The Genetic Codes Compiled by Andrzej (Anjay) Elzanowski and Jim
Ostell National Center for Biotechnology Information (NCBI), Bethesda,
Maryland, U.S.A.

Last update of the Genetic Codes: October 05, 2000

NCBI takes great care to ensure that the translation for each coding
sequence (CDS) present in GenBank records is correct. Central to this
effort is careful checking on the taxonomy of each record and
assignment of the correct genetic code (shown as a /transl_table
qualifier on the CDS in the flat files) for each organism and
record. This page summarizes and references this work.

The synopsis presented below is based primarily on the reviews by
Osawa et al. (1992) and Jukes and Osawa (1993). Listed in square
brackets [ ] (under Systematic Range) are tentative assignments of a
particular code based on sequence homology and/or phylogenetic
relationships.

The print-form ASN.1 version of this document, which includes all the
genetic codes outlined below, is also available here. Detailed
information on codon usage can be found at the Codon Usage Database.

The following genetic codes are described here: 

The Standard Code 
The Vertebrate Mitochondrial Code 
The Yeast Mitochondrial Code 
The Mold, Protozoan, and Coelenterate Mitochondrial Code and the
    Mycoplasma/Spiroplasma Code 
The Invertebrate Mitochondrial Code 
The Ciliate, Dasycladacean and Hexamita Nuclear Code 
The Echinoderm and Flatworm Mitochondrial Code 
The Euplotid Nuclear Code 
The Bacterial and Plant Plastid Code 
The Alternative Yeast Nuclear Code 
The Ascidian Mitochondrial Code 
The Alternative Flatworm Mitochondrial Code 
Blepharisma Nuclear Code 
Chlorophycean Mitochondrial Code 
Trematode Mitochondrial Code 
Scenedesmus Obliquus Mitochondrial Code 
Thraustochytrium Mitochondrial Code 
       

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1. The Standard Code (transl_table=1)
By default all transl_table in GenBank flatfiles are equal to id 1,
and this is not shown. When transl_table is not equal to id 1, it is
shown as a qualifier on the CDS feature.

    AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = ---M---------------M---------------M----------------------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Initiation Codon:
AUG 

Alternative Initiation Codons
In rare cases, translation in eukaryotes can be initiated from codons
other than AUG. A well documented case (including direct protein
sequencing) is the GUG start of a ribosomal P protein of the fungus
Candida albicans (Abramczyk et al.). Other examples can be found in
the following references: Peabody 1989; Prats et al. 1989; Hann et
al. 1992; Sugihara et al. 1990.

GUG, CUG, UUG 


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2. The Vertebrate Mitochondrial Code (transl_table=2)

    AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
  Starts = --------------------------------MMMM---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Differences from the Standard Code: 
        Code 2          Standard

 AGA    Ter  *          Arg  R
 AGG    Ter  *          Arg  R
 AUA    Met  M          Ile  I
 UGA    Trp  W          Ter  *


Alternative Initiation Codon:
Bos: AUA 
Homo: AUA, AUU
Mus: AUA, AUU, AUC
Coturnix, Gallus: also GUG (Desjardins and Morais, 1991)

Systematic Range:
Vertebrata

Comment: 
The transcripts of several vertebrate mitochondrial genes end in U or
UA, which become termination codons (UAA) upon subsequent
polyadenylation.

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3. The Yeast Mitochondrial Code (transl_table=3)

    AAs  = FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = ----------------------------------MM----------------------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Differences from the Standard Code: 
        Code 3          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, Hansenula saturnus, and
Kluyveromyces thermotolerans (Clark-Walker and Weiller, 1994)

Comments:
The remaining CGN codons are rare in Saccharomyces cerevisiae and
absent in Candida glabrata (= Torulopsis glabrata).

The AUA codon is common in the gene var1 coding for the single
mitochonLIial ribosomal protein, but rare in genes encoding the
enzymes.

The coding assignments of the AUA (Met or Ile) and CUU (possibly Leu,
not Thr) are uncertain in Hansenula saturnus.

