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SNP mRNA Flanking Sequence Retrieval

Hello!

Does anyone have any experience or tips for extracting an mRNA flanking sequence around a given SNP? I have SNP chromosome/position data (includes ref/alt alleles), and I am interested in looking at a flanking mRNA sequence (maybe 50 base pairs up and downstream of a given SNP: for a total of 101 BP [50 up + 50 down + 1 SNP allele).

Thanks!

snp mrna flanking sequence genomics
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updated by swbarnes2 swbarnes2 • written by RadiantZephyr • RadiantZephyr

2 answers

You can try using bedtools getfasta: http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html

First create a BED file with your positions of interest (chr<tab>start<tab>end).

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written by igor igor

Thanks for your response igor -- would this restrict the flanking sequence extracts to purely mRNA or would this include introns as well?

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written by RadiantZephyr • RadiantZephyr

That would be genomic sequence.

If you want to use coding sequence, you would have to create a different reference for just coding regions and transform your coordinates, which is not trivial.

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written by igor igor

Looks like ensembl.com BioMart can do this, if your SNPs are in their database. You want to start in the Variation database.

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written by swbarnes2 swbarnes2

Unfortunately many of the SNPs just have location data (chr/pos); is there a way to extract the mRNA flanking sequences without the need for rsIDs using this method?

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written by RadiantZephyr • RadiantZephyr

You should be able to do that in BioMart (use the multiple chromosomal regions under "filters" section).

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written by GenoMax GenoMax

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