Editing Open reading frame (section)

{{Short description|DNA section marked with start and stop codon of different length}}
[[File:Sampleorf.png|thumb|600px|Sample sequence showing three different possible [[reading frame]]s. [[Start codon]]s are highlighted in purple, and [[stop codon]]s are highlighted in red.]]

In [[molecular biology]], '''reading frames''' are defined as spans of [[DNA]] sequence between the start and stop [[Codon|codons]]. Usually, this is considered within a studied region of a [[Prokaryote|prokaryotic]] DNA sequence, where only one of the [[#Six-frame translation|six possible reading frames]] will be "open" (the "reading", however, refers to the RNA produced by [[Transcription (biology)|transcription]] of the DNA and its subsequent interaction with the [[ribosome]] in [[Translation (biology)|translation]]). Such an open reading frame (ORF) may<ref name="Sieber_2018"/> contain a [[start codon]] (usually AUG in terms of [[RNA]]) and by definition cannot extend beyond a [[stop codon]] (usually UAA, UAG or UGA in RNA).<ref>{{cite web| vauthors = Brody LC |date=2021-08-25|title=Stop Codon|url=https://www.genome.gov/genetics-glossary/Stop-Codon|access-date=2021-08-25|website=National Human Genome Research Institute|publisher=National Institutes of Health}}</ref> That start codon (not necessarily the first) indicates where translation may start. The [[transcription terminator|transcription termination]] site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, an incomplete [[protein]] would be made during translation.<ref>{{Cite book | vauthors = Slonczewski J, Foster JW |title=Microbiology: An Evolving Science |location=New York |publisher=W.W. Norton & Co. |year=2009 |isbn=978-0-393-97857-5 |oclc=185042615}}</ref>

In [[Eukaryote|eukaryotic]] [[gene]]s with multiple [[exon]]s, [[intron]]s are removed and exons are then joined together after transcription to yield the final [[mRNA]] for protein translation. In the context of [[Gene prediction|gene finding]], the start-stop [[definition]] of an ORF therefore only applies to spliced [[Messenger RNA|mRNAs]], not genomic DNA, since introns may contain stop codons and/or cause shifts between reading frames. An alternative definition says that an ORF is a sequence that has a length divisible by three and is bounded by stop codons.<ref name="Sieber_2018">{{cite journal | vauthors = Sieber P, Platzer M, Schuster S | title = The Definition of Open Reading Frame Revisited | journal = Trends in Genetics | volume = 34 | issue = 3 | pages = 167–170 | date = March 2018 | pmid = 29366605 | doi = 10.1016/j.tig.2017.12.009 }}</ref><ref name="Claverie_1997a">{{cite journal | vauthors = Claverie JM | title = Computational methods for the identification of genes in vertebrate genomic sequences | journal = Human Molecular Genetics | volume = 6 | issue = 10 | pages = 1735–44 | date = 1997 | pmid = 9300666 | doi = 10.1093/hmg/6.10.1735 | doi-access = free }}</ref> This more general definition can be useful in the context of [[Transcriptomics technologies|transcriptomics]] and [[metagenomics]], where a start or stop codon may not be present in the obtained sequences. Such an ORF corresponds to parts of a gene rather than the complete gene.