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RAP-DB specifications

Information


Unique identifier OMICS_04479
Name RAP-DB
Alternative name Rice Annotation Project Database
Restrictions to use None
Maintained Yes

Taxon


  • Plants and Fungi
    • Oryza sativa

Maintainer


  • person_outline Takeshi Itoh

Publication for Rice Annotation Project Database

RAP-DB citations

 (62)
library_books

Joint Exploration of Favorable Haplotypes for Mineral Concentrations in Milled Grains of Rice (Oryza sativa L.)

2018
Front Plant Sci
PMCID: 5906679
PMID: 29706977
DOI: 10.3389/fpls.2018.00447

[…] l., ). The regions containing the jointly detected QTLs were then subjected to candidate gene analysis. (2) We searched the regions in the annotation dataset with wet-lab supporting evidence from the Rice Annotation Project database (RAP-DB) (Ohyanagi et al., ). (3) We then screened the genes by annotation information. If there were any obvious supporting evidence from the functional annotation, r […]

library_books

Transcriptome Analysis of Two Rice Varieties Contrasting for Nitrogen Use Efficiency under Chronic N Starvation Reveals Differences in Chloroplast and Starch Metabolism Related Genes

2018
Genes
PMCID: 5924548
PMID: 29641510
DOI: 10.3390/genes9040206

[…] ns were subtracted from the total DEGs identified. For functional descriptions of the DEGs identified, the Cufflink gene IDs were first converted into both the Michigan State University (MSU) and the Rice Annotation Project Database (RAP-DB) IDs and the functional descriptions available in these two databases were made use of. For further understanding of the coordination of the gene expression un […]

call_split

Overexpression of OsNAC14 Improves Drought Tolerance in Rice

2018
Front Plant Sci
PMCID: 5855183
PMID: 29593766
DOI: 10.3389/fpls.2018.00310
call_split See protocol

[…] nd those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., ). To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/tophat/index.shtml). After mapping reads to a reference genome differentially expresse […]

call_split

QTL mapping and candidate gene analysis of peduncle vascular bundle related traits in rice by genome wide association study

2018
PMCID: 5840110
PMID: 29511908
DOI: 10.1186/s12284-018-0204-7
call_split See protocol

[…] D block where the significant trait-associated SNPs were situated was defined as the candidate gene regions. We can find all the genes located in the candidate regions for each important QTL from the Rice Annotation Project Database (RAP-DB).Secondly, all available non-synonymous SNPs located inside of these genes were searched from 32 M SNPs data generated from 3 K RGP in the Rice SNP-Seek Databa […]

library_books

Comparative Transcriptome Profiling of Rice Near Isogenic Line Carrying Xa23 under Infection of Xanthomonas oryzae pv. oryzae

2018
Int J Mol Sci
PMCID: 5877578
PMID: 29498672
DOI: 10.3390/ijms19030717

[…] Different genes from DEGs were selected to validate the RNA-Seq data. The corresponding sequences of the selected genes were retrieved from rice annotation project database. Primers of the DEGs were designed according to the transcript sequences by using AmplifX 1.5.4 software [], and primers used in the experiment are listed in . Moreove […]

call_split

Expression Profiling of Ribosomal Protein Gene Family in Dehydration Stress Responses and Characterization of Transgenic Rice Plants Overexpressing RPL23A for Water Use Efficiency and Tolerance to Drought and Salt Stresses

2017
PMCID: 5694489
PMID: 29184886
DOI: 10.3389/fchem.2017.00097
call_split See protocol

[…] The sequences of all the ribosomal protein-encoding genes of rice (RPL and RPS) were retrieved from RGAP-DB. The sequence identification and validation in RAP-DB, NCBI, and some other databases were carried out as described in Moin et al. (,) and Saha et al. () to ensure their specificity. Primers were designed specifically for each of the identified ge […]

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