# Quantification of EST/cDNA based retained intron transcripts

Note: this question has also been asked on Biostars

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 occurring so that we can do protein domain predictions. For example, we have transcript level expression support for DROSHA-203, which according to Ensembl is a retained intron transcript that potential gives rise to multiple splicing variants via the cDNA sequence information:

In theory, the orange sites indicate where a mutation might occur which could obliterate a splicing recognition site, thereby causing an retained intron event. So in total there are 6 potential mutational events which might give rise to 4 possible retention events. Given that 4 intronic regions might be retained, the number of unique retention events is a combinatorics question equal to 2^4, e.g., intron1 retained only, vs intron1 + 2 retained, all possible unique combination, etc, correct?

Is there a better way to more granularly quantify these possible transcripts? Or do we have to PCR validate all of them to figure out which one's are actually occurring? Is there a way that I can look at the reads mapping to the corresponding intronic regions to make even a probabilistic assessment of which transcripts are present and to what extent they are expressed? The libraries are prepped for total RNA with a ribozero depletion, so I should still be able to quantify any enrichment to these intronic regions, correct?

• Did you look up if there is any kind of LD between these positions? Maybe whenever a mutation in 359 occurs, there's also a mutation in the the previous splicing event.
– llrs
Nov 15, 2017 at 9:40

Unfortunately, if you want these tools to quantify intronic sequence (i.e. the $2^4$ possibilities you have suggested), then those sequences need to be included in the sequences provided. They won't estimate frequencies for non-existent sequence.