The coding assignment of Thr to CUN is uncertain in Kluyveromyces
thermotolerans (Clark-Walker and Weiller, 1994).

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4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the
   Mycoplasma/Spiroplasma Code (transl_table=4) 

    AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = --MM---------------M------------MMMM---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Differences from the Standard Code: 
        Code 4         Standard

 UGA    Trp  W          Ter  *


Alternative Initiation Codons: 
Trypanosoma: UUA, UUG, CUG
Leishmania: AUU, AUA 
Tertrahymena: AUU, AUA, AUG 
Paramecium: AUU, AUA, AUG, AUC, GUG, GUA(?) 
(Pritchard et al., 1990)

Systematic Range: 
Mycoplasmatales: Mycoplasma, Spiroplasma (Bove et al., 1989); Fungi:
Emericella nidulans, Neurospora crassa, Podospora anserina, Acremonium
(Fox, 1987), Candida parapsilosis (Guelin et al., 1991), Trichophyton
rubrum (de Bievre and Dujon, 1992), Dekkera/Brettanomyces, Eeniella
(Hoeben et al., 1993), and probably Ascobolus immersus, Aspergillus
amstelodami, Claviceps purpurea, and Cochliobolus heterostrophus.

Other Eukaryotes: Gigartinales among the red algae (Boyen et
al. 1994), and the protozoa Trypanosoma brucei, Leishmania tarentolae,
Paramecium tetraurelia, Tetrahymena pyriformis and probably Plasmodium
gallinaceum (Aldritt et al., 1989).

Metazoa: Coelenterata (Ctenophora and Cnidaria) 

Comments: 

This code is also used for the kinetoplast DNA (maxicircles,
minicircles). Kinetoplasts are modified mitochondria (or their parts).

This code is not used in the Acholeplasmataceae and plant-pathogenic
mycoplasma-like organisms (MLO) (Lim and Sears, 1992) Back to top


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5. The Invertebrate Mitochondrial Code (transl_table=5) 

    AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
  Starts = ---M----------------------------MMMM---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Comment: 
The codon AGG is absent in Drosophila. 
Differences from the Standard Code: 

        Code 5          Standard

 AGA    Ser  S          Arg  R
 AGG    Ser  S          Arg  R
 AUA    Met  M          Ile  I
 UGA    Trp  W          Ter  *


Alternative Initiation Codons: 
AUA, AUU
AUC: Apis (Crozier and Crozier, 1993)
GUG: Polyplacophora (Boore and Brown, 1994 GenBank Accession Number: U09810)
UUG: Ascaris, Caenorhabditis

Systematic Range:
Nematoda: Ascaris, Caenorhabditis;
Mollusca: Bivalvia (Hoffmann et al., 1992); Polyplacophora (Boore and
Brown, 1994)
Arthropoda/Crustacea: Artemia (Batuecas et al., 1988);
Arthropoda/Insecta: Drosophila [Locusta migratoria (migratory locust),
Apis mellifera (honeybee)]

Comments: 
GUG may possibly function as an initiator in Drosophila (Clary and
Wolstenholme, 1985; Gadaleta et al., 1988). AUU is not used as an
initiator in Mytilus (Hoffmann et al., 1992).

"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 and 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) Back to top


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6. The Ciliate, Dasycladacean and Hexamita Nuclear Code (transl_table=6) 

    AAs  = FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = -----------------------------------M----------------------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Differences from the Standard Code: 
          Code 6       Standard

 UAA      Gln  Q        Ter  *
 UAG      Gln  Q        Ter  *


Systematic Range: 
Ciliata: Oxytricha and Stylonychia (Hoffman et al. 1995), Paramecium,
Tetrahymena, Oxytrichidae and probably Glaucoma chattoni.
Dasycladaceae: Acetabularia (Schneider et al., 1989) and Batophora
(Schneider and de Groot, 1991).


