Splicing can happen either during transcription, or directly afterwards.

I am reading about single-cell RNA seq, and according to this paper, they observed that 15–25% of reads contained unspliced intronic sequences.

Now assuming that the majority of reads from RNA seq will come from RNA that has finished being transcribed...

Does this suggest that 75-85% of all genes are spliced during transcription? In other words, are 80% of our genes fully mature (spliced) immediately following transcription?


I don't think it will be possible to give a conclusive answer to this question, because a) it's a matter of active research and b) the rate / percentage of transcripts that are fully spliced co-transcriptionaly is almost certainly not constant but will depend on a lot of factors & regulatory mechanisms.

Another important detail is that this analysis / paper is based on mRNA sequencing, which uses oligo-dT primers to enrich for polyadenylated mRNA molecules. However, oligo-dT primers can also bind to stretches of A's inside of RNA molecules (this process is called internal priming) and since such stretches are more common in introns compared to exons this may contribute to the abundance of intronic reads in mRNA sequencing data (I don't have a good literature source for this specific case, but it's a known 'issue' for sure).

Maybe some of these reviews are also helpful (not sure if all are freely available):


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