Evidence to expect given a designer

Could it be because the dna sequence that is responsible for producing cytB in both mice and yeast are partially transcribed to produce miRNA that have other regulatory functions specific to each organism?

Cytochrome C is used by almost all organisms. I would say that several other proteins/enzymes are almost universal. If every little biochemical reaction that takes place in a cell requires transcription and translation, an enormous amount of dna would be needed and would likely be unable to be stored and utilized in an efficient manner if every biochemical reaction corresponded to a single exact sequence of DNA. It would be much more effective , for example, if you designed some of these enzymes/proteins to function the same under numerous different amino acid sequences. Doing so would allow you to use the corresponding gene for purposes other than transcribing the RNA necessary for that particular enzyme/protein. That same gene could be transcribed with other genes, and then spliced thousands of different ways to produce thousands of different miRNAs.The tuna, pidgeon, horse, drosophila fly, rat and yeast all have different biochemical pathways from each other, and yet all of these pathways use cytochrome C at some time or another. Why not design cytochrome C in such a way that it can perform the same function in a myriad of amino acid sequences? If every animal listed above had a cytochrome C protein that would only function with a specific amino acid sequence, the corresponding gene would likely only produce cytochrome C, and be less likely to be used for other regulatory functions. This would be because you would not be able to put other sequences in it that could serve other functions. If you did, you would destroy the function the gene was mainly designed for.To summarize: cytochrome C from one organism fits in to the cellular machinery of many other organisms in order to cut down on DNA storage space. One to one correspondence of gene to protein product is wasteful and inefficient.

Nested hierarchies are manmade inventions. Cytochrome C was not designed to make it look like evolution occurred. Men see evolution when there is none. That isn't God's fault. You are going to have to show me how cytC produces nested hierarchies and how morphologies produce nested hierarchies before I can decide if they do indeed look the same, and if so, what reason would be behind it.

I didn't say any other proteins would be produced. I said micro RNAs would be produced. These micro RNAs are known to have regulatory function, mainly transcription regulation. As you know, which genes are transcribed and which ones are not, at any one time, make an enormous difference in cellular chemistry.

If every protein/enzyme was only produced by a single gene, you would have over 2 million genes. There are only about 20,000 human genes instead of 2 million. That is efficiency. That is only half the story. When these 2 million proteins have their corresponding genes and/or gene fragments transcribed, and how those RNA strands are spliced and refitted, and when those RNA strands are translated into proteins makes a huge difference in cell chemistry and possibly what kind of organism is created.What determines when a gene gets transcribed and when it is turned off is partly determined by micro RNAs. If you had a seperate gene devoted to turning on and off another single gene for all the genes in a human, more DNA space would be required.In short, a one to one gene to gene product correspondence would require an enormous amount of DNA space. Doing more transcription work in less space is efficient. Not doing so is inefficient.