
                              THE GENETIC CODES
                     Compiled by Andrzej Elzanowski, MIPS
              Max Planck Institute for Biochemistry, Martinsried
                                April 1993
 
The following information is based on the review by Fox (1987) and a few more
recent sources.  The species covered by SYSTEMATIC RANGE are known to use a
particular code.  Codon assignments in OTHER TAXA are incompletely known, but
these organisms are likely to use an identical or a similar code.  TENTATIVE
ASSIGNMENTS, which are nothing more than compiler's guesses in the lack of any
direct evidence, are based on the taxonomic position of source organisms,
consistency with published ORFs, and parsimony with respect to differences from
the standard code.
 
 
 
>SGC0 - The Standard Code
 
UUU  F Phe      UCU  S Ser      UAU  Y Tyr      UGU  C Cys
UUC  F Phe      UCC  S Ser      UAC  Y Tyr      UGC  C Cys
UUA  L Leu      UCA  S Ser      UAA  * Ter      UGA  * Ter
UUG  L Leu      UCG  S Ser      UAG  * Ter      UGG  W Trp
 
CUU  L Leu      CCU  P Pro      CAU  H His      CGU  R Arg
CUC  L Leu      CCC  P Pro      CAC  H His      CGC  R Arg
CUA  L Leu      CCA  P Pro      CAA  Q Gln      CGA  R Arg
CUG  L Leu      CCG  P Pro      CAG  Q Gln      CGG  R Arg
 
AUU  I Ile      ACU  T Thr      AAU  N Asn      AGU  S Ser
AUC  I Ile      ACC  T Thr      AAC  N Asn      AGC  S Ser
AUA  I Ile      ACA  T Thr      AAA  K Lys      AGA  R Arg
AUG +M MET      ACG  T Thr      AAG  K Lys      AGG  R Arg
 
GUU  V Val      GCU  A Ala      GAU  D Asp      GGU  G Gly
GUC  V Val      GCC  A Ala      GAC  D Asp      GGC  G Gly
GUA  V Val      GCA  A Ala      GAA  E Glu      GGA  G Gly
GUG  V Val      GCG  A Ala      GAG  E Glu      GGG  G Gly
 
COMMENT
The in-frame opal nonsense codon, UGA, codes for selenocysteine in Escherichia
coli formate dehydrogenase and mammalian (at least human and murine)
glutathione peroxidase (Leinfelder et al., 1988, and references therein).
 
 
>SGC1 - The Vertebrate Mitochondrial Code
 
UUU  F Phe      UCU  S Ser      UAU  Y Tyr      UGU  C Cys
UUC  F Phe      UCC  S Ser      UAC  Y Tyr      UGC  C Cys
UUA  L Leu      UCA  S Ser      UAA  * Ter      UGA  W Trp
UUG  L Leu      UCG  S Ser      UAG  * Ter      UGG  W Trp
 
CUU  L Leu      CCU  P Pro      CAU  H His      CGU  R Arg
CUC  L Leu      CCC  P Pro      CAC  H His      CGC  R Arg
CUA  L Leu      CCA  P Pro      CAA  Q Gln      CGA  R Arg
CUG  L Leu      CCG  P Pro      CAG  Q Gln      CGG  R Arg
 
AUU  I Ile      ACU  T Thr      AAU  N Asn      AGU  S Ser
AUC  I Ile      ACC  T Thr      AAC  N Asn      AGC  S Ser
AUA  M Met      ACA  T Thr      AAA  K Lys      AGA  * Ter
AUG  M Met      ACG  T Thr      AAG  K Lys      AGG  * Ter
 
GUU  V Val      GCU  A Ala      GAU  D Asp      GGU  G Gly
GUC  V Val      GCC  A Ala      GAC  D Asp      GGC  G Gly
GUA  V Val      GCA  A Ala      GAA  E Glu      GGA  G Gly
GUG  V Val      GCG  A Ala      GAG  E Glu      GGG  G Gly
 
DIFFERENCES FROM THE STANDARD CODE
         SGC1          Standard
 AGA    Ter  *          Arg  R
 AGG    Ter  *          Arg  R
 AUA    Met  M          Ile  I
 UGA    Trp  W          Ter  *
 
Initiation codons
Bos: AUA
Homo: AUA, AUU
Mus: AUA, AUU, AUC
Coturnix, Gallus: also GUG
 
SYSTEMATIC RANGE
Mammalia including Bos, Homo, and Mus; Anura including Xenopus; Aves including
Coturnix and Gallus (Desjardins & Morais 1991)
 
COMMENT
The transcripts of several vertebrate mitochondrial genes end in U or UA, which
become termination codons (UAA) upon subsequent polyadenylation.
 
