ORF vs. CDS

[notwhereuareat]

Hello,

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

Thanks.

[blcr11]

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]

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

Thanks....

[Cat]

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]

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.