ArticleNucleic acids research2001
Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing.
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
What it found
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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.
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Who cites it
57 citing papers in PubMed, 117 citations in OpenAlex.
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- Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition.Nucleic acids research · 2017Article
- Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs.Nucleic acids research · 2016Article
- Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data.PloS one · 2016Article
- Rbfox3 controls the biogenesis of a subset of microRNAs.Nature structural & molecular biology · 2014Article
- RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing.Genome biology · 2014Article
- RNA binding proteins in the regulation of heart development.The international journal of biochemistry & cell biology · 2013Review
- Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules.Nature structural & molecular biology · 2012Article
- Rare inherited A2BP1 deletion in a proband with autism and developmental hemiparesis.American journal of medical genetics. Part A · 2012Article
- VERSE: a varying effect regression for splicing elements discovery.Journal of computational biology : a journal of computational molecular cell biology · 2012Article
- Muscle-specific splicing factors ASD-2 and SUP-12 cooperatively switch alternative pre-mRNA processing patterns of the ADF/cofilin gene in Caenorhabditis elegans.PLoS genetics · 2012Article
- RBFOX2 promotes protein 4.1R exon 16 selection via U1 snRNP recruitment.Molecular and cellular biology · 2012Article
- Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts.RNA (New York, N.Y.) · 2011Review
- Understanding splicing regulation through RNA splicing maps.Trends in genetics : TIG · 2011Review
- Nonsense mutation-associated Becker muscular dystrophy: interplay between exon definition and splicing regulatory elements within the DMD gene.Human mutation · 2011Article
- Efficient in vivo manipulation of alternative pre-mRNA splicing events using antisense morpholinos in mice.The Journal of biological chemistry · 2011Article
- Computational identification of tissue-specific alternative splicing elements in mouse genes from RNA-Seq.Nucleic acids research · 2010Article
- Article
- Fox-2 protein regulates the alternative splicing of scleroderma-associated lysyl hydroxylase 2 messenger RNA.Arthritis and rheumatism · 2010Article
- Fox-1 family of RNA-binding proteins.Cellular and molecular life sciences : CMLS · 2009Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Alternative pre-mRNA splicing is a major cellular process by which functionally diverse proteins can be generated from the primary transcript of a single gene, often in tissue-specific patterns. The current study investigates the hypothesis that splicing of tissue-specific alternative exons is regulated in part by control sequences in adjacent introns and that such elements may be recognized via computational analysis of exons sharing a highly specific expression pattern. We have identified 25 brain-specific alternative cassette exons, compiled a dataset of genomic sequences encompassing these exons and their adjacent introns and used word contrast algorithms to analyze key features of these nucleotide sequences. By comparison to a control group of constitutive exons, brain-specific exons were often found to possess the following: divergent 5' splice sites; highly pyrimidine-rich upstream introns; a paucity of GGG motifs in the downstream intron; a highly statistically significant over-representation of the hexanucleotide UGCAUG in the proximal downstream intron. UGCAUG was also found at a high frequency downstream of a smaller group of muscle-specific exons. Intriguingly, UGCAUG has been identified previously in a few intron splicing enhancers. Our results indicate that this element plays a much wider role than previously appreciated in the regulated tissue-specific splicing of many alternative exons.
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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.