DNA and RNA codon tables
List of standard rules to translate DNA encoded information into proteins From Wikipedia, the free encyclopedia
A codon table can be used to translate a genetic code into a sequence of amino acids.[1][2] The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis.[2][3] The mRNA sequence is determined by the sequence of genomic DNA.[4] In this context, the standard genetic code is referred to as 'translation table 1' among other tables.[3] It can also be represented in a DNA codon table. The DNA codons in such tables occur on the sense DNA strand and are arranged in a 5′-to-3′ direction. Different tables with alternate codons are used depending on the source of the genetic code, such as from a cell nucleus, mitochondrion, plastid, or hydrogenosome.[5]
The standard RNA codon table organized in a wheel
There are 64 different codons in the genetic code and the below tables; most specify an amino acid.[6] Three sequences, UAG, UGA, and UAA, known as stop codons,[note 1] do not code for an amino acid but instead signal the release of the nascent polypeptide from the ribosome.[7] In the standard code, the sequence AUG—read as methionine—can serve as a start codon and, along with sequences such as an initiation factor, initiates translation.[3][9][10] In rare instances, start codons in the standard code may also include GUG or UUG; these codons normally represent valine and leucine, respectively, but as start codons they are translated as methionine or formylmethionine.[3][10]
The classical table/wheel of the standard genetic code is arbitrarily organized based on codon position 1. Saier,[12] following observations from,[13] showed that reorganizing the wheel based instead on codon position 2 (and reordering from UCAG to UCGA) better arranges the codons by the hydrophobicity of their encoded amino acids. This suggests that early ribosomes read the second codon position most carefully, to control hydrophobicity patterns in protein sequences.
The first table—the standard table—can be used to translate nucleotide triplets into the corresponding amino acid or appropriate signal if it is a start or stop codon. The second table, appropriately called the inverse, does the opposite: it can be used to deduce a possible triplet code if the amino acid is known. As multiple codons can code for the same amino acid, the International Union of Pure and Applied Chemistry's (IUPAC) nucleic acid notation is given in some instances.
Translation table 1
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Perspective
Standard RNA codon table
| Amino-acid biochemical properties | Nonpolar (np) | Polar (p) | Basic (b) | Acidic (a) | Termination: stop codon * | Initiation: possible start codon ⇒ |
| 1st base |
2nd base | 3rd base | |||||||
|---|---|---|---|---|---|---|---|---|---|
| U | C | A | G | ||||||
| U | UUU | (Phe/F) Phenylalanine (np) | UCU | (Ser/S) Serine (p) | UAU | (Tyr/Y) Tyrosine (p) | UGU | (Cys/C) Cysteine (p) | U |
| UUC | UCC | UAC | UGC | C | |||||
| UUA | (Leu/L) Leucine (np) | UCA | UAA | Stop (Ochre) *[note 2] | UGA | Stop (Opal) *[note 2] | A | ||
| UUG ⇒ | UCG | UAG | Stop (Amber) *[note 2] | UGG | (Trp/W) Tryptophan (np) | G | |||
| C | CUU | CCU | (Pro/P) Proline (np) | CAU | (His/H) Histidine (b) | CGU | (Arg/R) Arginine (b) | U | |
| CUC | CCC | CAC | CGC | C | |||||
| CUA | CCA | CAA | (Gln/Q) Glutamine (p) | CGA | A | ||||
| CUG | CCG | CAG | CGG | G | |||||
