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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

From: COMIT: identification of noncoding motifs under selection in coding sequences

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
  1. 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.