ORF vs. CDS

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

Moderators: honeev, Leonid, amiradm, BioTeam

Post Reply
notwhereuareat
Garter
Garter
Posts: 3
Joined: Tue Feb 12, 2008 3:09 am

ORF vs. CDS

Post by notwhereuareat » Tue Feb 12, 2008 3:17 am

Hello,

What is the difference between an open reading frame (ORF) and a coding sequences (CDS)?

Thanks.

blcr11
Viper
Viper
Posts: 672
Joined: Fri Mar 30, 2007 4:23 am

Re: ORF vs. CDS

Post by blcr11 » Tue Feb 12, 2008 10:12 am

An ORF is only a potential coding sequence. When you scan a sequence of DNA for potential genes, the software looks for reading frames that could code for peptides of at least some minimal cut-off length, say 20-50 residues. If you don't know what gene is actually expressed, all you can do is label the sequence as an ORF. Sometimes ORFs will get annotated as being similar to another known gene, but it will still be only a hypothetical gene.

notwhereuareat
Garter
Garter
Posts: 3
Joined: Tue Feb 12, 2008 3:09 am

Post by notwhereuareat » Fri Feb 15, 2008 12:22 am

So ORFs are potential and unverified protein coding regions whereas CDS would be for known and verified genes.

Thanks....

Cat
King Cobra
King Cobra
Posts: 635
Joined: Thu Feb 14, 2008 7:40 pm

Re: ORF vs. CDS

Post by Cat » Fri Feb 15, 2008 12:40 am

No. CDC means only that the sequence is known to be transcribed and, therefore, it is coding for something -- neither gene nor protein has to be known. Any full mRNA sequence (obtained from cDNA sequencing) will have a full coding sequence. ORF is usually predicted based on DNA sequence and not proven to be transcribed.

notwhereuareat
Garter
Garter
Posts: 3
Joined: Tue Feb 12, 2008 3:09 am

Post by notwhereuareat » Sun Feb 17, 2008 10:12 am

Okay that makes sense:

ORFs:
- The base sequence is determined directly from DNA, not cDNA
- They are potentially coding for something, but no confirmed that actually do or are transcribed

CDS:
- Usually determined from cDNA
- and thus are known to be coding for something

Thanks.

Post Reply

Who is online

Users browsing this forum: Bing [Bot] and 4 guests