ArticleProceedings of the National Academy of Sciences of the United States of America2004
Genome annotation by high-throughput 5' RNA end determination.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons.G3 (Bethesda, Md.) · 2022Article
- Article
- Methods and strategies for gene structure curation in WormBase.Database : the journal of biological databases and curation · 2011Article
- PAR-3 mediates the initial clustering and apical localization of junction and polarity proteins during C. elegans intestinal epithelial cell polarization.Development (Cambridge, England) · 2010Article
- Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome.Genome research · 2009Article
- Identification and analysis of internal promoters in Caenorhabditis elegans operons.Genome research · 2007Article
- WormBase: new content and better access.Nucleic acids research · 2007Article
- Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans.Genome research · 2006Article
- WormBase: better software, richer content.Nucleic acids research · 2006Article
- WormBase: a comprehensive data resource for Caenorhabditis biology and genomics.Nucleic acids research · 2005Article
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Authors and funding
3 authors.
Funding
Abstract
Complete gene identification and annotation, including alternative transcripts, remains a challenge in understanding genome organization. Such annotation can be achieved by a combination of computational analysis and experimental confirmation. Here, we describe a high-throughput technique, trans-spliced exon coupled RNA end determination (TEC-RED), that identifies 5' ends of expressed genes in nematodes. TEC-RED can distinguish coding regions from regulatory regions and identify genes as well as their alternative transcripts that have different 5' ends. Application of TEC-RED to approximately 10% of the Caenorhabditis elegans genome yielded tags 75% of which experimentally verified predicted 5'-RNA ends and 25% of which provided previously unknown information about 5'-RNA ends, including the identification of 99 previously unknown genes and 32 previously unknown operons. This technique will be applicable in any organisms that have a trans-splicing reaction from spliced leader RNA. We also describe an efficient sequential method for concatenating short sequence tags for any serial analysis of gene expression-like techniques.
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