Differences of Translation Termination Sites Among the Three Stop Codons

Most organisms use different mechanisms of translation termination for the three types of stop codons, i.e. UAA, UAG, and UGA [1]. Using the GenBank database, we have conducted comprehensive computer analyses of translation termination sites in order to find the difference of consensus sequence patterns around each type of stop codons. We also systematically analyzed the preference of stop codons (O/E ratio: frequency of UAA, UAG, or UGA used as stop codons divided by frequency of the same triplet over the entire genome). It is known that Release Factor 1 (RF1) is required for translation termination for the stop codon UAG, and Release Factor 2 (RF2) for the stop codon UGA. The stop codon UAA requires either RF1 or RF2, but not necessarily both. For the five species of which genes for RF1 and RF2 are annotated in the GenBank database, we computed Codon Adaptation Index (CAI) values [2] for these genes.