Fast rate of evolution in alternatively spliced coding regions of mammalian genes.docVIP

BMC Genomics BioMedCentral Research article Open Access Fast rate of evolution in alternatively spliced coding regions of mammalian genes Ekaterina O Ermakova*1,2, Ramil N Nurtdinov1 and Mikhail S Gelfand1,2 Address: 1Department of Bioengineering and Bioinformatics, Moscow State University, Vorobevy gory, 1-73, 119992, Moscow, Russia and 2Research and Training Center Bioinformatics, Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny per. 19, 127994, Moscow, Russia Email: Ekaterina O Ermakova* - ermakova@iitp.ru; Ramil N Nurtdinov - n_ramil@mail.ru; Mikhail S Gelfand - gelfand@iitp.ru * Corresponding author Published: 18 April 2006 Received: 21 December 2005 Accepted: 18 April 2006 BMC Genomics2006, 7:84 doi:10.1186/1471-2164-7-84 This article is available from: /1471-2164/7/84 ? 2006Ermakova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: At least half of mammalian genes are alternatively spliced. Alternative isoforms are often genome-specific and it has been suggested that alternative splicing is one of the major mechanisms for generating protein diversity in the course of evolution. Another way of looking at alternative splicing is to consider sequence evolution of constitutive and alternative regions of protein-coding genes. Indeed, it turns out that constitutive and alternative regions evolve in different ways. Results: A set of 3029 orthologous pairs of human and mouse alternatively spliced genes was considered. The rate of nonsynonymous substitutions (d ), the rate of synonymous substitutions N (d ), and their ratio (ω = d /d ) appear to be significantly higher in alternatively spliced coding S