Table 1.
Abridged table of mouse-human genome-wide codon conservation frequencies, as a function of each of the 20 × 20 pairs of aligned amino acids
| AA1 | AA2 | # | 000 | 001 | 010 | 011 | 100 | 101 | 110 | 111 |
|---|---|---|---|---|---|---|---|---|---|---|
| F | F | 308,260 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.202 | 0.798 |
| F | S | 3,951 | 0.028 | 0.042 | 0.000 | 0.000 | 0.337 | 0.593 | 0.000 | 0.000 |
| F | T | 716 | 0.457 | 0.543 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| F | N | 220 | 0.377 | 0.623 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| F | K | 160 | 1.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| . | . | . | . | . | ||||||
| . | . | . | . | . | ||||||
| S | F | 3,660 | 0.022 | 0.050 | 0.000 | 0.000 | 0.322 | 0.607 | 0.000 | 0.000 |
| S | S | 616,045 | 0.004 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 | 0.302 | 0.691 |
| . | . | . | . | . | ||||||
| . | . | . | . | . | ||||||
| . | . | . | . | . | ||||||
| G | R | 7,924 | 0.000 | 0.000 | 0.393 | 0.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| G | G | 521,714 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.327 | 0.673 |
For a given pair of amino acids, there are eight possible conservation patterns for the underlying nucleotides (000, 001, 010, 011, 100, 101, 110, 111), where 1 means a conserved base and 0 means a non-conserved base. These frequencies provide a null model for the expected conservation patterns at the nucleotide level, given the amino acid sequence. Here '#' indicates the number of instances in which amino acid 1 (AA1) is aligned to AA2 in the complete set of coding alignments between mouse and human.