Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.

This work was supported by the Agence Nationale de la Recherche (ANR 143683); the National Health and Medical Research Council (grant #1061906, #1080530, #1128175, #1126306). BS and EE were supported by grants BIO2014-52566-R from the MINECO (Spanish Government) and FEDER funds, by AGAUR (2014-SGR1121), and by the Sandra Ibarra Foundation for Cancer (FSI2013).