DNA and RNA codon tables explained

A codon table can be used to translate a genetic code into a sequence of amino acids.[1] 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.[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]

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, 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] [8] [9] 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] [9]

The classical table/wheel of the standard genetic code is arbitrarily organized based on codon position 1. Saier,[10] following observations from,[11] 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 ⇒
1st
base! colspan=8
2nd base3rd
base
UCAG
UUUU(Phe/F) Phenylalanine (np)UCU(Ser/S) Serine (p)UAU(Tyr/Y) Tyrosine (p)UGU(Cys/C) Cysteine (p)U
UUCUCCUACUGCC
UUA(Leu/L) Leucine (np)UCAUAAStop (Ochre) *UGAStop (Opal) *A
UUG ⇒UCGUAGStop (Amber) *UGG(Trp/W) Tryptophan (np)G
CCUUCCU(Pro/P) Proline (np)CAU(His/H) Histidine (b)CGU(Arg/R) Arginine (b)U
CUCCCCCACCGCC
CUACCACAA(Gln/Q) Glutamine (p)CGAA
CUGCCGCAGCGGG
AAUU(Ile/I) Isoleucine (np)ACU(Thr/T) Threonine (p)AAU(Asn/N) Asparagine (p)AGU(Ser/S) Serine (p)U
AUCACCAACAGCC
AUAACAAAA(Lys/K) Lysine (b)AGA(Arg/R) Arginine (b)A
AUG ⇒(Met/M) Methionine (np)ACGAAGAGGG
GGUU(Val/V) Valine (np)GCU(Ala/A) Alanine (np)GAU(Asp/D) Aspartic acid (a)GGU(Gly/G) Glycine (np)U
GUCGCCGACGGCC
GUAGCAGAA(Glu/E) Glutamic acid (a)GGAA
GUG ⇒GCGGAGGGGG

As shown in the above table, NCBI table 1 includes the less-canonical start codons GUG and UUG.[3]

Inverse RNA codon table

Inverse table for the standard genetic code (compressed using IUPAC notation)[12]
Amino acid RNA codons CompressedAmino acid RNA codons Compressed
Ala, AGCU, GCC, GCA, GCGGCNIle, IAUU, AUC, AUAAUH
Arg, RCGU, CGC, CGA, CGG; AGA, AGGCGN, AGR; or
CGY, MGR
Leu, LCUU, CUC, CUA, CUG; UUA, UUGCUN, UUR; or
CUY, YUR
Asn, NAAU, AACAAYLys, KAAA, AAGAAR
Asp, DGAU, GACGAYMet, MAUG
Asn or Asp, BAAU, AAC; GAU, GACRAYPhe, FUUU, UUCUUY
Cys, CUGU, UGCUGYPro, PCCU, CCC, CCA, CCGCCN
Gln, QCAA, CAGCARSer, SUCU, UCC, UCA, UCG; AGU, AGCUCN, AGY
Glu, EGAA, GAGGARThr, TACU, ACC, ACA, ACGACN
Gln or Glu, ZCAA, CAG; GAA, GAGSARTrp, WUGG
Gly, GGGU, GGC, GGA, GGGGGNTyr, YUAU, UACUAY
His, HCAU, CACCAYVal, VGUU, GUC, GUA, GUGGUN
STARTAUG, CUG, UUG HUGSTOPUAA, UGA, UAGURA, 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! colspan=8
2nd base3rd
base
TCAG
T(Phe/F) Phenylalanine (np)C(Ser/S) Serine (p)A(Tyr/Y) Tyrosine (p)G(Cys/C) Cysteine (p)
CCCACGCC
A(Leu/L) Leucine (np)CAAAStop (Ochre) *GAStop (Opal) *A
G ⇒CGAGStop (Amber) *GG(Trp/W) Tryptophan (np)G
CCCC(Pro/P) Proline (np)CA (His/H) Histidine (b)CG(Arg/R) Arginine (b)
CCCCCCACCGCC
CACCACAA(Gln/Q) Glutamine (p)CGAA
CGCCGCAGCGGG
AA(Ile/I) Isoleucine (np)AC(Thr/T) Threonine (p)AA(Asn/N) Asparagine (p)AG(Ser/S) Serine (p)
ACACCAACAGCC
AAACAAAA(Lys/K) Lysine (b)AGA(Arg/R) Arginine (b)A
AG ⇒(Met/M) Methionine (np)ACGAAGAGGG
GG(Val/V) Valine (np)GC(Ala/A) Alanine (np)GA(Asp/D) Aspartic acid (a)GG(Gly/G) Glycine (np)
GCGCCGACGGCC
GAGCAGAA(Glu/E) Glutamic acid (a)GGAA
GG ⇒GCGGAGGGGG

