ArticleGenome biology2017
IRFinder: assessing the impact of intron retention on mammalian gene expression.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 187 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
187 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing.RNA (New York, N.Y.) · 2020Pooled it
- G970R-CFTR Mutation (c.2908G>C) Results Predominantly in a Splicing Defect.Clinical and translational science · 2021Trial
- The insulin/IGF axis is critically important for controlling gene transcription in the podocyte.eLife · 2026Article
- iMPI: An Integrative Database for MicroProteins Encoded by Intron Retention in Tumors.Proteomics · 2026Article
- Loss of cellular RNA homeostasis contributes to MDA5 activation during virus infection.Nature immunology · 2026Article
- Vitamin BNature communications · 2026Article
- Intermittent fasting rewires tissue-specific gene-transposable element regulatory networks.PNAS nexus · 2026Article
- The minor spliceosome component U4atac regulates JAK/STAT signaling to modulate hematopoiesis and immune responses in Drosophila melanogaster.Nature communications · 2026Article
- The competition between splicing and 3' processing shapes the human transcriptome.Genes & development · 2026Article
- Gene expression is stable despite widespread cis and trans regulatory divergence inbioRxiv : the preprint server for biology · 2026Article
- Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation.Genome research · 2026Article
- Alternative splicing-triggered mRNA decay informs splice-switching targets for neurodevelopmental disorders.The Journal of clinical investigation · 2026Article
- Article
- Elucidating the functional dynamics of DNASE1L2 intron retention in tuberculosis progression.Chinese medical journal · 2026Article
- Intron Retention Controls Localization of lncRNAsbioRxiv : the preprint server for biology · 2026Article
- Charting the multilevel molecular response to palbociclib in ER-positive breast cancer.NAR cancer · 2026Article
- RNA localization to nuclear speckles follows splicing logic.Nucleic acids research · 2026Article
- A conserved Lsm8-exosome module maintains RNA splicing fidelity to control fungal stress adaptation and virulence.Stress biology · 2026Article
- Neurofibromin 1 (International journal of molecular sciences · 2026Article
- Review
127 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.