the Tools menu I picked the option Find Motif and eventually typed TATA having in mind that this motif must not always indicate a promotor region, just for the sake of trying. What I got is thousand of spots aligned on two tracks below the pictogram of the VEGF gene displaying the exons and introns.

Can you help me finding gene regulatory elements, more particularly the promotor, of a given gene by using IGV ?

Many thanks.

Answer 1

[dariober]

As far as I know, promoters are still very loosely defined as the regulatory region upstream of a gene, usually 1kb upstream (things are further complicated by the fact that you have multiple transcripts per gene). So to find a promoter in IGV just go to the transcript start site of your gene and pick the region x kb upstream (of course, pay attention to the strand of the gene to get the start site). If available, you could use ChIP-Seq data to refine your region but that may become outside the scope of your work. Your question is not so much related to IGV, rather is about how to find a prometer and that's not an easy one I'm afraid.

[iibrams07]

Thanks. So a motif like TATA or other would not help here? Interestingly this motif was found in thousands of locations.