Figure 5—source data 1. | Splicing repression allows the gradual emergence of new Alu-exons in primate evolution

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

Figure 5—source data 1.

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 5—source data 1.List of Alu-exons across our datasets and UCSC annotation, including cross-species annotation.

We merged all Alu-exons identified from RNAseq data and annotated in UCSC (6731 exons), and filtered for non-overlapping exons. If any two exons overlapped, we retained the larger exon. This created a list of 6309 Alu-exons for which we selected the 3' splice site and mapped orthologues positions in four primate genomes. For each 3'splice site (if present), we predicted the splice site strength using MaxEntScan (Yeo and Burge, (2004) and searched for the longest U-tract within the Alu element. The table lists in order: Alu-exon co-ordinates (in hg19), and the annotation by UCSC as alternative or constitutive exon, if not present the exon is annotated as cryptic exon. Next, the furthest species in which we could identify the orthologous position, the exonisation group of the 3' splice site as defined in Figure 5 (see Materials and methods for details), the coordinates, repeat family, substitution group of the Alu element the exon arises from (in hg19), as well as the position, predicted strength of the 3' splice site and longest U-tract of the Alu element in human (hg19), in chimpanzee (panTro4), in gibbon (nomLeu1), in rhesus macaque (rheMac3) and in marmoset (calJac3). All 3' splice site positions start with the −2 position of the canonical 3' splice site (the AG nucleotide) consensus.

DOI: http://dx.doi.org/10.7554/eLife.19545.019

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