拟南芥外显子连接序列上最佳匹配片段的偏好

Biases of the Optimal Matching Segments on Exon-exon Sequences of Arabidopsis thaliana

内含子序列通过与相应mRNA序列的匹配参与基因表达调控。采用Smith-Waterman局部比对方法,以拟南芥全基因组基因序列为基础,获得了内含子序列与其对应的外显子连接序列的最佳匹配片段。为了揭示两者之间的序列匹配特征,给出匹配频率在外显子序列上的分布。研究发现,匹配频率分布在外显子的边界存在显著差异,长内含子序列和第一个内含子序列对外显子连接序列的分布偏好明显区别于其他内含子序列。对于长片段、低GC含量以及高配对率的最佳匹配片段在外显子连接序列上游EJC(exon-exon junction complex)结合区域分布有明显的最小值。结果显示内含子序列和编码序列存在共同进化关系。

Intron sequences involve gene expression and regulation by matching with the corresponding mRNA sequences.Based on the A.thalianagenome sequence,the Smith-Waterman local alignment method was used to obtain the optimal matching segments between intron sequences and the corresponding exonexon sequences.In order to reveal the sequence matching characteristics of the two sequences referred above,their distributions of matching frequency were analyzed on exon-exon sequences.The analysis points out that the matching frequency distribution has a distinct difference on exons’ boundary.The long introns and the first introns have different biases of distribution on exon-exon from other introns.In regard to long segments,segements with low GC content and segments with high match rate,their optimal matching segments exist an obvious minimum on EJC binding region of upstream exons.Results show that intron sequences are co-evolutionary with coding sequences.