 |
 |
Community annotation of rice gene families are provided by members of the rice community who have curated rice gene families and submitted their functional and/or structural annotation to TIGR. The community annotations are displayed in a tabular format on this page and also can be viewed along our the TIGR Annotation as a track in the Rice Genome Browser.
If you would like to contribute rice community annotation to the TIGR rice site, please go to the TIGR Rice Community Annotation Information page to learn more about the web based community annotation tool or bulk submissions of rice gene family community annotations.
Rice Gene Families
|
|
|
|
|
|
| Source: Zhen Xie, Zhong-Lin Zhang, Xiaolu Zou, Jie Huang, Paul Ruas, Daniel Thompson, and Qingxi J. Shen (2005) Annotations and Functional Analyses of the Rice WRKY Gene Superfamily Reveal Positive and Negative Regulators of Abscisic Acid Signaling in Aleurone Cells Plant Physiol. 137: 176-189 |
| WRKY Gene Superfamily |
|
|
| Wall-associated Kinases |
| Contact: Shibo Zhang |
| Organization: UC - Berkeley |
| Summary: 1 family - 144 members | + Show Details |
|
| Source: Shibo Zhang, Calvin Chen, Lei Li, Ling Meng, Jaswinder Singh, Ning Jiang, Xing-Wang Deng, Zheng-Hui He, and Peggy G. Lemaux (2005) Evolutionary Expansion, Gene Structure, and Expression of the Rice Wall-Associated Kinase Gene Family Plant Physiol. 139: 1107-1124. |
| Wall-associated Kinases gene family |
|
|
| Ascorbate Peroxidase (APx) Family |
| Contact: Marcia Margis-Pinheiro |
| Organization: Universidade Federal do Rio Grande do Sul (UFRGS) |
| Summary: 1 family - 8 members | + Show Details |
|
Source: Teixeira, F.K., Menezes-Benaventa, L., Margis, R. and Margis-Pinheiro, M. (2004) Analysis of the Molecular Evolutionary History of the Ascobrate Peroxidase Gene Family: Inferences from the Rice Genome. J Mol Evol 59:761-770.
Teixeira,F.K., Menezes-Benavente,L., Galvao,V.C., Margis,R., Margis-Pinheiro,M. (2006) Rice ascorbate peroxidase gene family encodes functionally diverse isoforms localized in different subcellular compartments. Planta DOI 10.1007/s00425-005-0214-8. |
| Ascorbate Peroxidase (APx) Family |
|
|
| Cellulose Synthase Gene Family |
| Contact: Jonathan Walton |
| Organization: Michigan State University |
| Website: http://www.prl.msu.edu/walton.shtml |
| Summary: 2 families - 45 members | + Show Details |
|
|
|
|
|
Source: Sweeney, M.T., Thomson, M.J., Pfiel, B.E., McCouch, S.R. (2006) Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell. 18:283-294.
|
| Red Pericarp Gene of Rice |
|
|
|
|
| Source:
Charron, J.-B. F., Ouellet, F., Pelletier, M., Chauve, C., Sarhan, F. (2005) Identification, expression, and evolutionary analyses of plant lipocalins. Plant Physiology 139:2017-2028.
|
| Temperature Induced Lipocalins |
| Chloroplastic Lipocalins |
|
|
| Phosphatidylethanolamine Binding Protein (PEBP) Gene Family |
| Contact: Fabien Chardon |
| Organization: INRA |
| Summary: 3 families - 18 members | + Show Details |
|
|
|
|
|
|
|
| Early Auxin-responsive GH3 Gene Family |
| Contact: Jitendra Khurana |
| Organization: University of Delhi |
| Website: http://genomeindia.org/DPMB/index.htm |
| Summary: 1 family - 14 members | + Show Details |
|
| Source:
Jain, M., Kaur, N., Tyagi, A.K. and Khurana, J.P. (2006) The auxin responsive GH3 gene family in rice (Oryza sativa). Funct Integr Genomics 6(1):47-59
|
| Early Auxin-responsive GH3 Gene Family |
|
|
| Early Auxin-responsive Aux/IAA Gene Family |
| Contact: Jitendra Khurana |
| Organization: University of Delhi |
| Website: http://genomeindia.org/DPMB/index.htm |
| Summary: 1 family - 31 members | + Show Details |
|
| Source:
Jain, M., Kaur, N., Garg, R., Thakur, J.K., Tyagi, A.K., and Khurana, J.P. (2006) Strucutre and expression analysis of early auxin responsive Aux/IAA gene family in rice (Oryza sativa). Funct Integ Genomics 6:47-59.
