ArticleNucleic acids research2010
Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome.
Article in Nucleic acids research, 2010. 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.
- Acute endothelial stresses identify microRNA let-7b-5p and non-coding SLC11A2 (NRAMP2/DMT1) exon as biomarkers that overlap with those detected in malignant and non-malignant diseases.QJM : monthly journal of the Association of Physicians · 2025Article
- Intron Retention and Alzheimer's Disease (AD): A Review of Regulation Genes Implicated in AD.Genes · 2025Review
- Alternative splicing ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Alternative splicing ofbioRxiv : the preprint server for biology · 2024Article
- Intron retention by a novel intronic mutation in DKC1 gene caused recurrent still birth and early death in a Chinese family.Molecular genetics & genomic medicine · 2022Article
- RNA-Seq is not required to determine stable reference genes for qPCR normalization.PLoS computational biology · 2022Article
- Spliceostatin C, a component of a microbial bioherbicide, is a potent phytotoxin that inhibits the spliceosome.Frontiers in plant science · 2022Article
- Alternative splicing level related to intron size and organism complexity.BMC genomics · 2021Article
- FLAME: long-read bioinformatics tool for comprehensive spliceome characterization.RNA (New York, N.Y.) · 2021Article
- AI applications in functional genomics.Computational and structural biotechnology journal · 2021Review
- Retracing Schwann Cell Developmental Transitions in Embryonic Dissociated DRG/Schwann Cell Cocultures in Mice.Frontiers in cellular neuroscience · 2021Article
- Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation.Molecular systems biology · 2020Article
- Systematic Analyses of the Differentially Expressed Alternative Splicing Events in Gastric Cancer and Its Clinical Significance.Frontiers in genetics · 2020Article
- Splicing the Clock to Maintain and Entrain Circadian Rhythms.Journal of biological rhythms · 2019Review
- A novel L1CAM isoform with angiogenic activity generated by NOVA2-mediated alternative splicing.eLife · 2019Article
- The cyclin-dependent kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A.The Plant journal : for cell and molecular biology · 2018Article
- Alternative splicing affects the targeting sequence of peroxisome proteins in Arabidopsis.Plant cell reports · 2017Article
- Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens.Scientific reports · 2017Article
- Alternative Splicing May Not Be the Key to Proteome Complexity.Trends in biochemical sciences · 2017Review
- JuncDB: an exon-exon junction database.Nucleic acids research · 2016Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mining massive amounts of transcript data for alternative splicing information is paramount to help understand how the maturation of RNA regulates gene expression. We developed an algorithm to cluster transcript data to annotated genes to detect unannotated splice variants. A higher number of alternatively spliced genes and isoforms were found compared to other alternative splicing databases. Comparison of human and mouse data revealed a marked increase, in human, of splice variants incorporating novel exons and retained introns. Previously unannotated exons were validated by tiling array expression data and shown to correspond preferentially to novel first exons. Retained introns were validated by tiling array and deep sequencing data. The majority of retained introns were shorter than 500 nt and had weak polypyrimidine tracts. A subset of retained introns matching small RNAs and displaying a high GC content suggests a possible coordination between splicing regulation and production of noncoding RNAs. Conservation of unannotated exons and retained introns was higher in horse, dog and cow than in rodents, and 64% of exon sequences were only found in primates. This analysis highlights previously bypassed alternative splice variants, which may be crucial to deciphering more complex pathways of gene regulation in human.
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