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Table 5 Candidate optimal codons in five species, determined as frequency increase by increased expression levela

From: Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

   

Species

       

Species

    

AA

 

Codon

AY

MI

OV

SR

TS

AA

 

Codon

AY

MI

OV

SR

TS

A

Ala

GCA

  

GCA

  

N

Asn

AAC

AAC

AAC

 

AAC

 

A

Ala

GCC

GCC

GCC

GCC

GCC

 

N

Asn

AAT

  

AAT

  

A

Ala

GCT

GCT

GCT

 

GCT

GCT

        
        

P

Pro

CCA

 

CCA

CCA

CCA

CCA

C

Cys

TGC

TGC

TGC

TGC

TGC

 

P

Pro

CCC

CCC

    
        

P

Pro

CCG

 

CCG

   

D

Asp

GAC

GAC

GAC

GAC

GAC

 

P

Pro

CCT

    

CCT

D

Asp

GAT

    

GAT

        
        

Q

Gln

CAA

   

CAA

CAA

E

Glu

GAA

  

GAA

GAA

GAA

Q

Gln

CAG

CAG

CAG

CAG

  

E

Glu

GAG

GAG

GAG

           
        

R

Arg

AGA

    

AGA

F

Phe

TTC

TTC

TTC

TTC

TTC

 

R

Arg

CGA

    

CGA

F

Phe

TTT

    

TTT

R

Arg

AGG

  

AGG

  
        

R

Arg

CGC

CGC

CGC

 

CGC

 

G

Gly

GGA

GGA

 

GGA

GGA

GGA

R

Arg

CGG

  

CGG

  

G

Gly

GGC

 

GGC

   

R

Arg

CGT

CGT

CGT

 

CGT

 

G

Gly

GGT

GGT

            
        

S

Ser

AGC

AGC

AGC

AGC

AGC

AGC

H

His

CAC

CAC

CAC

CAC

CAC

CAC

S

Ser

TCA

  

TCA

 

TCA

        

S

Ser

TCC

TCC

TCC

TCC

TCC

 

I

Ile

ATA

    

ATA

S

Ser

AGT

    

AGT

I

Ile

ATC

ATC

ATC

ATC

ATC

 

S

Ser

TCG

TCG

TCG

TCG

  

I

Ile

ATT

   

ATT

 

S

Ser

TCT

   

TCT

 

K

Lys

AAA

    

AAA

T

Thr

ACC

ACC

ACC

ACC

ACC

 

K

Lys

AAG

AAG

AAG

AAG

AAG

 

T

Thr

ACG

 

ACG

ACG

  
        

T

Thr

ACT

   

ACT

ACT

L

Leu

CTA

    

CTA

        

L

Leu

CTC

CTC

CTC

 

CTC

 

V

Val

GTA

    

GTA

L

Leu

CTG

  

CTG

  

V

Val

GTC

GTC

GTC

GTC

GTC

 

L

Leu

CTT

CTT

CTT

 

CTT

CTT

V

Val

GTG

 

GTG

   

L

Leu

TTA

    

TTA

V

Val

GTT

 

GTT

 

GTT

 

L

Leu

TTG

 

TTG

TTG

TTG

         
        

Y

Tyr

TAC

TAC

TAC

TAC

TAC

TAC

  1. aExpression level inferred by EST number. Definitions of species two letter codes are provided in Table 1. AA, amino acid; EST, expressed sequence tag.