The expression of Per3 varies widely among the BXD family with differences that range from approximately twofold to fivefold depending on the specific probe set (Supplementary Table S2). Higher expression is invariably associated with the D allele; an effect seen most prominently in the 3′ UTR (1460662_at and 1421087_at), and the 3′ UTR and last three exons of Per3 (1421086_at) (Figure 1a). None of the probe sets overlap SNPs between D and B genotypes (SNPs will tend to increase the apparent expression of the B genotype; see ref. 46) Additional probe sets targeting introns are either not abundantly expressed (1442243_at) or overlap SNPs (1458176_at and 1441445_at) and were excluded from analysis (Figure 1a).
