What proportion of the (coding) genome is actually expressed at any given time?
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Dunois ★ 2.2k

(Please forgive me if this is a trivial/stupid question.)

Say a genome has n genes that code for proteins. Sampling the mRNA pool produced by this genome at time t yields m distinct mRNAs.

My question is, are there any estimates for what m/n is in general. (Like 5%, 50%, etc.) That is, what fraction of the genome (that codes for genes) is expressed at any give arbitrary time point?

If I were to pose this question a bit differently: say I have RNA-seq reads for an organism with a fully sequenced genome. What is the "typical" (?) mapping rate I should expect if I were to have the reads mapped to the genome (or to its CDS subset)?

genome gene expression RNA-Seq • 459 views
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Mensur Dlakic ★ 22k

It depends on the exact organism, genome size, tissue sample, developmental stage(s), day-night cycle and many other things. Larger number of genes are expressed in liver than brain. Larger proportion of genome is expressed in micro-organisms with reduced genomes than in salamanders. Impossible to answer globally without knowing more details about your experiment, and may be possible only in general terms even with that information.

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GenoMax 125k

What is the "typical" (?) mapping rate I should expect if I were to have the reads mapped to the genome (or to its CDS subset)?

While you will not likely see 100% mapping, a large fraction of reads should map to the genome you expect to see (anywhere from 70% upwards). Quality of the libraries will directly impact this number.

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