Fig. 3

Summary of identified CLN3 transcripts. A Data processing pipeline for ENCODE long-read RNA sequencing data is shown. B Valid transcripts are categorised based on transcript novelty, open reading frame (ORF) and untranslated region (UTR) novelty, coding potential and nonsense-mediated decay (NMD) prediction. Numbers of transcripts within different categories are shown in the bar plot. Bars showing the number of transcripts with novel ORFs are highlighted. C Top 15 CLN3 transcripts based on the number of samples in which they are detected (occurrence, left panel) are selected. The occurrence numbers are shown in the left panel, coloured by categories of these transcripts. The middle panel shows the structures of transcripts, the coloured taller boxes show the ORFs while the grey shorter boxes show the UTRs. The transcript usage is shown in the right panel. Note, CLN3 transcripts are present on the antisense strand, so read right to left. Transcription start sites (TSSs) and polyadenylation sites (PASs) signals are shown under the transcript structures, aligned by genomic coordinates. D Eight transcripts with the same ORF as the ‘major’ disease-associated transcript but different UTRs are detected. This plot shows the structural differences between these ‘major’ transcripts and the canonical CLN3 transcript “CLN3_24_438aa_5UTR_136_3UTR_49”. All grey boxes show structures of the ‘major’ transcripts, with taller grey boxes showing the ORF and shorter grey boxes showing the UTRs. The pink boxes show sequences in the canonical transcript but not in the ‘major’ transcripts, blue boxes show sequences in the ‘major’ transcripts but not in the canonical transcript