tag:blogger.com,1999:blog-37148773.post4919957642415076001..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Junk in Your Genome: Protein-Encoding GenesLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger11125tag:blogger.com,1999:blog-37148773.post-44428732155227785472008-02-12T19:52:00.000-05:002008-02-12T19:52:00.000-05:00It includes a number of introns of extraordinary l...<I>It includes a number of introns of extraordinary length lying between exons of dubious existence (often non-coding).</I><BR/><BR/>A non-protein-coding exon is still an exon. Many 5' exons are not translated, but are still functional sequences (3'UTRs). I agree that computationally predicted 5' exons are often errors, but that doesn't mean that some 5' exons are important. Also, those introns of extraordinary length often contain important cis regulatory sequences (long introns are under more selective constraint than short introns).RPMhttps://www.blogger.com/profile/00344508931818143159noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77922734869444315822008-02-09T17:52:00.000-05:002008-02-09T17:52:00.000-05:00If stuff is either "essential" or "junk", you migh...<I>If stuff is either "essential" or "junk", you might as well trim off all those junky crystallographically-unstructured loop domains from the coding sequences of protein-encoding exons too</I><BR/><BR/>Not really, depending on the protein that unstructured loop actually has functions, typically allowing protein domains to move quite bit.Nick Sullivanhttps://www.blogger.com/profile/07492463380069893463noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-89849077334236551242008-02-09T16:02:00.000-05:002008-02-09T16:02:00.000-05:00If stuff is either "essential" or "junk", you migh...If stuff is either "essential" or "junk", you might as well trim off all those junky crystallographically-unstructured loop domains from the coding sequences of protein-encoding exons too. Out of 635 amino acids in the average protein, you could probably toss out a third of those, maybe more.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63142551865152752162008-02-09T12:30:00.000-05:002008-02-09T12:30:00.000-05:00Larry, if the amount of necessary sequences within...Larry, if the amount of necessary sequences within introns are as small as you suggest wouldn't this this allow us to make a prediction. Couldn't we predict that due to drift there should be very little similarity in intron lengths between different species. If, by any chance, there is similarity then what would your explanation be?Sigmundhttps://www.blogger.com/profile/00262375488263086844noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-47187030257761992382008-02-09T12:03:00.000-05:002008-02-09T12:03:00.000-05:00Fair enough - as student pursuing a Ph.D in Bioinf...Fair enough - as student pursuing a Ph.D in Bioinformatics, and studying Alternative Splicing in particular, I find your posts very interesting, and something that helps retain some sort of "perspective" via exposure to the other extreme of opinion, so to say.Optimistixhttps://www.blogger.com/profile/17927346995555238063noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68813659741494497622008-02-09T11:56:00.000-05:002008-02-09T11:56:00.000-05:00rileen asks,Do you believe that the "typical human...rileen asks,<BR/><BR/><I>Do you believe that the "typical human exon" is about 250 bp in size?<BR/><BR/>You're saying there 8.2 exons on average, and 2,200 bp of mRNA, which would imply an average exon size of ~250 bp - about 100 bp more than what I've read in several papers.</I><BR/><BR/>The short answer is "yes," I do believe that the average exon is about 250 bp. <BR/><BR/>The long answer requires an extended discussion about the reliability of EST databases and the predictions of alternative splicing. That's why I choose to use values from well-characterized genes where real live human scientists have looked at the data and weeded out the nonsense.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10061596204762059212008-02-09T09:51:00.000-05:002008-02-09T09:51:00.000-05:00Do you believe that the "typical human exon" is ab...Do you believe that the "typical human exon" is about 250 bp in size?<BR/><BR/>You're saying there 8.2 exons on average, and 2,200 bp of mRNA, which would imply an average exon size of ~250 bp - about 100 bp more than what I've read in several papers.<BR/><BR/><BR/>(sorry if my comment shows up twice, I tried posting a few hours but it hasn't shown up, while your replies to previous comments have - hence this second attempt)Optimistixhttps://www.blogger.com/profile/17927346995555238063noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75446130972021334472008-02-09T08:46:00.000-05:002008-02-09T08:46:00.000-05:00soparc asks,Shouldn't that be1.3% coding and 0.1% ...soparc asks,<BR/><BR/><I>Shouldn't that be<BR/>1.3% coding and 0.1% UTRs?</I><BR/><BR/>Yes it should. Thanks.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31281295493311080822008-02-09T08:45:00.000-05:002008-02-09T08:45:00.000-05:00rob,I don't think it would make any significant im...rob,<BR/><BR/><I>I don't think it would make any significant impact on your calculations but there are microRNAs encoded within introns, intronic microRNA. I wonder if there is any other essential noncoding RNA that you might miss in your calculations.</I><BR/><BR/>I haven't covered small RNAs yet. Wait for it. <BR/><BR/>I also haven't covered all the essential non-transcribed sequences in "noncoding" DNA.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55626994137715661462008-02-09T00:57:00.000-05:002008-02-09T00:57:00.000-05:00Thus, total essential exons comprise 2200 bp on av...<I>Thus, total essential exons comprise 2200 bp on average per gene. Since there are 20,500 protein-encoding genes, this means 20,500 × 2.2 kb = 45.1 Mb or 1.4% of the genome (<B>about 13% coding and 1% UTRs</B>).</I><BR/>Shouldn't that be <BR/><B>1.3% coding and 0.1% UTRs</B>?SPARChttps://www.blogger.com/profile/09563722742249547887noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21744064950772831642008-02-09T00:11:00.000-05:002008-02-09T00:11:00.000-05:00I don't think it would make any significant impact...I don't think it would make any significant impact on your calculations but there are microRNAs encoded within introns, intronic microRNA. I wonder if there is any other essential noncoding RNA that you might miss in your calculations.Robhttps://www.blogger.com/profile/11878582460269426199noreply@blogger.com