What is the ratio of spliced to unspliced introns in a cell? I found, that the median half-life of a human mRNA is roughly 10h [1], while transcription and splicing each take around half a minute [2, 3]. Based on this 1200x time-ratio, my default assumption is that the ratio between pre-mRNA and mRNA of the same genes follows a similar ratio.

Does this estimate seem reasonable? Are there any more direct experiments, that address this?

The context is crosslinking immunoprecipitation (CLIP), where some fragmented (and poly-(T) purified) RNA-reads might be only uniquely mapped if limiting mapping to the the pool of spliced mRNAs, while the same read may show up in introns. Knowing the ratio between introns and exons can help to evaluate the associated risk of such a simplification and to find suitable cut-offs.

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    $\begingroup$ Does this answer your question? What percentage of introns are spliced in polyadenylated mRNAs? $\endgroup$ Commented Nov 2, 2022 at 20:54
  • $\begingroup$ I see that you previously asked a very similar question. I think it is a duplicate, if not then it would be helpful to know in what ways it differs, or to have a single edited question. $\endgroup$ Commented Nov 2, 2022 at 20:55
  • $\begingroup$ I agree that it could make sense to ask these questions next to each other, but IMO those are dichotomous questions, requiring entirely different knowledge to be answered: One question asks about the ratio between pre-mRNAs and mRNAs, which is a question of life-times, while the other question asks about the ratio of spliced to non-spliced introns within polyadenylated mRNAs, ignoring the fraction of non-polydaenylated mRNAs. $\endgroup$
    – KaPy3141
    Commented Jan 2, 2023 at 11:55


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