title: Distribution bias of the sequence matching between exons and introns in exon joint and EJC binding region in C. elegans.
abstract: 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 λCG values show the minimum distribution in exon junction complex (EJC) binding region. High λCG 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.
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China. Electronic address: ndlihong@imu.edu.cn.
authors.forename: Hong
authors.initials: H
authors.lastname: Li
authors.affiliation: Biotechnology Research Centre, Inner Mongolia Academy of Agricultural and Animal Husbandry Science, Hohhot, 010021, China.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
authors.forename: Deliang
authors.initials: D
authors.lastname: Zhou
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D019295:Computational Biology; D005091:Exons; D005786:Gene Expression Regulation; D007438:Introns; D035683:MicroRNAs / Q000378:metabolism; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics; D012326:RNA Splicing; D012333:RNA, Messenger / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D009711:Nucleotides; D012333:RNA, Messenger; D034741:RNA, Small Interfering
keywords: EJC; Exon-exon sequences; Introns; Local matched alignment; Optimal matched segments