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Protocols

Oryzabase specifications

Information


Unique identifier OMICS_03278
Name Oryzabase
Restrictions to use None
Maintained Yes

Taxon


  • Plants and Fungi
    • Oryza sativa

Publication for Oryzabase

Oryzabase citations

 (7)
library_books

Genome wide analyses of direct target genes of four rice NAC domain transcription factors involved in drought tolerance

2018
BMC Genomics
PMCID: 5767043
PMID: 29329517
DOI: 10.1186/s12864-017-4367-1

[…] f an AtNAC TF, ANAC092/AtNAC2/ORE1 []. We also identified an ENODL gene (Os06g0681200), which is associated with root architecture by trait ontology in the NBRP database (http://shigen.nig.ac.jp/rice/oryzabase/), as being involved in drought tolerance (Table ). Among the direct targets were also four genes (Os03g0216700, Os03g0571900, Os10g0195000 and Os06g0494400) encoding a multi antimicrobial e […]

library_books

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement

2017
BMC Bioinformatics
PMCID: 5622590
PMID: 28964253
DOI: 10.1186/s12859-017-1846-y

[…] nd.meiji.ac.jp/OryzaExpress/ ), RicePLEX ([], http://www.plexdb.org/plex.php?database=Rice ), Rice Oligonucleotide Array database (ROAD) [], RiceSRTFDB ([], http://www.nipgr.res.in/RiceSRTFDB.html ), Oryzabase ([], http://shigen.nig.ac.jp/rice/oryzabase/ ), QlicRice ([], http://nabg.iasri.res.in:8080/qlic-rice ), OryGenesDB ([], http://orygenesdb.cirad.fr/ ), RiceXPro ([], http://ricexpro.dna.affr […]

call_split

Shotgun proteomics of the barley seed proteome

2017
BMC Genomics
PMCID: 5219712
PMID: 28061743
DOI: 10.1186/s12864-016-3408-5
call_split See protocol

[…] e Uniprot identifiers were then used to identify the corresponding TIGR loci using Biomart tool in the Phytozome database (https://phytozome.jgi.doe.gov/biomart/martview), Rice ID checker tool in the Oryzabase (http://shigen.nig.ac.jp/rice/oryzabase/tool/riceIdChecker/search) and the Rice Pseudomolecule Version Converter tool in the MSU rice database (http://rice.plantbiology.msu.edu/analyses_sear […]

library_books

High resolution QTL mapping for grain appearance traits and co localization of chalkiness associated differentially expressed candidate genes in rice

2016
PMCID: 5033801
PMID: 27659284
DOI: 10.1186/s12284-016-0121-6

[…] ted to be sharply down-regulated in the L-Pool and PYZX compared to the H-Pool and P02428. OsUAM3 gene has an annotated as having UDP-arabinopyranose mutase activity (http://www.shigen.nig.ac.jp/rice/oryzabase/) and was predicted to be analpha-1,4-glucan-protein synthase and UDP-glucose/protein transglucosylase 1 (http://rapdb.dna.affrc.go.jp/). Given that carbohydrate metabolism is considered to […]

library_books

JAZ Repressors: Potential Involvement in Nutrients Deficiency Response in Rice and Chickpea

2015
Front Plant Sci
PMCID: 4639613
PMID: 26617618
DOI: 10.3389/fpls.2015.00975

[…] the protein blast and HMM searches. The identified chickpea JAZs were named according to their homology with Arabidopsis JAZs (Table ; Figure ). The chromosomal localization of JAZs was analyzed with Oryzabase for rice. Fifteen JAZs were located on six chromosomes. Five OsJAZ genes were present on chromosome 3, two each on chromosome 4 and 7, one on chromosome 8, two on chromosome 9, and three on […]

library_books

cDNA AFLP analysis of gene expression differences between the flower bud and sprout shoot apical meristem of Angelica sinensis (Oliv.) Diels

2011
Genet Mol Biol
PMCID: 3115322
PMID: 21734829
DOI: 10.1590/S1415-47572011000200018

[…] es from 26 TDFs were selected and sequenced. The resultant sequences were analyzed for homologs by BLAST searches against public nonredundant databases (GenBank, Arabidopsis Information Resource, and Oryzabase) using BLASTN and BLASTX algorithms (Altschul et al.,1997).Semi-quantitative reverse transcription-PCR (sqRT-PCR) was carried out on 2 μg of total RNA, by using a two-step RT-PCR kit (Takara […]

Citations

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Oryzabase institution(s)
Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan

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