Question: How to find polyA sites from gtf/gff?
1
gravatar for goodez
2.4 years ago by
goodez480
United States
goodez480 wrote:

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?

gene genome • 893 views
ADD COMMENTlink modified 2.4 years ago by Friederike6.2k • written 2.4 years ago by goodez480
2
gravatar for Friederike
2.4 years ago by
Friederike6.2k
United States
Friederike6.2k wrote:

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

ADD COMMENTlink written 2.4 years ago by Friederike6.2k
3
gravatar for Devon Ryan
2.4 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

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.

ADD COMMENTlink written 2.4 years ago by Devon Ryan96k
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