Diplomonadida: 
Scope: Hexamita inflata, Diplomonadida ATCC50330, and ATCC50380. 
Ref.: Keeling, P.J. and Doolittle, W.F. 1996.. A non-canonical genetic
code in an early diverging eukaryotic lineage. The EMBO Journal 15,
2285-2290.

Comment: 
The ciliate macronuclear code has not been determined completely. The
codon UAA is known to code for Gln only in the Oxytrichidae.

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Tables 7 and 8 have been deleted 

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9. The Echinoderm and Flatworm Mitochondrial Code (transl_table=9) 

    AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
  Starts = -----------------------------------M---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Differences from the Standard Code: 

          Code 9        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) Rhabditophora among the
Platyhelminthes (Telford et al. 2000)

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10. The Euplotid Nuclear Code (transl_table=10) 

    AAs  = FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = -----------------------------------M----------------------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Differences from the Standard Code: 
          Code 10     Standard

 UGA      Cys  C        Ter  *


Systematic Range: 
Ciliata: Euplotidae (Hoffman et al. 1995). 
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11. The Bacterial and Plant Plastid Code (transl_table=11) 

    AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = ---M---------------M------------MMMM---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Systematic Range and Comments: 
Table 11 is used for Bacteria, Archaea, prokaryotic viruses and
chloroplast proteins. As in the standard code, initiation is most
efficient at AUG. In addition, GUG and UUG starts are documented in
Archaea and Bacteria (Kozak 1983, Fotheringham et al. 1986, Golderer
et al. 1995, Nolling et al. 1995, Sazuka & Ohara 1996, Genser et
al. 1998, Wang et al. 2003). In E. coli, UUG is estimated to serve as
initiator for about 3% of the bacterium's proteins (Blattner et
al. 1997). CUG is known to function as an initiator for one
plasmid-encoded protein (RepA) in Escherichia coli (Spiers and
Bergquist, 1992). In addition to the NUG initiations, in rare cases
Bacteria can initiate translation from an AUU codon as e.g. in the
case of poly(A) polymerase PcnB and the InfC gene that codes for
translation initiation factor IF3 (Polard et al. 1991, Liveris et
al. 1993, Sazuka & Ohara 1996, Binns & Masters 2002). The internal
assignments are the same as in the standard code though UGA codes at
low efficiency for Trp in Bacillus subtilis and, presumably, in
Escherichia coli (Hatfiled and Diamond, 1993).

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12. The Alternative Yeast Nuclear Code (transl_table=12) 

    AAs  = FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = -------------------M---------------M----------------------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Differences from the Standard Code: 
           Code 12      Standard

 CUG       Ser          Leu
       

Alternative Initiation Codons: 
CAG may be used in Candida albicans (Santos et al., 1993). 
Systematic Range: 
Endomycetales (yeasts): Candida albicans, Candida cylindracea, Candida
melibiosica, Candida parapsilosis, and Candida rugosa (Ohama et al.,
1993).

Comment: 
However, other yeast, including Saccharomyces cerevisiae, Candida
azyma, Candida diversa, Candida magnoliae, Candida rugopelliculosa,
Yarrowia lipolytica, and Zygoascus hellenicus, definitely use the
standard (nuclear) code (Ohama et al., 1993).

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13. The Ascidian Mitochondrial Code (transl_table=13) 

    AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
  Starts = ---M------------------------------MM---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Differences from the Standard Code: 
          Code 13     Standard

 AGA      Gly  G        Arg  R
 AGG      Gly  G        Arg  R
 AUA      Met  M        Ile  I
 UGA      Trp  W        Ter  *


Systematic range and Comments:
There is evidence from a phylogenetically diverse sample of tunicates
(Urochordata) that AGA and AGG code for glycine. In other organisms,
AGA/AGG code for either arginine or serine and in vertebrate
mitochondria they code a STOP. Evidence for glycine translation of
AGA/AGG has been found in Pyura stolonifera (Durrheim et al. 1993),
Halocynthia roretzi (Kondow et al. 1999, Yokobori et al., 1993,
Yokobori et al. 1999) and Ciona savignyi (Yokobori et al. 2003). In
addition, the Halocynthia roretzi mitochondrial genome encodes an
additional tRNA gene with the anticodon U*CU that is thought to enable
the use of AGA or AGG codons for glycine and the gene has been shown
to be transcribed in vivo (Kondow et al. 1999, Yokobori et al. 1999).

