ArticleNAR genomics and bioinformatics2021
Assessing the functional relevance of splice isoforms.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 48 citations in OpenAlex.
- IRCAS: a novel end-to-end approach to identify, rectify, and classify comprehensive alternative splicing events in a transcriptome without genome reference.Briefings in bioinformatics · 2026Article
- Disease-associated genetic variants can cause missense effects in tissue-specific protein isoforms.Nature communications · 2026Article
- VGLUT1 and PSD-95 Expression Remains Stable in the Prefrontal and Cerebellar Cortices of the VPA Autism Rat Model.Developmental neurobiology · 2026Article
- Cataloging the potential functional diversity of Cacna1e splice variants using long-read sequencing.BMC genomics · 2025Article
- Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain.Genome biology · 2025Article
- LincRNA-ASAO promotes dental pulp repair through interacting with PTBP1 to increase ALPL alternative splicing.Stem cell research & therapy · 2025Article
- Conservation assessment of human splice site annotation based on a 470-genome alignment.Nucleic acids research · 2025Article
- Conservation assessment of human splice site annotation based on a 470-genome alignment.bioRxiv : the preprint server for biology · 2025Article
- Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain.Journal of molecular neuroscience : MN · 2025Article
- Transcriptomic Profiling Provides Insight into the Molecular Basis of Heterosis in Philippine-RearedInsects · 2025Article
- Discovery and characterization of a novel telomerase alternative splicing isoform that protects lung cancer cells from chemotherapy induced cell death.Scientific reports · 2025Article
- Toward a comprehensive profiling of alternative splicing proteoform structures, interactions and functions.Current opinion in structural biology · 2025Review
- GENCODE 2025: reference gene annotation for human and mouse.Nucleic acids research · 2025Article
- Human introns contain conserved tissue-specific cryptic poison exons.NAR genomics and bioinformatics · 2024Article
- Steering research on mRNA splicing in cancer towards clinical translation.Nature reviews. Cancer · 2024Review
- IsopretGO-analysing and visualizing the functional consequences of differential splicing.NAR genomics and bioinformatics · 2024Article
- The rapid degradation of translated upstream regions points to an inefficient translation initiation process.bioRxiv : the preprint server for biology · 2024Article
- Profiling genetically driven alternative splicing across the Indonesian archipelago.American journal of human genetics · 2024Article
- Protein language models learn evolutionary statistics of interacting sequence motifs.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Alternative splicing of messenger RNA can generate an array of mature transcripts, but it is not clear how many go on to produce functionally relevant protein isoforms. There is only limited evidence for alternative proteins in proteomics analyses and data from population genetic variation studies indicate that most alternative exons are evolving neutrally. Determining which transcripts produce biologically important isoforms is key to understanding isoform function and to interpreting the real impact of somatic mutations and germline variations. Here we have developed a method, TRIFID, to classify the functional importance of splice isoforms. TRIFID was trained on isoforms detected in large-scale proteomics analyses and distinguishes these biologically important splice isoforms with high confidence. Isoforms predicted as functionally important by the algorithm had measurable cross species conservation and significantly fewer broken functional domains. Additionally, exons that code for these functionally important protein isoforms are under purifying selection, while exons from low scoring transcripts largely appear to be evolving neutrally. TRIFID has been developed for the human genome, but it could in principle be applied to other well-annotated species. We believe that this method will generate valuable insights into the cellular importance of alternative splicing.
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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.