ArticleGenome research2009
Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome.
Article in Genome research, 2009. 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.
- Detecting gene expression in Caenorhabditis elegans.Genetics · 2025Review
- Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons.G3 (Bethesda, Md.) · 2022Article
- CANT1 lncRNA Triggers Efficient Therapeutic Efficacy by Correcting Aberrant lncing Cascade in Malignant Uveal Melanoma.Molecular therapy : the journal of the American Society of Gene Therapy · 2017Article
- Analysis of a lin-42/period Null Allele Implicates All Three Isoforms in Regulation of Caenorhabditis elegans Molting and Developmental Timing.G3 (Bethesda, Md.) · 2016Article
- Full-length enriched cDNA libraries and ORFeome analysis of sugarcane hybrid and ancestor genotypes.PloS one · 2014Article
- The significance of alternative transcripts for Caenorhabditis elegans transcription factor genes, based on expression pattern analysis.BMC genomics · 2013Article
- RNA-seq analysis of the C. briggsae transcriptome.Genome research · 2012Article
- Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping.Nature methods · 2011Article
- Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii.BMC genomics · 2011Article
- Targeted rapid amplification of cDNA ends (T-RACE)--an improved RACE reaction through degradation of non-target sequences.Nucleic acids research · 2010Article
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Authors and funding
16 authors.
Funding
Abstract
Although a highly accurate sequence of the Caenorhabditis elegans genome has been available for 10 years, the exact transcript structures of many of its protein-coding genes remain unsettled. Approximately two-thirds of the ORFeome has been verified reactively by amplifying and cloning computationally predicted transcript models; still a full third of the ORFeome remains experimentally unverified. To fully identify the protein-coding potential of the worm genome including transcripts that may not satisfy existing heuristics for gene prediction, we developed a computational and experimental platform adapting rapid amplification of cDNA ends (RACE) for large-scale structural transcript annotation. We interrogated 2000 unverified protein-coding genes using this platform. We obtained RACE data for approximately two-thirds of the examined transcripts and reconstructed ORF and transcript models for close to 1000 of these. We defined untranslated regions, identified new exons, and redefined previously annotated exons. Our results show that as much as 20% of the C. elegans genome may be incorrectly annotated. Many annotation errors could be corrected proactively with our large-scale RACE platform.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.