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In viable yellow agouti mice, a transposable element inserted into the agouti gene drives ectopic agouti expression. This leads to various phenotypic effects, including yellow coat color. Individual variability in CpG methylation at this locus causes differences in coat color among genetically identical heterozygous viable yellow agouti littermates, as shown here. Maternal nutrition affects the phenotype of viable yellow agouti offspring by influencing the degree of CpG methylation at the agouti locus.