PMID: 9419356Feb 21, 1998Paper

Relationship between "proto-splice sites" and intron phases: evidence from dicodon analysis

Proceedings of the National Academy of Sciences of the United States of America
M LongWalter Gilbert

Abstract

The coding sequence at the boundaries of exons flanking nuclear introns shows some degree of conservation. To the extent that such sequences might be recognized by the splicing machinery, this conservation may be a derived result of evolution for efficient splicing. Alternatively, such conserved sequences might be remnants of proto-splice sites, which might have existed early in eukaryotic genes and served as the targets for the insertion of introns, as has been proposed by the introns-late theory. The distribution of intron phases, the position of the intron within a codon, is biased with an over-representation of phase 0 introns. Could any distribution of proto-splice sites account for today's intron phase distribution? Here, we examine the dicodon usage in six model organisms, based on current sequences in the GenBank database, and predict the phase distribution that would be expected if introns had been inserted into proto-splice sites. However, these predictions differ between the various model organisms and disagree with the observed intron phase distributions. Thus, we reject the hypothesis that introns are inserted into hypothetical proto-splice sites. Finally, we analyze the sequences around the splice sites of introns...Continue Reading

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Citations

Aug 13, 2008·Journal of Molecular Evolution·Rubens N Akamine, Carlos Eduardo Winter
Mar 26, 2010·Journal of Molecular Evolution·Vladimir BabenkoAnatoly Ruvinsky
Nov 26, 1999·Gene·S W RoyW Gilbert
Oct 30, 2001·Current Opinion in Genetics & Development·M Long
Jan 23, 1999·Current Opinion in Genetics & Development·J M Logsdon
Apr 1, 2000·RNA·D LibriM Rosbash
Feb 2, 2006·Heredity·R Belshaw, D Bensasson
Aug 24, 1999·Nucleic Acids Research·M Deutsch, M Long
Sep 13, 2000·Nucleic Acids Research·J Trzcinska-Danielewicz, J Fronk
Feb 13, 2003·Nucleic Acids Research·Elisabeth BonClaude Gaillardin
Mar 25, 2005·Nucleic Acids Research·Alexander V SverdlovEugene V Koonin
Jul 21, 2006·Nucleic Acids Research·Eyal KamhiJoseph Sperling
Apr 8, 2011·Nucleic Acids Research·Yuri KapustinNick J Dibb
Mar 29, 2002·Molecular Biology and Evolution·Toshinori EndoWalter Gilbert
Nov 11, 2006·Annual Review of Genetics·Francisco Rodríguez-TrellesFrancisco J Ayala
Sep 9, 2006·BMC Evolutionary Biology·Hung D NguyenNaoya Kenmochi
Oct 13, 2006·BMC Genomics·Henrik Nielsen, Rasmus Wernersson
Mar 7, 2006·PLoS Genetics·Maki YoshihamaNaoya Kenmochi
Nov 29, 2007·PloS One·Necat HavliogluJane Y Wu
Nov 1, 2001·Proceedings of the National Academy of Sciences of the United States of America·A FedorovW Gilbert
Jun 6, 1998·Proceedings of the National Academy of Sciences of the United States of America·S J de SouzaW Gilbert
Nov 22, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alexei FedorovWalter Gilbert
Jul 10, 2004·Proceedings of the National Academy of Sciences of the United States of America·Avril Coghlan, Kenneth H Wolfe
Apr 5, 2001·Proceedings of the National Academy of Sciences of the United States of America·B LiebK I Miller
Apr 14, 2005·Proceedings of the National Academy of Sciences of the United States of America·Scott William Roy, Walter Gilbert
Jan 12, 2005·Proceedings of the National Academy of Sciences of the United States of America·Scott W Roy, Walter Gilbert
Jul 27, 2001·American Journal of Human Genetics·L A MetherellA J Clark
Dec 26, 2006·Molecular Phylogenetics and Evolution·Davids FridmanisJanis Klovins
Apr 18, 2006·Journal of Molecular Biology·Gordon S Whamond, Janet M Thornton
Dec 19, 2003·Current Biology : CB·Alexander V SverdlovEugene V Koonin
Aug 25, 2004·Current Biology : CB·Alexander V SverdlovEugene V Koonin
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May 17, 2002·The Journal of Biological Chemistry·Feike R van der LeijNigel T Price
Feb 8, 2005·Journal of Molecular Evolution·A RuvinskyL D Hurst
Feb 18, 2006·Nature Reviews. Genetics·Scott William Roy, Walter Gilbert

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