Potential relations between post-spliced introns and mature mRNAs in the Caenorhabditis elegans genome

There are potential interactions between introns and their corresponding coding sequences (CDSs) in ribosomal protein genes that have been proposed by our group and the interactions are achieved by sequence matches between the two kinds of sequences. Here, the optimal matching relations between mature mRNAs and their corresponding introns in Caenorhabditis elegans (C.elegans) were investigated by improved Smith-Waterman local alignment software. Our results showed that the remarkably matched regions appear in the untranslated regions (UTRs) of mRNAs, especially in the 3' UTR. The optimal matched segments (OMSs) are highly organized segments. In addition, the optimal matching relations were analysed between mature mRNAs and other introns. The matching strengths in the UTRs are clearly lower than those in their corresponding introns. Our studies indicate that there are potential interactions between mature mRNAs and their corresponding introns and the post-spliced introns should have other novel functions in the gene expression process.