ArticleNucleic acids research2006
Comprehensive splice-site analysis using comparative genomics.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 219 papers.
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Who cites it
219 citing papers in PubMed.
- Convergent genome streamlining accompanies independent miniaturization in the world's smallest fishes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- ZRSR1 protects against obesity-associated hepatic lipogenesis independent of minor intron splicing.Life metabolism · 2026Article
- Pervasive noise in human pre-mRNA splice site selection.Molecular cell · 2026Article
- The minor spliceosome component U4atac regulates JAK/STAT signaling to modulate hematopoiesis and immune responses in Drosophila melanogaster.Nature communications · 2026Article
- The splice of life: an isoform-centric view of disease, technology, and therapeutics.The Journal of clinical investigation · 2026Review
- IRCAS: a novel end-to-end approach to identify, rectify, and classify comprehensive alternative splicing events in a transcriptome without genome reference.Briefings in bioinformatics · 2026Article
- Improving splice site usage prediction with SPLAIRE.bioRxiv : the preprint server for biology · 2026Article
- 5' leader defects drive persistent HIV-1 viremia on long-term ART.Nature communications · 2026Article
- Splicing deficiency is driven by genomic erosion in non-recombining algal mating-type chromosomes.PLoS biology · 2026Article
- Muscleblind-like proteins dimerize by forming disulfide bonds to regulate alternative splicing and pathogenic RNA foci formation.Nucleic acids research · 2026Article
- UniSplicer: A deep-learning framework for accurate splice-site prediction and splice-altering mutation detection across diverse taxa.Plant communications · 2026Article
- Transient molecular chimerism for exploiting xenogeneic organelles.Nature communications · 2026Article
- Identity rather than 3D position informs splicing of rare introns in the human genome.iScience · 2026Article
- Utilisation of Machine Learning Approaches Improves RNA-Seq Transcriptome Analyses in Alzheimer's Disease Brain.Journal of molecular neuroscience : MN · 2026Article
- Extensive splicing deficiency in a degenerating mating-type chromosome.bioRxiv : the preprint server for biology · 2025Article
- Alternative splicing of the Snap23 microexon is regulated by MBNL, QKI, and RBFOX2 in a tissue-specific manner and is altered in striated muscle diseases.RNA biology · 2025Article
- A Plot Twist: When RNA Yields Unexpected Findings in Paired DNA-RNA Germline Genetic Testing.Genes · 2025Article
- Molecular Analysis of the HGD Gene in 9 Families With Alkaptonuric Ochronosis in Iran and Identification of Two Novel Variants.Molecular genetics & genomic medicine · 2025Article
- Alternative splicing events of three rare variants in CHKB gene causing megaconial congenital dystrophy.Neurogenetics · 2025Article
159 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
We have collected over half a million splice sites from five species-Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana-and classified them into four subtypes: U2-type GT-AG and GC-AG and U12-type GT-AG and AT-AC. We have also found new examples of rare splice-site categories, such as U12-type introns without canonical borders, and U2-dependent AT-AC introns. The splice-site sequences and several tools to explore them are available on a public website (SpliceRack). For the U12-type introns, we find several features conserved across species, as well as a clustering of these introns on genes. Using the information content of the splice-site motifs, and the phylogenetic distance between them, we identify: (i) a higher degree of conservation in the exonic portion of the U2-type splice sites in more complex organisms; (ii) conservation of exonic nucleotides for U12-type splice sites; (iii) divergent evolution of C.elegans 3' splice sites (3'ss) and (iv) distinct evolutionary histories of 5' and 3'ss. Our study proves that the identification of broad patterns in naturally-occurring splice sites, through the analysis of genomic datasets, provides mechanistic and evolutionary insights into pre-mRNA splicing.
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