Figure 4—figure supplement 2. | Splicing repression allows the gradual emergence of new Alu-exons in primate evolution

Open accessCopyright infoDownload PDFDownload figures

Splicing repression allows the gradual emergence of new Alu-exons in primate evolution

Figure 4—figure supplement 2.

Affiliation details

UCL Institute of Neurology, United Kingdom; MRC-Laboratory of Molecular Biology, United Kingdom; Institute de Biologie de l’ENS (IBENS), CNRS UMR 8197, France; University College London Genetics Institute, United Kingdom; Goethe University Frankfurt, Germany; Institute of Molecular Biology (IMB), Germany
Figure 4—figure supplement 2.
Download figureOpen in new tabFigure 4—figure supplement 2. Features of Alu-exons grouped by substitution rate.

All Alu-exons in protein-coding genes that were validated by junction-spanning reads at both the 5' and the 3' splice site (SS; 798 exons in total, were stratified by the number of substitutions from the Alu consensus sequences annotated by RepeatMasker (Smit et al., 1996-2010), as proxy for evolutionary age (A) The maximum entropy score of 5' and 3' splice sites of each exon was predicted based on nucleotide sequence (Yeo and Burge, 2004). The correlation between substitutions and splice site score was tested by a linear model, *** indicates p-value < 0.001. For comparison, the distribution of silent Alu elements is shown in grey; for visualisation, the lower whisker of the silent Alu elements is cut-off at −4. Actual lower whisker values are −7.9 at 5' SS and −13.2 at 3' SS. (B) The length of the U-tract at the 3' splice site of each Alu-exon is shown. For comparison, we show the length of the longest U-tract in silent Alu elements (‘silent’ Alu elements, i.e. non-exonising). Only U-stretches within Alu elements were considered. Thirteen of 798 Alu-exons were removed in (C) because no U-tract of at least three nucleotides was found in the Alu element sequence upstream of the 3' splice site. These exons are likely to utilise a polypyrimidine tract in the close-by genomic sequence. (C) Alu-exons arising from highly diverged Alu elements are not depleted of PTCs. Shown is the number of Alu-exons in each group, which do or do not contain a PTC, or potentially cause a frame-shift, as well as those which are outside of the coding region of the transcript.

DOI: http://dx.doi.org/10.7554/eLife.19545.017