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Table 5 Optimal codons of genes in Bombyx mori

From: Non-uniqueness of factors constraint on the codon usage in Bombyx mori

Amino acid Codon High Low Amino acid Codon High Low
RSCU N RSCU N RSCU N RSCU N
Ala GCU 0.64 288 1.66 315 Asn AAU 0.34 130 1.39 549
GCC * 1.80 818 0.46 88 AAC * 1.66 631 0.61 239
GCA 0.29 133 1.65 313 Gln CAA 0.44 174 1.43 370
GCG * 1.27 575 0.23 43 CAG * 1.56 615 0.57 146
Phe UUU 0.24 91 1.48 396 Ser UCU 0.71 153 1.49 233
UUC * 1.76 680 0.52 140 UCC * 1.71 366 0.44 69
Gly GGU 0.65 240 1.49 291 UCA 0.42 90 1.77 276
GGC * 1.91 703 0.58 113 UCG * 1.56 335 0.34 53
GGA 0.75 277 1.55 303 AGU 0.34 72 1.40 219
GGG * 0.69 254 0.39 76 AGC * 1.26 271 0.55 86
Ile AUU 0.34 99 1.37 407 Thr ACU 0.57 146 1.49 275
AUC * 2.23 652 0.39 115 ACC * 1.68 433 0.43 79
AUA 0.43 126 1.24 368 ACA 0.43 110 1.85 343
Leu UUA 0.17 49 2.18 442 ACG * 1.32 339 0.23 43
UUG 0.61 179 1.30 264 Asp GAU 0.38 226 1.46 587
CUU 0.30 88 0.89 181 GAC * 1.62 958 0.54 217
CUC * 2.05 602 0.35 71 Glu GAA 0.57 414 1.59 769
CUA 0.27 78 0.75 152 GAG * 1.43 1036 0.41 197
CUG * 2.60 764 0.53 108 His CAU 0.38 97 1.44 196
Pro CCU 0.48 122 1.46 204 CAC * 1.62 416 0.56 76
CCC * 1.65 418 0.35 49 Lys AAA 0.48 278 1.55 924
CCA 0.36 91 1.87 261 AAG * 1.52 870 0.45 269
CCG * 1.50 380 0.32 45 Arg CGU 0.63 126 0.76 81
Val GUU 0.41 144 1.59 363 CGC * 2.49 495 0.21 22
GUC * 1.32 469 0.48 109 CGA 0.37 74 0.87 93
GUA 0.36 126 1.26 289 CGG * 1.04 207 0.23 24
GUG * 1.91 678 0.67 153 AGA 0.61 121 3.05 325
Cys UGU 0.35 64 1.50 179 AGG 0.86 172 0.89 95
UGC * 1.65 302 0.50 60 Trp UGG 1.00 219 1.00 157
Tyr UAU 0.29 100 1.40 322 TER UGA 0.94 17 0.61 11
UAC * 1.71 595 0.60 138 UAA 1.50 27 1.83 33
Met AUG 1.00 507 1.00 359 UAG 0.56 10 0.56 10
  1. Note: N is codon frequency, RSCU is relative synonymous codon usage. The codon usage of eleven genes (5% of the total number of genes) from the extremes of the principal were pooled. The codon usage of both pools was compared using a two-way Chi squared contingency test, to identify optimal codons. For the purposes of this test dataset with the lower ENc were putatively assigned as highly expressed. The codon usage and RSCU of both datasets is shown. Those codons that occur significantly more often (p < 0.01) in the highly biased dataset relative to the lower biased dataset are putatively considered optimal, and are indicated with a (*).