Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns.docVIP

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Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns.doc

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Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns

BMC Genomics BioMedCentral Research article Open Access Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns Colin N Dewey1,2, Igor B Rogozin1 and Eugene V Koonin*1 Address: 1National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda MD 20894, USA and 2Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, USA Email: Colin N Dewey - cdewey@; Igor B Rogozin - rogozin@; Eugene V Koonin* - koonin@ * Corresponding author Published: 08 December 2006 Received: 18 July 2006 Accepted: 08 December 2006 BMC Genomics 2006, 7:311 doi:10.1186/1471-2164-7-311 This article is available from: /1471-2164/7/311 ? 2006 Dewey 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: The signals that determine the specificity and efficiency of splicing are multiple and complex, and are not fully understood. Among other factors, the relative contributions of different mechanisms appear to depend on intron size inasmuch as long introns might hinder the activity of the spliceosome through interference with the proper positioning of the intron-exon junctions. Indeed, it has been shown that the information content of splice sites positively correlates with intron length in the nematode, Drosophila, and fungi. We explored the connections between the length of vertebrate introns, the strength of splice sites, exonic splicing signals, and evolution of flanking exons. Results: A compensatory relationship is shown to exist between different types of signals, namely, the splice sites and the exonic splicing enhancers (ESEs). In the range of relatively short introns (approximatel