All cells in an organism have the same genome, so all segments of an organism do have the same master genes. What’s important is when and where they are turned on during development.
If a gene is at the ‘top’ of a regulatory pathway, it can influence other genes further down the pathway. If there is a problem with a gene, the further up the pathway it is, the more widespread its effects will be. If a gene that’s important for many different segments of an organism is damaged, then all of those segments will be damaged.
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