Analysis on the interaction between post-spliced introns and corresponding protein coding sequences in ribosomal protein genes

Many experiments show that intron loss/gain can influence many stages of mRNA metabolism. However, in the current work, post-spliced introns are not considered directly. Here, the optimal matched regions between introns and their protein coding sequences in ribosomal protein genes are intensively investigated by using the improved Smith–Waterman local alignment software. In introns, it is found that optimal matched regions are located in the central non-conserved regions, and their distribution characteristics are different from each intron group. We find two optimal matched regions in long introns, and the former one is more conservative than the latter one. We also find only one optimal matched region in short introns. In protein coding sequences, there are some optimal matched regions and forbidden regions, especially two conserved forbidden regions located at about 10% and 80% in the length of protein coding sequences. The forbidden regions may be potential protein-binding regions. Match rates of most optimal matched segments range among 65% and 75% and they belonged to weak match. The interaction between post-spliced introns and corresponding protein coding sequences may play a key role in gene expression.