NCBI Alternative Genetic Codes
The standard genetic code is nearly universal, but it is not the only one. NCBI maintains a numbered set of translation tables (the transl_table value in GenBank) for alternative codes used by mitochondria, bacteria, ciliates and other lineages. This page lists those tables and shows exactly how each one differs from the standard code. For the full standard code itself, see the codon table.
| NCBI ID | Name | Used by | Key differences from the standard code (table 1) |
|---|---|---|---|
| 1 | Standard | Most nuclear genomes | None — the reference code (61 sense codons, starts ATG, stops TAA/TAG/TGA) |
| 2 | Vertebrate Mitochondrial | Vertebrate mitochondria | AGA & AGG = Stop (not Arg); ATA = Met (not Ile); TGA = Trp (not Stop) |
| 3 | Yeast Mitochondrial | Saccharomyces mitochondria | ATA = Met; CTT/CTC/CTA/CTG = Thr (not Leu); TGA = Trp |
| 4 | Mold/Protozoan/Coelenterate Mito & Mycoplasma/Spiroplasma | e.g. Mycoplasma, many fungal mitochondria | TGA = Trp (not Stop); several alternative start codons |
| 5 | Invertebrate Mitochondrial | Invertebrate mitochondria | AGA & AGG = Ser (not Arg); ATA = Met; TGA = Trp |
| 6 | Ciliate/Dasycladacean/Hexamita Nuclear | e.g. Tetrahymena, Paramecium | TAA & TAG = Gln (only TGA remains a stop) |
| 9 | Echinoderm/Flatworm Mitochondrial | Echinoderm & flatworm mitochondria | AAA = Asn; AGA & AGG = Ser; TGA = Trp |
| 10 | Euplotid Nuclear | Euplotes ciliates | TGA = Cys (not Stop) |
| 11 | Bacterial, Archaeal & Plant Plastid | Bacteria, archaea, plastids | Same amino-acid assignments as standard, but broad use of alternative starts (GTG, TTG, ATT, CTG…) |
| 12 | Alternative Yeast Nuclear | Some Candida species | CTG = Ser (not Leu) |
| 13 | Ascidian Mitochondrial | Ascidian (tunicate) mitochondria | AGA & AGG = Gly; ATA = Met; TGA = Trp |
| 14 | Alternative Flatworm Mitochondrial | Some flatworm mitochondria | AAA = Asn; AGA & AGG = Ser; TAA = Tyr; TGA = Trp |
| 25 | Candidate Division SR1 & Gracilibacteria | SR1/Gracilibacteria bacteria | TGA = Gly (not Stop) |
Codons are written as DNA; “=” means “encodes”. The NCBI ID is the transl_table number used in sequence records.
Why there is more than one genetic code
The standard code is so widely shared that it was long called the universal code. In practice a few lineages — above all mitochondria, but also some bacteria and ciliate nuclei — have reassigned one or more codons. There are two kinds of reassignment: a stop → amino-acid change (a codon that normally terminates translation instead encodes a residue, e.g. TGA = Trp), and an amino-acid → amino-acid change (a sense codon encodes a different residue, e.g. CTG = Ser instead of Leu). Each NCBI table captures one such variant.
The most common reassignments
A handful of changes recur across many tables. TGA = Trp appears in numerous mitochondrial codes and in Mycoplasma (tables 2, 3, 4, 5, 9, 13, 14). The arginine codons AGA and AGG are frequently reassigned — to Stop in vertebrate mitochondria, to Ser in invertebrate, echinoderm and flatworm mitochondria, and to Gly in ascidian mitochondria. ATA = Met (rather than Ile) is shared by several mitochondrial codes. And in the ciliate nuclear code, TAA and TAG = Gln, leaving TGA as the lone stop codon.
Start codons
In the standard code the usual start codon is ATG (Met). Many other codes also permit alternative start codons: bacteria, archaea and plastids (table 11) routinely initiate at GTG, TTG or ATT, and several mitochondrial codes recognise additional starts as well. The amino acid placed at the start is still formylmethionine/methionine — it is the codon used to begin the open reading frame that varies.
A curated subset — verify with NCBI
The table above is a curated subset of the most commonly encountered codes. The full, authoritative list — including the rarer organelle- and lineage-specific tables — is maintained by NCBIon its “Genetic Codes” page. For organelle or lineage-specific work, always verify the exact transl_table assignment there, as codon assignments and start codons can vary by source.
Frequently asked questions
- Is the genetic code universal?
- Nearly. The standard code (NCBI table 1) is used by almost all nuclear genomes, which is why it is often called the universal code. But it is not strictly universal: mitochondria and a handful of nuclear lineages reassign a few codons, which is why NCBI maintains several alternative translation tables.
- What is a translation table or transl_table number?
- NCBI assigns each variant of the genetic code a number (the transl_table value seen in GenBank feature qualifiers). Table 1 is the standard code; higher numbers — such as 2 for vertebrate mitochondria or 11 for bacteria — specify which codon-to-amino-acid mapping to use when translating a given sequence.
- Which genetic code do mitochondria use?
- There is no single mitochondrial code — it depends on the lineage. Vertebrate mitochondria use table 2, invertebrate mitochondria table 5, yeast mitochondria table 3, and so on. A reassignment many of them share is TGA encoding tryptophan instead of acting as a stop codon.
- What is special about the ciliate code?
- In the ciliate/dasycladacean/hexamita nuclear code (table 6), TAA and TAG encode glutamine (Gln) rather than acting as stop codons, leaving TGA as the only stop. It is one of the clearest examples of a stop-to-amino-acid reassignment in a nuclear genome.
- Does SeqBench support alternative genetic codes?
- SeqBench's Translate and ORF tools use only the standard code (table 1). This page is a reference for the alternative NCBI tables; if you need to translate with a non-standard code, consult the authoritative NCBI Genetic Codes list and a tool that supports the relevant transl_table number.
See also
Related tools and references
Use these related pages when this table raises a practical calculation or workflow question.