How to find polyA sites from gtf/gff?

I need a list of polyA site positions. For instance, I extracted TSS positions from a gtf file by taking the starting position of all transcript features. Would the end position of the transcript be the polyA site?

genome gene

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updated 4.4 years ago by ks.bis •

• written 8.2 years ago by goodez

3 answers

Many gtf files contain the coordinates for the 3'UTR, too (check the 3rd column). Its end coordinate might be a suitable proxy.

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written 8.2 years ago by Friederike

Poly-A sites aren't typically annotated, since they often don't exist in the genome, but are rather post-transcriptionally added. See, for example wikipedia for an overview.

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written 8.2 years ago by Devon Ryan

Looking for something similar and I found:
https://polyasite.unibas.ch/atlas http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Utils_1_1PolyA.html

• 0 views • link

written 4.4 years ago by ks.bis •

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