Table 1 |
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|
Abridged table of mouse-human genome-wide codon conservation frequencies, as a function of each of the 20 × 20 pairs of aligned amino acids |
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|
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 |
|
|
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|
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. |
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|
Kural et al. Genome Biology 2009 10:R133 doi:10.1186/gb-2009-10-11-r133 |
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