Comparison of sequence conservation for genes and pseudogenes in the context of adjacent genomic sequences. The orthologous sequences in chimp, macaque, mouse, and dog were retrieved from the MSA data for protein “coding” regions (CDS) of genes and pseudogenes. Their regions were divided into 10 blocks, and pairwise nucleotide sequence identities were calculated for each block. The data shown here are the means for all genes or processed (PS) or nonprocessed (NPS) pseudogenes. For comparison, 500-bp upstream and downstream sequences of CDSs were also analyzed. The P-values of the t-test for the differences between genes and pseudogenes (for all four species) and between NPS and PS (in chimp and macaque) are <0.01.
