How to find polyA sites from gtf/gff?
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4.7 years ago
goodez ▴ 630

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 • 1.6k views
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4.7 years ago

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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4.7 years ago

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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