| A | AUU | (Ile/I) Isoleucine (np) | ACU | (Thr/T) Threonine (p) | AAU | (Asn/N) Asparagine (p) | AGU | (Ser/S) Serine (p) | U |
| AUC | ACC | AAC | AGC | C | |||||
| AUA | ACA | AAA | (Lys/K) Lysine (b) | AGA | (Arg/R) Arginine (b) | A | |||
| AUG ⇒ | (Met/M) Methionine (np) | ACG | AAG | AGG | G | ||||
| G | GUU | (Val/V) Valine (np) | GCU | (Ala/A) Alanine (np) | GAU | (Asp/D) Aspartic acid (a) | GGU | (Gly/G) Glycine (np) | U |
| GUC | GCC | GAC | GGC | C | |||||
| GUA | GCA | GAA | (Glu/E) Glutamic acid (a) | GGA | A | ||||
| GUG ⇒ | GCG | GAG | GGG | G | |||||
As shown in the above table, NCBI table 1 includes the less-canonical start codons GUG and UUG.[3]
Inverse RNA codon table
| Amino acid | RNA codons | Compressed | Amino acid | RNA codons | Compressed | |
|---|---|---|---|---|---|---|
| Ala, A | GCU, GCC, GCA, GCG | GCN | Ile, I | AUU, AUC, AUA | AUH | |
| Arg, R | CGU, CGC, CGA, CGG; AGA, AGG | CGN, AGR; or CGY, MGR |
Leu, L | CUU, CUC, CUA, CUG; UUA, UUG | CUN, UUR; or CUY, YUR | |
| Asn, N | AAU, AAC | AAY | Lys, K | AAA, AAG | AAR | |
| Asp, D | GAU, GAC | GAY | Met, M | AUG | ||
| Asn or Asp, B | AAU, AAC; GAU, GAC | RAY | Phe, F | UUU, UUC | UUY | |
| Cys, C | UGU, UGC | UGY | Pro, P | CCU, CCC, CCA, CCG | CCN | |
| Gln, Q | CAA, CAG | CAR | Ser, S | UCU, UCC, UCA, UCG; AGU, AGC | UCN, AGY | |
| Glu, E | GAA, GAG | GAR | Thr, T | ACU, ACC, ACA, ACG | ACN | |
| Gln or Glu, Z | CAA, CAG; GAA, GAG | SAR | Trp, W | UGG | ||
| Gly, G | GGU, GGC, GGA, GGG | GGN | Tyr, Y | UAU, UAC | UAY | |
| His, H | CAU, CAC | CAY | Val, V | GUU, GUC, GUA, GUG | GUN | |
| START | AUG, CUG, UUG | HUG | STOP | UAA, UGA, UAG | URA, UAG; or UGA, UAR | |
Standard DNA codon table
| Amino-acid biochemical properties | Nonpolar (np) | Polar (p) | Basic (b) | Acidic (a) | Termination: stop codon * | Initiation: possible start codon ⇒ |
| 1st base |
2nd base | 3rd base | |||||||
|---|---|---|---|---|---|---|---|---|---|
| T | C | A | G | ||||||
| T | TTT | (Phe/F) Phenylalanine (np) | TCT | (Ser/S) Serine (p) | TAT | (Tyr/Y) Tyrosine (p) | TGT | (Cys/C) Cysteine (p) | T |
| TTC | TCC | TAC | TGC | C | |||||
| TTA | (Leu/L) Leucine (np) | TCA | TAA | Stop (Ochre) *[note 2] | TGA | Stop (Opal) *[note 2] | A | ||
| TTG ⇒ | TCG | TAG | Stop (Amber) *[note 2] | TGG | (Trp/W) Tryptophan (np) | G | |||
| C | CTT | CCT | (Pro/P) Proline (np) | CAT | (His/H) Histidine (b) | CGT | (Arg/R) Arginine (b) | T | |
| CTC | CCC | CAC | CGC | C | |||||
| CTA | CCA | CAA | (Gln/Q) Glutamine (p) | CGA | A | ||||
| CTG | CCG | CAG | CGG | G | |||||
| A | ATT | (Ile/I) Isoleucine (np) | ACT | (Thr/T) Threonine (p) | AAT | (Asn/N) Asparagine (p) | AGT | (Ser/S) Serine (p) | T |
| ATC | ACC | AAC | AGC | C | |||||
| ATA | ACA | AAA | (Lys/K) Lysine (b) | AGA | (Arg/R) Arginine (b) | A | |||
| ATG ⇒ | (Met/M) Methionine (np) | ACG | AAG | AGG | G | ||||
| G | GTT | (Val/V) Valine (np) | GCT | (Ala/A) Alanine (np) | GAT | (Asp/D) Aspartic acid (a) | GGT | (Gly/G) Glycine (np) | T |
| GTC | GCC | GAC | GGC | C | |||||
| GTA | GCA | GAA | (Glu/E) Glutamic acid (a) | GGA | A | ||||
| GTG ⇒ | GCG | GAG | GGG | G | |||||
Inverse DNA codon table
| Amino acid | DNA codons | Compressed | Amino acid | DNA codons | Compressed | |
|---|---|---|---|---|---|---|
| Ala, A | GCT, GCC, GCA, GCG | GCN | Ile, I | ATT, ATC, ATA | ATH | |
| Arg, R | CGT, CGC, CGA, CGG; AGA, AGG | CGN, AGR; or CGY, MGR |
Leu, L | CTT, CTC, CTA, CTG; TTA, TTG | CTN, TTR; or CTY, YTR | |
