Notes. NMD = nonsense-mediated mRNA decay. ω (Human), ω (Mouse) and ω (Dog) are the Ka/Ks ratios in human, mouse and dog lineages, respectively. a NMD-specific exon alignment was concatenated alignment from the human NMD-specific exon regions of human-mouse-dog three-way CDS alignments, and the rest regions in the CDS alignments were concatenated together to construct the remained NMD alignment. b similar to the NMD-specific case, the human non-NMD-single exon regions of human-mouse-dog three-way CDS alignments were clipped out to construct the concatenated alignment, and the rest regions to construct the remained non-NMD alignment. See Methods for details.