ArticleNucleic acids research2011
An SF1 affinity model to identify branch point sequences in human introns.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- U2 snRNP recognizes the branch site through a loaded-spring strand-invasion mechanism.Nucleic acids research · 2026Article
- SPAT inhibits LUAD metastasis by targeting SF1-mediated splicing.Cell death & disease · 2025Article
- A Comprehensive Map of Intron Branchpoints and Lariat RNAs in Plants.The Plant cell · 2019Article
- A heuristic model for computational prediction of human branch point sequence.BMC bioinformatics · 2017Article
- Article
- Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression.Nature communications · 2016Article
- Intron definition and a branch site adenosine at nt 385 control RNA splicing of HPV16 E6*I and E7 expression.PloS one · 2012Article
- RNA splicing and debranching viewed through analysis of RNA lariats.Molecular genetics and genomics : MGG · 2011Article
- Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans.RNA (New York, N.Y.) · 2011Article
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Authors and funding
6 authors.
Funding
Abstract
Splicing factor 1 (SF1) binds to the branch point sequence (BPS) of mammalian introns and is believed to be important for the splicing of some, but not all, introns. To help identify BPSs, particularly those that depend on SF1, we generated a BPS profile model in which SF1 binding affinity data, validated by branch point mapping, were iteratively incorporated into computational models. We searched a data set of 117,499 human introns for best matches to the SF1 Affinity Model above a threshold, and counted the number of matches at each intronic position. After subtracting a background value, we found that 87.9% of remaining high-scoring matches identified were located in a region upstream of 3'-splice sites where BPSs are typically found. Since U2AF65 recognizes the polypyrimidine tract (PPT) and forms a cooperative RNA complex with SF1, we combined the SF1 model with a PPT model computed from high affinity binding sequences for U2AF65. The combined model, together with binding site location constraints, accurately identified introns bound by SF1 that are candidates for SF1-dependent 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.