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?