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Distribution bias of the sequence matching between exons and introns in exon joint and EJC binding region in C. elegans

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文献类型：外文期刊

作者： Zhang, Qiang ¹ ; Li, Hong ¹ ; Zhao, Xiaoqing ² ; Zheng, Yan ¹ ; Zhou, Deliang ¹ ;

作者机构： 1.Inner Mongolia Univ, Sch Phys Sci & Technol, Lab Theoret Biophys, Hohhot 010021, Peoples R China

2.Inner Mongolia Acad Agr & Anim Husb Sci, Biotechnol Res Ctr, Hohhot 010021, Peoples R China

关键词： Exon-exon sequences;Introns;Local matched alignment;Optimal matched segments;EJC

期刊名称：JOURNAL OF THEORETICAL BIOLOGY （影响因子：2.691；五年影响因子：2.374 ）

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收录情况： SCI

摘要： We propose a mechanism that there are matching relations between mRNA sequences and corresponding post-spliced introns, and introns play a significant role in the process of gene expression. In order to reveal the sequence matching features, Smith-Waterman local alignment method is used on C elegans mRNA sequences to obtain optimal matched segments between exon-exon sequences and their corresponding introns. Distribution characters of matching frequency on exon-exon sequences and sequence characters of optimal matched segments are studied. Results show that distributions of matching frequency on exon-exon junction region have obvious differences, and the exon boundary is revealed. Distributions of the length and matching rate of optimal matched segments are consistent with sequence features of siRNA and miRNA. The optimal matched segments have special sequence characters compared with their host sequences. As for the first introns and long introns, matching frequency values of optimal matched segments with high GC content, rich CG dinucleotides and high lambda(CG) values show the minimum distribution in exon junction complex (EJC) binding region. High lambda(CG) values in optimal matched segments are main characters in distinguishing EJC binding region. Results indicate that EJC and introns have competitive and cooperative relations in the process of combining on protein coding sequences. Also intron sequences and protein coding sequences do have concerted evolution relations. (C) 2014 Elsevier Ltd. All rights reserved.

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