ArticleJournal of molecular evolution1997
Analysis of donor splice sites in different eukaryotic organisms.
Article in Journal of molecular evolution, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 154 citations in OpenAlex.
- U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs.Nucleic acids research · 2024Article
- Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies.BMC bioinformatics · 2022Article
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- What's Wrong in a Jump? Prediction and Validation of Splice Site Variants.Methods and protocols · 2021Review
- Electroretinograms of eyes with Stickler syndrome.Documenta ophthalmologica. Advances in ophthalmology · 2020Article
- Analysis of macaque BTN3A genes and transcripts in the extended MHC: conserved orthologs of human γδ T cell modulators.Immunogenetics · 2019Article
- Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes.Cancers · 2019Article
- Splicing mutations in human genetic disorders: examples, detection, and confirmation.Journal of applied genetics · 2018Review
- The role of transposable elements in functional evolution of amphioxus genome: the case of opsin gene family.Scientific reports · 2018Article
- Extensive Alternative Splicing of KIR Transcripts.Frontiers in immunology · 2018Article
- Cap-independent translation ensures mTOR expression and function upon protein synthesis inhibition.RNA (New York, N.Y.) · 2017Article
- Computational Identification of Novel Genes: Current and Future Perspectives.Bioinformatics and biology insights · 2016Review
- Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.Frontiers in microbiology · 2015Article
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- In silico tools for splicing defect prediction: a survey from the viewpoint of end users.Genetics in medicine : official journal of the American College of Medical Genetics · 2014Review
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- Assessment and reconstruction of novel HSP90 genes: duplications, gains and losses in fungal and animal lineages.PloS one · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present here a new algorithm for functional site analysis. It is based on four main assumptions: each variation of nucleotide composition makes a different contribution to the overall binding free energy of interaction between a functional site and another molecule; nonfunctioning site-like regions (pseudosites) are absent or rare in genomes; there may be errors in the sample of sites; and nucleotides of different site positions are considered to be mutually dependent. In this algorithm, the site set is divided into subsets, each described by a certain consensus. Donor splice sites of the human protein-coding genes were analyzed. Comparing the results with other methods of donor splice site prediction has demonstrated a more accurate prediction of consensus sequences AG/GU(A,G), G/GUnAG, /GU(A,G)AG, /GU(A,G)nGU, and G/GUA than is achieved by weight matrix and consensus (A,C)AG/GU(A,G)AGU with mismatches. The probability of the first type error, E1, for the obtained consensus set was about 0.05, and the probability of the second type error, E2, was 0.15. The analysis demonstrated that accuracy of the functional site prediction could be improved if one takes into account correlations between the site positions. The accuracy of prediction by using human consensus sequences was tested on sequences from different organisms. Some differences in consensus sequences for the plant Arabidopsis sp., the invertebrate Caenorhabditis sp., and the fungus Aspergillus sp. were revealed. For the yeast Saccharomyces sp. only one conservative consensus, /GUA(U,A,C)G(U,A,C), was revealed (E1 = 0.03, E2 = 0.03). Yeast is a very interesting model to use for analysis of molecular mechanisms of splicing.
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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.