Codon Table

Q: How many codons encode each amino acid?

The genetic code is degenerate: most amino acids are encoded by 2-6 codons. Leucine (Leu) and Arginine (Arg) have the most with 6 codons each. Serine (Ser) also has 6. Methionine (Met, AUG) and Tryptophan (Trp, UGG) each have only 1 codon. The three stop codons (UAA, UAG, UGA) do not encode amino acids but signal translation termination.

Q: What is the wobble hypothesis?

The wobble hypothesis, proposed by Francis Crick in 1966, states that the third position of a codon can form non-standard base pairs with the first position of the anticodon. G can pair with C or U, U can pair with A or G, and inosine (I) in the anticodon can pair with U, C, or A. This explains how fewer than 61 tRNAs can recognize all 61 sense codons.

Q: What is the Codon Adaptation Index (CAI)?

CAI measures how closely a gene's codon usage matches the preferred codons of a host organism. It is calculated as exp(1/L * sum(ln(w_i))) where w_i is the relative adaptiveness of each codon and L is the gene length in codons. CAI = 1.0 means only preferred codons are used. Values above 0.8 predict high expression; below 0.5 predict low expression in the host.

Q: Why is AUG both a start codon and a methionine codon?

AUG serves a dual role: it is the universal start codon that initiates translation (recognized by the initiator tRNA fMet-tRNA in prokaryotes or Met-tRNA in eukaryotes) and also encodes internal methionine residues within a protein. The ribosome distinguishes the start AUG from internal AUGs using the Shine-Dalgarno sequence (prokaryotes) or Kozak consensus sequence (eukaryotes).

Q: What amino acids can be phosphorylated?

Serine (Ser, S), Threonine (Thr, T), and Tyrosine (Tyr, Y) are the three amino acids that undergo phosphorylation by protein kinases. Their hydroxyl (-OH) side chains accept a phosphate group. In human cells, approximately 86% of phosphorylation occurs on serine, 12% on threonine, and 2% on tyrosine. Histidine phosphorylation also occurs in bacteria.

Q: How does GC content affect codon usage?

Organisms with high genomic GC content (>60%, e.g., Streptomyces at ~72%) strongly prefer codons ending in G or C at the third position. Low-GC organisms (<40%, e.g., Plasmodium at ~19%) prefer codons ending in A or U. This bias must be accounted for when designing synthetic genes for heterologous expression in a different host organism.

Q: What makes UGA special among stop codons?

UGA (Opal) is unique because it can encode selenocysteine (Sec, U), the 21st amino acid, when a SECIS (Selenocysteine Insertion Sequence) element is present in the mRNA. Additionally, in mitochondrial genetic codes of many organisms, UGA is reassigned to encode tryptophan instead of functioning as a stop codon, demonstrating that the genetic code is not truly universal.

Q: What is codon optimization and when is it needed?

Codon optimization replaces rare codons in a gene with synonymous preferred codons of the expression host to improve translation efficiency and protein yield. It is essential when expressing a gene from one organism (e.g., human) in a different host (e.g., E. coli) where codon usage patterns differ significantly. The CAI score and host-specific codon usage tables guide the optimization process.

Free reference guide: Codon Table

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About Codon Table

The Codon Table Reference provides a comprehensive, searchable lookup of all 64 RNA triplet codons mapped to the 20 standard amino acids and 3 stop codons. Each entry includes the codon sequences (RNA and DNA), the encoded amino acid with one-letter and three-letter abbreviations, molecular weight in Daltons, key biochemical properties (pKa values, functional groups), and biological roles such as post-translational modification sites (phosphorylation, glycosylation, acetylation, ubiquitination) and enzyme active site residues.

The reference is organized into six categories: Start/Stop codons (AUG initiation, UAA Ochre, UAG Amber, UGA Opal with selenocysteine insertion), hydrophobic amino acids (Phe, Leu, Ile, Val, Ala, Pro), polar amino acids (Ser, Thr, Tyr, Asn, Gln), charged amino acids (Asp, Glu, Lys, Arg, His), special amino acids (Cys disulfide bonds, Trp single codon, Gly achiral), and codon optimization topics (wobble base pairing, Codon Adaptation Index, GC content bias). E. coli codon usage frequencies per 1000 codons are included for recombinant protein expression planning.

