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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: analysis service resource, data analysis service, data or information resource, database, production service resource, 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
Funding: NSF IOS-0606909; NSF DBI-0110254; NSF DBI-0321600
Availability: THIS RESOURCE IS NO LONGER IN SERVICE
Resource Name: Arabidopsis thaliana Genome Database
Resource ID: SCR_001901
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Source: SciCrunch Registry (RRID:SCR_005400)
Description: Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch have assigned RRIDs which are used to cite resources in scientific manuscripts. SciCrunch Registry, formerly NIF Registry, provides resources catalog. Allows to add new resources. Allows edit existing resources after registration. Curators are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping contents current.
URL: https://rrid.site/rin/sources/SCR_005400
The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
