I apologise for the basic molecular biology question but I've been away from this area for quite a while. I was looking at a gene today and noticed that it had different exon boundaries for its splice variants. I had always thought splice variants had the different combinations of the same exons (e.g. splice variant 1 might contain exons 1,2 and 4, splice variant 2 might contain exons 1, 3 and 4). Sometimes you also get intron retention where you get a 'exon' which might be exons 1 and 2 plus the intron between them. In my mind I have a model of making plug and play proteins from different exon combinations
i was a little surprised to find an exon which had different start and end points in different transcripts of the gene. I thought this might still be ok if the exons are still translated from the same starting point and/or have the same reading frame. When I inspected it closer the exon was not translated in either transcript so the gene was still consistent my plug and play model. But this then begs the question, do you ever find genes where exons are translated in different reading frames. This would give a totally different protein sequence in the splice variants. I've never heard of this but that doesn't mean it hasn't been discovered in the ten years since I studied this!