5' UTR Length of C.elegans genes

Hello wormers! I have a naive question: can we state that C.elegans gene have a particularly short 5’UTR when compared to other eukariotic organisms?
If yes: could this be due to policistronic transcription and subsequent transsplicing of genes belonging to operons ?

Thanks in advance for any feedback you may have,

Alessandro Guffanti
(ex wormer…)

From one ex-wormer to another…

I don’t think it is easy to answer this question because I don’t think you can get a reliable set of 5’ UTRs from WormBase. Many 5’ UTRs will be designated as such due to a very short overlap between an EST and the coding transcript. E.g. WormMart allows you to export just over 4,000 5’ UTRs from C. elegans genes. Over a third of these are 10 bp or less (nearly 150 of these are 1 bp!). The average size for these UTRs is about 50 bp. Contrast that to A. thaliana where there are full-length mRNAs for most genes. Nearly 15,000 5’ UTRs gives you an average length in A. thaliana of ~110 bp and only about 4% of these are 10 bp or less.

So if you believe that all of these short 5’ UTRs are real, then yes C. elegans UTRs are shorter than (one) other eukaryotes.



P.S. You could try downloading 5’ UTRs from http://www.ba.itb.cnr.it/UTR/. They make EMBL format files of 5’ UTR sequences from each EMBL division.

Thanks a lot Keith a very helpful set of hints :smiley: