ORF vs. CDS

last updated by

notwhereuareat 16 years, 9 months ago

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- February 12, 2008 at 3:17 am #9093
  notwhereuareat
  Participant
  Hello,
  What is the difference between an open reading frame (ORF) and a coding sequences (CDS)?
  Thanks.
- February 12, 2008 at 10:12 am #81738
  blcr11
  Participant
  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.
- February 15, 2008 at 12:22 am #81840
  notwhereuareat
  Participant
  So ORFs are potential and unverified protein coding regions whereas CDS would be for known and verified genes.
  Thanks….
- February 15, 2008 at 12:40 am #81845
  Cat
  Participant
  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.
- February 17, 2008 at 10:12 am #81913
  notwhereuareat
  Participant
  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.
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