ArticleGenome research2011
Quantitative evaluation of all hexamers as exonic splicing elements.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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Who cites it
142 citing papers in PubMed, 232 citations in OpenAlex.
- An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal.Nucleic acids research · 2026Article
- Control of gene output by intron RNA structure.bioRxiv : the preprint server for biology · 2025Article
- Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation.bioRxiv : the preprint server for biology · 2025Article
- Massively parallel assay of human splice variants reveals cis-regulatory drivers of disease-associated and cell type-specific splicing regulation.bioRxiv : the preprint server for biology · 2025Article
- Core splicing architecture and early spliceosomal recognition determine microexon sensitivity to SRRM3/4.Nature structural & molecular biology · 2025Article
- Non-viral intron knock-ins for targeted gene integration into human T cells and for T-cell selection.Nature biomedical engineering · 2025Article
- OpenASO: RNA Rescue-designing splice-modulating antisense oligonucleotides through community science.RNA (New York, N.Y.) · 2025Article
- Single Antisense Oligonucleotides Correct Diverse Splicing Mutations in Hotspot Exons.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Fully haplotyped genome assemblies of healthy individuals reveal variability in 5'ss strength and support by splicing regulatory proteins.NAR genomics and bioinformatics · 2025Article
- From benign to pathogenic variants and vice versa: pyrimidine transitions at position -3 of TAG and CAG 3' splice sites.Journal of human genetics · 2025Article
- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.Nature reviews. Genetics · 2025Review
- Pre-mRNA Splicing Modulation by Antisense Oligonucleotides.Methods in molecular biology (Clifton, N.J.) · 2025Article
- In silico splicing analysis of the PMS2 gene: exploring alternative molecular mechanisms in PMS2-associated Lynch syndrome.BMC genomic data · 2024Article
- Decoding biology with massively parallel reporter assays and machine learning.Genes & development · 2024Review
- Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs.Nucleic acids research · 2024Article
- The debranching enzyme Dbr1 regulates lariat turnover and intron splicing.Nature communications · 2024Article
- Copper-binding proteins and exonic splicing enhancers and silencers.Metallomics : integrated biometal science · 2024Article
- Exonic splicing code and coordination of divalent metals in proteins.Nucleic acids research · 2024Article
- Article
- An intronic RNA element modulates Factor VIII exon-16 splicing.Nucleic acids research · 2024Article
82 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
We describe a comprehensive quantitative measure of the splicing impact of a complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts. All 4096 6-mers were substituted at five positions within two different internal exons in a 3-exon minigene, and millions of successfully spliced transcripts were sequenced after transfection of human cells. The results allowed the assignment of a relative splicing strength score to each mutant molecule. The effect of 6-mers on splicing often depended on their location; much of this context effect could be ascribed to the creation of different overlapping sequences at each site. Taking these overlaps into account, the splicing effect of each 6-mer could be quantified, and 6-mers could be designated as enhancers (ESEseqs) and silencers (ESSseqs), with an ESRseq score indicating their strength. Some 6-mers exhibited positional bias relative to the two splice sites. The distribution and conservation of these ESRseqs in and around human exons supported their classification. Predicted RNA secondary structure effects were also seen: Effective enhancers, silencers and 3' splice sites tend to be single stranded, and effective 5' splice sites tend to be double stranded. 6-mers that may form positive or negative synergy with another were also identified. Chromatin structure may also influence the splicing enhancement observed, as a good correspondence was found between splicing performance and the predicted nucleosome occupancy scores of 6-mers. This approach may prove of general use in defining nucleic acid regulatory motifs, substitute for functional SELEX in most cases, and provide insights about splicing mechanisms.
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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.