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)[reply]

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)[reply]

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)[reply]

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)[reply]

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)[reply]