 
>SGC2 - The Yeast Mitochondrial Code
 
UUU  F Phe      UCU  S Ser      UAU  Y Tyr      UGU  C Cys
UUC  F Phe      UCC  S Ser      UAC  Y Tyr      UGC  C Cys
UUA  L Leu      UCA  S Ser      UAA  * Ter      UGA  W Trp
UUG  L Leu      UCG  S Ser      UAG  * Ter      UGG  W Trp
 
CUU  T Thr      CCU  P Pro      CAU  H His      CGU  R Arg
CUC  T Thr      CCC  P Pro      CAC  H His      CGC  R Arg
CUA  T Thr      CCA  P Pro      CAA  Q Gln      CGA  R Arg
CUG  T Thr      CCG  P Pro      CAG  Q Gln      CGG  R Arg
 
AUU  I Ile      ACU  T Thr      AAU  N Asn      AGU  S Ser
AUC  I Ile      ACC  T Thr      AAC  N Asn      AGC  S Ser
AUA  M Met      ACA  T Thr      AAA  K Lys      AGA  R Arg
AUG  M Met      ACG  T Thr      AAG  K Lys      AGG  R Arg
 
GUU  V Val      GCU  A Ala      GAU  D Asp      GGU  G Gly
GUC  V Val      GCC  A Ala      GAC  D Asp      GGC  G Gly
GUA  V Val      GCA  A Ala      GAA  E Glu      GGA  G Gly
GUG  V Val      GCG  A Ala      GAG  E Glu      GGG  G Gly
 
DIFFERENCES FROM THE STANDARD CODE
         SGC2          Standard
 AUA    Met  M          Ile  I
 CUU    Thr  T          Leu  L
 CUC    Thr  T          Leu  L
 CUA    Thr  T          Leu  L
 CUG    Thr  T          Leu  L
 UGA    Trp  W          Ter  *
 
 CGA    absent          Arg  R
 CGC    absent          Arg  R
 
SYSTEMATIC RANGE
Saccharomyces cerevisiae, Candida glabrata (= Torulopsis glabrata)
 
OTHER TAXA
Hansenula saturnus, Schizosaccharomyces pombe
 
COMMENT
The remaining CGN codons are rare in S. cerevisiae and absent in T. glabrata.
 
COMMENT
The AUA codon is common in the gene var1 coding for the single mitochondrial
ribosomal protein, but rare in genes encoding the enzymes.
 
COMMENT
In H. saturnus, the coding assignments of the AUA (Met or Ile) and CUU
(possibly Leu, not Thr) are uncertain.
 
COMMENT
In S. pombe, the codon UGA is rarely used and probably encodes Trp. Sequence
comparisons do not suggest other nonstandard codon assignments in this species.
 
 
>SGC3 - The Mold Mitochondrial and Mycoplasma Code
 
UUU  F Phe      UCU  S Ser      UAU  Y Tyr      UGU  C Cys
UUC  F Phe      UCC  S Ser      UAC  Y Tyr      UGC  C Cys
UUA  L Leu      UCA  S Ser      UAA  * Ter      UGA  W Trp
UUG  L Leu      UCG  S Ser      UAG  * Ter      UGG  W Trp
 
CUU  L Leu      CCU  P Pro      CAU  H His      CGU  R Arg
CUC  L Leu      CCC  P Pro      CAC  H His      CGC  R Arg
CUA  L Leu      CCA  P Pro      CAA  Q Gln      CGA  R Arg
CUG  L Leu      CCG  P Pro      CAG  Q Gln      CGG  R Arg
 
AUU  I Ile      ACU  T Thr      AAU  N Asn      AGU  S Ser
AUC  I Ile      ACC  T Thr      AAC  N Asn      AGC  S Ser
AUA  I Ile      ACA  T Thr      AAA  K Lys      AGA  R Arg
AUG  M Met      ACG  T Thr      AAG  K Lys      AGG  R Arg
 
GUU  V Val      GCU  A Ala      GAU  D Asp      GGU  G Gly
GUC  V Val      GCC  A Ala      GAC  D Asp      GGC  G Gly
GUA  V Val      GCA  A Ala      GAA  E Glu      GGA  G Gly
GUG  V Val      GCG  A Ala      GAG  E Glu      GGG  G Gly
 
DIFFERENCES FROM THE STANDARD CODE
         SGC3          Standard
 UGA    Trp  W          Ter  *
 
SYSTEMATIC RANGE
Mycoplasma, Spiroplasma (Bove et al. 1989)
Emericella nidulans, Neurospora crassa
Candida parapsilosis (Guelin et al. 1991)
Trichophyton rubrum (de Bievre & Dujon, 1992)
 
OTHER TAXA
Podospora anserina, Acremonium sp.
 
