Random monoallelic expression in the mouse genome. (a) Assessed genes. Based on the identity of SNP probes present on the array and the genotypes of mice used, a total of 4,361 genes contained at least one heterozygous assessable SNP within exons or introns. The actual number assessed (shown in grey) was lower, since not all genes were expressed in the given cell type and not all SNPs passed the stringent quality control filters, which maximize specificity at the cost of sensitivity. Among these 1,358 assessed genes, 212 demonstrate random monoallelic expression (RMAE; dark green is RMAE class I, light green is RMAE class II, yellow is biallelic expression). The mean number of SNPs assessed per gene is 1.53 and the most common number of SNPs assessed per gene (mode) is 1. (b) Map of assessed genes on the mouse autosomes. Biallelic and RMAE genes identified in this study are located throughout the autosomes. Yellow indicates biallelic genes, light green represents class II RMAE genes and dark green indicates a class I RMAE gene. (c) Individual clones show unique patterns of monoallelic expression. A representative autosome, chromosome 2, is shown - all autosomes show a similar diversity of expression states. There is no coordination along the chromosome in terms of the direction of monoallelic expression. Individual clones show distinct patterns of allelic expression along the length of the chromosome, including biallelic expression.