ORF finder
Every open reading frame on both strands, with coordinates and the protein.
Every open reading frame on both strands, with coordinates and the protein.
An open reading frame is a run of codons from a start codon to the next in-frame stop codon. This tool scans all three frames of your sequence and, by default, all three frames of its reverse complement, and lists every ORF longer than the minimum you set, with its strand, frame, coordinates and translated protein. It is the quickest way to find the gene in a raw sequence, check that a cloned insert is intact, or see what a stretch of unknown DNA might encode. Use the six-frame translation to see the frames side by side, and the DNA to protein translator once you know which frame you want.
In ATG-to-stop mode each ORF runs from the first ATG after the previous stop to the next stop in the same frame; that is the longest ORF for each stop and the way NCBI ORFfinder reports them. In stop-to-stop mode the ORF is the entire open stretch between two stops, whatever codon it begins with, which catches bacterial genes with GTG or TTG starts and coding sequences whose beginning lies outside your sequence. An ORF that reaches the end of the sequence without a stop is kept and marked. Lengths in nucleotides include the stop codon; lengths in amino acids do not.
That is why the minimum length matters. Short ORFs arise by chance in any sequence, and a 25-amino-acid threshold, the NCBI default, removes most of them. An ORF of a hundred codons or more with no stop is very unlikely to be chance, especially in GC-rich DNA, where stops are rarer still because all three stop codons are AT-rich.
Positions are 1-based on the forward strand as pasted. A forward ORF has start < end. A reverse-strand ORF is reported with its start at the higher coordinate and its end at the lower, because it is read right to left, and its frame is −1, −2 or −3 counted from the 3′ end of the pasted sequence. Select an ORF in the table to see its protein.
Start and stop codons follow the genetic code you choose, so in the vertebrate mitochondrial code TGA is read through as tryptophan and AGA and AGG end the frame. IUPAC ambiguity codes are translated when every reading agrees and shown as X otherwise; an ambiguous codon never counts as a start or a stop. U is read as T, and each record of a FASTA file is scanned separately.
A stretch of DNA that can be read as codons from a start codon to a stop codon without any stop in between. Every protein-coding gene contains an ORF, but not every ORF is a gene; short ORFs occur by chance in any sequence.
It depends on what you are looking for. Random sequence produces ORFs of up to about 30 codons quite often, so 75 nucleotides (25 amino acids), the NCBI ORFfinder default, filters most noise in short sequences. For whole-genome scans 100 amino acids is common. Lower the threshold when hunting small peptides.
ATG-to-stop reports ORFs that begin at a methionine codon, which is how most genes start. Stop-to-stop reports the whole open stretch between two stops regardless of start codon, which is useful for bacterial genes with alternative starts such as GTG and TTG, and for sequences whose 5′ end is missing.
Coordinates are always given on the forward strand as you pasted it, with the strand marked − and the frame numbered −1 to −3. The start position of a reverse ORF is therefore the higher coordinate, because the gene runs right to left on the pasted sequence.
Because the sequence ends before a stop is reached. Such ORFs are marked as running off the end. They are common in partial sequences, reads and PCR products, and mean the real gene may continue beyond your sequence.