Retained intron transcripts

Question

[mforde84]

Hi,

We are seeing a retained intron transcript event for some RNAseq samples, and we want to assess at the sequence level which intron retention events are actually occuring. For example, we have support for DROSHA-203 which according to Ensembl is a retained intron transcript. However DROSHA-203 appears to give rise to multiple potential splicing variants given the supplied cDNA information from Ensembl:

So in theory, the orange sites indicate where a mutation causing an retained intronic event might occur, so in total there are 6 potential mutational events which may give rise to removal of a splice site for 4 intronic regions. Given that 4 intronic regions might be retained, the number of unique retention events is equal to 2^4, e.g., intron1 retained only, vs intron1 + 2 retained, etc....

Is there a better way to more granularly quantify these possible transcripts? Or do we have to PCR validate all of them to get reliable quantification estimates?

Martin

[Devon Ryan]

Hello mforde84!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/2848/quantification-of-est-cdna-based-retained-intron-transcripts

This is typically not recommended as it runs the risk of annoying people in both communities.

[mforde84]

I disagree. They are independent communities. Respectfully, it's none of your business where I post. Nor should you have any say in the moderation of my posts on another site.

[Devon Ryan]

1. That's a template from biostars.
2. I'm a moderator on both sites.
3. It's generally considered polite to cross-reference posts across sites so people can at least check if questions have been answered elsewhere (and if so, to see what said answers are).