Skip to main content

Table 1 Codon usage in 2009 H1N1 pdm Influenza A Virus, displayed as RSCU a values

From: Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development

AA

Cod

HC

Swine

H1N1pdm

H1N1b

H3N2

AA

Cod

HC

Swine

H1N1pdm

H1N1

H3N2

Phe

UUU

0.92

0.79

0.85

0.98

0.96

Ser

UCU

1.14

0.99

1.08

1.12

0.91

UUC

1.08

1.21

1.15

1.02

1.04

UCC

1.32

1.50

0.74

0.87

0.97

Leu

UUA

0.48

0.32

0.62

0.91

0.62

UCA

0.90

0.73

1.57

1.62

1.34

UUG

0.78

0.67

1.00

1.27

1.30

UCG

0.30

0.39

0.31

0.14

0.21

CUU

0.78

0.65

1.16

0.97

1.24

Pro

CCU

1.16

1.05

1.00

1.04

1.29

CUC

1.20

1.35

0.95

0.59

0.78

CCC

1.28

1.46

0.80

0.72

0.84

CUA

0.42

0.33

1.20

1.00

0.96

CCA

1.12

0.94

1.70

1.74

1.29

CUG

2.40

2.68

1.07

1.27

1.11

CCG

0.44

0.56

0.50

0.49

0.58

Ile

AUU

1.08

0.91

1.07

1.07

1.03

Thr

ACU

1.00

0.83

1.01

1.11

1.28

AUC

1.41

1.67

0.77

0.78

0.89

ACC

1.44

1.68

0.79

0.96

0.72

AUA

0.51

0.42

1.16

1.16

1.08

ACA

1.12

0.92

1.88

1.74

1.67

Met

AUG

1.00

1.00

1.00

1.00

1.00

ACG

0.44

0.57

0.32

0.19

0.34

Val

GUU

0.72

0.57

0.83

0.97

1.06

Ala

GCU

1.08

0.96

0.98

1.13

1.06

GUC

0.96

1.07

0.77

0.74

0.69

GCC

1.60

1.80

0.87

0.87

0.93

GUA

0.48

0.34

1.12

1.07

1.02

GCA

0.92

0.74

1.87

1.74

1.73

GUG

1.84

2.03

1.28

1.22

1.23

GCG

0.44

0.50

0.27

0.26

0.28

Tyr

UAU

0.88

0.73

1.04

1.09

1.13

Cys

UGU

0.92

0.79

0.88

1.09

0.79

UAC

1.12

1.27

0.96

0.91

0.87

UGC

1.08

1.21

1.12

0.91

1.21

TER

UAA

**

**

**

**

**

TER

UGA

**

**

**

**

**

UAG

**

**

**

**

**

Trp

UGG

1.00

1.00

1.00

1.00

1.00

His

CAU

0.84

0.70

1.23

1.05

1.21

Arg

CGU

0.48

0.44

0.11

0.24

0.10

CAC

1.16

1.30

0.77

0.95

0.79

CGC

1.08

1.31

0.33

0.18

0.24

Gln

CAA

0.54

0.44

1.05

1.33

1.36

CGA

0.66

0.60

0.63

0.41

0.43

CAG

1.46

1.56

0.95

0.67

0.64

CGG

1.20

1.29

0.43

0.28

0.57

Asn

AAU

0.94

0.79

1.15

1.20

1.15

Ser

AGU

0.90

0.77

1.14

1.15

0.95

GAC

1.08

1.21

0.95

0.80

0.85

AGC

1.44

1.62

1.16

1.11

1.38

Lys

AAA

0.86

0.76

1.10

1.27

1.39

Arg

AGA

1.26

1.12

2.89

3.08

2.84

AAG

1.14

1.24

0.90

0.73

0.61

AGG

1.26

1.23

1.61

1.81

1.83

Asp

GAU

0.92

0.80

1.05

1.13

1.08

Gly

GGU

0.64

0.57

0.57

0.60

0.69

GAC

1.08

1.20

0.95

0.87

0.92

GGC

1.36

1.46

0.62

0.55

0.62

Glu

GAA

0.84

0.72

1.20

1.15

1.14

GGA

1.00

0.91

1.73

1.84

1.65

GAG

1.16

1.28

0.80

0.85

0.86

GGG

1.00

1.05

1.08

1.01

1.04

  1. aRSCU, relative synonymous codon usage; AA, amino acid; Cod, codons; HC, human cells; H1N1pdm, 2009 H1N1 pdm Influenza A virus; H1N1 and H3N2, seasonal H1N1 and H3N2 Influenza A virus, respectively. Highly increased codons with respect to host cells (∆ ≥ 0.30) are shown in bold. Codons containing de dinucleotide CG are shown in italics. b RSCU codon usage of seasonal H1N1 and H3N2 according to Wong et al. (2010) [12].
Back to article page

Virology Journal

ISSN: 1743-422X