Increased intron retention in wild-type T cells correlates with exon-skipping events in Ptprc . (a) Exons 4, 5 and 6 of the Ptprc (CD45) gene are alternatively spliced in T cells and may be combined to produce eight distinct CD45 isoforms. The longest isoform, CD45RABC, is primarily expressed in B cells whereas T cells express different CD45 isoforms through their development and activation. (b) RNA-seq data along the length of the Ptprc gene show the introns flanking alternative exons 4, 5 and 6 are covered by a greater depth of sequence reads and indicates incomplete splicing of these introns in both wild-type (WT; in red) and thunder (THU; in blue) CD8+ T cells. (c) Read depth over retained introns is consistent within biological replicate samples, but is different between wild-type (red) and thunder (blue) samples, as shown in the purple trace, which plots the wild-type minus thunder per nucleotide read depth through the alternatively spliced region of the Ptprc gene. Introns and exons are labeled as I- and E-, respectively, followed by their corresponding number. Thunder mutants with a hypomorphic Hnrpll gene show fewer reads aligned to introns 3, 4, 5, 6 and 7.