ArticleGenome research2007
A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 66 citations in OpenAlex.
- p-LoopF is associated with chromatin looping in large introns of Ginkgo biloba.Cell research · 2026Article
- Exon-intron boundary inhibits mNature communications · 2023Article
- Article
- Activation of cryptic splice sites in three patients with chronic granulomatous disease.Molecular genetics & genomic medicine · 2019Article
- A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions.Molecular cell · 2019Article
- At Least Two Genes Encode Many Variants of Irak3 in Rainbow Trout, but Neither the Full-Length Factor Nor Its Variants Interfere Directly With the TLR-Mediated Stimulation of Inflammation.Frontiers in immunology · 2019Article
- Mutations of Pre-mRNA Splicing Regulatory Elements: Are Predictions Moving Forward to Clinical Diagnostics?International journal of molecular sciences · 2017Review
- Does conservation account for splicing patterns?BMC genomics · 2016Article
- Systematical identification of splicing regulatory cis-elements and cognate trans-factors.Methods (San Diego, Calif.) · 2014Article
- Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation.RNA (New York, N.Y.) · 2013Article
- Function of alternative splicing.Gene · 2013Review
- A biophysical model for identifying splicing regulatory elements and their interactions.PloS one · 2013Article
- An exon splice enhancer primes IGF2:IGF2R binding site structure and function evolution.Science (New York, N.Y.) · 2012Article
- Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules.Nature structural & molecular biology · 2012Article
- VERSE: a varying effect regression for splicing elements discovery.Journal of computational biology : a journal of computational molecular cell biology · 2012Article
- Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans.RNA (New York, N.Y.) · 2011Article
- Quantitative evaluation of all hexamers as exonic splicing elements.Genome research · 2011Article
- The population genetics of chronic kidney disease: insights from the MYH9-APOL1 locus.Nature reviews. Nephrology · 2011Review
- Fox-3 and PSF interact to activate neural cell-specific alternative splicing.Nucleic acids research · 2011Article
- Context-dependent robustness to 5' splice site polymorphisms in human populations.Human molecular genetics · 2011Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Orthologous mammalian introns contain many highly conserved sequences. Of these sequences, many are likely to represent protein binding sites that are under strong positive selection. In order to identify conserved protein binding sites that are important for splicing, we analyzed the composition of intronic sequences that are conserved between human and six eutherian mammals. We focused on all completely conserved sequences of seven or more nucleotides located in the regions adjacent to splice-junctions. We found that these conserved intronic sequences are enriched in specific motifs, and that many of these motifs are statistically associated with either alternative or constitutive splicing. In validation of our methods, we identified several motifs that are known to play important roles in alternative splicing. In addition, we identified several novel motifs containing GCT that are abundant and are associated with alternative splicing. Furthermore, we demonstrate that, for some of these motifs, conservation is a strong indicator of potential functionality since conserved instances are associated with alternative splicing while nonconserved instances are not. A surprising outcome of this analysis was the identification of a large number of AT-rich motifs that are strongly associated with constitutive splicing. Many of these appear to be novel and may represent conserved intronic splicing enhancers (ISEs). Together these data show that conservation provides important insights into the identification and possible roles of cis-acting intronic sequences important for alternative and constitutive 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.