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Table 3 Preferentially used codons in the target region in US and EU serotypes of PRRSV

From: Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome

  ORF1a ORF2 ORF3
Codon US EU US EU US EU
aGCA b1.69 b1.43 0 0.91 0.15 0.64
GCC 1.00 0.98 1.42 2.16 0 0.91
aGCG b2.25 b1.34 0 0 b2.17 0
GCU 0 0.76 1.03 0.83 2.94 1.88
aAGA 0 0 0.5 b1.37 0 0
AGG 1.22 0 0 0 3.72 0
aCGA b2.42 0 0 0 0 0
CGC 0 0 0 0 0 2.05
CGG 3.07 5.63 3.79 1.14 0 0
aCGU 0 0 0 b1.07 0.47 b2.90
AAC 0.43 0.90 1.86 0 0.12 1.01
aAAU b1.72 0.68 0.40 0 b1.35 1.00
aGAC 0 b1.56 0 0 0 0
GAU 2.31 0.37 0 1.26 0.38 0.25
UGC 1.08 1.62 1.25 0 0.36 0.18
aUGU 0.92 0.50 b1.01 b1.51 b1.44 b1.43
aCAA b1.89 b1.08 0.50 0.86 0 0
CAG 0.17 0.92 0 1.21 0 2.15
aGAA 0.55 0.28 0 0 b1.50 0
GAG 1.30 1.38 0 1.14 0.27 1.30
aGGA 0 0.39 0 b2.46 0 0
GGC 1.40 1.63 3.13 0 1.51 3.82
GGG 2.00 1.16 0 0.29 0 0
GGU 0.15 0.48 1.40 1.25 2.58 0.42
aCAC 0 0 0 b1.58 0 0.72
CAU 0 0 0 0.21 1.41 1.32
aAUA b8.26 0 b2.55 b3.19 0 0
AUC 0 0 0 0 0 2.58
AUU 0 0.59 0 0 4.31 0
aCUA b2.32 0.24 0.32 0 0 b4.42
CUC 1.90 1.87 0 0 1.84 0.77
CUG 0.92 0 0 0.65 1.39 0.43
CUU 1.01 1.34 0.66 0.24 0 1.02
aUUA 0.28 0.22 0.64 b3.54 0 0
UUG 0 0.80 1.99 2.04 0.74 1.29
aAAA 0 0 b1.27 b2.64 0 0
AAG 0 0 0 0 0 0
aUUC b1.01 0.48 0.17 b1.09 0.99 0.95
UUU 1.01 1.46 1.14 0.78 1.02 1.07
CCA 0 0.98 1.50 1.04 0 4.51
CCC 2.27 0.11 0 0 0.39 0
aCCG 0 b2.43 b1.36 b1.07 b3.79 0
CCU 1.01 0.81 0 3.21 0 0.24
aAGC 0.42 b1.56 0 0.43 b2.02 b1.26
aAGU b6.36 b8.28 b4.94 b4.13 0 b1.87
UCA 1.89 1.68 0.28 0.41 0 1.17
UCC 0.21 0.98 0.09 0.60 0.83 0.59
aUCG 0 0 b1.58 b1.70 0 b1.30
UCU 2.79 1.33 1.16 0.63 2.21 1.22
aACA b1.97 b1.48 b6.17 0 b1.24 0.70
ACC 0.89 0.58 0 0 0 0.70
aACG b2.22 b1.49 0 b1.83 b1.74 b2.11
aACU 0 b1.06 0 0 0.96 0.82
UAC 1.33 0 0 1.36 1.32 2.03
aUAU 0.37 0.30 b1.77 0.53 0 0.11
aGUA 0 b2.67 0 b4.79 0 0
GUC 0.77 1.77 3.78 0.33 0.11 0.33
GUG 1.71 0.31 0 2.04 1.88 0
GUU 0.76 0.53 2.96 0 1.08 4.14
  ORF4 ORF5 ORF6 ORF7
Codon US EU US EU US EU US EU
aGCA b1.25 0.16 0 0 0 b1.60 0 b1.09
GCC 0.55 0.96 1.91 3.08 0.65 1.69 1.22 1.75
aGCG b1.27 b1.09 0.85 0.57 b1.60 0 0 0
GCU 0.98 1.20 1.35 0 2.24 0.21 1.50 0.74
aAGA 0 0 0 b3.69 0 0 b2.78 0.71
