Jan 29, 2016

Human splicing diversity across the Sequence Read Archive

BioRxiv : the Preprint Server for Biology
Abhinav NelloreJeffrey T Leek

Abstract

We aligned 21,504 publicly available Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. 56,865 junctions (18.6%) found in at least 1,000 samples were not annotated, and their expression associated with tissue type. Newer samples contributed few novel well-supported junctions, with 96.1% of junctions detected in at least 20 reads across samples present in samples before 2013. Junction data is compiled into a resource called intropolis available at http://intropolis.rail.bio. We discuss an application of this resource to cancer involving a recently validated isoform of the ALK gene.

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Mentioned in this Paper

Steroid receptor RNA activator
Exons
Histocompatibility Testing
Rallidae
Nuclear mRNA Cis Splicing, via Spliceosome
Reading Frames (Nucleotide Sequence)
RNA Splicing
Molecular Genetic Technique
Protein Isoforms
Gene Annotation

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