This is not a stupid question at all. In fact, it is the subject of much active research. The short and extremely oversimplified answer is that a given gene wil

This is not a stupid question at all. In fact, it is the subject of much active research. The short and extremely oversimplified answer is that a given gene will produce approximately the same protein product no matter where it is in the genome, but the regulation of where and when and how much and under what conditions that protein is produced is highly dependent on the genomic context of the gene.