We recently learned in genetics class that exons always cap the ends of nascent RNA. I have been trying to figure out the reason why introns can't instead be found on the ends instead of exons. The end introns would still have their 5' and 3' splice sites, and assuming the splicing machinery functions correctly, these introns would be removed. The only thing I could imagine occurring is inappropriate nucleophilic attack of the end 3' hydroxy group at the end 5' phosphate leading to a single circular RNA. However, in a normal situation where exons are at the ends, if introns in an RNA are all removed simultaneously than it is possible that the free 3' hydroxy group of say intron 2 could attack the 5' end of another intron leading to inappropriate cleavage of the intervening exon so having exons at the ends does not solve that problem. I don't think my explanation is correct, any ideas?
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$\begingroup$ You should revise splicing mechanisms. Splicing requires that the intron be flanked by exons. There can be nucleolytic clipping of the ends- as in case of tRNAs, but they are not generally referred to as introns (though one technically can). $\endgroup$– WYSIWYGCommented Sep 16, 2014 at 16:41
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$\begingroup$ I was unclear..I was asking why introns are not found before the 1st exon and after the last. $\endgroup$– Zach MillerCommented Sep 16, 2014 at 16:44
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$\begingroup$ There are untranslated regions of mRNA flanking the exons, even after splicing. These are creatively called the 5' and 3' untranslated regions. These regions help regulate translation and mRNA stability. I've never heard of it, but maybe there are cases where RNA gets cut out from between an exon and an untranslated region. $\endgroup$– user137Commented Sep 16, 2014 at 16:58
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$\begingroup$ Neither pre-mRNA or mature mRNA begin with exons, they begin with the 5'UTR. Are you asking why the sequence after the 5'UTR is always an exon? Or are you asking why there can't be introns before the 5'UTR? $\endgroup$– ArmatusCommented Sep 16, 2014 at 18:49
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1$\begingroup$ @user137 (and Armatus) UTRs are exons, some of them even contain introns and are spliced just like coding exons. $\endgroup$– terdonCommented Sep 16, 2014 at 22:22
2 Answers
RNA splicing refers to a certain kind of RNA processing mechanism which leads to the excision and exclusion of some regions of the primary transcript. You should note that this is not the only method by which such a thing can happen; Endo-ribonucleases can clip the ends of the transcript and this happens in the case of tRNA-processing. But as "splicing" happens it is essential that the excised region be in the interior of the transcript. See the figure.
RNA splicing begins with assembly of helper proteins at the intron/exon borders. These splicing factors act as beacons to guide small nuclear ribo proteins to form a splicing machine, called the spliceosome. These animation is showing this happening in real time. see>
http://www.youtube.com/watch?v=FVuAwBGw_pQ
http://www.sumanasinc.com/webcontent/animations/content/mRNAsplicing.html
