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AtGDB specifications

Information


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

Maintainer


  • person_outline GeneMap Team

Publication for AtGDB

AtGDB citations

 (5)
library_books

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

2018
Genes
PMCID: 5852552
PMID: 29360757
DOI: 10.3390/genes9020035

[…] db.org/BdGDB/), Oryza sativa (http://www.plantgdb.org/OsGDB/), Glycine max (http://www.plantgdb.org/GmGDB/), Brassica rapa (http://brassicadb.org/brad/), Arabidopsis thaliana (http://www.plantgdb.org/AtGDB/), Arabidopsis lyrata (https://genome.jgi.doe.gov/Araly1), Chenopodium quinoa from Phytozome v12 (http://phytozome.jgi.doe.gov/pz/), Picea abies (http://congenie.org/) and Hordeum vulgare (http: […]

library_books

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

2017
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 [] [http://genome.crg.es/software/geneid/]. Both analyses were considered for the selection of microsatellites loca […]

call_split

Virus like attachment sites as structural landmarks of plants retrotransposons

2016
Mob DNA
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 […]

library_books

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

2012
BMC Genomics
PMCID: 3473312
PMID: 22748146
DOI: 10.1186/1471-2164-13-297

[…] We used the proteomes of S. cerevisiae from http://www.yeastgenome.org/, H. sapiens from http://www.ncbi.nlm.nih.gov, A. thaliana from http://www.plantgdb.org/AtGDB/ and E. histolytica from the http://amoebadb.org 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 […]

library_books

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

2010
BMC Plant Biol
PMCID: 3017805
PMID: 20565830
DOI: 10.1186/1471-2229-10-116

[…] SS and a perl script, MISA http://pgrc.ipk-gatersleben.de/misa/, respectively. For comparison, cDNA data of Arabidopsis and rice were downloaded from public databases PlantGDB http://www.plantgdb.org/AtGDB/ and NCBI ftp://ftp.ncbi.nih.gov, 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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