title: Analysis on the preference for sequence matching between mRNA sequences and the corresponding introns in ribosomal protein genes.
abstract: Introns after splicing still play an important role. Introns can accomplish gene expression and regulation by interaction with corresponding mRNA sequences. Based on the Smith-Waterman method, local comparing makes us get the optimal matched segments between intron sequences and mRNA sequences. Analyzing the distribution regulation of the optimal matching region on mRNA sequences of ribosomal protein genes about 27 species, we find a strong interaction between UTR region sequences and introns. There are a lot of the optimal matching regions and low matching ones, and the latter are supposed to be the combined regions of protein complexes. The optimal matching frequency distributions have obvious differences nearby the mRNA functional sites such as translation initiation and termination sites, exon-exon joints and EJC regions. This conclusion shows that intron sequences and mature mRNA sequences are co-evolved and interactive to play their functions.
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: Hu
authors.initials: H
authors.lastname: Meng
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Jia
authors.affiliation: School of Foreign Languages, Inner Mongolia University, Hohhot 010021, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Xue
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
authors.forename: Sulin
authors.initials: S
authors.lastname: Bo
mesh_terms: D000818:Animals; D006801:Humans; D007438:Introns; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012269:Ribosomal Proteins / Q000096:biosynthesis / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012333:RNA, Messenger; D012269:Ribosomal Proteins
keywords: Introns; Local matched alignment; MRNA sequences; Optimal matched segments; Ribosomal protein genes