retained introns in knownAlt annotation table, mm10

[Colin Wilson]

   Thank you for your business. I'd be grateful if you may convey the origin of the data/evidence on intron retention events, or refer me to it. I found there are many IR events (about 15 thousands) in mice. Are these annotated as some gene isoforms (transcripts)?

   Sorry for the kind of question, but it's currently rather acute. I believe some could be just temporary aberrant unspliced transcripts.

   With kind Regards,

Vladimir

[Luis Nassar]

Hello, Vladimir.

Thank you for your interest in the Genome Browser.

The knownAlt table was generated from the GENCODE (https://www.gencodegenes.org/mouse/) models. However, it does appear that it was built using pseudogene and non-coding transcripts in addition to protein-coding transcripts. When we recreate the data without those, we see 3814 retained introns in mm10.

We appreciate you bringing this to our attention, and we will look into making these updated tables live. In the meantime you may find this new data in the following location:

http://hgwdev.gi.ucsc.edu/~braney/knownAltCoding.bed

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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