I'm not an expert on protein folding, but here goes:
protein folding is not always guaranteed to end up being the same everytime even if its AA sequence is the same. Take example prions, which has perfectly normal AA Sequences despite the fact that it is infectious. There are a few protein-folding enzymes that can be regulated via gene expression.
But as for the genetic transcripts responsible, every eukaryotic gene has a basal promoter and possibly an upstream promoter. The basal promoter should be the same in all circumstances because that's what the GTF's need to bind to. The upstream promoter's sequences can vary. Also, most transcription start only with AUG coding for methionine, so there really shouldn't be different products in different places if the gene is the same.