DNA and RNA codon tables

A codon table can be used to translate a genetic code into a sequence of amino acids. 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. The mRNA sequence is determined by the sequence of genomic DNA. In this context, the standard genetic code is referred to as 'translation table 1' among other tables. 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.

There are 64 different codons in the genetic code and the below tables; most specify an amino acid. Three sequences, UAG, UGA, and UAA, known as stop codons, do not code for an amino acid but instead signal the release of the nascent polypeptide from the ribosome. 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. 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.

The classical table/wheel of the standard genetic code is arbitrarily organized based on codon position 1. Saier, following observations from Muto, 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 Standard RNA codon table Amino-acid biochemical properties Nonpolar (np) Polar (p) Basic (b) Acidic (a) Termination: stop codon * Initiation: possible start codon ⇒ + Standard genetic code 1stbase 2nd base 3rdbase 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) * UGA Stop (Opal) * AUUG ⇒ UCG UAG Stop (Amber) * UGG (Trp/W) Tryptophan (np) G C CUU CCU (Pro/P) Proline (np) CAU (His/H) Histidine (b)CGU (Arg/R) Arginine (b) U CUCCCCCACCGC CCUACCACAA (Gln/Q) Glutamine (p)CGA ACUGCCGCAGCGG G AAUU (Ile/I) Isoleucine (np)ACU (Thr/T) Threonine (p)AAU (Asn/N) Asparagine (p)AGU (Ser/S) Serine (p) UAUCACCAACAGC CAUAACAAAA (Lys/K) Lysine (b)AGA (Arg/R) Arginine (b) AAUG ⇒ (Met/M) Methionine (np)ACGAAGAGG G GGUU (Val/V) Valine (np)GCU (Ala/A) Alanine (np)GAU (Asp/D) Aspartic acid (a)GGU (Gly/G) Glycine (np) UGUCGCCGACGGC CGUAGCAGAA (Glu/E) Glutamic acid (a)GGA AGUG ⇒GCGGAGGGG G

As shown in the above table, NCBI table 1 includes the less-canonical start codons GUG and UUG.

Inverse RNA codon table + Inverse table for the standard genetic code (compressed using IUPAC notation) 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 ⇒ + Standard genetic code 1stbase 2nd base 3rdbase 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) * TGA Stop (Opal) * A TTG ⇒ TCG TAG Stop (Amber) * TGG (Trp/W) Tryptophan (np) G C CTT CCT (Pro/P) Proline (np) CAT (His/H) Histidine (b)CGT (Arg/R) Arginine (b) TCTCCCCCACCGC CCTACCACAA (Gln/Q) Glutamine (p)CGA ACTGCCGCAGCGG G AATT (Ile/I) Isoleucine (np)ACT (Thr/T) Threonine (p)AAT (Asn/N) Asparagine (p)AGT (Ser/S) Serine (p) TATCACCAACAGC CATAACAAAA (Lys/K) Lysine (b)AGA (Arg/R) Arginine (b) AATG ⇒ (Met/M) Methionine (np)ACGAAGAGG G GGTT (Val/V) Valine (np)GCT (Ala/A) Alanine (np)GAT (Asp/D) Aspartic acid (a)GGT (Gly/G) Glycine (np) TGTCGCCGACGGC CGTAGCAGAA (Glu/E) Glutamic acid (a)GGA AGTG ⇒GCGGAGGGG G

Inverse DNA codon table + Inverse table for the standard genetic code (compressed using IUPAC notation) 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 NTG STOP TAA, TGA, TAG TRA, TAR

Alternative codons in other translation tables

The genetic code was once believed to be universal: 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, resulting in discrepancies in how a codon is translated depending on the genetic source. 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. Stop codons can also be affected: in ciliated protozoa, the universal stop codons UAA and UAG code for glutamine. 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. The following table displays these alternative codons.

Amino-acid biochemical properties Nonpolar (np) Polar (p) Basic (b) Acidic (a) Termination: stop codon *

+ Comparison between codon translations with alternative and standard genetic codes Code Translation table DNA codon involved RNA codon involved Translation with this code Standard translation Notes Standard 1Includes translation table 8 (plant chloroplasts). Vertebrate mitochondrial 2AGAAGA 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 34 AGG AGG Met (M) (np) Arg (R) (b) Peptacetobacter 35 CGG CGG Gln (Q) (p) Arg (R) (b) Anaerococcus and Onthovivens 36 CGG CGG Trp (W) (np) Arg (R) (b) Absconditabacterales 37 CGA CGA Trp (W) (np) Arg (R) (b) CGG CGG Trp (W) (np) Arg (R) (b) TGA UGA Gly (G) (np) Stop *

DNA and RNA codon tables

Bron en licentie