DNA to Protein Translator (Transcription & Translation)

About the DNA to Protein Translator (Transcription & Translation)

Paste a DNA or mRNA sequence to see its mRNA (or either DNA strand) and its protein. You can translate one reading frame, all three forward frames, all six frames (both strands), or the protein a ribosome would make from the first AUG to the next stop codon. Choose any of NCBI’s 27 genetic codes: the standard code, the vertebrate and yeast mitochondrial codes, the bacterial and plastid code, the ciliate codes, and the rest. Amino acids can be shown in one-letter or three-letter code.

The ORF finder lists open reading frames on both strands. You can choose the start codons it accepts and a minimum length, and download the ORFs as FASTA or CSV. A codon-by-codon view marks starts, stops and ambiguous codons. The tool reads plain text, FASTA (with a menu for multi-record files) and GenBank records, and IUPAC ambiguity codes such as N or R are translated wherever the amino acid is certain. Everything runs in your browser — your sequence is never uploaded.

Common uses

• Biology homework on transcription and translation, including template-strand questions.
• Checking that a cloned or synthetic gene is in frame and has no premature stop codons.
• Translating mitochondrial, bacterial, plastid or ciliate genes with the right genetic code.
• Finding candidate protein-coding regions (ORFs) in a new sequence, on both strands.

From DNA to protein

The coding strand of a gene has the same sequence as its mRNA, with T in place of U. The template strand is its complement, the strand RNA polymerase reads. To get the mRNA from a template written 3′→5′, take the complement base by base. From a template written 5′→3′, take the reverse complement.

The ribosome reads the mRNA 5′→3′ in codons of three bases, starting at an initiator codon (usually AUG) and stopping at a stop codon. A sequence has three reading frames on each strand:

• +1, +2 and +3 start at its 1st, 2nd and 3rd base;
• −1, −2 and −3 do the same on the reverse complement.

Positions in the tool are always counted on the coding strand.

The genetic codes

The tables are NCBI’s “The Genetic Codes” (Elzanowski & Ostell), taken from NCBI’s gc.prt file, version 4.6. They cover tables 1–6, 9–16 and 21–33, which differ in a few codons. For example, UGA is Trp in vertebrate mitochondria (table 2), where AGA and AGG are stops and AUA is Met. As NCBI specifies, an initiator codon — AUG, or an alternative such as GUG, UUG or CUG — is translated as Met when it starts a protein (the first-AUG translation and the ORFs). Inside a frame it keeps its usual meaning: GUG is Val.

In tables 27, 28 and 31 some codons (UAA, UAG or UGA) can be read either as an amino acid or as a stop, depending on context. The frame translations show the amino acid and the codon view marks the codon; the translation from the first AUG and the ORF finder end there, as at a stop.

Open reading frames

An ORF here runs from a start codon to the next stop codon in the same frame, stop included. Its length is counted in nucleotides, stop included, and it must reach the minimum length you choose. You can accept:

• ATG only;
• ATG and the table’s alternative initiators (for the standard code, also CTG and TTG);
• any sense codon, which gives stop-to-stop ORFs.

For each stop the longest ORF is reported — the one from the first start after the previous stop. You can also ask for ORFs that run off the end without a stop, and hide ORFs lying entirely inside a longer one on any strand or frame. Minus-strand ORFs are given in coding-strand coordinates, so their start is the higher number. The table shows the 200 longest; the FASTA and CSV downloads contain up to 2,000.

Ambiguity codes and gaps

IUPAC-IUB ambiguity codes are expanded to every codon they could stand for:

• if all those codons give one amino acid, it is shown — GCN is Ala;
• if they give only stops, a stop is shown;
• if they give Asp or Asn, the result is B (Asx);
• if they give Glu or Gln, the result is Z (Glx);
• anything else is X (the IUPAC-IUB amino-acid symbols).

Gap characters (- and .) are removed before translating, and a note says how many.

Sources

• NCBI, The Genetic Codes, by A. Elzanowski and J. Ostell, and its data file gc.prt (version 4.6).
• NC-IUB, Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (Cornish-Bowden, Nucleic Acids Res. 13, 3021–3030).
• IUPAC-IUB JCBN, Nomenclature and Symbolism for Amino Acids and Peptides, 3AA-1.
• The translations were checked against NCBI’s own proteins for human insulin (NM_000207.3 → NP_000198.1), human mitochondrial COX1 and ND5 (NC_012920.1, table 2) and E. coli lacI (NC_000913.3, table 11).

Limitations

• Introns are not removed. Translate a spliced sequence (mRNA or CDS), not genomic DNA with introns.
• Special recoding is not modelled: selenocysteine at UGA, pyrrolysine at UAG, ribosomal frameshifts, and stop codons completed by polyadenylation in mitochondrial mRNAs.
• Input is limited to 2,000,000 characters. The codon view shows up to 6,000 codons and the ORF list up to 2,000 ORFs.
• An ORF is only a candidate: whether it is really translated depends on promoters, ribosome binding sites, splicing and other signals not checked here.

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