Fig. 6.

Novel isoforms of existing genes with six different types of novel junctions. The genome browser setting is the same as in Fig. 2D. The GENCODE annotation is in the dark blue track. The novel junction uses are highlighted by a pink dashed box and are not reported by existing annotations but are supported by both long reads and short reads. Other: a novel exon in novel isoform TMEM142.2 is detected with two novel flanking junctions that are categorized in the “Other” group in Fig. 2C. InterG: A novel junction in novel isoform INO80C.1 is categorized as “intergenic proximal” junctions from annotated genes, but is a 3′-end junction of a novel isoform of INO80C (note that this gene is in the reverse strand). IR: A novel junction in novel isoform YTHDF1.1 indicates a splice within an annotated exon; i.e., the RefSeq annotation has a retained intron relative to YTHDF1.1. N3S: A novel junction in novel isoform MBD1.1 has a novel 3′-splice site (note that this gene is in the reverse strand). N5S: A novel junction in novel isoform TTC32.1 has a novel 5′-splice site (note that this gene is in the reverse strand). ES: Novel isoform HSD17B14.1 contains a novel junction that skips an annotated exon.