Conservation/Mutation in the Splice Sites of Cytokine Receptor Genes of Mouse and Human

Conservation/mutation in the intronic initial and terminal hexanucleotides was studied in 26 orthologous cytokine receptor genes of Mouse and Human. Introns began and ended with the canonical dinucleotides GT and AG, respectively. Identical configurations were found in 57% of the 5′ hexanucleotides and 28% of the 3′ hexanucleotides. The actual conservation percentages of the individual variable nucleotides at each position in the hexanucleotides were determined, and the theoretical rates of conservation of groups of three nucleotides were calculated under the hypothesis of a mutual evolutionary independence of the neighboring nucleotides (random association). Analysis of the actual conservation of groups of variable nucleotides showed that, at 5′, GTGAGx was significantly more expressed and GTAAGx was significantly less expressed, as compared to the random association. At 3′, TTTxAG and xTGCAG were overexpressed as compared to a random association. Study of Mouse and Human transcript variants involving the splice sites showed that most variants were not inherited from the common ancestor but emerged during the process of speciation. In some variants the silencing of a terminal hexanucleotide determined skipping of the downstream exon; in other variants the constitutive splicing hexanucleotide was replaced by another potential, in-frame, splicing hexanucleotide, leading to alterations of exon lengths. 1. Introduction In most protein-coding genes of eukaryotes the coding exons alternate with noncoding introns. The nuclear pre-mRNA is a transcript of the whole gene, including the introns. However, before it is exported to the cytoplasm, the introns are removed through a process called pre-mRNA splicing and the exons orderly joined to form the mature coding mRNA. Cutting at splicing sites is usually accomplished with a high degree of precision, as needed for the synthesis of the correct protein products in the process of translation. Precision splicing requires the existence of specific sequence arrangements at appropriate pre-mRNA sites (signals) and is affected by a massive ribonucleoprotein complex, the spliceosome, which has evolved to interact with these sequences. Most often the splicing signal is univocal and robust enough to allow one single splicing pattern only at each site. But when the splicing signals are less robust or possibly not univocal, “physiological” alternative splicing patterns may occur, with total or partial deletion of some exons or retention of in-frame introns resulting in alterations of the encoded protein product. In most of