ArticleGenome biology2002
Full-length messenger RNA sequences greatly improve genome annotation.
Article in Genome biology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers, 1 of them a synthesis that pooled it.
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Who cites it
86 citing papers in PubMed, 1 synthesis or guideline pooled it, 177 citations in OpenAlex.
- Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.Genome biology · 2002Pooled it
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- RNA-Seq improves annotation of protein-coding genes in the cucumber genome.BMC genomics · 2011Article
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- RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis.Plant molecular biology · 2011Article
- A white spruce gene catalog for conifer genome analyses.Plant physiology · 2011Article
- Ustilago maydis transcript features identified through full-length cDNA analysis.Molecular genetics and genomics : MGG · 2011Article
- Twenty-first century plant biology: impacts of the Arabidopsis genome on plant biology and agriculture.Plant physiology · 2010Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundAnnotation of eukaryotic genomes is a complex endeavor that requires the integration of evidence from multiple, often contradictory, sources. With the ever-increasing amount of genome sequence data now available, methods for accurate identification of large numbers of genes have become urgently needed. In an effort to create a set of very high-quality gene models, we used the sequence of 5,000 full-length gene transcripts from Arabidopsis to re-annotate its genome. We have mapped these transcripts to their exact chromosomal locations and, using alignment programs, have created gene models that provide a reference set for this organism.
resultsApproximately 35% of the transcripts indicated that previously annotated genes needed modification, and 5% of the transcripts represented newly discovered genes. We also discovered that multiple transcription initiation sites appear to be much more common than previously known, and we report numerous cases of alternative mRNA splicing. We include a comparison of different alignment software and an analysis of how the transcript data improved the previously published annotation.
conclusionsOur results demonstrate that sequencing of large numbers of full-length transcripts followed by computational mapping greatly improves identification of the complete exon structures of eukaryotic genes. In addition, we are able to find numerous introns in the untranslated regions of the genes.
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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.