Fig. 2

Assigning CLN3 transcripts to the CLN3-NPIPB7 readthrough gene affects the accurate quantification of CLN3 in ENCODE long-read RNA sequencing data. A The CLN3, NPIPB7, and CLN3-NPIPB7 readthrough gene (ENSG00000261832) loci are shown according to their genomic coordinates from Ensembl 110. B The readthrough gene, ENSG00000261832, contains exons of CLN3 and NPIPB7. This plot shows representative transcripts of CLN3 and ENSG00000261832. Coding sequences are coloured by red for CLN3 and cyan for ENSG00000261832, grey boxes show the UTRs. Note, CLN3 transcript is present on the antisense strand, so it reads right to left. C Over 10% of CLN3 transcripts were assigned to the readthrough gene in selected ENCODE data, affecting the accurate annotation and gene-level quantification of CLN3. D The gene-level quantification of CLN3 and the readthrough gene ENSG00000261832 across nine ENCODE-defined organs are plotted. The readthrough gene has rather lower transcripts per million (TPMs) across all samples compared with CLN3