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Codon usage

Codon Usage in Arabidopsis thaliana (At% is the frequency of the codon for each AAcid) and E. coli ( reference: HÉNAUT and DANCHIN). Class I (EcI) contains genes involved in most metabolic processes. Class II genes correspond to genes highly and continuously expressed during exponential growth. Class III genes are implicated in horizontal transfer of DNA. The distribution of codons in class III genes is more or less even, whereas it is extremely biased in class II genes.

Rare codons (<5%) of E. coli class II are in bold.

AAcid Codon At (n) n/N
1000		 At% Ec I Ec II* Ec III
Ala GCA 1336 16.56 0.22 19.63 24.01 31.27
Ala GCC 1208 14.97 0.2 27.62 16.14 23.67
Ala GCG 665 8.24 0.11 38.23 32.3 22.19
Ala GCT 2861 35.46 0.47 14.52 27.54 22.86
Arg AGA 1305 16.17 0.32 1.75 0.62 15.63
Arg AGG 1027 12.73 0.25 1.54 0.29 9.96
Arg CGA 404 5.01 0.1 5.52 1.07 12.8
Arg CGC 280 3.47 0.07 42.23 32.97 21.94
Arg CGG 278 3.45 0.07 8.97 0.8 13.62
Arg CGT 822 10.19 0.2 38.99 64.25 26.05
Asn AAC 1968 24.39 0.6 59.13 82.75 35.94
Asn AAT 1319 16.35 0.4 40.87 17.25 64.06
Asp GAC 1719 21.3 0.41 37.17 53.95 29.53
Asp GAT 2516 31.18 0.59 62.83 46.05 70.47
Cys TGC 634 7.86 0.47 59.1 61.15 44.29
Cys TGT 724 8.97 0.53 40.9 38.85 55.71
End TAA 140 1.74 0.38 nd nd nd
End TAG 66 0.82 0.18 nd nd nd
End TGA 165 2.04 0.44 nd nd nd
Gln CAA 1414 17.52 0.5 33.4 18.65 37.06
Gln CAG 1439 17.83 0.5 66.6 81.35 62.94
Glu GAA 2337 28.96 0.47 68.33 75.35 66.25
Glu GAG 2675 33.15 0.53 31.67 24.65 33.75
Gly GGA 2418 29.97 0.38 9.19 1.97 24.75
Gly GGC 871 10.79 0.14 43.17 42.83 24.51
Gly GGG 747 9.26 0.12 14.74 4.36 18.95
Gly GGT 2308 28.6 0.36 32.91 50.84 31.79
His CAC 765 9.48 0.5 43.2 70.23 38.31
His CAT 771 9.55 0.5 56.8 29.77 61.69
Ile ATA 724 8.97 0.16 4.43 0.57 25.78
Ile ATC 1935 23.98 0.43 44.37 65.94 26.65
Ile ATT 1857 23.01 0.41 51.2 33.49 47.57
Leu CTA 698 8.65 0.1 3.09 0.83 6.81
Leu CTC 1461 18.11 0.2 10.4 8.03 9.04
Leu CTG 703 8.71 0.1 52.79 76.67 29.99
Leu CTT 1914 23.72 0.27 9.7 5.56 19
Leu TTA 736 9.12 0.1 10.99 3.44 20.09
Leu TTG 1648 20.42 0.23 13.02 5.47 15.05
Lys AAA 1989 24.65 0.39 75.44 78.55 72.21
Lys AAG 3161 39.17 0.61 24.56 21.45 27.79
Met ATG 2093 25.94 1 100 100 100
Phe TTC 1933 23.96 0.58 44.91 70.92 32.86
Phe TTT 1400 17.35 0.42 55.09 29.08 67.14
Pro CCA 1334 16.53 0.35 18.63 15.25 31.5
Pro CCC 534 6.62 0.14 11.19 1.63 16.26
Pro CCG 612 7.58 0.16 56.47 71.89 23.94
Pro CCT 1358 16.83 0.35 13.71 11.23 28.3
Ser AGC 957 11.86 0.15 30.04 24.33 17.61
Ser AGT 958 11.87 0.15 13.96 4.52 18.73
Ser TCA 1126 13.95 0.18 10.83 4.79 22.09
Ser TCC 921 11.41 0.15 15.02 26.56 11.34
Ser TCG 589 7.3 0.1 16.88 7.39 10.6
Ser TCT 1644 20.37 0.27 13.26 32.41 19.63
Thr ACA 1189 14.74 0.27 10.52 4.67 27.93
Thr ACC 1171 14.51 0.26 46.83 53.6 24.45
Thr ACG 560 6.94 0.13 27.81 12.65 20.8
Thr ACT 1538 19.06 0.34 14.85 29.08 26.83
Trp TGG 929 11.51 1 100 100 100
Tyr TAC 1423 17.64 0.62 45.58 64.77 30.4
Tyr TAT 877 10.87 0.38 54.42 35.23 69.6
Val GTA 568 7.04 0.1 14.86 19.97 21.78
Val GTC 1319 16.35 0.24 22.48 13.45 18.95
Val GTG 1459 18.08 0.26 38.92 26.81 24.94
Val GTT 2191 27.15 0.4 23.74 39.77 34.33
 
N=80691