Intron Framing Exonic Nucleotides: A Compromise Between Protein Coding and Splicing Constraints

Introns in eukaryotic genes are located either between codons (phase 0) or within codons (phase 1 and 2). Phase 0 introns are more frequent. Several factors might contribute to this phenomenon with codon usage bias playing a significant role. The nucleotides located at the very ends of intermediate exons are involved not only in protein coding but also in splicing regulation. This study indicates that phase 0 introns create more flexibility for protein coding without affecting splicing sensitive exonic nucleotides than the other two intron types. The canonic AG↓G site, for instance, is particularly frequent around phase 0 introns. In humans the observed frequency of AG↓G sites framing phase 0 introns is at least 2 to 3 times higher than in phase 1 and 2 introns. It is possible that the higher flexibility of exonic nucleotides surrounding phase 0 introns may serve as a driving force increasing frequencies of sites like AG↓G and this could lead to more stable or efficient splicing without compromising protein coding. If so, this type of selection might also contribute to higher frequency of phase 0 introns.