2423.02 Depiction of Coding Regions [R-07.2015]
If applicant chooses to depict coding regions, 37 CFR 1.822(c)(3) requires the amino acids corresponding to the codons in the coding parts of a nucleotide sequence to be typed immediately below the corresponding codons. Further, in 37 CFR 1.822(c)(3), the situation in which a codon spans an intron has been addressed. In those situations, the "amino acid symbol shall be typed below the portion of the codon containing two nucleotides." This requirement clarifies the representation of an amino acid that corresponds to a codon that spans an intron.
It should be noted that the sequence rules do not, in any way, require the depiction of coding regions or the amino acids corresponding to the codons in those coding regions. 37 CFR 1.822(d) only requires that where amino acids corresponding to the codons in the coding parts of a nucleotide sequence are depicted, they must be depicted below the corresponding codons. There is absolutely no requirement in the rules to depict coding regions. However, when the coding parts of a nucleotide sequence and their corresponding amino acids have been enumerated by their residues, those amino acids must also be set forth as a separate sequence if the amino acid sequence meets the length thresholds in 37 CFR 1.821(a).