This tool is designed for molecular biologists, biochemistry students, bioinformatics researchers, and anyone working with gene synthesis, codon optimization, or protein engineering. All content is presented in a filterable RefTool component with bilingual Korean/English support, running entirely in the browser with no data sent to any server.

Key Features

All 64 codons mapped to 20 amino acids + 3 stop codons with RNA/DNA sequences and one/three-letter codes
Molecular weights, pKa values, and functional group details for each amino acid
Post-translational modification sites: Ser/Thr/Tyr phosphorylation, N/O-glycosylation, Lys acetylation/methylation/ubiquitination
E. coli preferred codons and usage frequencies per 1000 codons for recombinant expression optimization
Wobble base pairing rules: anticodon-codon 3rd position pairing including inosine (I) base
Codon Adaptation Index (CAI) formula and interpretation: CAI > 0.8 = high expression, CAI < 0.5 = low expression
GC content bias effects on codon usage: high-GC organisms (Streptomyces ~72%) vs. low-GC (Plasmodium ~19%)
Searchable, filterable interface organized by amino acid property categories with bilingual Korean/English content

Frequently Asked Questions

How many codons encode each amino acid?

The genetic code is degenerate: most amino acids are encoded by 2-6 codons. Leucine (Leu) and Arginine (Arg) have the most with 6 codons each. Serine (Ser) also has 6. Methionine (Met, AUG) and Tryptophan (Trp, UGG) each have only 1 codon. The three stop codons (UAA, UAG, UGA) do not encode amino acids but signal translation termination.

What is the wobble hypothesis?

The wobble hypothesis, proposed by Francis Crick in 1966, states that the third position of a codon can form non-standard base pairs with the first position of the anticodon. G can pair with C or U, U can pair with A or G, and inosine (I) in the anticodon can pair with U, C, or A. This explains how fewer than 61 tRNAs can recognize all 61 sense codons.

What is the Codon Adaptation Index (CAI)?

CAI measures how closely a gene's codon usage matches the preferred codons of a host organism. It is calculated as exp(1/L * sum(ln(w_i))) where w_i is the relative adaptiveness of each codon and L is the gene length in codons. CAI = 1.0 means only preferred codons are used. Values above 0.8 predict high expression; below 0.5 predict low expression in the host.

Why is AUG both a start codon and a methionine codon?

AUG serves a dual role: it is the universal start codon that initiates translation (recognized by the initiator tRNA fMet-tRNA in prokaryotes or Met-tRNA in eukaryotes) and also encodes internal methionine residues within a protein. The ribosome distinguishes the start AUG from internal AUGs using the Shine-Dalgarno sequence (prokaryotes) or Kozak consensus sequence (eukaryotes).

What amino acids can be phosphorylated?

Serine (Ser, S), Threonine (Thr, T), and Tyrosine (Tyr, Y) are the three amino acids that undergo phosphorylation by protein kinases. Their hydroxyl (-OH) side chains accept a phosphate group. In human cells, approximately 86% of phosphorylation occurs on serine, 12% on threonine, and 2% on tyrosine. Histidine phosphorylation also occurs in bacteria.

How does GC content affect codon usage?

Organisms with high genomic GC content (>60%, e.g., Streptomyces at ~72%) strongly prefer codons ending in G or C at the third position. Low-GC organisms (<40%, e.g., Plasmodium at ~19%) prefer codons ending in A or U. This bias must be accounted for when designing synthetic genes for heterologous expression in a different host organism.

What makes UGA special among stop codons?

UGA (Opal) is unique because it can encode selenocysteine (Sec, U), the 21st amino acid, when a SECIS (Selenocysteine Insertion Sequence) element is present in the mRNA. Additionally, in mitochondrial genetic codes of many organisms, UGA is reassigned to encode tryptophan instead of functioning as a stop codon, demonstrating that the genetic code is not truly universal.

What is codon optimization and when is it needed?

Codon optimization replaces rare codons in a gene with synonymous preferred codons of the expression host to improve translation efficiency and protein yield. It is essential when expressing a gene from one organism (e.g., human) in a different host (e.g., E. coli) where codon usage patterns differ significantly. The CAI score and host-specific codon usage tables guide the optimization process.