Alpha 2.0
Login Register
» Articles » PMID: 16381971

The Rice Annotation Project Database (RAP-DB): Hub for Oryza Sativa Ssp. Japonica Genome Information

Overview
Journal Nucleic Acids Res
Publisher Oxford University Press
Specialty Biochemistry
Date 2005 Dec 31
PMID 16381971
Citations 94
Authors
Hajime Ohyanagi
Tsuyoshi Tanaka
Hiroaki Sakai
Yasumasa Shigemoto
Kaori Yamaguchi
Takuya Habara
Yasuyuki Fujii
Baltazar A Antonio
Yoshiaki Nagamura
Tadashi Imanishi
Kazuho Ikeo
Takeshi Itoh
Takashi Gojobori
Takuji Sasaki
Affiliations
Soon will be listed here.
Abstract

With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through http://rapdb.lab.nig.ac.jp/.

Citing Articles

Breeding of a promising isogenic line of rice ( L.) variety 'Koshihikari' with low cadmium and brown spot () resistance.

Mizobuchi R, Ohashi S, Matsumoto K, Ota Y, Yamakawa T, Abe T Breed Sci. 2025; 74(5):462-467.

PMID: 39897662 PMC: 11780335. DOI: 10.1270/jsbbs.24027.

Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 () Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance.

Al-Bader N, Meier A, Geniza M, Gongora Y, Oard J, Jaiswal P Genes (Basel). 2023; 14(9).

PMID: 37761813 PMC: 10530950. DOI: 10.3390/genes14091673.

Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes.

Imbert B, Kreplak J, Flores R, Aubert G, Burstin J, Tayeh N Front Artif Intell. 2023; 6:1191122.

PMID: 37601035 PMC: 10435283. DOI: 10.3389/frai.2023.1191122.

High-quality reference transcriptome construction improves RNA-seq quantification in indica.

Srikakulam N, Sridevi G, Pandi G Front Genet. 2022; 13:995072.

PMID: 36246658 PMC: 9558114. DOI: 10.3389/fgene.2022.995072.

Improvement of millets in the post-genomic era.

Ajeesh Krishna T, Maharajan T, Ceasar S Physiol Mol Biol Plants. 2022; 28(3):669-685.

PMID: 35465206 PMC: 8986959. DOI: 10.1007/s12298-022-01158-8.

References
1.
Imanishi T, Itoh T, Suzuki Y, ODonovan C, Fukuchi S, Koyanagi K . Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2004; 2(6):e162. PMC: 393292. DOI: 10.1371/journal.pbio.0020162. View
2.
Moore G, Devos K, Wang Z, Gale M . Cereal genome evolution. Grasses, line up and form a circle. Curr Biol. 1995; 5(7):737-9. DOI: 10.1016/s0960-9822(95)00148-5. View
3.
Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View
4.
Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H . The institute for genomic research Osa1 rice genome annotation database. Plant Physiol. 2005; 138(1):18-26. PMC: 1104156. DOI: 10.1104/pp.104.059063. View
5.
Dowell R, Jokerst R, Day A, Eddy S, Stein L . The distributed annotation system. BMC Bioinformatics. 2001; 2:7. PMC: 58584. DOI: 10.1186/1471-2105-2-7. View