Allele-resolved isoform expression and sequences. (A) Computational strategy for determining allele-resolved isoforms. (B–E) SNHG5, HLA-A, HLA-DPA1, and HLA-DRA gene loci are shown in a genome browser view. GENCODE annotation (top), Mandalorion isoforms (center), and allele-resolved R2C2 reads (bottom) are shown. Direction of shown features is indicated by color (“top strand”: blue, “bottom strand”: yellow). Mismatches of R2C2 reads to the genome reference are shown in black. Both HLA-A and HLA-DPA show allele-resolved differential expression of isoforms with alternative poly(A) sites. (E) Red arrows indicate allele-specific variants in the HLA-DRA gene.