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.