ArticleBMC genomics2008
Computational analysis of splicing errors and mutations in human transcripts.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 39 citations in OpenAlex.
- A novel heterozygous splicing variant in theFrontiers in cell and developmental biology · 2026Article
- Aberrant splicing caused by exonic single nucleotide variants positioned 2nd or 3rd to the last nucleotide in the COL4A5 gene.Clinical and experimental nephrology · 2023Article
- Splice2Deep: An ensemble of deep convolutional neural networks for improved splice site prediction in genomic DNA.Gene: X · 2020Article
- Clinical, immunological and genetic characteristic of patients with clinical phenotype associated to LRBA-deficiency in Colombia.Colombia medica (Cali, Colombia) · 2019Article
- [The clinical characteristics and molecular pathogenesis of a variant Glanzmann's thrombasthenia-like pedigree].Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi · 2018Article
- Systematic evaluation of isoform function in literature reports of alternative splicing.BMC genomics · 2018Article
- regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution.Human genetics · 2017Article
- Natural variation of gene models in Drosophila melanogaster.BMC genomics · 2015Article
- Polymorphisms in DNA repair genes of XRCC1, XPA, XPC, XPD and associations with lung cancer risk in Chinese people.Thoracic cancer · 2014Article
- Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.Genome biology · 2013Article
- Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements.Frontiers in plant science · 2012Article
- Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders.Nucleic acids research · 2011Article
- Evolution of prokaryotic genes by shift of stop codons.Journal of molecular evolution · 2011Article
- Identification and characterization of a null-activity mutant containing a cryptic pre-mRNA splice site for cytosolic fructose-1,6-bisphosphatase in Flaveria linearis.Plant molecular biology · 2010Article
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- Accurate distinction of pathogenic from benign CNVs in mental retardation.PLoS computational biology · 2010Article
- Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay.BMC biology · 2009Article
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
backgroundMost retained introns found in human cDNAs generated by high-throughput sequencing projects seem to result from underspliced transcripts, and thus they capture intermediate steps of pre-mRNA splicing. On the other hand, mutations in splice sites cause exon skipping of the respective exon or activation of pre-existing cryptic sites. Both types of events reflect properties of the splicing mechanism.
resultsThe retained introns were significantly shorter than constitutive ones, and skipped exons are shorter than exons with cryptic sites. Both donor and acceptor splice sites of retained introns were weaker than splice sites of constitutive introns. The authentic acceptor sites affected by mutations were significantly weaker in exons with activated cryptic sites than in skipped exons. The distance from a mutated splice site to the nearest equivalent site is significantly shorter in cases of activated cryptic sites compared to exon skipping events. The prevalence of retained introns within genes monotonically increased in the 5'-to-3' direction (more retained introns close to the 3'-end), consistent with the model of co-transcriptional splicing. The density of exonic splicing enhancers was higher, and the density of exonic splicing silencers lower in retained introns compared to constitutive ones and in exons with cryptic sites compared to skipped exons.
conclusionThus the analysis of retained introns in human cDNA, exons skipped due to mutations in splice sites and exons with cryptic sites produced results consistent with the intron definition mechanism of splicing of short introns, co-transcriptional splicing, dependence of splicing efficiency on the splice site strength and the density of candidate exonic splicing enhancers and silencers. These results are consistent with other, recently published analyses.
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