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-   -   CDS vs cDNA (http://seqanswers.com/forums/showthread.php?t=17199)

s13ep 01-29-2012 11:29 AM

CDS vs cDNA
 
Hi everyone,

I need a help please. I need to verify my understanding of the difference between cDNA and CDS.

From the definition, CDS is a region of nucleotide that corresponds to the sequence of aa in the predicted protein . The CDS contains start & stop codon and does not include any UTR and introns. Therefore, CDS does not correspond to the actual mRNA sequence.

On the other hand, cDNA is the DNA version of mature mRNA (ie, does not include introns, but include the UTR, such as Kozak sequence etc).

Am I right?

One of the web that I was reading (I forgot which one, but it's a reliable source) mentions that CDS should start with a start codon. However, when I was browsing through NCBI, one of the nucleotide sequences of a protein that I found says "complete cds" does not start with ATG. And this nucleotide sequence does not correspond to the translated protein seq (from the same author). Why is that?

Any help is appreciated. Thank you so much.

regards,
:o s13ep

pmiguel 02-04-2012 12:18 PM

Quote:

Originally Posted by s13ep (Post 63157)


On the other hand, cDNA is the DNA version of mature mRNA (ie, does not include introns, but include the UTR, such as Kozak sequence etc).

Am I right?

Yes.

Quote:

Originally Posted by s13ep (Post 63157)

One of the web that I was reading (I forgot which one, but it's a reliable source) mentions that CDS should start with a start codon. However, when I was browsing through NCBI, one of the nucleotide sequences of a protein that I found says "complete cds" does not start with ATG. And this nucleotide sequence does not correspond to the translated protein seq (from the same author). Why is that?

Hard to say without know which CDS you refer to. While ATG is a very common start codon, it is not universally utilized. Bacteria, especially, will use others. See this for some additional information.

--
Phillip

Jerry_Zhao 02-13-2012 12:38 PM

CDS means coding sequences. It is start from the transcription start site to the end site.
The "CDS" in your posts might be ORF, open reading frame, which is start from the ATG to the stop codon.

In my opinion, the CDS in database is the longest/most abundant one of all the cDNAs/mRNAs transcribed from the particular gene.

steven 02-17-2012 10:21 AM

Quote:

Originally Posted by Jerry_Zhao (Post 64736)
CDS means coding sequences. It is start from the transcription start site to the end site.

I think that this is the transcription unit. As said above, a CDS starts from the start codon and ends at the stop codon. UTRs are transcribed but not coding and therefore do not belong to the CDS.

Quote:

Originally Posted by Jerry_Zhao (Post 64736)
The "CDS" in your posts might be ORF, open reading frame, which is start from the ATG to the stop codon.

ORF is a sequence with no in-frame stop. You typically have several ORFs in any mRNA. Considering the 3 (or 6 if you don't know the strand) possible phases the CDS is often the longest ORF, but not always.
Most of the CDS in human do start by an ATG. See pmiguel's post and link.

billstevens 04-20-2012 03:19 PM

In regards to RNA-seq, the difference between CDS and exon however is that the CDS does not include the UTR, but the exon does right?


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