Alternative initiation codons: ATA, GTG and TTG (Yokobori et al. 1999).

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14. The Alternative Flatworm Mitochondrial Code (transl_table=14) 

    AAs  = FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
  Starts = -----------------------------------M----------------------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Differences from the Standard Code: 
          Code 14      Standard

 AAA      Asn  N       Lys  K
 AGA      Ser  S       Arg  R
 AGG      Ser  S       Arg  R
 UAA      Tyr  Y       Ter  *
 UGA      Trp  W       Ter  *


Systematic Range: 
Platyhelminthes (flatworms) 

Comments: 
Code 14 differs from code 9 only by translating UAA to Tyr rather than
STOP. A recent study [PMID:11027335] has found no evidence that the
codon UAA codes for Tyr in the flatworms but other opinions
exist. There are very few GenBank records that are translated with
code 14 but a test translation shows that retranslating these records
with code 9 can cause premature terminations. Therefore, GenBank will
maintain code 14 until further information becomes available.  Back to
top


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15. Blepharisma Nuclear Code (transl_table=15) 

    AAs  = FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = -----------------------------------M----------------------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Differences from the Standard Code: 
          Code 10       GStandard

UAG       Gln  Q        Ter  *


Systematic Range: 
Ciliata: Blepharisma (Liang and Heckman, 1993) 

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16. Chlorophycean Mitochondrial Code (transl_table=16) 

    AAs  = FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = -----------------------------------M----------------------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format
Systematic Range: 

Chlorophyceae: Hayashi-Ishiimaru, Y, T. Ohama, Y. Kawatsu,
K. Nakamura, S. Osawa, 1996. Current Genetics 30: 29-33

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21. Trematode Mitochondrial Code (transl_table=21) 

    AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
  Starts = -----------------------------------M---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Systematic Range: 
Trematoda: Ohama, T, S. Osawa, K. Watanabe, T.H. Jukes, 1990. J. Molec Evol. 30
Garey, J.R. and D.R. Wolstenholme, 1989. J. Molec. Evol. 28: 374-387 329-332. 

Other Alternative Initiation Codons
GUG, UUG (and possibly CUG) in the Archaea (Noelling et al., unpublished) 

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).

ACG initiates translation of certain proteins in the adeno-associated
virus type 2 (Becerra et al., 1985), the phage T7 mutant CR17
(Anderson and Buzash-Pollert, 1985), Sendai virus (Gupta and
Patwardhan, 1988), and rice chloroplast (Hiratsuka et al.,
1989). Also, it is the most effective non-AUG initiation codon in
mammalin cells (Koepke and Leggatt, 1991).

CUG is the initiation codon for one of the two alternative products of
the human c-myc gene (Hann et al., 1987).

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22. Scenedesmus obliquus mitochondrial Code (transl_table=22) 

    AAs  = FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = -----------------------------------M----------------------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Systematic Range:
Scenedesmus obliquus: Nedelcu A, Lee RW, Lemieux C, Gray MW and Burger
G. "The complete mitochondrial DNA sequence of Scenedesmus obliquus
reflects an intermediate stage in the evolution of the green algal
mitochondrial genome." Genome Research (in press).

Other Alternative Initiation Codons
GUG, UUG (and possibly CUG) in the Archaea (Noelling et al., unpublished) 

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).

ACG initiates translation of certain proteins in the adeno-associated
virus type 2 (Becerra et al., 1985), the phage T7 mutant CR17
(Anderson and Buzash-Pollert, 1985), Sendai virus (Gupta and
Patwardhan, 1988), and rice chloroplast (Hiratsuka et al.,
1989). Also, it is the most effective non-AUG initiation codon in
mammalin cells (Koepke and Leggatt, 1991).

