I am trying to convert exon start/end from genomic coordinates to protein. I have been using Ensembl-Biomart exon attribute: Genomic coding start/end. I assume that this one refers to the start and end of the exon of only of the coding region. So if for each gene I start from exon 1 and I start counting by three from Genomic coding start I should have an exact number of aminoacids (and then I can convert easily from genomic to protein coordinates). In other words ( Genomic coding start - Genomic coding end ) should be divisible by 3. However, it is not.
I have been trying to use CDS start/end cDNA start/end too, but same happens. Any clue on what is going on here? Thank you.