ArticleNature structural & molecular biology2009
Recognition of atypical 5' splice sites by shifted base-pairing to U1 snRNA.
Article in Nature structural & molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
56 citing papers in PubMed, 85 citations in OpenAlex.
- PCRD-seq: proximity crosslinking-induced RNA depletion sequencing for low-input chromatin-associated transcriptome profiling.Nucleic acids research · 2026Article
- An antisense method for efficient exon skipping and its application to Duchenne muscular dystrophy.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Utargetome: A targetome prediction tool for modified U1-snRNAs to identify distal-target positions with improved selectivity.PLoS computational biology · 2025Article
- Splicing accuracy varies across human introns, tissues, age and disease.Nature communications · 2025Article
- Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs.Nucleic acids research · 2024Article
- Identification and characterization of a novel intronic splicing mutation in CSF1R-related leukoencephalopathy.CNS neuroscience & therapeutics · 2024Article
- Specificity, synergy, and mechanisms of splice-modifying drugs.Nature communications · 2024Article
- Examining the capacity of human U1 snRNA variants to facilitate pre-mRNA splicing.RNA (New York, N.Y.) · 2024Article
- RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells.Nature communications · 2023Article
- Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects.Nature reviews. Genetics · 2023Review
- Article
- ZAP isoforms regulate unfolded protein response and epithelial- mesenchymal transition.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Principles and correction of 5'-splice site selection.RNA biology · 2022Review
- Field-theoretic density estimation for biological sequence space with applications to 5' splice site diversity and aneuploidy in cancer.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Human spliceosomal snRNA sequence variants generate variant spliceosomes.RNA (New York, N.Y.) · 2021Article
- A Reporter Based Cellular Assay for Monitoring Splicing Efficiency.Journal of visualized experiments : JoVE · 2021Article
- An in vitro reconstituted U1 snRNP allows the study of the disordered regions of the particle and the interactions with proteins and ligands.Nucleic acids research · 2021Article
- Restriction of an intron size en route to endothermy.Nucleic acids research · 2021Article
- Intron exon boundary junctions in human genome have in-built unique structural and energetic signals.Nucleic acids research · 2021Article
- Profiling of cis- and trans-acting factors supporting noncanonical splice site activation.RNA biology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Accurate pre-mRNA splicing is crucial for gene expression. The 5' splice site (5' ss)--the highly diverse element at the 5' end of introns--is initially recognized via base-pairing to the 5' end of the U1 small nuclear RNA (snRNA). However, many natural 5' ss have a poor match to the consensus sequence, and are predicted to be weak. Using genetic suppression experiments in human cells, we demonstrate that some atypical 5' ss are actually efficiently recognized by U1, in an alternative base-pairing register that is shifted by one nucleotide. These atypical 5' ss are phylogenetically widespread, and many of them are conserved. Moreover, shifted base-pairing provides an explanation for the effect of a 5' ss mutation associated with pontocerebellar hypoplasia. The unexpected flexibility in 5' ss-U1 base-pairing challenges an established paradigm and has broad implications for splice-site prediction algorithms and gene-annotation efforts in genome projects.
Indexed as
Identifiers
What OpenQuestion holds
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.