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AtGDB specifications


Unique identifier OMICS_14938
Name AtGDB
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • person_outline GeneMap Team

Publication for AtGDB

AtGDB citations


Genome Wide Characterization of Heat Shock Protein 70s from Chenopodium quinoa and Expression Analyses of Cqhsp70s in Response to Drought Stress

PMCID: 5852552
PMID: 29360757
DOI: 10.3390/genes9020035

[…], Oryza sativa (, Glycine max (, Brassica rapa (, Arabidopsis thaliana (, Arabidopsis lyrata (, Chenopodium quinoa from Phytozome v12 (, Picea abies ( and Hordeum vulgare (http: […]


Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims)

BMC Genomics
PMCID: 5520361
PMID: 28732469
DOI: 10.1186/s12864-017-3881-5

[…] listed and quantified. Sequence repeats located in putative coding regions were identified with the gene model version TAIR 9 using P. edulis contigs blasted against Arabidopsis thaliana transcripts (AtGDB171). An ab initio prediction of coding regions was also performed using geneid [] []. Both analyses were considered for the selection of microsatellites loca […]


Virus like attachment sites as structural landmarks of plants retrotransposons

PMCID: 4963935
PMID: 27471551
DOI: 10.1186/s13100-016-0069-5
call_split See protocol

[…] Ten fully sequenced genomes (A. thaliana - At - AtGDB171/TAIR9 – GenBank current version is TAIR10 at GCA_000001735.1, M. truncatula - Mt – Mt3.5 – GenBank current version is MedtrA17_4.0 at GCA_000219495.2, P. trichocarpa - Pt - Ptr v2.2 – GenBank […]


Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism

BMC Genomics
PMCID: 3473312
PMID: 22748146
DOI: 10.1186/1471-2164-13-297

[…] We used the proteomes of S. cerevisiae from, H. sapiens from, A. thaliana from and E. histolytica from the to generate our database. Each of the 95 077 proteins was compared to the whole database using BLASTP [] with a cutoff E value of 10-10. This all […]


Genome wide characterization of the biggest grass, bamboo, based on 10,608 putative full length cDNA sequences

BMC Plant Biol
PMCID: 3017805
PMID: 20565830
DOI: 10.1186/1471-2229-10-116

[…] SS and a perl script, MISA, respectively. For comparison, cDNA data of Arabidopsis and rice were downloaded from public databases PlantGDB and NCBI, respectively.To identify putative alternative splicing variants, program CAP3 [] was first used to filter singletons with default parameters. The remaining sequ […]


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AtGDB institution(s)
Department of Zoology and Genetics, Iowa State University, Ames, IA, USA; Department of Statistics, Iowa State University, Ames, IA, USA
AtGDB funding source(s)
This work was supported in part by the National Science Foundation (grant no. DBI–0110254).

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