TENTATIVE ASSIGNEMENTS
Ascobolus immersus, Aspergillus amstelodami, Claviceps purpurea,
Cochliobolus heterostrophus
 
COMMENT This code is NOT used in Acholeplasmataceae and the plant-pathogenic
mycoplasma-like organisms (MLO) (Lim and Sears, 1992)
 
 
>SGC4 - The Invertebrate Mitochondrial Code:
 
UUU  F Phe      UCU  S Ser      UAU  Y Tyr      UGU  C Cys
UUC  F Phe      UCC  S Ser      UAC  Y Tyr      UGC  C Cys
UUA  L Leu      UCA  S Ser      UAA  * Ter      UGA  W Trp
UUG  L Leu      UCG  S Ser      UAG  * Ter      UGG  W Trp
 
CUU  L Leu      CCU  P Pro      CAU  H His      CGU  R Arg
CUC  L Leu      CCC  P Pro      CAC  H His      CGC  R Arg
CUA  L Leu      CCA  P Pro      CAA  Q Gln      CGA  R Arg
CUG  L Leu      CCG  P Pro      CAG  Q Gln      CGG  R Arg
 
AUU  I Ile      ACU  T Thr      AAU  N Asn      AGU  S Ser
AUC  I Ile      ACC  T Thr      AAC  N Asn      AGC  S Ser
AUA  M Met      ACA  T Thr      AAA  K Lys      AGA  S Ser
AUG  M Met      ACG  T Thr      AAG  K Lys      AGG  S Ser
 
GUU  V Val      GCU  A Ala      GAU  D Asp      GGU  G Gly
GUC  V Val      GCC  A Ala      GAC  D Asp      GGC  G Gly
GUA  V Val      GCA  A Ala      GAA  E Glu      GGA  G Gly
GUG  V Val      GCG  A Ala      GAG  E Glu      GGG  G Gly
 
DIFFERENCES FROM THE STANDARD CODE
         SGC4          Standard
 AGA    Ser  S          Arg  R
 AGG    Ser  S          Arg  R
 AUA    Met  M          Ile  I
 UGA    Trp  W          Ter  *
 
Initiation codons
AUA, AUU
Ascaris, Caenorhabditis: UUG
 
COMMENT
GUG may possibly function as an initiator in Drosophila (Clary & Wolstenholme,
1985; Gadaleta et al. 1988). AUU is not used as an initiator in Mytilus
(Hoffmann et al. 1992).
 
SYSTEMATIC RANGE
Drosophila (Insecta); Artemia (Crustacea) (Batuecas et al. 1988);
Mytilus (Bivalvia) ((Hoffmann et al. 1992)
Ascaris, Caenorhabditis (Nematoda)
 
TENTATIVE ASSIGNMENTS
Locusta migratoria (migratory locust), Apis mellifera (honeybee)
 
COMMENT
The codon AGG is absent in Drosophila.
 
COMMENT
"An exceptional mechanism must operate for initiation of translation of the
cytochrome oxidase subunit I mRNA in both D. melanogaster (de Bruijn, 1983) and
D. yakuba (Clary & Wolstenholme 1983), since its only plausible initiation
codon, AUA, is out of frame with the rest of the gene. Initiation appears to
require the "reading" of of an AUAA quadruplet, which would be equivalent to
initiation at AUA followed immediately by a specific ribosomal frameshift.
Another possible mechanism ... is that the mRNA is "edited" to bring the AUA
initiation into frame." (Fox, 1987)
 
 
>SGC5 - The Ciliate Macronuclear and Dasycladacean Nuclear Code
 
UUU  F Phe      UCU  S Ser      UAU  Y Tyr      UGU  C Cys
UUC  F Phe      UCC  S Ser      UAC  Y Tyr      UGC  C Cys
UUA  L Leu      UCA  S Ser      UAA  Q Gln      UGA  * Ter
UUG  L Leu      UCG  S Ser      UAG  Q Gln      UGG  W Trp
 
