Proline Codons — CCT, CCC, CCA, CCG
Proline (Pro, one-letter code P) is encoded by 4 synonymous codons — CCT, CCC, CCA, CCG in DNA, CCU, CCC, CCA, CCG in RNA.
It is four-fold degenerate, with only the third position — the wobble base — differing between them. Which one a host actually uses is a different question, and the eight organisms below split across 4 different favourites.
Proline codon usage by organism
Each number is that codon's share of all proline codons in that organism, so every column sums to 100%. The highest in each column is the preferred codon a codon optimizer would pick.
| DNA | RNA | E. coli | Human | Yeast | CHO | Pichia | Insect | Arabidopsis | Zebrafish |
|---|---|---|---|---|---|---|---|---|---|
| CCT | CCU | 16% | 29% | 31% | 31% | 35% | 29% | 38% | 31% |
| CCC | CCC | 12% | 32% | 15% | 32% | 15% | 28% | 11% | 24% |
| CCA | CCA | 19% | 28% | 42% | 29% | 42% | 28% | 33% | 30% |
| CCG | CCG | 53% | 11% | 12% | 8% | 9% | 16% | 18% | 15% |
Reference approximations derived from the Kazusa Codon Usage Database — the same tables the codon optimizer runs on. Verify against your own expression system for critical work.
Preferred codon by host
Use this
Frequently asked questions
Which codons code for proline?
4 codons: CCT, CCC, CCA, CCG in DNA, or CCU, CCC, CCA, CCG in RNA. Proline is four-fold degenerate, and only the third (wobble) position varies.
Which proline codon should I use?
It depends on the host, and the eight organisms here do not agree — they split across 4 different favourites (CCG, CCC, CCA, CCT). E. coli (K-12) prefers CCG, Human (H. sapiens) prefers CCC, Yeast (S. cerevisiae) prefers CCA. The table below gives every fraction.
Does CCG behave the same in every organism?
No — it is the codon that varies most across these eight. E. coli (K-12) uses it for 53% of its proline codons, CHO (C. griseus) for 8%. That gap is the reason a gene that expressed well in one host can stall in another without a single amino acid changing.
What is the proline one-letter code?
P, and the three-letter code is Pro. Those are what the sequence tools on this site read and write — paste a protein in either alphabet and it is understood.
Where do these usage numbers come from?
They are reference approximations derived from the Kazusa Codon Usage Database and are the same tables the codon optimizer on this site runs on. For critical work, check them against your own expression system rather than treating any single table as definitive.
Codons for the other amino acids
Or go back to the full codon table for the codon-to-amino-acid direction.