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I'm browsing in the UCSC genome browser and found that the UTRs length of KIAA0040 gene in the genomic sequences is too much longer than the corresponding the Refseq mRNA sequence. In fact, the total length of Refseq mRNA sequence is 4,721 and the length of its genomic sequence is about 36,107bp, of which the length of CDS is just 300 bp. How to explain this event? This gene has 4 transcript variant and I know something about that UTR can span multiple exons, but I'm not sure about it and would like to hear more from you.

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  • $\begingroup$ Doesn't the genomic sequence you refer to contain intron sequence? $\endgroup$
    – 243
    Sep 4, 2015 at 22:49
  • $\begingroup$ What do you mean by "length of the gene" ? The UCSC browser displays the mRNA sequences aligned to the genome, so the sequences can differ only if there were errors in alignment. Are you saying the UTR is longer in the genomic alignment than in the refseq mRNA sequence? Which mRNA are you referring to? $\endgroup$
    – Roland
    Sep 6, 2015 at 7:13

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UTRs are involved in post-transcriptional regulation. See the wikipedia articles on the 5' and 3' UTRs. Alternative splicing of UTRs allows for exposing/hiding these regulation sites, which may then be useful for differential regulation in differing tissues.

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