CUU  L Leu      CCU  P Pro      CAU  H His      CGU  R Arg
CUC  L Leu      CCC  P Pro      CAC  H His      CGC  R Arg
CUA  L Leu      CCA  P Pro      CAA  Q Gln      CGA  R Arg
CUG  L Leu      CCG  P Pro      CAG  Q Gln      CGG  R Arg
 
AUU  I Ile      ACU  T Thr      AAU  N Asn      AGU  S Ser
AUC  I Ile      ACC  T Thr      AAC  N Asn      AGC  S Ser
AUA  I Ile      ACA  T Thr      AAA  K Lys      AGA  R Arg
AUG  M Met      ACG  T Thr      AAG  K Lys      AGG  R Arg
 
GUU  V Val      GCU  A Ala      GAU  D Asp      GGU  G Gly
GUC  V Val      GCC  A Ala      GAC  D Asp      GGC  G Gly
GUA  V Val      GCA  A Ala      GAA  E Glu      GGA  G Gly
GUG  V Val      GCG  A Ala      GAG  E Glu      GGG  G Gly
 
DIFFERENCES FROM THE STANDARD CODE
           SGC5        Standard
 UAA      Gln  Q        Ter  *
 UAG      Gln  Q        Ter  *
 
SYSTEMATIC RANGE
 
Ciliata including Paramecium, Tetrahymena, and Stylonychia (UAA -> Q) but NOT
the Euplotidae (see SGC9). Dasycladaceae including Acetabularia (Schneider et
al. 1989) and Batophora (Schneider & de Groot 1991).
 
TENTATIVE ASSIGNEMENTS
Glaucoma chattoni
 
COMMENT
The ciliate macronuclear code has not been fully determined.
 
 
>SGC6 - The Protozoan Mitochondrial Code:
 
UUU  F Phe      UCU  S Ser      UAU  Y Tyr      UGU  C Cys
UUC  F Phe      UCC  S Ser      UAC  Y Tyr      UGC  C Cys
UUA  L Leu      UCA  S Ser      UAA  * Ter      UGA  W Trp
UUG  L Leu      UCG  S Ser      UAG  * Ter      UGG  W Trp
 
CUU  L Leu      CCU  P Pro      CAU  H His      CGU  R Arg
CUC  L Leu      CCC  P Pro      CAC  H His      CGC  R Arg
CUA  L Leu      CCA  P Pro      CAA  Q Gln      CGA  R Arg
CUG  L Leu      CCG  P Pro      CAG  Q Gln      CGG  R Arg
 
AUU  I Ile      ACU  T Thr      AAU  N Asn      AGU  S Ser
AUC  I Ile      ACC  T Thr      AAC  N Asn      AGC  S Ser
AUA  I Ile      ACA  T Thr      AAA  K Lys      AGA  R Arg
AUG  M Met      ACG  T Thr      AAG  K Lys      AGG  R Arg
 
GUU  V Val      GCU  A Ala      GAU  D Asp      GGU  G Gly
GUC  V Val      GCC  A Ala      GAC  D Asp      GGC  G Gly
GUA  V Val      GCA  A Ala      GAA  E Glu      GGA  G Gly
GUG  V VAL      GCG  A Ala      GAG  E Glu      GGG  G Gly
 
DIFFERENCES FROM THE STANDARD CODE
         SGC6          Standard
 UGA    Trp  W          Ter  *
 
Initiation codons
Trypanosoma: UUA, UUG, CUG
Leishmania: AUU, AUA
Tertrahymena: AUU, AUA, AUG
Paramecium: AUU, AUA, AUG, AUC, GUG, GUA(?) (Pritchard, A.E. et al., 1990)
 
SYSTEMATIC RANGE
Trypanosoma brucei, Leishmania tarentolae, Paramecium tetraurelia,
Tetrahymena pyriformis
 
TENTATIVE ASSIGNEMENTS
Plasmodium gallinaceum (Aldritt, S.M. et al., 1989)
 
COMMENT
SGC6 is also valid for the kinetoplast DNA (maxicircles, minicircles).
Kinetoplasts are modified mitochondria (or their parts).
 
 
>SGC7 - Plant Mitochondrial Code
DELETED. ALL DIFFERENCES FROM THE STANDARD CODE PROVED TO BE DUE TO RNA
EDITING.
 
