ArticleGenome research2001
The contribution of exon-skipping events on chromosome 22 to protein coding diversity.
Article in Genome research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Article
- Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.G3 (Bethesda, Md.) · 2018Article
- Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing.Oncology letters · 2017Article
- Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison.BMC genomics · 2007Article
- Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome.BMC bioinformatics · 2006Article
- Intronic alternative splicing regulators identified by comparative genomics in nematodes.PLoS computational biology · 2006Article
- Evolution of alternative splicing after gene duplication.Genome research · 2006Article
- Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.Nucleic acids research · 2006Article
- An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs.Nucleic acids research · 2006Article
- Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms.Nucleic acids research · 2005Article
- A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.Nucleic acids research · 2005Article
- A transcript finishing initiative for closing gaps in the human transcriptome.Genome research · 2004Article
- The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures.Genome research · 2004Article
- Exon repetition: a major pathway for processing mRNA of some genes is allele-specific.Nucleic acids research · 2004Article
- The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Computational discovery of internal micro-exons.Genome research · 2003Article
- Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Reevaluating human gene annotation: a second-generation analysis of chromosome 22.Genome research · 2003Article
- Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.Genome biology · 2003Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Completion of the human genome sequence provides evidence for a gene count with lower bound 30,000-40,000. Significant protein complexity may derive in part from multiple transcript isoforms. Recent EST based studies have revealed that alternate transcription, including alternative splicing, polyadenylation and transcription start sites, occurs within at least 30-40% of human genes. Transcript form surveys have yet to integrate the genomic context, expression, frequency, and contribution to protein diversity of isoform variation. We determine here the degree to which protein coding diversity may be influenced by alternate expression of transcripts by exhaustive manual confirmation of genome sequence annotation, and comparison to available transcript data to accurately associate skipped exon isoforms with genomic sequence. Relative expression levels of transcripts are estimated from EST database representation. The rigorous in silico method accurately identifies exon skipping using verified genome sequence. 545 genes have been studied in this first hand-curated assessment of exon skipping on chromosome 22. Combining manual assessment with software screening of exon boundaries provides a highly accurate and internally consistent indication of skipping frequency. 57 of 62 exon skipping events occur in the protein coding regions of 52 genes. A single gene, (FBXO7) expresses an exon repetition. 59% of highly represented multi-exon genes are likely to express exon-skipped isoforms in ratios that vary from 1:1 to 1:>100. The proportion of all transcripts corresponding to multi-exon genes that exhibit an exon skip is estimated to be 5%.
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