Hi, I have googled a lot about this query but I could not find a suitable answer.
I downloaded some genomes from NCBI; predicted and annotated genes by prokka. But later, I found that there are few genomes that have 2-3 CDS regions of the same gene while other genomes have the same full-length gene (1245bp) with one CDS. I have aligned them by using MAUVE and figured out that these CDS are parts of one gene. (Further, I have also done blast to confirm this.)
My question is:
- Why there are multiple CDS regions in one gene? (While all other genomes having this gene as intact or one CDS)
- If this is not a gene prediction problem then what it could be?
Sorry, I couldn't upload the MAUVE aligned figure for further clarification.
thanks
Awan
Yes, you are right there are stop codons at the end of each these newly formed CDS. But why there are newly formed stop codons? Thanks, I will definitely find out the functional ability of this protein.
As I said: mutations.