Codons
A protein-coding sequence is read three bases at a time. Each three-base codon stands for one amino acid, or for stop. ATG codes for methionine and is the usual start codon. TAA, TAG and TGA are the stop codons in the standard code. ATGGCTTAA translates to M A *, where * marks the stop.
Six reading frames
Starting on the first, second or third base gives three different translations of one strand, and the reverse complement gives three more. Only one of the six is usually the real protein. The right frame is normally a long stretch without stop codons, called an open reading frame.
Find the protein in a longer sequence
- Paste the DNA into the ORF Finder and set a minimum length, such as 100 codons.
- Check the longest open reading frames on both strands.
- Copy the one you want into Translate DNA to Protein to see it codon by codon.
Genetic codes
Most organisms use the standard code, but not all. In vertebrate mitochondria TGA codes for tryptophan and AGA and AGG are stops, and some bacteria, yeasts and ciliates have their own variations. Pick the matching NCBI genetic code, or a mitochondrial gene will seem full of stops.
Going backwards
Several codons code for most amino acids, so a protein does not give one exact DNA sequence. Reverse Translate writes the possibilities with IUPAC codes, or uses the most frequent codon from a codon usage table.
One sequence, three frames
The sequence ATGGCCATTGTAATGGGCCGCTGA read from each of its first three bases:
| Frame | Codons | Protein |
|---|---|---|
| 1 | ATG GCC ATT GTA ATG GGC CGC TGA | M A I V M G R * |
| 2 | TGG CCA TTG TAA TGG GCC GCT | W P L * W A A |
| 3 | GGC CAT TGT AAT GGG CCG CTG | G H C N G P L |
Frame 1 starts with ATG and ends cleanly at a stop codon, which marks it as the likely coding frame.
Common problems
- The protein is full of stops. The sequence may be genomic DNA with introns. Translate the coding sequence or the mRNA instead, not the gene as it sits in the genome.
- X appears in the protein. A codon contains N or another ambiguity code, so its amino acid cannot be known.
- Bacterial genes start without ATG. Bacteria also use GTG and TTG as start codons. At the start of a gene they still code for methionine.
- A stop sits inside a known protein. A few proteins insert selenocysteine at a UGA codon, guided by a special structure in the mRNA. Translation tools show a stop there.