Analysis on the preference for sequence matching between mRNA sequences and the corresponding introns in ribosomal protein genes

•We have given a propose that the sequence matching relation between mRNA sequences and corresponding post-spliced introns plays a significant role in the process of gene expression and regulation.•Functional sites such as translation initiation and termination sites, exon–exon joints and EJC regions can be revealed by our method.•EJC and introns have competitive and cooperative relations in the process of combining on mRNA sequences.•Intron sequences and mature mRNA sequences are co-evolved and interactive to play their functions.

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.