Intron retention events in GETs. (A) Relative amount of transcript isoform classes based on GENCODE/Ensembl annotation in All-expressed transcripts and in GETs. (B) Schematic representation of intron retention event and its quantification using IRFinder to calculate the IRratio. (C) Representative retained-intron events of GETs compared to the nonretained-intron isoform. IRratios values are indicated for retained intron (RI) and neighbor intron (NI) (not-retained). (D) Distribution of IRratio values for neighbor introns and retained introns. Dashed line represents IRratio = 0.1. (E) Genome browser tracks of RNA-seq data at CENPT locus for the various gradient fractions. Dashed line indicates intron retention and accumulation of reads peaking in F3–F4. (F) RNA abundance throughout the gradient for CENPT isoforms. CENPT-233 is a retained-intron isoform and GET, whereas CENPT-235 is a fully spliced mRNA and not a GET.