Codon Map/Freqency/Optimization

Codon Map/Freqency/Optimization

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Codon map and codon freqnency

Followings are triplet, amino acid and codon frequencies for wheat (Triticum aestivum), human (Homo sapiens)and  e-coli (Escherichia coli) in  F/1000

 Triplet  Amino Acid Wheat Homo sapiens E-coli
TTT Phe(F) 12.3 17.6 24.4
TTC Phe(F) 24.8 20.3 13.9
TTA Leu(L) 3.7 7.7 17.4
TTG Leu(L) 12.1 12.9 12.9
         
CTT Leu(L) 12.3 13.2 14.5
CTC Leu(L) 27.4 19.6 9.5
CTA Leu(L) 7.4 7.2 5.6
CTG Leu(L) 22.3 39.6 37.4
         
ATT Ile(I) 11.7 16.0 29.6
ATC Ile(I) 24.3 20.8 19.4
ATA Ile(I) 6.7 7.5 13.3
ATG Met(M), START 24.3 22.0 23.7
         
GTT Val(V) 14.3 11.0 21.6
GTC Val(V) 21.3 14.5 13.1
GTA Val(V) 5.3 7.1 13.1
GTG Val(V) 25.0 28.1 19.9

 

  Amino Acid Wheat Homo sapiens E-coli
TCT Ser(S) 10.3 15.2 13.1
TCC Ser(S) 18.0 17.7 9.7
TCA Ser(S) 10.6 12.2 13.1
TCG Ser(S) 10.7 4.4 8.2
         
CCT Pro(P) 11.7 17.5 9.5
CCC Pro(P) 14.6 19.8 6.2
CCA Pro(P) 23.4 16.9 9.1
CCG Pro(P) 16.4 6.9 14.5
         
ACT Thr(T) 9.2 13.1 13.1
ACC Thr(T) 19.1 18.9 18.9
ACA Thr(T) 9.1 15.1 15.1
ACG Thr(T) 9.7 6.1 13.6
         
GCT Ala(A) 16.4 18.4 18.9
GCC Ala(A) 32.7 27.7 21.6
GCA Ala(A) 15.4 15.8 23.0
GCG Ala(A) 22.2 7.4 21.1

 

  Amino Acid Wheat Homo sapiens E-coli
TAT Tyr(Y) 8.3 12.2 21.6
TAC Tyr(Y) 20.6 15.3 11.7
TAA STOP 0.6 1.0 2.0
TAG STOP 0.6 0.8 0.3
         
CAT His(H) 8.4 10.9 12.4
CAC His(H) 13.8 15.1 7.3
CAA Gln(Q) 42.2 12.3 14.4
CAG Gln(Q) 38.2 34.2 26.7
         
AAT Asn(N) 10.5 17.0 29.3
AAC Asn(N) 21.4 19.1 20.3
AAA Lys(K) 10.5 24.4 37.2
AAG Lys(K) 37.6 31.9 15.3
         
GAT Asp(D) 17.1 21.8 33.7
GAC Asp(D) 29.0 25.1 17.9
GAA Glu(E) 15.3 29.0 35.1
GAG Glu(E) 38.2 39.6 19.4

 

  Amino Acid Wheat Homo sapiens E-coli
TGT Cys(C) 5.1 10.6 5.9
TGC Cys(C) 13.6 12.6 5.5
TGA STOP 1.5 1.6 1.1
TGG Trp(W) 12.0 13.2 13.4
         
CGT Arg(R) 5.6 4.5 15.9
CGC Arg(R) 12.8 10.4 14.0
CGA Arg(R) 3.0 6.2 4.8
CGG Arg(R) 8.9 11.4 7.9
         
AGT Ser(S) 6.6 12.1 13.2
AGC Ser(S) 16.6 19.5 14.3
AGA Arg(R) 6.7 12.2 7.1
AGG Arg(R) 13.0 12.0 4.0
         
GGT Gly(G) 13.7 10.8 23.7
GGC Gly(G) 31.1 22.2 20.6
GGA Gly(G) 14.9 16.5 13.6
GGG Gly(G) 17.9 16.5 12.3

 

Ref:

  • Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nakamura, Y., Gojobori, T. and Ikemura, T. (2000) Nucl. Acids Res. 28, 292.
  • Wheat (Triticum aestivum) : http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=4565
  • Homo sapiens :http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606
  • Escherichia coli: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=37762
Codon Optimization Services

Codon optimization service are provided by various companies as services for gene synthesis.

  • Eurofinsgenomics : GENEius
  • Integrated DNA Technologies : Codon Optimization
  • GenScript : OptimumGene