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The following term was not found in PMC: RiceAnnotation.

Select item 67641011.

RiceRelativesGD: a genomic database of rice relatives for rice research

Lingfeng Mao, Meihong Chen, Qinjie Chu, Lei Jia, Most Humaira Sultana, Dongya Wu, Xiangdong Kong, Jie Qiu, Chu-Yu Ye, Qian-Hao Zhu, Xi Chen, Longjiang Fan

Database (Oxford) 2019; 2019: baz110. Published online 2019 Sep 27. doi: 10.1093/database/baz110

PMCID:: PMC6764101

Abstract Article PDF–874K

Select item 77061802.

ThRSDB: a database of Thai rice starch composition, molecular structure and functionality

Kwanjeera Wanichthanarak, Maysaya Thitisaksakul

Database (Oxford) 2020; 2020: baaa068. Published online 2020 Dec 1. doi: 10.1093/database/baaa068

PMCID:: PMC7706180

Abstract Article PDF–2.1M

Select item 93565363.

NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions

Sanchari Sircar, Mayank Musaddi, Nita Parekh

Database (Oxford) 2022; 2022: baac060. Published online 2022 Aug 6. doi: 10.1093/database/baac060

PMCID:: PMC9356536

Abstract Article PDF–8.2M

Select item 35830254.

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

Hiroaki Sakai, Sung Shin Lee, Tsuyoshi Tanaka, Hisataka Numa, Jungsok Kim, Yoshihiro Kawahara, Hironobu Wakimoto, Ching-chia Yang, Masao Iwamoto, Takashi Abe, Yuko Yamada, Akira Muto, Hachiro Inokuchi, Toshimichi Ikemura, Takashi Matsumoto, Takuji Sasaki, Takeshi Itoh

Plant Cell Physiol. 2013 Feb; 54(2): e6. Published online 2013 Jan 7. doi: 10.1093/pcp/pcs183

PMCID:: PMC3583025

Abstract Article PDF–1.6M

Select item 85540985.

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

Zahra Iqbal, Mohammed Shariq Iqbal, M. Iqbal R. Khan, Mohammad Israil Ansari

Front Plant Sci. 2021; 12: 741419. Published online 2021 Oct 15. doi: 10.3389/fpls.2021.741419

PMCID:: PMC8554098

Abstract Article PDF–1.5M

Select item 96303316.

Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger

Mushtaq Ahmad

Front Plant Sci. 2022; 13: 1002596. Published online 2022 Oct 20. doi: 10.3389/fpls.2022.1002596

PMCID:: PMC9630331

Abstract Article PDF–2.0M

Select item 36496417.

RiceSRTFDB: A database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis

Pushp Priya, Mukesh Jain

Database (Oxford) 2013; 2013: bat027. Published online 2013 May 9. doi: 10.1093/database/bat027

PMCID:: PMC3649641

Abstract Article PDF–462K

Select item 110091578.

Oryza CLIMtools: A genome–environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits

Ángel Ferrero-Serrano, David Chakravorty, Kobie J. Kirven, Sarah M. Assmann

Plant Commun. 2024 Apr 8; 5(4): 100813. Published online 2024 Jan 11. doi: 10.1016/j.xplc.2024.100813

PMCID:: PMC11009157

Abstract Article PDF–8.8M

Select item 43833479.

LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study

Kun Wang, Jiao Deng, Rebecca Njeri Damaris, Mei Yang, Liming Xu, Pingfang Yang

Database (Oxford) 2015; 2015: bav023. Published online 2015 Mar 27. doi: 10.1093/database/bav023

PMCID:: PMC4383347

Abstract Article PDF–1.5M

Select item 641194810.

Rice Genomics: over the Past Two Decades and into the Future

Shuhui Song, Dongmei Tian, Zhang Zhang, Songnian Hu, Jun Yu

Genomics Proteomics Bioinformatics. 2018 Dec; 16(6): 397–404. Published online 2019 Feb 13. doi: 10.1016/j.gpb.2019.01.001

PMCID:: PMC6411948

Abstract Article PDF–780K

Select item 954753811.

HSDatabase—a database of highly similar duplicate genes from plants, animals, and algae

Xi Zhang, Yining Hu, David Roy Smith

Database (Oxford) 2022; 2022: baac086. Published online 2022 Oct 8. doi: 10.1093/database/baac086

PMCID:: PMC9547538

Abstract Article PDF–3.5M

Select item 546754312.

PCPPI: a comprehensive database for the prediction of Penicillium–crop protein–protein interactions

Junyang Yue, Danfeng Zhang, Rongjun Ban, Xiaojing Ma, Danyang Chen, Guangwei Li, Jia Liu, Michael Wisniewski, Samir Droby, Yongsheng Liu

Database (Oxford) 2017; 2017: baw170. Published online 2017 Feb 26. doi: 10.1093/database/baw170

PMCID:: PMC5467543

Abstract Article PDF–811K

Select item 550245513.

The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies

Guotian Li, Rashmi Jain, Mawsheng Chern, Nikki T. Pham, Joel A. Martin, Tong Wei, Wendy S. Schackwitz, Anna M. Lipzen, Phat Q. Duong, Kyle C. Jones, Liangrong Jiang, Deling Ruan, Diane Bauer, Yi Peng, Kerrie W. Barry, Jeremy Schmutz, Pamela C. Ronald

Plant Cell. 2017 Jun; 29(6): 1218–1231. Published online 2017 Jun 2. doi: 10.1105/tpc.17.00154

PMCID:: PMC5502455

Abstract Article PDF–1.6M

Select item 134745614.

