Intron retention and candidate decoy exons in targeted erythroid genes. (A) Annotation of key features in IR regions of four prominent erythroid genes. (Top panel) Refseq gene annotations, lacking indications of intron retention isoforms or decoy exons predicted within the introns. For SF3B1, only the four most frequently spliced decoys are shown, from a total of six (Parra et al. 2018). Lower panels show a reannotation that includes predicted decoy exons (boxed), RNA-seq data from early stage (D9) and late stage (D15) erythroblasts, and phylogenetic conservation of the relevant gene regions. (B) 5′ splice site features of targeted decoy exons. Upper case, decoy exon sequence; lower case, downstream intron sequence. Vertical bars show 5′ splice site junctions identified in RNA-seq data from erythroblasts inhibited for nonsense-mediated decay. Shaded regions indicate regions targeted by antisense MOs.
