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Table 4 Synonymous codon usage bias for the whole coding sequence of PRRSV

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

aAA

Codon

bCUB ij

AAa

Codon

bCUB ij

Ala

GCA

-0.143

Leu

CUA

-0.490

 

GCC

0.309

 

CUC

0.164

 

GCG

-0.350

 

CUG

0.377

 

GCU

0.184

 

CUU

0.096

Arg

AGA

-0.107

 

UUA

-0.670

 

AGG

0.092

 

UUG

0.522

 

CGA

-0.258

Lys

AAA

-0.003

 

CGC

0.411

 

AAG

0.003

 

CGG

0.012

Phe

UUC

-0.083

 

CGU

-0.149

 

UUU

0.083

Asn

AAC

0.040

Pro

CCA

0.047

 

AAU

-0.04

 

CCC

0.059

Asp

GAC

-0.045

 

CCG

-0.198

 

GAU

0.045

 

CCU

0.092

Cys

UGC

0.001

Ser

AGC

-0.128

 

UGU

-0.001

 

AGU

-0.194

Gln

CAA

-0.018

 

UCA

0.075

 

CAG

0.018

 

UCC

0.418

Glu

GAA

-0.116

 

UCG

-0.317

 

GAG

0.116

 

UCU

0.145

Gly

GGA

-0.441

Thr

ACA

-0.031

 

GGC

0.369

 

ACC

0.439

 

GGG

0.016

 

ACG

-0.347

 

GGU

0.056

 

ACU

-0.061

His

CAC

-0.153

Tyr

UAC

0.174

 

CAU

0.153

 

UAU

-0.174

Ile

AUA

-0.234

Val

GUA

-0.635

 

AUC

0.166

 

GUC

0.110

 

AUU

0.068

 

GUG

0.406

    

GUU

0.118

  1. a mean amino acid
  2. bThe CUB ij value was calculated following by the equation: CUB ij = RSCU ij -RSCU 0 , and RSCU ij value came from the previous study [30].