Open reading frame

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In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of DNA beginning with a start codon, usually methionine (ATG), and ending with a stop codon (TAA, TAG or TGA in most genomes).[1] The transcription termination pause site is located after the ORF, beyond the translation stop codon, because if transcription were to cease before the stop codon, an incomplete protein would be made during translation.[2]

Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop codons.


One common use of open reading frames is as one piece of evidence to assist in gene prediction. Long ORFs are often used, along with other evidence, to initially identify candidate protein coding regions in a DNA sequence.[3] The presence of an ORF does not necessarily mean that the region is ever translated. For example in a randomly generated DNA sequence with an equal percentage of each nucleotide, a stop-codon would be expected once every 21 codons.[3] A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode a typical protein, where the codon usage of that region matches the frequency characteristic for the given organism's coding regions.[3] By itself even a long open reading frame is not conclusive evidence for the presence of a gene.[3]


If a portion of a genome has been sequenced, ORFs can be located by examining each of the three possible reading frames on each strand. Possible stop codons in DNA are "TGA", "TAA" and "TAG".

Sample sequence showing three different reading frames. Start codons are highlighted in purple, and stop codons are highlighted in red.

Six-frame translation[edit]

Since DNA has two anti-parallel strands, an additional three reading frames arise, giving a possible six frame translations.

Example of a six-frame translation

ORF finding tools[edit]


See also[edit]


  1. ^ Brown, T. A (2010). Gene Cloning and DNA Analysis: An Introduction. Wiley-Blackwell. ISBN 978-1-4051-8173-0. 
  3. ^ a b c d Deonier, Richard; Simon Tavaré, Michael Waterman (2005). Computational Genome Analysis: an introduction. Springer-Verlag. p. 25. ISBN 0-387-98785-1. 

External links[edit]

  • [1] - A web page where you can buy the book 'Gene Cloning and DNA analysis' by BROWN, T. A (2010)
  • Translation and Open Reading Frames
  • NCBI ORF finder - A web based interactive tool for predicting and analysing ORFs from nucleotide sequences.
  • ORF finder - A web based interactive tool for predicting and analysing ORFs from nucleotide sequences - hosted at
  • hORFeome V5.1 - A web based interactive tool for CCSB Human ORFeome Collection
  • StarORF - A multi-platform, java based, GUI tool for predicting and analyzing ORFs and obtaining reverse complement sequence