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Fig. 5 | Genome Biology

Fig. 5

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

Fig. 5

a Regions used to calculate MaxEnt and mean conservation scores surrounding unannotated alternative 3′ and 5′ splice sites and new introns (top) or new cassette exons (bottom). b, c Scatterplots comparing MaxEnt scores to mean conservation scores (phyloP, 30-way) at 5′ (left) or 3′ (right) splice sites for b annotated and random or c observed unannotated events. Smaller points are used to represent splice sites with either score lower than 0 as these may result from splicing noise. Annotated splice sites were downsampled by random selection (5′, N = 2268; 3′, N = 2693; same as unannotated splice site numbers in c from the 159,335 observed in our libraries. Additional file 1: Figure S4A shows the same plot for all observed annotated splice sites. b also contains 2268 random GT-containing (left) and 2693 random AG-containing (right) sites; identical plots for four additional sets of randomized locations are shown in Additional file 1: Figure S4B. The top 5% mean conservation scores of random sites is indicated and marked by a dashed line. Genes for which genome browser tracks are shown in panels d and e and in Additional file 1: Figure S5A and B are indicated. d, e Genome browser tracks of library coverage across CNOT1 (d) and EEA1 (e). Annotated transcripts are shown in gray and unannotated alternative 3′ splice site use in orange. Conservation tracks and annotations are as in Fig. 1b–d

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