| Asn, N | AAT, AAC | AAY | Lys, K | AAA, AAG | AAR | |
| Asp, D | GAT, GAC | GAY | Met, M | ATG | ||
| Asn or Asp, B | AAT, AAC; GAT, GAC | RAY | Phe, F | TTT, TTC | TTY | |
| Cys, C | TGT, TGC | TGY | Pro, P | CCT, CCC, CCA, CCG | CCN | |
| Gln, Q | CAA, CAG | CAR | Ser, S | TCT, TCC, TCA, TCG; AGT, AGC | TCN, AGY | |
| Glu, E | GAA, GAG | GAR | Thr, T | ACT, ACC, ACA, ACG | ACN | |
| Gln or Glu, Z | CAA, CAG; GAA, GAG | SAR | Trp, W | TGG | ||
| Gly, G | GGT, GGC, GGA, GGG | GGN | Tyr, Y | TAT, TAC | TAY | |
| His, H | CAT, CAC | CAY | Val, V | GTT, GTC, GTA, GTG | GTN | |
| START | ATG, TTG, GTG, CTG[20] | NTG | STOP | TAA, TGA, TAG | TRA, TAR | |
Alternative codons in other translation tables
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The genetic code was once believed to be universal:[21] a codon would code for the same amino acid regardless of the organism or source. However, it is now agreed that the genetic code evolves,[22] resulting in discrepancies in how a codon is translated depending on the genetic source.[21][22] For example, in 1981, it was discovered that the use of codons AUA, UGA, AGA and AGG by the coding system in mammalian mitochondria differed from the universal code.[21] Stop codons can also be affected: in ciliated protozoa, the universal stop codons UAA and UAG code for glutamine.[22][note 4] Four novel alternative genetic codes (numbered here 34–37) were discovered in bacterial genomes by Shulgina and Eddy, revealing the first sense codon changes in bacteria.[23] The following table displays these alternative codons.
| Amino-acid biochemical properties | Nonpolar (np) | Polar (p) | Basic (b) | Acidic (a) | Termination: stop codon * |
| Code | Translation table |
DNA codon involved | RNA codon involved | Translation with this code |
Standard translation | Notes | ||
|---|---|---|---|---|---|---|---|---|
| Standard | 1 | Includes translation table 8 (plant chloroplasts). | ||||||
| Vertebrate mitochondrial | 2 | AGA | AGA | Stop * | Arg (R) (b) | |||
| AGG | AGG | Stop * | Arg (R) (b) | |||||
| ATA | AUA | Met (M) (np) | Ile (I) (np) | |||||
| TGA | UGA | Trp (W) (np) | Stop * | |||||
| Yeast mitochondrial | 3 | ATA | AUA | Met (M) (np) | Ile (I) (np) | |||
| CTT | CUU | Thr (T) (p) | Leu (L) (np) | |||||
| CTC | CUC | Thr (T) (p) | Leu (L) (np) | |||||
| CTA | CUA | Thr (T) (p) | Leu (L) (np) | |||||
| CTG | CUG | Thr (T) (p) | Leu (L) (np) | |||||
| TGA | UGA | Trp (W) (np) | Stop * | |||||
| CGA | CGA | absent | Arg (R) (b) | |||||
| CGC | CGC | absent | Arg (R) (b) | |||||
| Mold, protozoan, and coelenterate mitochondrial + Mycoplasma / Spiroplasma | 4 | TGA | UGA | Trp (W) (np) | Stop * | Includes the translation table 7 (kinetoplasts). | ||
| Invertebrate mitochondrial | 5 | AGA | AGA | Ser (S) (p) | Arg (R) (b) | |||
| AGG | AGG | Ser (S) (p) | Arg (R) (b) | |||||
| ATA | AUA | Met (M) (np) | Ile (I) (np) | |||||
| TGA | UGA | Trp (W) (np) | Stop * | |||||
| Ciliate, dasycladacean and Hexamita nuclear | 6 | TAA | UAA | Gln (Q) (p) | Stop * | |||
| TAG | UAG | Gln (Q) (p) | Stop * | |||||
| Echinoderm and flatworm mitochondrial | 9 | AAA | AAA | Asn (N) (p) | Lys (K) (b) | |||
| AGA | AGA | Ser (S) (p) | Arg (R) (b) | |||||
| AGG | AGG | Ser (S) (p) | Arg (R) (b) | |||||
| TGA | UGA | Trp (W) (np) | Stop * | |||||
| Euplotid nuclear | 10 | TGA | UGA | Cys (C) (p) | Stop * | |||
| Bacterial, archaeal and plant plastid | 11 | See translation table 1. | ||||||
