|
||||||
|
||||||
|
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 summerizes 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:
|
||||||
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
Initiation Codon:AUG
Alternative Initiation Codons |
||||||
2. The Vertebrate Mitochondrial Code (transl_table=2)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
Starts = --------------------------------MMMM---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
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 Systematic Range:Vertebrata
Comment:The transcripts of several vertebrate mitochondrial genes end in U or UA, which become termination codons (UAA) upon subsequent polyadenylation. |
||||||
3. The Yeast Mitochondrial Code (transl_table=3)
AAs = FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
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, Schizosaccharomyces pombe, 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 codon UGA is rarely used and probably encodes Trp in Schizosaccharomyces pombe. Sequence comparisons do not suggest other nonstandard codon assignments in this species.
The coding assignment of Thr to CUN is uncertain in Kluyveromyces thermotolerans Clark-Walker and Weiller, 1994). |
||||||
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
Differences from the Standard Code:
Code 4 Standard
UGA Trp W Ter *
Alternative Initiation Codons:Trypanosoma: UUA, UUG, CUG 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. 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 not used in the Acholeplasmataceae and plant-pathogenic mycoplasma-like organisms (MLO) (Lim and Sears, 1992) |
||||||
5. The Invertebrate Mitochondrial Code (transl_table=5)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
Starts = ---M----------------------------MMMM---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
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 Systematic Range:Nematoda: Ascaris, Caenorhabditis; Comments:
"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) |
||||||
6. The Ciliate, Dasycladacean and Hexamita Nuclear Code (transl_table=6)
AAs = FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
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: Comment:
|
||||||
tables 7 and 8 have been deleted |
||||||
9. The Echinoderm Mitochondrial Code (transl_table=9)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
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) |
||||||
10. The Euplotid Nuclear Code (transl_table=10)
AAs = FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Differences from the Standard Code:
Code 10 Standard
UGA Cys C Ter *
Systematic Range:Ciliata: Euplotidae (Hoffman et al. 1995). |
||||||
11. The Bacterial "Code" (transl_table=11)
AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = ---M---------------M------------MMMM---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Differences from the Standard Code:None
Alternative Initiation Codons:GUG, UUG, AUU, CUG Systematic Range:Prokaryotes including the eubacteria (Kozak, 1983) and archaebacteria (Brown et al. 1989; Noelling et al., unpublished). Comments:
|
||||||
12. The Alternative Yeast Nuclear Code (transl_table=12)
AAs = FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -------------------M---------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
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:
|
||||||
13. The Ascidian Mitochondrial Code (transl_table=13)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
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:Ascidiacea (sea squirts): Pyuridae (Durrheim et al. 1993; Yokobori et al., 1993) |
||||||
14. The Flatworm Mitochondrial Code (transl_table=14)
AAs = FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
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) |
||||||
15. Blepharisma Nuclear Code (transl_table=15)
AAs = FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Differences from the Standard Code:
Code 10 GStandard
UAG Gln Q Ter *
Systematic Range:Ciliata: Blepharisma (Liang and Heckman, 1993) |
||||||
|
||||||
|
||||||
For Educational purposes only.Note NCBI Entries are copies of originals for computers without internet access. Computers with internet access can directly access the database. |
||||||
|
m.hill@unsw.edu.au |