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information

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

Nucleic Acids Res. 2006 Jan 1; 34(Database issue): D741–D744. Published online 2005 Dec 28. doi: 10.1093/nar/gkj094

PMCID:: PMC1347456

Abstract Article PDF–330K

Select item 1123210415.

Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome

Kerry A. Ramsbottom, Ananth Prakash, Yasset Perez-Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J. Kundu, Emily Bowler-Barnett, Maria Martin, Jun Fan, Dmytro Chebotarov, Kenneth L. McNally, Eric W. Deutsch, Juan Antonio Vizcaíno, Andrew R. Jones

J Proteome Res. 2024 Jul 5; 23(7): 2518–2531. Published online 2024 May 29. doi: 10.1021/acs.jproteome.4c00187

PMCID:: PMC11232104

Abstract Article PDF–7.1M

Select item 641966616.

Infrastructures of systems biology that facilitate functional genomic study in rice

Woo-Jong Hong, Yu-Jin Kim, Anil Kumar Nalini Chandran, Ki-Hong Jung

Rice (N Y) 2019; 12: 15. Published online 2019 Mar 14. doi: 10.1186/s12284-019-0276-z

PMCID:: PMC6419666

Abstract Article PDF–799K

Select item 1068082917.

A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome

Kerry A Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J. Kundu, Emily Bowler-Barnett, Maria Martin, Jun Fan, Dmytro Chebotarov, Kenneth L McNally, Eric W Deutsch, Juan Antonio Vizcaíno, Andrew R Jones

Version 1. bioRxiv. Preprint. 2023 Nov 17. doi: 10.1101/2023.11.17.567512

Published in:: J Proteome Res. 2024 Jul 5; 23(7): 2518–2531.

PMCID:: PMC10680829

Abstract Article PDF–7.4M

Select item 692818218.

Rice Stress-Resistant SNP Database

Samuel Tareke Woldegiorgis, Shaobo Wang, Yiruo He, Zhenhua Xu, Lijuan Chen, Huan Tao, Yu Zhang, Yang Zou, Andrew Harrison, Lina Zhang, Yufang Ai, Wei Liu, Huaqin He

Rice (N Y) 2019; 12: 97. Published online 2019 Dec 23. doi: 10.1186/s12284-019-0356-0

PMCID:: PMC6928182

Abstract Article PDF–1.9M

Select item 727224319.

Current status of genomic resources on wild relatives of rice

Richa Kamboj, Balwant Singh, Tapan Kumar Mondal, Deepak Singh Bisht

Breed Sci. 2020 Apr; 70(2): 135–144. Published online 2020 Mar 19. doi: 10.1270/jsbbs.19064

PMCID:: PMC7272243

Abstract Article PDF–642K

Select item 1048583320.

Fine mapping and sequence analysis reveal a promising candidate gene encoding a novel NB-ARC domain derived from wild rice (Oryza officinalis) that confers bacterial blight resistance

Pragya Sinha, Dilip Kumar T., Hajira Sk, Manish Solanki, C. G. Gokulan, Ayyappa Das, Anila Miriyala, Rekha Gonuguntala, Punniakoti Elumalai, Kousik M. B. V. N, Masthani S. K., Chaitra Kumboju, Yugander Arra, Laha G. S., N. Neerja Chirravuri, Hitendra Kumar Patel, Irfan Ahmad Ghazi, Sung-Ryul Kim, Kshirod K. Jena, Surekha Rani Hanumanth, Ricardo Oliva, Satendra K. Mangrauthia, Raman Menakshi Sundaram

Front Plant Sci. 2023; 14: 1173063. Published online 2023 Aug 25. doi: 10.3389/fpls.2023.1173063

PMCID:: PMC10485833

Abstract Article PDF–1.0M

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PMC Images search for RiceAnnotation Project DataBase (RAP-DB): An integrative and interactive database for rice genomics.

Fig. 4

Integrative Database of Cereal Gene Phylogeny (IDCGP). (A) Main window of IDCGP showing the phylogenetic trees, hyperlinks to the downloadable data and buttons for adding sequences and editing multiple sequence alignments. (B) A window for editing multiple sequence alignments.

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

Plant Cell Physiol. 2013 Feb;54(2):e6-e6.
Fig. 2

Gene details view. The ‘Details’ tab shows the detailed annotation information including the literature-based manual curation data. The ‘DB references’ tab provides hyperlinks to the external databases including the two satellite databases, Plant Gene Family Database and Integrative Database of Cereal Gene Phylogeny.

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

Plant Cell Physiol. 2013 Feb;54(2):e6-e6.
Fig. 3

Short-Read Assembly Browser (S-RAB). The S-RAB window consists of (i) a Gene information view (upper left); (ii) an Alignment view (bottom); and (iii) a Short-read information view (upper right).

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

Plant Cell Physiol. 2013 Feb;54(2):e6-e6.
Fig. 1

Gene map view. In RNA-Seq tracks, gene expression levels are shown as a histogram generated from the depth of mapped reads. At the bottom, two tracks, ‘Koshihikari’ and ‘Guangluai-4’, are linked to the Short-Read Assembly Browser.

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

Plant Cell Physiol. 2013 Feb;54(2):e6-e6.

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