ArticleProceedings of the National Academy of Sciences of the United States of America2008
Identification of gene 3' ends by automated EST cluster analysis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 45 citations in OpenAlex.
- Genome-wide polyadenylation site mapping datasets in the rice blast fungus Magnaporthe oryzae.Scientific data · 2018Article
- Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites.Nucleic acids research · 2014Article
- GATA-3 regulates the self-renewal of long-term hematopoietic stem cells.Nature immunology · 2013Article
- All's well that ends well: alternative polyadenylation and its implications for stem cell biology.Current opinion in cell biology · 2013Review
- Dual suppression of hemangiogenesis and lymphangiogenesis by splice-shifting morpholinos targeting vascular endothelial growth factor receptor 2 (KDR).FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2013Article
- Misfolded human tRNA isodecoder binds and neutralizes a 3' UTR-embedded Alu element.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Article
- POLYAR, a new computer program for prediction of poly(A) sites in human sequences.BMC genomics · 2010Article
- Pseudogenes as an alternative source of natural antisense transcripts.BMC evolutionary biology · 2010Article
- GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs.BMC bioinformatics · 2010Article
- Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.BMC genomics · 2009Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The properties and biology of mRNA transcripts can be affected profoundly by the choice of alternative polyadenylation sites, making definition of the 3' ends of transcripts essential for understanding their regulation. Here we show that 22-52% of sequences in commonly used human and murine "full-length" transcript databases may not currently end at bona fide polyadenylation sites. To identify probable transcript termini over the entire murine and human genomes, we analyzed the EST databases for positional clustering of EST ends. The analysis yielded 58,282 murine- and 86,410 human-candidate polyadenylation sites, of which 75% mapped to 23,091 known murine transcripts and 22,891 known human transcripts. The murine dataset correctly predicted 97% of the 3' ends in a manually curated and experimentally supported benchmark transcript set. Of currently known genes, 15% had no associated prediction and 25% had only a single predicted termination site. The remaining genes had an average of 3-4 alternative polyadenylation sites predicted for each murine or human transcript, respectively. The results are made available in the form of tables and an interactive web site that can be mined for rapid assessment of the validity of 3' ends in existing collections, enumeration of potential alternative 3' polyadenylation sites of known transcripts, direct retrieval of terminal sequences for design of probes, and detection of polyadenylation sites not currently mapped to known genes.
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