ArticlePlant physiology2003
Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping.
Article in Plant physiology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Difference Analysis Among Six Kinds of Acceptor Splicing Sequences by the Dispersion Features of 6-mer Subsets in Human Genes.Biology · 2025Article
- Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD.Nucleic acids research · 2024Article
- Insights into sweet potato SR proteins: from evolution to species-specific expression and alternative splicing.Planta · 2022Article
- The comparison of alternative splicing among the multiple tissues in cucumber.BMC plant biology · 2018Article
- Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence.BMC research notes · 2017Article
- Seed Dormancy in Arabidopsis Requires Self-Binding Ability of DOG1 Protein and the Presence of Multiple Isoforms Generated by Alternative Splicing.PLoS genetics · 2015Article
- Evolutionary Character of Alternative Splicing in Plants.Bioinformatics and biology insights · 2015Review
- Genome-wide analysis of alternative splicing in Volvox carteri.BMC genomics · 2014Article
- Genome-wide survey of Alternative Splicing in Sorghum Bicolor.Physiology and molecular biology of plants : an international journal of functional plant biology · 2014Article
- Alternative splicing in plant immunity.International journal of molecular sciences · 2014Review
- Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes.Plant physiology · 2014Article
- Complexity of the alternative splicing landscape in plants.The Plant cell · 2013Review
- 5' Regulatory region of ubiquitin 2 gene from Porteresia coarctata makes efficient promoters for transgene expression in monocots and dicots.Plant cell reports · 2013Article
- Catalyzing plant science research with RNA-seq.Frontiers in plant science · 2013Article
- Alternative splicing in plants--coming of age.Trends in plant science · 2012Review
- Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis.Genome research · 2012Article
- Estimation of Gene Expression at Isoform Level from mRNA-Seq Data by Bayesian Hierarchical Modeling.Frontiers in genetics · 2012Article
- Genome-wide mapping of alternative splicing in Arabidopsis thaliana.Genome research · 2010Article
- ESTPiper--a web-based analysis pipeline for expressed sequence tags.BMC genomics · 2009Article
- Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure.BMC genomics · 2008Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Expressed sequence tags (ESTs) currently encompass more entries in the public databases than any other form of sequence data. Thus, EST data sets provide a vast resource for gene identification and expression profiling. We have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing. All results of this study were parsed into a database and are accessible via a flexible Web interface at http://www.plantgdb.org/AtGDB/.
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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.