ArticleNature genetics2008
Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines.
Article in Nature genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 204 papers.
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Who cites it
204 citing papers in PubMed, 322 citations in OpenAlex.
- Differential alternative splicing in skeletal muscle after 14 days immobilization-induced atrophy in young men.Pflugers Archiv : European journal of physiology · 2026Article
- Human-specific SRGAP2 paralogs synchronize neotenic microglial maturation and synaptic development.Neuron · 2026Article
- Transcriptomic regulation of pancreatic acinar cell homeostasis and plasticity.Biochemical Society transactions · 2026Review
- Epigenetic regulation by gut microbiota-derived metabolites in celiac disease.Biochemistry and biophysics reports · 2026Review
- Article
- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- A neuron type-specific microexon in Ank3/ankyrin-G modulates calcium activity and neuronal excitability.Nature communications · 2026Article
- ASPECT: Alternative Splicing Event Classification with Transformers.bioRxiv : the preprint server for biology · 2026Article
- mRNA splicing in turkey muscle satellite cells is dynamically altered upon thermal challenge.PloS one · 2026Article
- A neuron type-specific microexon inbioRxiv : the preprint server for biology · 2025Article
- Alternative splicing of the Snap23 microexon is regulated by MBNL, QKI, and RBFOX2 in a tissue-specific manner and is altered in striated muscle diseases.RNA biology · 2025Article
- Reverse engineering neuron-type-specific and type-orthogonal splicing-regulatory networks using diverse cellular transcriptomes.Cell reports · 2025Article
- Role of circulating microRNAs in tetralogy of Fallot.Postepy w kardiologii interwencyjnej = Advances in interventional cardiology · 2025Article
- Article
- Formation of Circular RNAs.Advances in experimental medicine and biology · 2025Review
- The Spatial-Temporal Alternative Splicing Profile Reveals the Functional Diversity of FXR1 Isoforms in Myogenesis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation.Genome research · 2024Article
- Human-specific paralogs of SRGAP2 induce neotenic features of microglia structural and functional maturation.bioRxiv : the preprint server for biology · 2024Article
- Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms.Nature communications · 2024Article
- scaRNA20 promotes pseudouridylatory modification of small nuclear snRNA U12 and improves cardiomyogenesis.Experimental cell research · 2024Article
144 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
7 authors at 3 institutions in 1 country.
Funding
Abstract
Alternative pre-messenger RNA splicing influences development, physiology and disease, but its regulation in humans is not well understood, partially because of the limited scale at which the expression of specific splicing events has been measured. We generated the first genome-scale expression compendium of human alternative splicing events using custom whole-transcript microarrays monitoring expression of 24,426 alternative splicing events in 48 diverse human samples. Over 11,700 genes and 9,500 splicing events were differentially expressed, providing a rich resource for studying splicing regulation. An unbiased, systematic screen of 21,760 4-mer to 7-mer words for cis-regulatory motifs identified 143 RNA 'words' enriched near regulated cassette exons, including six clusters of motifs represented by UCUCU, UGCAUG, UGCU, UGUGU, UUUU and AGGG, which map to trans-acting regulators PTB, Fox, Muscleblind, CELF/CUG-BP, TIA-1 and hnRNP F/H, respectively. Each cluster showed a distinct pattern of genomic location and tissue specificity. For example, UCUCU occurs 110 to 35 nucleotides preceding cassette exons upregulated in brain and striated muscle but depleted in other tissues. UCUCU and UGCAUG seem to have similar function but independent action, occurring 5' and 3', respectively, of 33% of the cassette exons upregulated in skeletal muscle but co-occurring for only 2%.
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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.