The stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals the termination of translation. Premature stop codons (premature termination of transcription) occurs when a mutation in which one of the three terminator codons in the mRNA used to signal the end of a polypeptide appears in the middle of a genetic message (nonsense mutation). Two genetically-encoded amino acids, selenocysteine and pyrrolysine, are encoded by what normally would be a stop codon – mechanism called translational recoding and depends on the presence of different compounds and translation initiation factors. Premature stop codons interfere with gene regulation, and can result in phenotypic consequences. Though often associated with diseases, they can give rise to interesting agronomic characteristics.