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Table 1.

Categories of overlapping codon pairs that are the basis for codon blocks (c-blocks)

Codon pair status	General category	C-block category	Codon topology	Description	Positional identity
Paired	Simple	Match	Both: contiguous or split	Exact match in genomic position and nucleotide triplet identity	3/3 overlap
Unpaired: empty “placeholder” codon		Deletion	Both contiguous	Codon missing in the alternative isoform	0/3 or 1/3 overlap
Unpaired: empty “placeholder” codon		Insertion	Both contiguous	Codon missing in the reference isoform	0/3 or 1/3 overlap
Unpaired: “placeholder” codon that represents an untranslated position	Translational status	Untranslated	Both: contiguous or split	Nucleotide triplet not translated in the alternative isoform	0/3 or 1/3 overlap
	Translational status	Translated	Both: contiguous or split	Nucleotide triplet not translated in the reference isoform	0/3 or 1/3 overlap
Paired	Frameshift	Ahead	Both contiguous	Alternative isoform codon one position downstream	2/3 overlap
	Frameshift	Behind	Both contiguous	Alternative isoform codon one position upstream	2/3 overlap
	Split codon patterns	Edge^a	Both split	Codons overlapping at the junction	Different
	Split codon patterns	Complex^a	Both split or 1 of the 2 codons split	Codons overlapping at the junction, and are frameshifted	Different

[i] ^aA subset of these paired codons can result in AA differences, or “ragged” codon pairs.