AGG 0 0 0 0.15 0 0 0.17 2.19
aCGA 0 0 b7.83 0 b4.58 0.99 0 0.33
CGC 0 0 0 0 2.29 5.79 0 0.75
CGG 0 0 0 0 0 0.23 0 0.29
aCGU 0 0 0 b1.80 0 0 0 0
AAC 3.67 1.36 1.34 1.42 0 0.31 1.09 1.42
aAAU 0 0.56 0 0.20 0.29 0.86 0.89 0.83
aGAC b1.38 b1.39 0.58 0.18 b1.33 0.64 0.50 0
GAU 0.50 0.69 0 2.65 0.67 0.86 0.75 0
UGC 0.64 0.67 0.82 0.99 0.44 1.38 1.92 1.00
aUGU b1.41 0.99 b1.13 b1.02 b1.33 0.24 0 0.29
aCAA 0.42 b1.14 0.25 1.00 b1.50 b1.38 0.64 0.78
CAG 1.46 0.95 2 0 0.33 0 1.13 1.07
aGAA 0.50 0 0 0 0.17 0.45 0 0
GAG 0.19 2.14 1.49 0.29 0 0 0 0
aGGA 0 0 0 0 0 0.84 b1.31 b1.14
GGC 0.63 0 1.63 1.98 0.79 0.77 1.05 0.89
GGG 0 0 1.03 0.54 1.87 1.97 0.63 0.85
GGU 4.00 3.33 0.17 0 0 0.56 1.35 1.11
aCAC 0 0 0 b2.90 0.78 b2.05 0 0
CAU 0 1.48 1.94 0 1.46 0 0 0
aAUA 0 0 0 b2.58 b1.12 b1.86 0 b3.29
AUC 1.26 1.24 1.07 0.12 1.19 0.90 1.46 0
AUU 0.73 1.20 1.34 0.37 0.80 0.08 0 0
aCUA 0 b2.26 b1.37 0 b1.66 b1.35 0 0
CUC 1.52 1.15 0.60 0 0.19 0.74 0 0
CUG 0 1.14 0.70 0.99 1.19 1.48 1.46 1.78
CUU 1.19 1.81 0.62 0.77 1.27 0.94 0 0
aUUA 0 0.23 0.55 0 0.77 0.16 0 0
UUG 1.50 0.19 1.69 2.16 0.73 0.84 0.22 1.05
aAAA b1.21 0.20 b1.34 1.00 0 0.31 b1.08 b1.21
AAG 0.69 1.82 0.23 0.38 2.43 1.32 0.98 0.86
aUUC b1.28 b1.18 b1.88 0.99 1.00 0.42 0 0
UUU 0.76 0.12 0.84 0.98 0.87 1.49 0 0
CCA 3.83 0 0 0.76 3.00 0 2.25 1.85
CCC 0.40 1.67 0 0 0 0.79 0 0.59
aCCG 0 0.43 b4.25 b1.29 0 0 b2.00 0.33
CCU 0 0.24 0.17 0 0 1.65 0 0.50
aAGC b1.34 0 b1.69 0.57 0.98 b3.10 1.00 b2.47
aAGU b3.67 b2.57 0 0 b4.28 0 0 b2.51
UCA 4.31 0.64 0 0 2.20 0 0 2.99
UCC 0.78 0 0.32 1.17 0.79 0 1.35 1.26
aUCG b1.91 b1.95 b1.58 b1.48 b2.20 0 0 0
UCU 0.47 0.86 1.45 1.78 2.02 0.31 0 0
aACA 0 0 0 b1.32 0.17 b1.76 0 b1.63
ACC 1.78 1.41 0.98 0.67 0.83 0.56 0 0
aACG 0 b1.69 b6.79 b2.13 b2.35 0 0 0
aACU 0.78 0.21 0 0.53 0.18 0.43 0 0
UAC 0 0 1.80 1.11 0.67 1.05 0 0
aUAU 0 0 0.48 0.90 b1.50 0.55 0 0
aGUA 0 0 0 0 0.98 0.27 0 0
GUC 0.92 1.04 0.34 0 0 0 1.72 2.96
GUG 0.52 0.10 2.79 0 2.10 2.29 0 0
GUU 2.25 1.77 0 0 0 0 0 0
  1. a presented the non-preferential codon.
  2. b presented that the non-preferential codon was more preferentially chosen in the translation initiation region than that of the whole coding sequence.