What is the difference between Coding Sequences (CDS) and cDNA?

Are Coding sequences the sequences that is transcribed to mRNA and cDNA in contrast DNA obtained by reverse polymerization of matured mRNA?


2 Answers 2


The difference boils down to UnTranslated Regions. A CDS or coding sequence is the part of a transcript that is actually translated into protein. Therefore a CDS will (almost) always start with an AUG codon and stop at one of the three STOP codons (UAA,UGA,UAG).

The transcript however (note that I am referring to mature transcripts that have already been spliced so introns have been removed) will also contain the UTRs which are not actually translated into protein. A cDNA sequence is derived from the transcript by reverse transcription and will, therefore, also contain the 5' and 3' UTRs. For example, see this schematic diagram of an unspliced transcript:

enter image description here

The CDS of the gene depicted in image above will only contain the ATG, the STOP and the two green regions (exons). The cDNA will contain all that and, in addition, the two UTRs. Of course, both the cDNA and the CDS will not contain the introns.

  • $\begingroup$ Actually, exons include 5' UTR, CDS and 3'UTR. And CDS should not include STOP codon as it's not translated into an amino acid. Your diagram isn't very accurate with where you draw Exon 1 and Exon 2. $\endgroup$
    – olala
    Aug 5, 2016 at 21:42
  • $\begingroup$ @olala that's just a simple diagram to illustrate the existence of UTRs. Yes, of course they are exonic but that is not really relevant here. As for the CDS, no it also includes the stop codon. First because the stops are recognized by specific tRNAs, just like any other codon, and because that's the convention in the field. See, for example, the CDS described here: p53.iarc.fr/p53Sequence.aspx $\endgroup$
    – terdon
    Aug 7, 2016 at 10:37
  • $\begingroup$ i have to disagree on CDS and stop codon. If you look at at GTF format annotations, they listed stop codon separately from CDS, see an example from this post at the bottom of the page: mblab.wustl.edu/GTF22.html, also see this post Istvan's answer biostars.org/p/65162 $\endgroup$
    – olala
    Aug 8, 2016 at 17:12

The definition of coding sequence is, to my mind, a little confusing. It is actually the sequence of DNA in the gene which has the same sequence as the corresponding mRNA (except it has T instead of U). Now, you will often see definitions that say that the coding sequence is the DNA that is transcribed, but this isn't really correct because during transcription the RNA polymerase actually copies (transcribes) the other strand of the DNA (i.e. the one that is complementary to the coding sequence). And I would go one step further and say that the coding sequence excludes introns. You could also refer to the coding strand of the DNA, to encompass the entire transcriptional unit including introns as a way of referring to the strand which carries the coding sequence.

You are correct in your definition of cDNA (except its reverse transcription not reverse polymerisation). The the full-length cDNA sequence for a protein-coding gene will encompass the CDS but, as @terdon points out in his comment, will also include untranslated regions at the 5' and 3' ends.

  • $\begingroup$ so the difference in sequence to a given gene among its CDS and cDNA would be? $\endgroup$
    – Katz
    Nov 8, 2013 at 15:43
  • $\begingroup$ The CDS sequence is not identical to the cDNA sequence. That will only be the case for genes with no UTR regions. $\endgroup$
    – terdon
    Nov 8, 2013 at 17:56
  • $\begingroup$ Yes, @terdon is correct - I'm so protein-oriented I overlooked this. So the cDNA sequence will encompass the CDS. Will add a correction to the answer. $\endgroup$
    – Alan Boyd
    Nov 8, 2013 at 21:14

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