| Alternative yeast nuclear | 12 | CTG | CUG | Ser (S) (p) | Leu (L) (np) | |||
| Ascidian mitochondrial | 13 | AGA | AGA | Gly (G) (np) | Arg (R) (b) | |||
| AGG | AGG | Gly (G) (np) | Arg (R) (b) | |||||
| ATA | AUA | Met (M) (np) | Ile (I) (np) | |||||
| TGA | UGA | Trp (W) (np) | Stop * | |||||
| Alternative flatworm mitochondrial | 14 | AAA | AAA | Asn (N) (p) | Lys (K) (b) | |||
| AGA | AGA | Ser (S) (p) | Arg (R) (b) | |||||
| AGG | AGG | Ser (S) (p) | Arg (R) (b) | |||||
| TAA | UAA | Tyr (Y) (p) | Stop * | |||||
| TGA | UGA | Trp (W) (np) | Stop * | |||||
| Blepharisma nuclear | 15 | TAG | UAG | Gln (Q) (p) | Stop * | As of Nov. 18, 2016: absent from the NCBI update. Similar to translation table 6. | ||
| Chlorophycean mitochondrial | 16 | TAG | UAG | Leu (L) (np) | Stop * | |||
| Trematode mitochondrial | 21 | TGA | UGA | Trp (W) (np) | Stop * | |||
| ATA | AUA | Met (M) (np) | Ile (I) (np) | |||||
| AGA | AGA | Ser (S) | Arg (R) (b) | |||||
| AGG | AGG | Ser (S) (p) | Arg (R) (b) | |||||
| AAA | AAA | Asn (N) (p) | Lys (K) (b) | |||||
| Scenedesmus obliquus mitochondrial | 22 | TCA | UCA | Stop * | Ser (S) (p) | |||
| TAG | UAG | Leu (L) (np) | Stop * | |||||
| Thraustochytrium mitochondrial | 23 | TTA | UUA | Stop * | Leu (L) (np) | Similar to translation table 11. | ||
| Pterobranchia mitochondrial | 24 | AGA | AGA | Ser (S) (p) | Arg (R) (b) | |||
| AGG | AGG | Lys (K) (b) | Arg (R) (b) | |||||
| TGA | UGA | Trp (W) (np) | Stop * | |||||
| Candidate division SR1 and Gracilibacteria | 25 | TGA | UGA | Gly (G) (np) | Stop * | |||
| Pachysolen tannophilus nuclear | 26 | CTG | CUG | Ala (A) (np) | Leu (L) (np) | |||
| Karyorelict nuclear | 27 | TAA | UAA | Gln (Q) (p) | Stop * | |||
| TAG | UAG | Gln (Q) (p) | Stop * | |||||
| TGA | UGA | Stop * | or | Trp (W) (np) | Stop * | |||
| Condylostoma nuclear | 28 | TAA | UAA | Stop * | or | Gln (Q) (p) | Stop * | |
| TAG | UAG | Stop * | or | Gln (Q) (p) | Stop * | |||
| TGA | UGA | Stop * | or | Trp (W) (np) | Stop * | |||
| Mesodinium nuclear | 29 | TAA | UAA | Tyr (Y) (p) | Stop * | |||
| TAG | UAG | Tyr (Y) (p) | Stop * | |||||
| Peritrich nuclear | 30 | TA | UAA | Glu (E) (a) | Stop * | |||
| TAG | UAG | Glu (E) (a) | Stop * | |||||
| Blastocrithidia nuclear | 31 | TAA | UAA | Stop * | or | Glu (E) (a) | Stop * | |
| TAG | UAG | Stop * | or | Glu (E) (a) | Stop * | |||
| TGA | UGA | Trp (W) (np) | Stop * | |||||
| Cephalodiscidae mitochondrial code | 33 | AGA | AGA | Ser (S) (p) | Arg (R) (b) | Similar to translation table 24. | ||
| AGG | AGG | Lys (K) (b) | Arg (R) (b) | |||||
| TAA | UAA | Tyr (Y) (p) | Stop * | |||||
| TGA | UGA | Trp (W) (np) | Stop * | |||||
| Enterosoma[23] | 34 | AGG | AGG | Met (M) (np) | Arg (R) (b) | |||
| Peptacetobacter[23] | 35 | CGG | CGG | Gln (Q) (p) | Arg (R) (b) | |||
| Anaerococcus and Onthovivens[23] | 36 | CGG | CGG | Trp (W) (np) | Arg (R) (b) | |||
| Absconditabacteraceae[23] | 37 | CGA | CGA | Trp (W) (np) | Arg (R) (b) | |||
| CGG | CGG | Trp (W) (np) | Arg (R) (b) | |||||
| TGA | UGA | Gly (G) (np) | Stop * | |||||
See also
Notes
- The historical basis for designating the stop codons as amber, ochre and opal is described in the autobiography of Sydney Brenner[15] and in a historical article by Bob Edgar.[16]
- Euplotes octacarinatus is an exception.[22]
References
Further reading
External links
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