Talk:Open reading frame

Template:WikiProject Geneticsfixed the notion that there is difficulty in reading possible ORF's in eukaryotic mRNA. It is normally monocistronic, so usually only a single ORF is contained therefore looking for the longest possible gene sequence between a start and stop codon should give you the correct amino acid sequence. Active contributor 17:27, 20 March 2007 (UTC)

This isn't rigorously true at all... the 'largest possible gene sequence between a start codon and a stop codon' would almost never give you the correct amino acid sequence. The 'largest possible gene sequence between a start codon and a stop codon' would include many downstream genes.24.240.37.200 (talk) 02:34, 28 October 2010 (UTC)

ORFs do not imply a protein

It is very important to note that not all ORFs ever encode a protein. There are ORFs within ORFs depending on the reading frame you look at. There are ORFs in non-coding regions of the genome. ORFs simply mean that you have a start codon and a stop codon in the same reading frame. They can be used as an initial filter to find potential genes, but many ORFs found this way are false positives. Any good gene finding algorithm looks at much more than just whether or not there is a stretch of DNA in the same reading frame with a start followed by a stop codon.

The meaning of the word "open"

Is there any source for the meaning of the word "open"? -Huggie (talk) 11:10, 28 October 2009 (UTC)

ORF without stop codon!?

The article claims that the "open" in ORF means that there is no stop codon. Surely this is incorrect! An ORF as far as I know extends from a start to a stop codon. So if in the example only one of the three frames has a stop codon then that one is the only ORF - right?

[1] which is even referenced in the article also says: "An open reading frame starts with an atg (Met) in most species and ends with a stop codon (taa, tag or tga)."

--203.109.144.209 23:11, 16 May 2007 (UTC)

An ORF must contain both a start and stop codon, so none of the examples provided are necessarily open, but number 1 probably is, since there is likely a stop codon downstream that is not shown. Number three might be as well, but the beginning of an ORF and the reading frame is defined by a start codon, so it is meaningless just to talk about in-frame stop codons.24.240.37.200 (talk) 02:48, 28 October 2010 (UTC)

ORFs do not begin at start codons

Yes, the article is incorrect, on several points. The "open" means that there is no stop codon encoded in the frame.

The earliest citation I can find is that an open reading frame is "a long run of amino acid codons before the appearance of a terminator codon" R.F. Doolittle, Of URFs and ORFs, 1986; a start codon is not required for the definition of an ORF. The citation [2] above also ignores the real possibility that a start codon other than ATG may be used. In addition, the exons of a eukaryotic gene, after the first exon, although they do not (necessarily) contain a functioning in-frame start codon, are also contained within ORFs.

An ORF is simply a contiguous section of nucleotide sequence that when, read in frame, contains no stop codons.

A portion of a reading frame that runs from a start to a stop codon is just a (putative) coding sequence (CDS, which page incidentally also provides an incorrect definition of coding sequence). Note that since many eukaryotic genes are intronic, you may not find a contiguous run from a start to a stop codon, and not all portions of a gene are necessarily used for coding (splice variation), nor must they all lie in the same frame.

143.234.97.119 (talk) 08:17, 20 October 2008 (UTC)

I've looked through a bunch of different sources and the only common thread I can find is that a) it appears to encode a protein and b) it is not interrupted by start or stop codons. As you say, alternate splicing might ignore the apparent stop codon, but the preceding sequence would still be considered an open reading frame. I'm not sure whether the start/stop codons would be considered part of the ORF, but they definitely don't have to be there. It's all very vague, one definition for example says that an ORF "begins with" and "ends with" an initiation codon and ends with a termination codon. Then again, a gene technically does not have to include stop/start and so really the only difference between a CDS and an ORF is that a CDS encodes a known polypeptide and an ORF is just a sequence which is presumed to. I agree that the wikipedia definition of CDS isn't much good. It would be awesome if anyone could clarify all this. Master gopher (talk) 07:31, 19 August 2009 (UTC)

Open reading frames are defined in terms of the stop codon. They are simply the reading frames that are "open"-- through which a ribosome could pass. A start codon cannot "interrupt" a reading frame because it would just be read as Met. The oldest use of the term that I can find is this one [3], though I would guess that the term originates with Crick or his colleagues[4].173.75.148.131 (talk) 04:05, 25 May 2010 (UTC)

Really?

An ORF must contain a start codon, which defines the reading frame, and necessarily ends at a stop codon. Example 2 at the bottom of the introduction to the current revision of the article is not in frame.24.240.37.200 (talk) 02:34, 28 October 2010 (UTC)

If ORFs had no in frame stop codons, proteins would rarely be terminated. Excision of introns must be accounted for in locating an in-frame stop codon. It may not be in-frame prior to excision, but must be afterwards. All coding sequences are ORFs, and all ORFs are putative coding sequences.24.240.37.200 (talk) 02:51, 28 October 2010 (UTC)