Evolutionary signatures are specific, common patterns in the way that DNA sequence has changed over time due to the process of evolution. In my thesis I observe these signatures to understand the sources of highly mutable coding regions in mammals and elucidate a new candidate function for a stop codon readthrough candidate gene, BRI3BP. First, I identify deviations from the normal evolutionary signatures in protein coding genes to recognize synonymous acceleration elements (SAEs): regions with unusually high rates of synonymous substitution. These SAEs are driven by an increased mutation rate, which persists in the human lineage, in otherwise evolutionarily constrained protein-coding regions. SAEs provide an important resource to better characterize protein-coding constraint in mammals and within humans. Second, I combine evolutionary signatures at the protein-coding and protein-folding level to characterize the functional implication of stop-codon readthrough in BRI3BP. I demonstrate that this readthrough region has conserved spaced hydrophobic residues that pattern match to the c-terminal helix forming a coiled-coil-like domain. Readthrough alters BRI3BP function from pro-growth to pro-apoptotic, similarly to another human stop-codon readthrough gene. This suggests that readthrough-triggered apoptosis may represent a general mechanism for limiting growth of cells with aberrant ribosomal termination.