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Obviously, the only way for one to be male is to inherit the Y chromosome, but are there alleles on the y chromosomes? Or is it just automatically the recessive trait without an allele.

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The question are there alleles on the y chromosomes is unclear. Here are two possible things you might mean

  • Is there genetic variation among individuals on the y chromosomes
  • Is there anything functional on the Y chromosome

Is there genetic variation among individuals on the y chromosomes

Yes, of course, there is genetic variation of the Y chromosome just like there is genetic variation other chromosomes. Talking about SNPs (Single Nucleotide Polymorphism) only, we have already detected tens of thousands of SNPs on the Y chromosome (see this page).

Is there anything functional on the Y chromosome

Yes! As an example, one of the most famous gene on the Y chromosome is the Test determination factor (as already indicated in a comment by @L.Diagio).

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