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Why are the sum of all exons so much longer than CDS?

Is this because of non-coding RNA? I thought these would have been at least comparable.

library(GenomicFeatures)
txdb <- makeTxDbFromEnsembl("Homo Sapiens",server="useastdb.ensembl.org")
gr<-cds(txdb)
sum(width(reduce(gr)))
[1] 41901692

gr<-exons(txdb)
sum(width(reduce(gr)))
[1] 153094341
exons cds
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updated by swbarnes2 swbarnes2 • written by Jeremy Leipzig Jeremy Leipzig

yes, there are a bunch of non-coding RNA families (rRNA, tRNA, miRNA, snRNA, lncRNA, ...) which can be in your exon list but not in your CDS

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written by JC JC

2 answers

3' and 5' UTR as well as non-coding species.

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written by Eric Lim Eric Lim

how about that!

sum(width(unlist(fiveUTRsByTranscript(txdb))))
[1] 21299710
sum(width(unlist(threeUTRsByTranscript(txdb))))
[1] 86927764
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written by Jeremy Leipzig Jeremy Leipzig

Yeah, the mean 3' UTR is around 40% of the length of a transcript and a not insubstantial number of UTRs are more than 75% of the transcript.

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written by i.sudbery i.sudbery

Also, ensembl will count an exon as unique if it overlaps with other exons, so a lot of sequence is being counted over and over again because it belongs to multiple slightly different exons.

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written by swbarnes2 swbarnes2

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