Middleton, RobertGao, DadiThomas, AubinSingh, Babita, 1986-Au, AmyWong, Justin J.-L.Bomane, AlexandraCosson, BertrandEyras Jiménez, EduardoRasko, John E.J.Ritchie, William2017-05-232017-05-232017Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJ-L et al. IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biology. 2017;18:51. DOI: 10.1186/s13059-017-1184-41474-760Xhttp://hdl.handle.net/10230/32143Intron 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.application/pdfeng© The Author(s). 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.info:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/s13059-017-1184-4mRNA splicingIntron retentionGene regulationinfo:eu-repo/semantics/openAccess