Question: Retrieving sequences/locations for conserved elements only from specific region of a gene-UCSC
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gravatar for nash.claire
2.7 years ago by
nash.claire330
Canada
nash.claire330 wrote:

Hi all,

Apologies if this question is a bit similar to others but I haven't found the exact answer I'm looking for.

For my project, I'd like to be able to look for potential miRNA binding sites in my gene of interest, specifically in 5'UTR and 3'UTR of my gene. However, I only want to find these miRNA binding sites in highly conserved regions of the 5'UTR and 3'UTR. Therefore, I would like to download FASTA sequences or a BED file for conserved regions within the UTR regions of my gene to run on miRNA algorithms further down the line.

I believe UCSC Table Browser can do this for me but I'm hoping someone can give me step by step instructions on how to do this. I've had a play with it and I'm not sure I'm pulling out the right thing. I appear to be getting results back for the 3'UTR that aren't in the location where I expect the 3'UTR to be. Perhaps this is the 3'UTRs for other mammals than human? I'm not sure and don't know how to find out. Also, I don't know if there is a way to pull out conserved elements that have a PhastCons score of greater than a threshold? Or whether using the PhastCons conserved elements track is enough? I was going to use the 20 mammal PhastCons track to do this.

Any help and advice would be greatly appreciated.

sequence genome gene • 1.5k views
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