Expression of pseudoautosomal gene Mid1 in F1 hybrids. (A) Total expression in adult whole brains, quantified as transcripts per million (TPM), in all nine possible reciprocal crosses between CAST/EiJ, PWK/PhJ, and WSB/EiJ. Group assignments for several tests of differential expression are shown as color-coded dots beneath the x-axis, with corresponding adjusted P-values at right. (B) Aggregate allele-specific read depth over Ensembl-annotated exons of Mid1 (transcript ENSMUST00000112107) in F1 females (top row) and males (bottom row), with a CAST/EiJ X or Y chromosome. Maternal reads are shown above the horizontal axis and paternal reads below, shaded according to strain origin (green, CAST/EiJ; red, PWK/PhJ; and purple, WSB/EiJ). Vertical axis truncated at ± 200. (C) Transcript isoforms assembled from RNA sequencing read alignments in the parental strains compared to Mid1 transcript models from Ensembl, plotted in genomic coordinates. Gray dashed line shows canonical pseudoautosomal region boundary. (D) Same transcripts as (C), but drawn with introns compressed, exons to scale, and vertically aligned to facilitate comparison of splice sites. Coding region of Ensembl transcripts shown as tall boxes. CAST/EiJ splicing differences in exons corresponding to canonical exons 4 and 5 emphasized by light gray-shaded box.