Retrieve Information About The Exons Of A Gene
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8.1 years ago
9606 ▴ 330

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?

genes exon database • 2.6k views
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Entering edit mode
8.1 years ago
brentp 23k

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.

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

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Entering edit mode
8.1 years ago

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.