Intron distribution in ancient paralogs supports random insertion and not random loss - PubMed (original) (raw)
Intron distribution in ancient paralogs supports random insertion and not random loss
G Cho et al. J Mol Evol. 1997 Jun.
Erratum in
- J Mol Evol 1997 Aug;45(2):206
Abstract
The intron positions of ten different protein families were examined to determine (the statistical likelihood of) whether spliceosomal introns are the result of random insertion events into previously intronless genes, on the one hand, or the result of random loss from common ancestral introns, on the other. The number of expected matches for the alternative scenarios was calculated for a binomial distribution by considering currently observed introns relative to all possible locations for insertion or loss. Introns occurring at approximately the same location (hereafter called a "match") were tallied for each of the paired proteins. Matches were identified by their positions in the multiple alignment and were defined as any two introns occurring within a window of 11 possible nucleotide positions, thereby allowing for possible alignment errors and "intron sliding." Matches were tallied from the raw data and compared with the expected number of matches for the two different scenarios. The results suggest that the distribution of introns in genes encoding proteins is due to random insertion and not random loss.
Similar articles
- Formation of new genes explains lower intron density in mammalian Rhodopsin G protein-coupled receptors.
Fridmanis D, Fredriksson R, Kapa I, Schiöth HB, Klovins J. Fridmanis D, et al. Mol Phylogenet Evol. 2007 Jun;43(3):864-80. doi: 10.1016/j.ympev.2006.11.007. Epub 2006 Nov 17. Mol Phylogenet Evol. 2007. PMID: 17188520 - Large-scale comparison of intron positions among animal, plant, and fungal genes.
Fedorov A, Merican AF, Gilbert W. Fedorov A, et al. Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16128-33. doi: 10.1073/pnas.242624899. Epub 2002 Nov 20. Proc Natl Acad Sci U S A. 2002. PMID: 12444254 Free PMC article. - The evolutionary gain of spliceosomal introns: sequence and phase preferences.
Qiu WG, Schisler N, Stoltzfus A. Qiu WG, et al. Mol Biol Evol. 2004 Jul;21(7):1252-63. doi: 10.1093/molbev/msh120. Epub 2004 Mar 10. Mol Biol Evol. 2004. PMID: 15014153 - Models of spliceosomal intron proliferation in the face of widespread ectopic expression.
Rodríguez-Trelles F, Tarrío R, Ayala FJ. Rodríguez-Trelles F, et al. Gene. 2006 Feb 1;366(2):201-8. doi: 10.1016/j.gene.2005.09.004. Epub 2005 Nov 8. Gene. 2006. PMID: 16288838 Review. - Intron-rich ancestors.
Roy SW. Roy SW. Trends Genet. 2006 Sep;22(9):468-71. doi: 10.1016/j.tig.2006.07.002. Epub 2006 Jul 20. Trends Genet. 2006. PMID: 16857287 Review.
Cited by
- Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization.
Wang Y, Tao XF, Su ZX, Liu AK, Liu TL, Sun L, Yao Q, Chen KP, Gu X. Wang Y, et al. Evol Bioinform Online. 2016 Dec 12;12:303-312. doi: 10.4137/EBO.S40703. eCollection 2016. Evol Bioinform Online. 2016. PMID: 27980385 Free PMC article. - Divergence and adaptive evolution of the gibberellin oxidase genes in plants.
Huang Y, Wang X, Ge S, Rao GY. Huang Y, et al. BMC Evol Biol. 2015 Sep 29;15:207. doi: 10.1186/s12862-015-0490-2. BMC Evol Biol. 2015. PMID: 26416509 Free PMC article. - Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process.
Wang L, Stein LD. Wang L, et al. BMC Evol Biol. 2013 Feb 28;13:57. doi: 10.1186/1471-2148-13-57. BMC Evol Biol. 2013. PMID: 23448166 Free PMC article. - Origin and evolution of spliceosomal introns.
Rogozin IB, Carmel L, Csuros M, Koonin EV. Rogozin IB, et al. Biol Direct. 2012 Apr 16;7:11. doi: 10.1186/1745-6150-7-11. Biol Direct. 2012. PMID: 22507701 Free PMC article. Review. - Evolutionary dynamics of spliceosomal intron revealed by in silico analyses of the P-Type ATPase superfamily genes.
Oda T, Ohniwa RL, Suzuki Y, Denawa M, Kumeta M, Okamura H, Takeyasu K. Oda T, et al. Mol Biol Rep. 2011 Apr;38(4):2285-93. doi: 10.1007/s11033-010-0360-3. Epub 2010 Nov 3. Mol Biol Rep. 2011. PMID: 21046256