(A) Strategy for detecting allelic expression from RNA-seq data from 23 mouse tissues and developmental stages using Allelome.PRO. Every gene in the annotation is classified into one of seven different allelic expression categories indicated by different colors in the key and explained in the text. These colors are used in figures throughout the manuscript. The sex of the tissues is indicated by XX (female) and XY (male). Individuals were used except for indicated embryonic tissues where an entire litter was pooled (XX/XY). (B) Allelome.PRO classification of the allelic expression status of protein-coding genes in each tissue. (C) Allelome.PRO classification of non-coding genes. Tissues examined were placenta (Pl embryonic day (E) 12.5, E16.5), visceral yolk sac endoderm (VE E9.5, E12.5, E16.5), embryonic stem cells (ESC), mouse embryonic fibroblasts (MEF E12.5), embryonic liver (Li E12.5, E16.5), embryonic heart (He E16.5), embryonic and neonatal brain (Br E16.5, 3 days postnatal (dpn)), neonatal tongue (To 3dpn), adult brain (aBr), adult lactating female brain (lfBr), adult virgin mammary glands (vMG), adult lactating female mammary glands (lfMG), adult lung (aLu), adult leg muscle (aLM), adult heart (aHe), adult thymus (aTh), adult liver (aLi) and adult spleen (aSp). Embryo and placenta diagrams adapted from Hudson et al. (2011). Allelome.PRO settings: FDR 1%, allelic-ratio cutoff 0.7, minread 2.