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Eye color comes from a pigment called melanin; blue eyes have no melanin and brown eyes have lots in a part of the eye called the stroma. First, it is possible that very early in the pregnancy, one cell of the developing fetus had a change or mutation in an eye color gene. As the fetus developed, that cell gave rise to parts of the body that included one eye while the “normal” cells developed the other eye. This condition is called somatic mosaicism. Another possibility is that two fertilized eggs fuse together to form a single person (kind of like the reverse of twins). This is called chimerism after the mythological chimera. The difference between this and somatic mosaicism is that in chimerism, lots of genes are different instead of just the one. Finally, for genes to work, they must be turned on or expressed.There are well known cases where a gene is turned on in one cell and turned off in another part of the body. For example, the pigment gene is shut off in one eye and is on in the other. Reference Link: http://www.thetech.org/genetics/ask.php?id=26
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