Bioinformatics analysis of alternative splicing
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Summary
A number of groups have used a combination of bioinformatics, comparative genomics and experimental validation to identify new motifs for splice regulatory factors, analyse the balance of factors that regulateAlternative splicing, and propose a new mechanism for regulation based on the interaction of alternative splicing and nonsense-mediated decay.
- Type
- review
- Published
- 2005-03-01
- Cited by
- 98
- References
- 49
- Access
- Open access
- OpenAlex
- https://openalex.org/W2113322429
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:1229007
Keywords
Alternative splicing, RNA splicing, Biology, Computational biology, Exon
References
- Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers
- Negative selection pressure against premature protein truncation is reduced by both alternative splicing and diploidy
- Genomic variants in exons and introns: identifying the splicing spoilers
- DEDB: a database of Drosophila melanogaster exons in splicing graph form
- No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions
- Increase of functional diversity by alternative splicing.
- The Birth of an Alternatively Spliced Exon: 3' Splice-Site Selection in Alu Exons
- Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons.
- ESTGenes: alternative splicing from ESTs in Ensembl.
- Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform.
- Genome-wide detection of alternative splicing in expressed sequences of human genes
- Alternative splice variants encoding unstable protein domains exist in the human brain.
- Detection of Novel Splice Forms in Human and Mouse Using Cross-Species Approach
- Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data.
- Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity
- A non-EST-based method for exon-skipping prediction.
- The Effects of Alternative Splicing on Transmembrane Proteins in the Mouse Genome
- The impact of very short alternative splicing on protein structures and functions in the human genome.
- Extensive Search for Discriminative Features of Alternative Splicing
- Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss
Cited by
- Bioinformatics detection of alternative splicing.
- Genomic analysis of RNA alternative splicing in cancers.
- Analysis of alternative splicing in plants with bioinformatics tools.
- Methods and platforms for the quantification of splice variants' expression.
- Computational analysis of gene expression data
- Reconstruction of full-length isoforms from splice graphs.
- Assessing the impact of alternative splicing on the diversity and evolution of the proteome in plants
- Genome-wide survey and analysis of allele-specific mRNA splicing in human and mouse
- Genome Mapping and Genomics in Laboratory Animals
- The role of hnRNP H in the splicing response to genotoxic stress
- Identification and expression analysis of three novel splice variants of protein kinase A catalytic β subunit gene in the mouse using combinatorial in silico and molecular biology approaches
- Alternative splicing: a perspective of the nematode model-Caenorhabditis elegans.
- Global detection and identification of developmental stage specific transcripts in mouse brain using subtractive cross-screening algorithm.
- Sequence Variability and Sequence Evolution: An Explanation of Molecular Polymorphisms and Why Many Molecular Structures Can Be Preserved Although They Are Not Predominant
- Plant SET domain-containing proteins: structure, function and regulation.
- Platelet GPIIb/IIIa receptor: how prone to mutation?
- Weak linkage in androgen receptor: identification of mutation-prone points.
- Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse
- Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events
- New perspectives on neoplasia and the RNA world
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