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

Attig J, Ruiz de los Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, König J, Ule J

Date Published: November 21, 2016

DOI: http://dx.doi.org/10.5061/dryad.7h81d

 

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Title List of exons and DEXseq analysis in RNAseq data set E-MTAB-6008.
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Description This data set was created using cufflinks and DEXseq, using Ensembl GRCh37 version 72 as input annotation. For detailled description, see associated publication. Columns included are genomic position, Ensembl transcript and exon ID, base mean across conditions, and statistical testing by DEXseq. Exon_class indicated if the exon is an Alu-exon, a cryptic exon, or not. UCSCoverlap and type indicate if the exon is annotated by UCSC, and if it is a constitutive or alternative exon. If the exon is not annotated in UCSC, it's called a cryptic exon. Stand_alone exons are not predicted by cufflinks to overlap with another exon. The table also includes the number of junction reads confirming either splice site. In addition, we predicted premature stop codons in protein coding genes; for PTC+ exons it includes the distance between the PTC and downstream exon-exon junction, the following (second) exon-exon junction, the number of downstream exons. The last two columns show the ID after merging all discovered Alu-exons with UCSC annotated Alu-exons, and the grouping of evolutionary groups shown in Figure 5 of the associated publication.
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When using this data, please cite the original publication:

Attig J, Ruiz de los Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, König J, Ule J (2016) Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. eLife 5: e19545. http://dx.doi.org/10.7554/elife.19545

Additionally, please cite the Dryad data package:

Attig J, Ruiz de los Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, König J, Ule J (2016) Data from: Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7h81d
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