Fig. 2

Characterization of novel transcripts from long-read data in zebrafish embryos. A The heatmap represents the H3K4me3 signal distribution in the promoter region (± 3 kb) of the transcriptional start sites (TSSs) of annotated transcripts and the classical TSSs of novel isoform transcripts. The columns correspond to unfertilized, 2-cell, 128-cell, and 1 k-cell stages, respectively. B The heatmap represents the H3K4me3 signal distribution in the promoter region (± 3 kb) of the TSSs except for the classic TSSs in the novel isoform transcripts and the TSSs of novel gene transcripts. C The CAGE data of zebrafish at stage 1-cell, oblong, shield, 14–19 somites, prim-5, and prim-25 were compared with annotated TSSs, classical TSSs, novel TSSs belonging to novel isoforms, and novel gene TSSs. The blue bars represent the TSSs supported by CAGE data. Red bars indicate TSSs that CAGE data does not support. D An example of a novel isoform, located at positions 2,248,323–2,311,225 on chromosome 13. IGV view of the next-generation RNA-Seq alignment density, H3K4me3 peak, CAGE-seq capping site and reference genome annotation in novel isoform regions. The novel isoform was demonstrated by next-generation RNA-seq density, the H3K4me3 peak, and CAGE-seq capping site. E An example of a novel gene located at positions 989,552–1,015,458 on chromosome 1. IGV view of the RNA-Seq alignment density, the H3K4me3 peak, CAGE-seq capping site, and reference genome annotation in the novel gene region. The novel gene was also demonstrated by next-generation RNA-seq density, H3K4me3 peak, and CAGE-seq capping site. F Homology and domain annotation of novel coding transcripts. The significance threshold e-value was set to 1e − 5, and the blue points show that both BlastP and pfam were significant. The purple points indicate that only pfam was significant; the green points mean that only BlastP was significant, and none of the gray points were significant. G The scatter plot shows a conservation analysis of Novel lncRNA transcripts. The X-axis represents the maximum phastCons score for the 200-bp sliding window, and the Y-axis represents the fragment phyloP score for conserved bases. The significance threshold was set to the 95 th percentile of the randomized control-region scores. Blue plots mean both were significant; purple plots mean only phastCons was significant; green plots mean only phyloP was significant, and gray plots mean neither was significant