CUG is the initiation codon for one of the two alternative products of
the human c-myc gene (Hann et al., 1987).

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23. Thraustochytrium Mitochondrial Code (transl_table=23) 

    AAs  = FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = --------------------------------M--M---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format
This code has been created for the mitochondrial genome of the
labyrinthulid Thraustochytrium aureum sequenced by the The Organelle
Genome Megasequencing Program (OGMP).

It is the similar to the bacterial code (trans_table 11) but it
contains an additional stop codon (TTA) and also has a different set
of start codons.


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Cited References 

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Aldritt, S.M., Joseph, J.T., and Wirth, D.F. (1989)
Mol. Cell. Biol. 9, 3614-3620. [PubMed]

Anderson, C.W. and Buzash-Pollert, E. (1985) Mol. Cell. Biol. 5,
3621-3624. [PubMed]

Batuecas, B., Garesse, R., Calleja, M., Valverde, J.R., and Marco,
R. (1988) Nucleic Acids Res. 16, 6515-6529. [PubMed]

Becerra, S.P., Rose, J.A., Hardy, M., Baroudy, B.M., and Anderson,
C.W. (1985) Proc. Natn. Acad. Sci. USA 82: 7919-7923. [PubMed]

Boore, J. L. and Brown, W. M. (1994) (GenBank Accession Number:
U09810).

Bove, J.M. Carle, P., Garnier, M., Laigret, F., Renaudin, J., and
Saillard, C. (1989) in The Mycoplasmas, R.F. Whitcomb and J.G. Tully,
eds., 5: 244-364. Academic Press, New York.

Brown, J. W., Daniels, C. J., and Reeve, J. N. (1989)
Crit. Rev. Microbiol. 16: 287-337. [PubMed]

de Bievre, C. and Dujon, B. (1992) Curr. Genet. 22: 229-234. [PubMed]

de Bruijn, M.H.L. (1983) Nature 304, 234-241. [PubMed] 

Cantatore, P., Roberti, M., Rainaldi, G., Gadaleta, M.N., and Saccone,
C. (1989) J. Biol. Chem. 264: 10965-10974. [PubMed]

Clark-Walker G.D., Weiller G.F. (1994) J. Mol. Evol. 38:
593-601(1994). [PubMed]

Clary, D.O. and Wolstenholme, D.R. (1983) Nucleic Acids Res. 11,
6859-6872. [PubMed]

Clary, D.O. and Wolstenholme, D.R. (1985) J. Mol. Evol. 22, 252-271. [PubMed] 

Crozier, R. H. and Crozier, Y. C. (1993) Genetics 133: 97-117. [PubMed] 

Desjardins, P. and Morais, R. (1991) J. Mol. Evol. 32: 153-161. [PubMed] 

Durrheim, G. A., Corfield, V. A., Harley, E. H., and Ricketts,
M. H. (1993) Nucleic Acids Res. 21: 3587-8. [PubMed]

Fox, T.D. (1987) Ann. Rev. Genet. 21, 67-91. 

Gadaleta, G., Pepe, G., De Candia, G., Quagliariello, C., Sbisa, E.,
and Saccone, C. (1988) Nucleic Acids Res. 16, 6233. [PubMed]

Guelin E., Guerin M., and Velours J. (1991) Eur. J. Biochem. 197:
105-111. [PubMed]

Gupta, K.C. and Patwardhan, S. (1988) J. Biol. Chem. 263, 8553-8556. [PubMed] 

Hann, S. R., King, M. W., Bentley, D. L., Anderson, C. W., and
Eisenman, R. N. (1988) Cell 52: 185-195. [PubMed]

Hatfield, D. and Diamond, A. (1993) TIG 9: 69-70. [PubMed] 

Hiesel, R. Wissinger, B., Schuster, W., and Brennicke, A. (1989)
Science 246, 1632-1634. [PubMed]

