As per my knowledge prokaryotic genes are usually continuous only. CDS (Coding DNA sequences) are just the part of genes that functionally codes for the resultant protein or transcription factor. And yes CDS may also overlap because of the fact that many genes in the prokaryotes also show overlapping existence and they share a common promoter sequence for the transcription. As there is no introns in prokaryotes, so both CDS and the corresponding gene can also be present on the same coordinates.

@Satyabrata Yeah I agree totally with you.

But, how come a gene and CDS have same coordinates, that is what is making me sick. And it is not the case with one or two, there are many with such case. Is it a mistake with the NCBI Annotation System or is it that the definition of gene and CDS are more or less same.

Isn't it that a gene should have the promoter sequence and the terminator sequence along with the CDS. Then calling it a gene would be more apt. Then why is it that annotation systems annotate gene and CDS in the same way..? :(

@Manual

Why is it that annotation systems don't include promoters and terminators of a CDS in a gene? In such an annotation there is no differentiation between Gene and CDS

CDS is the protein coding region of a gene, so it obviously has the same coordinates as the gene. Another important feature is the transcribed region, that is CDS plus additional 5'- and 3' - UTR (untranslated regions) on both ends. Often the precise ends of the transcript are not known (cannot be predicted, have to be determined experimentally), or even there might be several initiation and termination sites. As for introns (additional non-coding regions within the CDS), they are very rare in prokaryotes, but they do exist (I seem to remember that the nitrogen fixation genes in A. tumefaciens have introns). Now the fact that this is annotated as a pseudogene is also important. I would suggest to search for homologues in the same or other species to see whether these introns are a general feature of this gene.

Concerning continuous genes. Even if the vast majority of genes in prokaryotes are continuous, there are a few introns. These introns are self-splicing and are akin to mobile elements (read on group I and group II introns if you want to find out more).

Ravi,

As said above, CDS is the coding sequence, and gene is the whole gene. You will notice the difference more easily (or at all) when you look at eukaryotic genes.

The CDS is therefore made of the parts of the sequence that will be in the protein, while gene contains introns and UTRs too, if defined. UTRs being relatively rarely defined in genomic sequences, it happens that start and end coordinates of CDS and gene features coincide, but it needs not to be the case.

As an example, look at this gene:

http://www.ncbi.nlm.nih.gov/nuccore/KF112870.1

Here, the coordinates of gene and CDS are not the same:

gene 1285..45402

CDS join(2073..2550,10331..10378,35742..35807,39696..39900,

40291..40354,44111..44227)

Also, refer to the NCBI definition (from http://www.ncbi.nlm.nih.gov/books/NBK21106/):

CDS

coding region, coding sequence. CDS refers to the portion of a genomic DNA sequence that is translated, from the start codon to the stop codon, inclusively, if complete. A partial CDS lacks part of the complete CDS (it may lack either or both the start and stop codons). Successful translation of a CDS results in the synthesis of a protein.

Notice they do not get into the hairy business of trying to define gene. ;-)

Cheers

J

Ravi,

Agree with Joao, the reason that UTR's and promoter regions are not included in most prokaryotic annotations is that the precise mapping is (still) largely missing; main technical problem is the unstable mRNA in bacteria.

My first advise is always: look at what you have in your hands!

Here it translates into: go and blast the intervening sequence (use a BLASTX), learn that it is either phage related or IS-related; then blast (use TBLASTN) your translation of the CDS and look at the results; they will tell you.

go ahead!

O