Fig. 3

(A and B) Genome browser tracks at the top of each panel show the intron (grey lines) / exon (yellow boxes) annotations of the different transcripts of the BAG1 (A) and UTP11 (B) genes according to ENSEMBL (original annotation) and according to the new transcriptome expanded by the long-read data (new annotation). Arrows denote the direction of transcription. The coverage of long (Nanopore) and short reads (Illumina) of the control (CTR) and SMG6/SMG7 double knockdown (dKD) samples is shown in dark blue. In the scheme underneath the genome browser tracks, constitutive exons are depicted by grey boxes, those that induce NMD by purple and light green boxes. The relative positions of primers used for splice-isoform-specific RT-PCR are shown by arrows. Agarose gels show the products of PCR reactions using the designated primers