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Fig. 4 | Genome Biology

Fig. 4

From: Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways

Fig. 4

a Distribution of unannotated splice sites relative to the closest annotated splice site observed in analyzed libraries (solid colored lines). Gray dotted line: Frequency of available GT or AG dinucleotides surrounding the annotated 5′ (left) and 3′ (right) splice sites with open circles indicating in-frame positions and solid gray dots indicating out-of-frame positions. b Distribution of the ratio of unannotated alternative 3′ splice site use (RPMUnanno) over all events using the same 5′ splice site (RPMUnanno + RPMAnno) in each library type. (Left) Unannotated alternative 3′ splice sites at positions + 3, + 4, and + 5 relative to closest annotated 3′ splice site. Gray lines show how the top 15% (highest RPMUnanno) of unannotated junctions detected in EJC RIPiT-Seq libraries differ between library types. Results of one-way ANOVA and Tukey’s post hoc tests comparing EJC RIPiT-Seq to RNA-Seq libraries are indicated; ****P < 0.0001. (Right) Median [RPMUnanno/(RPMUnanno + RPMAnno)] values per library at the + 3, + 4, and + 5 positions. (Bottom) Sequence motifs for unannotated 3′ splice sites used at positions + 3, + 4, and + 5. Sequence logos were generated in R using ggseqlogo [28]; letter height signifies the relative abundance of that nucleotide at each position. N: number of splice sites contributing to each logo. Dashed lines indicate location of annotated (black) and unannotated (orange) splice sites

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