Retrieve Information About The Exons Of A Gene

Question

[9606]

Given a gene, I would like to get the coordinates (left-end and right-end) of all of its exons.

I can do it manually, looking at the gene in the UCSC Genome Browser, but I need to automatize this procedure.

Where can I find the information that I need?

Thank you for your help

Answer 1

[brentp]

Here's a way to do this in python with cruzdb using the TRIM13 from hg19 gene as an example:

from cruzdb import Genome
g = Genome('hg19')

for transcript in g.refGene.filter_by(name2='TRIM13'):
    print transcript.exons

the output is a list of start, end tuples for each transcript.

[Steve Lianoglou]

First time I've come across your cruzdb package -- nice work!

Answer 2

[Steve Lianoglou]

Similar questions like these pop up quite often here, so please search the archives.

That having been said:

• Genomic Cordinates From Ucsc to one such question that you can adapt to get what you want.
• If you are familiar with R/Bioconductor, you can easily address such questions with facilities provided by the GenomicFeatures, and you can read through its vignette to become more familiar with it.