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URL: http://www.plantgdb.org/AtGDB/
Proper Citation: Arabidopsis thaliana Genome Database (RRID:SCR_001901)
Description: Database providing a sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on gene structure annotation. The current genome assembly displayed at AtGDB is version TAIR9. Annotated gene models are TAIR10. They 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.
Abbreviations: AtGDB
Synonyms: Arabidopsis thaliana Genome DB
Resource Type: service resource, data analysis service, data or information resource, database, production service resource, analysis service resource
Defining Citation: PMID:16219921, PMID:14681433, PMID:12805580
Keywords: expressed sequence tag, est sequence, contig, gene structure, genome, arabidopsis thaliana, cdna, plant database, blast, annotation
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