Altered mRNA splicing between wild-type and mutant Hnrpll CD8+T cells validated with RT-PCR. A selection of ten genes that ranked highly in one or more tests for differential alternative splicing in Hnrpllthu T cells were validated using RT-PCR. Six genes showed differential PCR bands between samples and are show alongside an ideogram of the inferred sequence included in each product, determined from band sizes and the expected included sequence indicated by RNA-seq junction read information. (a) Ptprc gene, oligonucleotide PCR primers located in exons 2 and 7, amplifying across the regions of alternative exons 4, 5 and 6. (b) Senp2 gene, primers located in exons 8 and 11, amplifying the intron between exons 10 and 11 containing a variably included unannotated or cryptic exon. The sequence of each band in the accompanying ideogram was confirmed by Sanger sequencing. (c) Ctse gene, primers located in exon 1 and 2, amplifying unannotated exon in intron 1. (d) Trpv2 gene, primers located in exons 1 and 3 to amplify unannotated exons in introns 1 and 2. (e) Ash1l gene, primers located in exons 20 and 21, spanning variably included unannotated exon in intron 20. (f) Slc12a7 gene, primers located in an alternative first exon, such that preference to the other first exon there would be no product. (g) Lck gene, primers were designed with a forward primer spanning across exons 1 and 4 and a reverse primer in exon 5, amplifying products of exon 1 and 4 joining (skipping exons 2 and 3) with variable length of exon 4. Oligonucleotide primer locations are displayed against read depth and gene intron/structure in Figure S2 in Additional file 4. WT, wild type.