Himeno, H., Masaki, H., Kawai, T., Ohta, T., Kumagai, I., Miura,
K. and Watanabe, K. (1987) Gene 56: 219-230. [PubMed]

Hiratsuka, J., Shimada, H., Whittier, R., Ishibashi, T., Sakamoto, M.,
Mori, M., Kondo, C., Honji, Y., Sun, C. R., Meng, B. Y., Li, Y. Q.,
Kanno, A., Nishizawa, Y., Hirai, A., Shinozaki, K., and Sugiura,
M. (1989) Mol. Gen. Genet. 217: 185-194. [PubMed]

Hoeben, P., Weiller, G., and Clark-Walker, G. D. (1993)
J. Mol. Evol. 36: 263-269. [PubMed]

Hoffman, D. C., Anderson. R., C., DuBois, M. L., and Prescott,
D. M. (1995) Nucleic Acids Res. 23: 1279-1283. [PubMed]

Hoffmann, R. J, Boore, J. L, and Brown, W. M. (1992) Genetics
131:397-412. [PubMed]

Jacobs, H. T., Elliott, D. J., Math, V. B., and Farquharson, A. (1988)
J. Mol. Biol. 202, 185-217. [PubMed]

Jukes, T. H. and Osawa, S. (1993) Comp. Biochem. Physiol. 106B:
489-494. [PubMed]

Kopke, A. K. E. and Leggatt, P. A. (1991) Nucleic Acids Res. 19:
5169-5172. [PubMed]

Kozak, M. (1983) Microbiol. Rev. 47, 1-45. [PubMed]

Leinfelder, W., Zehelein, E., Mandrand-Berthelot, M.-A., and Boeck,
A. (1988) Nature 331, 723-725. [PubMed]

Liang, A. and Heckmann, K. (1993) Naturwissenschaften 80,
225-226. [PubMed]

Lim, P. and Sears, B. B. (1992) J. Bacteriol. 174, 2606-2611. [PubMed]

Noelling J., Pihl T., Vriesema A., Reeve J. (Unpublished) Organization
and growth phase dependent transcription of methane genes in two
regions of the Methanobacterium thermoautotrophicum genome.

Ohama, T., Suzuki, T., Mori, M., Osawa, S., Ueda, T., Watanabe, K.,
and Nakase, T. (1993) Nucl. Acids Res. 21: 4039-4045. [PubMed]

Olsen, O. (1987) Carlsberg Res. Comm. 52: 83-90.

Osawa, S., Jukes, T. H., Watanabe, K., and Muto, A. (1992)
Microbiol. Rev. 56: 229-264. [PubMed]

Prats H, Kaghad M, Prats AC, Klagsbrun M, Lelias JM, Liauzun P, Chalon
P, Tauber JP, Amalric F, Smith JA, et al. (1989). High molecular mass
forms of basic fibroblast growth factor are initiated by alternative
CUG codons. Proc Natl Acad Sci U S A 86 (6): 1836-1840. [PubMed]

Pritchard, A.E., Seilhamer, J.J., Mahalingam, R. Sable, C.L., Venuti,
S.E., and Cummings, D.J. (1990) Nucleic Acids Research 18:
173-180. [PubMed]

Santos, M.A., Keith, G., and Tuite, M.F. (1993) EMBO J. 12:
607-616. [PubMed]

Schneider, S.U. and de Groot, E.J. (1991) Curr. Genet. 20:
173-175. [PubMed]

Schneider, S.U., Leible, M.B., and Yang, X.-P. (1989)
Mol. Gen. Genet. 218: 445-452. [PubMed]

Spiers, A. J. and Berquist, P. L. (1992) J. Bacter. 174:
7533-7541. [PubMed]

Yokobori, S., Ueda, T., and Watanabe, K. (1993) J. Mol. Evol. 36:
1-8. [PubMed]


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Comments and questions to info@ncbi.nlm.nih.gov 
Credits: Andrzej (Anjay) Elzanowski, Jim Ostell, Detlef Leipe,
Vladimir Soussov. 
