Xenbase Image ID: 138113

Figure 2. Analysis of Alternative Splicing in tra2b Morphants Shows Intron Retention as the Most Common Splice Change (A) Outline of the RNA-seq analysis pipeline. Condition-specific transcript assemblies are merged with JGI annotation, resulting in an augmented transcriptome assembly that forms the basis for DEXSeq testing of differential exon expression. (B) Table showing the number of novel transcripts found in this study and the number of significant splice changes in tra2b morphants. (C) RNA-seq reads from X. tropicalis control and morphants in tra2b locus show MO-induced intron retention (RI, blue box) and an increase in variable exon 2 (black arrow). (D) DEXSeq output showing fitted splicing (a proxy for the number of reads aligned) across all exonic regions. Control (black) and morphant (red) exon expression is similar except for the variable exon 2 and MO-induced retained intron, where the graphs diverge. Both events are significant (purple exons indicate adjusted p < 0.05). (E) Alternative splicing changes in morphants grouped by category show RI (red) as the most common event, followed by skipped or included exons (ESI, yellow). (F) A plot of individual alternative splicing events shows that retained introns are always included in morphants, whereas ESI events in all but two instances are included in normal embryos. (G) Most of the alternative splicing events detected are novel and are not described in the annotation. See also Figure S2 and Tables S1 and S2. Image published in: Dichmann DS et al. (2015) Copyright © 2015. Image reproduced with permission of the publisher and the copyright holder. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. Larger Image Printer Friendly View

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