The transcriptome and allele-specific expression analyses consistently detected higher expression for the D allele of Per3 relative to the B allele. This difference is accompanied by a large number of sequence differences between strains that inherit these alternative B and D alleles and haplotypes. By resequencing the Per3 gene we detected 163 SNPs that differentiated the B and D genotypes. The majority of these SNPs—142 of 163—are in introns. However, we detected four missense mutations, two of which are predicted by both SIFT and PolyPhen 2 to produce significant functional changes in the PER3 protein.