 
>SGC8 - The Echinoderm Mitochondrial Code
 
UUU  F Phe      UCU  S Ser      UAU  Y Tyr      UGU  C Cys
UUC  F Phe      UCC  S Ser      UAC  Y Tyr      UGC  C Cys
UUA  L Leu      UCA  S Ser      UAA  * Ter      UGA  W Trp
UUG  L Leu      UCG  S Ser      UAG  * Ter      UGG  W Trp
 
CUU  L Leu      CCU  P Pro      CAU  H His      CGU  R Arg
CUC  L Leu      CCC  P Pro      CAC  H His      CGC  R Arg
CUA  L Leu      CCA  P Pro      CAA  Q Gln      CGA  R Arg
CUG  L Leu      CCG  P Pro      CAG  Q Gln      CGG  R Arg
 
AUU  I Ile      ACU  T Thr      AAU  N Asn      AGU  S Ser
AUC  I Ile      ACC  T Thr      AAC  N Asn      AGC  S Ser
AUA  I Ile      ACA  T Thr      AAA  N Asn      AGA  S Ser
AUG +M MET      ACG  T Thr      AAG  K Lys      AGG  S Ser
 
GUU  V Val      GCU  A Ala      GAU  D Asp      GGU  G Gly
GUC  V Val      GCC  A Ala      GAC  D Asp      GGC  G Gly
GUA  V Val      GCA  A Ala      GAA  E Glu      GGA  G Gly
GUG  V Val      GCG  A Ala      GAG  E Glu      GGG  G Gly
 
DIFFERENCES FROM THE STANDARD CODE
           SGC8       Standard
 AAA      Asn  N        Lys K
 AGA      Ser  S        Arg R
 AGG      Ser  S        Arg R
 UGA      Trp  W        Ter *
 
SYSTEMATIC RANGE
Asterozoa (starfishes)(Himeno et al. 1987)
Echinozoa (sea urchins) (Jacobs et al. 1988, Cantatore et al. 1989)
 
 
>SGC9 - The Euplotid Macronuclear Code
 
UUU  F Phe      UCU  S Ser      UAU  Y Tyr      UGU  C Cys
UUC  F Phe      UCC  S Ser      UAC  Y Tyr      UGC  C Cys
UUA  L Leu      UCA  S Ser      UAA  * Ter      UGA  C Cys
UUG  L Leu      UCG  S Ser      UAG  Q Gln      UGG  W Trp
 
CUU  L Leu      CCU  P Pro      CAU  H His      CGU  R Arg
CUC  L Leu      CCC  P Pro      CAC  H His      CGC  R Arg
CUA  L Leu      CCA  P Pro      CAA  Q Gln      CGA  R Arg
CUG  L Leu      CCG  P Pro      CAG  Q Gln      CGG  R Arg
 
AUU  I Ile      ACU  T Thr      AAU  N Asn      AGU  S Ser
AUC  I Ile      ACC  T Thr      AAC  N Asn      AGC  S Ser
AUA  I Ile      ACA  T Thr      AAA  K Lys      AGA  R Arg
AUG  M Met      ACG  T Thr      AAG  K Lys      AGG  R Arg
 
GUU  V Val      GCU  A Ala      GAU  D Asp      GGU  G Gly
GUC  V Val      GCC  A Ala      GAC  D Asp      GGC  G Gly
GUA  V Val      GCA  A Ala      GAA  E Glu      GGA  G Gly
GUG  V Val      GCG  A Ala      GAG  E Glu      GGG  G Gly
 
DIFFERENCES FROM THE STANDARD CODE
           SGC9        Standard
 UAG      Gln  Q        Ter  *
 UGA      Cys  C        Ter  *
 
SYSTEMATIC RANGE
Euplotidae (Harper and Jahn 1989, Meyer et al. 1991)
 
 
           Other cases of nonstandard translation initiation codons
 
The codons GUG, UUG and AUU (in order of decreasing frequency) are used
alternatively to AUG in the eubacterian prokaryotes (Kozak 1983). The codons
AUA, GUG, UUG, and AUC or AAG may be used (at least in experimental systems) by
the yeasts Saccharomyces cerevisiae (Olsen 1987, and references therein). The
codon ACG initiates translation of certain proteins in the adeno-associated
virus type 2 (Becerra et al. 1985), the phage T7 mutant CR17 (Anderson &
Buzash-Pollert 1985), Sendai virus (Gupta & Patwardhan, 1988), and rice
chloroplast (Hiratsuka et al. 1989)
 
 
                                  References
 
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Becerra, S.P., Rose, J.A., Hardy, M., Baroudy, B.M., and Anderson, C.W. (1985)
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