Inverse DNA codon table

Inverse table for the standard genetic code (compressed using IUPAC notation)
Amino acid DNA codons CompressedAmino acid DNA codons Compressed
Ala, AGC, GCC, GCA, GCGGCNIle, IA, AC, AAAH
Arg, RCG, CGC, CGA, CGG; AGA, AGGCGN, AGR; or
CGY, MGR
Leu, LC, CC, CA, CG; A, GCN, R; or
CY, YR
Asn, NAA, AACAAYLys, KAAA, AAGAAR
Asp, DGA, GACGAYMet, MAG
Asn or Asp, BAA, AAC; GA, GACRAYPhe, F, CY
Cys, CG, GCGYPro, PCC, CCC, CCA, CCGCCN
Gln, QCAA, CAGCARSer, SC, CC, CA, CG; AG, AGCCN, AGY
Glu, EGAA, GAGGARThr, TAC, ACC, ACA, ACGACN
Gln or Glu, ZCAA, CAG; GAA, GAGSARTrp, WGG
Gly, GGG, GGC, GGA, GGGGGNTyr, YA, ACAY
His, HCA, CACCAYVal, VG, GC, GA, GGGN
STARTATG, TTG, GTG, CTG[13] NTGSTOPAA, GA, AGRA, AR

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.[14] [15] 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.[14] Stop codons can also be affected: in ciliated protozoa, the universal stop codons UAA and UAG code for glutamine.[15] 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.[16] The following table displays these alternative codons.

Amino-acid biochemical properties Nonpolar (np)Polar (p)Basic (b)Acidic (a)Termination: stop codon *
Code! scope="col" style="width: 25px;"
Translation
table
DNA codon involvedRNA codon involvedTranslation
with this code
Standard translationNotes
scope=rowStandard1Includes translation table 8 (plant chloroplasts).
scope=row rowspan="4"Vertebrate mitochondrial2AGAAGAStop *Arg (R) (b)
AGG AGG Stop * Arg (R) (b)
ATA AUA Met (M) (np)Ile (I) (np)
TGA UGA Trp (W) (np)Stop *
scope=row rowspan="8" Yeast mitochondrial3ATA 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)
scope=row rowspan="1" Mold, protozoan, and coelenterate mitochondrial + Mycoplasma / Spiroplasma4TGA UGA Trp (W) (np) Stop * Includes the translation table 7 (kinetoplasts).
scope=row rowspan="4" Invertebrate mitochondrial5AGA 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 *
scope=row rowspan="2" Ciliate, dasycladacean and Hexamita nuclear6TAA UAA Gln (Q) (p)Stop *
TAGUAG Gln (Q) (p)Stop *
scope=row rowspan="4" Echinoderm and flatworm mitochondrial9AAA 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 *
scope=row rowspan="1" Euplotid nuclear10TGA UGA Cys (C) (p)Stop *
scope=row rowspan="1" Bacterial, archaeal and plant plastid11See translation table 1.
scope=row rowspan="1" Alternative yeast nuclear12CTG CUG Ser (S) (p)Leu (L) (np)
scope=row rowspan="4" Ascidian mitochondrial13AGA 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 *
scope=row rowspan="5" Alternative flatworm mitochondrial14AAA 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 *
scope=row rowspan="1" Blepharisma nuclear15TAG UAG Gln (Q) (p)Stop * As of Nov. 18, 2016: absent from the NCBI update. Similar to translation table 6.
scope=row rowspan="1" Chlorophycean mitochondrial16TAG UAG Leu (L) (np) Stop *
scope=row rowspan="5" Trematode mitochondrial21TGA 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)
scope=row rowspan="2" Scenedesmus obliquus mitochondrial22TCA UCA Stop * Ser (S) (p)
TAG UAG Leu (L) (np) Stop *
scope=row rowspan="1" Thraustochytrium mitochondrial23TTA UUA Stop * Leu (L) (np) Similar to translation table 11.
scope=row rowspan="3" Pterobranchia mitochondrial24AGA AGA Ser (S) (p)Arg (R) (b)
AGG AGG Lys (K) (b) Arg (R) (b)
TGA UGA Trp (W) (np) Stop *
scope=row rowspan="1" Candidate division SR1 and Gracilibacteria25TGA UGA Gly (G) (np) Stop *
scope=row rowspan="1" Pachysolen tannophilus nuclear26CTG CUG Ala (A) (np) Leu (L) (np)
scope=row rowspan="3" Karyorelict nuclear27TAA UAA Gln (Q) (p)Stop *
TAG UAG Gln (Q) (p)Stop *
TG UGA Stop * or Trp (W) (np) Stop *
scope=row rowspan="3" Condylostoma nuclear28TAA UAA Stop * or Gln (Q) (p)Stop *
TAG UAG Stop * or Gln (Q) (p)Stop *
TGA UGA Stop * or Trp (W) (np)Stop *
scope=row rowspan="2" Mesodinium nuclear29TAA UAA Tyr (Y) (p)Stop *
TAG UAG Tyr (Y) (p)Stop *
scope=row rowspan="2" Peritrich nuclear30TA UAA Glu (E) (a)Stop *
TAG UAG Glu (E) (a)Stop *
scope=row rowspan="3" Blastocrithidia nuclear31TAA UAA Stop * or Glu (E) (a)Stop *
TAG UAG Stop * or Glu (E) (a)Stop *
TGA UGA Trp (W) (np) Stop *
scope=row rowspan="4" Cephalodiscidae mitochondrial code33AGA 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 *
scope=row rowspan="1" Enterosoma34AGG AGG Met (M) (np)Arg (R) (b)
scope=row rowspan="1" Peptacetobacter35CGG CGG Gln (Q) (p)Arg (R) (b)
scope=row rowspan="1" Anaerococcus and Onthovivens36CGG CGG Trp (W) (np)Arg (R) (b)
scope=row rowspan="3" Absconditabacteraceae37CGA CGA Trp (W) (np)Arg (R) (b)
CGG CGG Trp (W) (np)Arg (R) (b)
TGA UGA Gly (G) (np) Stop *

