PEIJ_PIEJ DB: A Putative Database for Intron Retention

Abstract

Abstract Unlike exon skipping, intron retention is another type of important mechanism of alternative splicing in higher eukaryotes. Although high throughput tandem (MS/MS) mass spectrometry provides extensive information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets, the possibility to identify alternative splicing events through tandem mass spectrometry relies on the database with which the spectra will be searched. In this research, the previous putative exon-exon junction database (PEEJ DB) aimed at and specified for putative exon skipping events in all kinds of alternative splicing studies is extended and a theoretical exon-intron junction and putative intron-exon junction database (PEIJ_PIEJ DB) to account for all possible exon-intron (or intron-exon) combinations and all possible intron internal retention events for every gene in the human genome from the EnsEMBL core database has been built up.Application of the constructed PEIJ_PIEJ DB to non-ETS gene fusion sequences in human prostate cancer RNA-Seq data demonstrates the putative exon-intron junction and putative intron-exon junction database (PEIJ_PIEJ DB) can identify intron retentions with reliable confidence in the non-ETS gene fusion sequences, suggesting that this putative database is helpful for scientific researchers in alternative splicing studies involving intron retention events from high-throughput experimental datasets such as proteomics datasets and next generation sequencing ones. The sourcecode implementing the database is freely available at https://sourceforge.net/projects/peij-piej.