See also

Further reading

External links

Notes and References

  1. Web site: Amino Acid Translation Table. Oregon State University. 2 December 2020. 29 May 2020. https://web.archive.org/web/20200529000711/http://sites.science.oregonstate.edu/genbio/otherresources/aminoacidtranslation.htm. dead.
  2. Book: Bartee. Lisa. Brook. Jack. MHCC Biology 112: Biology for Health Professions. Open Oregon. 42. 6 December 2020. 6 December 2020. https://web.archive.org/web/20201206173711/https://mhccbiology112.pressbooks.com/. live.
  3. Web site: The Genetic Codes. National Center for Biotechnology Information. Elzanowski A, Ostell J. 7 January 2019. 21 February 2019. https://web.archive.org/web/20201005105339/https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi. 5 October 2020.
  4. Web site: RNA Functions. Scitable. Nature Education. 5 January 2021. https://web.archive.org/web/20081018170459/https://www.nature.com/scitable/topicpage/rna-functions-352/. 18 October 2008. live.
  5. Web site: The Genetic Codes. National Center for Biotechnology Information. 2 December 2020. 13 May 2011. https://web.archive.org/web/20110513014234/http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi. live.
  6. Web site: Codon. National Human Genome Research Institute. 10 October 2020. 22 October 2020. https://web.archive.org/web/20201022081214/https://www.genome.gov/genetics-glossary/Codon. live.
  7. Web site: How nonsense mutations got their names. Maloy S.. 29 November 2003. Microbial Genetics Course. San Diego State University. 10 October 2020. https://web.archive.org/web/20200923075442/http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/rev-sup/amber-name.html. 23 September 2020.
  8. Hinnebusch AG. 2011. Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes. Microbiology and Molecular Biology Reviews. 75. 3. 434–467. 10.1128/MMBR.00008-11. 21885680. 3165540. free.
  9. Touriol C, Bornes S, Bonnal S, Audigier S, Prats H, Prats AC, Vagner S. Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons. Biology of the Cell. 95. 3–4. 169–78. 2003. 12867081. 10.1016/S0248-4900(03)00033-9. free.
  10. Saier . Milton H. Jr. . 10 July 2019 . Understanding the Genetic Code. . J Bacteriol . 201 . 15 . e00091-19 . 10.1128/JB.00091-19. 31010904 . 6620406 .
  11. Muto . A. . Osawa . S. . January 1987 . The guanine and cytosine content of genomic DNA and bacterial evolution. . Proc Natl Acad Sci USA . 84 . 1 . 166–9 . 10.1073/pnas.84.1.166. 3467347 . 304163 .
  12. Web site: Abbreviations and Symbols for Nucleic Acids, Polynucleotides and Their Constituents. IUPAC—IUB Commission on Biochemical Nomenclature. International Union of Pure and Applied Chemistry. 5 December 2020. 9 July 2021. https://web.archive.org/web/20210709183441/http://publications.iupac.org/pac/1974/pdf/4003x0277.pdf. live.
  13. Web site: Choose a start codon . 2024-08-14 . depts.washington.edu.
  14. Osawa. A. November 1993. Evolutionary changes in the genetic code. Comparative Biochemistry and Physiology. 106. 2. 489–94. 10.1016/0305-0491(93)90122-l. 8281749. 2020-12-05. 2020-12-06. https://web.archive.org/web/20201206173716/https://pubmed.ncbi.nlm.nih.gov/8281749/. live.
  15. Osawa S, Jukes TH, Watanabe K, Muto A. March 1992. Recent evidence for evolution of the genetic code. Microbiological Reviews. 56. 1. 229–64. 10.1128/MR.56.1.229-264.1992. 372862. 1579111.
  16. Shulgina . Yekaterina . Eddy . Sean R. . 9 November 2021 . A computational screen for alternative genetic codes in over 250,000 genomes. . eLife . 10 . 10.7554/eLife.71402. free . 34751130 . 8629427 .