|
| Early Auxin-responsive Aux/IAA Gene Family |
|
|
|
|
| Source:
Jain, M., Tyagi, A.K., and Khurana, J.P. (2006) Molecular characterization and differential expression of cytokinin-responsive type-A response regulators of rice (Oryza sativa). BMC Plant Biology. 6:1
|
| Rice Type-A Response Regulators |
|
|
| Mitogen-Activated Protein Kinases (MAPKs) and MAPK kinases (MAPKKs) |
| Contact: Brian Ellis |
| Organization: University of British Columbia |
| Summary: 2 families - 23 members | + Show Details |
|
| Source:
Louis-Philippe Hamel, Marie-Claude Nicole, Somrudee Sritubtim, Marie-Josee Morency, Margaret Ellis, Juergen Ehlting, Nathalie Beaudoin, Brad Barbazuk, Dan Klessig, Justin Lee, Greg Martin, John Mundy, Yuko Ohashi, Dierk Scheel, Jen Sheen, Tim Xing, Shuqun Zhang, Armand Seguin and Brian E. Ellis. (2006) Ancient signals: comparative genomics of plant MAPK and MAPKK gene families. Trends in Plant Science 11(4):192-8 |
| Rice homologs of Arabidopsis MAPKs (Mitogen-Activated Protein Kinases) |
| Rice homologs of Arabidopsis MAPKKs (Mitogen-Activated Protein Kinase Kinases) |
|
|
| Protein Phosphatase 2A family |
| Contact: Richard Yu |
| Organization: City University of Hong Kong |
| Summary: 1 family - 5 members | + Show Details |
|
| Source:
Yu, R.M.K., Wong, M.M.L., Jack, R.W. and Kong, R.Y.C. (2005) Structure, evolution and expression of a second subfamily of protein phosphatase 2A catalytic subunit gnees in the rice plant (Oryza sativa). Planta. 222:757-768.
|
| Rice Protein Phosphatase 2A family |
|
|
| Glutaredoxin family |
| Contact: Nicolas Rouhier |
| Organization: Nancy University |
| Summary: 1 family - 28 members | + Show Details |
|
| Source:
Rouhier, N., Couturier, J., and Jacquot, J-P. (2006) Genome-wide analysis of plant glutaredoxin systems. Journal of Experimental Botany 57(8):1685-96.
|
| Glutaredoxin family |
|
|
|
|
| Source:
Terol, J., Domingo, C., and Talon, M. (2006) The GH3 family in plants: Genome wide analysis in rice and evolutionary history based upon EST anlaysis. Gene 371:270-290.
|
| Indole-3-acetic-acid synthetase family |
|
|
|
|
| Source:
Jain, M., Tyagi, A.K., and Khurana, J.P. (2006) Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice (Oryza sativa) Genomics 88:360-371
|
| Small auxin-up gene family |
|
|
|
|
| Source:
Jain, M., Tyagi, AK, and Khurana, JP (2006) Overexpression of putative topoisomerase 6 genes from rice confers stress tolerance in transgenic Arabidopsis plants.FEBS J 273(23):5245-60.
|
| Topoisomerase 6 gene family |
|
|
| Calmodulin and calmodulin-related calcium sensor proteins |
| Contact: Teerapong Buaboocha |
| Organization: Department of Biochemistry, Faculty of Science, Chulalongkorn University |
| Summary: 2 families -37 members | + Show Details |
|
|
|
| MAP kinases with altered expression upon Magnaporthe grisea inoculation |
| Contact: Yinong Yang |
| Organization: Pennsylvania State University |
| Summary: 1 family - 17 members | + Show Details |
|
|
|
| HKT transporters |
| Contact: Olivier Cotsaftis |
| Organization: Australian Center for Plant Functional Genomics and University of Adelaide |
| Summary: 1 family - 8 members | + Show Details |
|
| Source:
Platten JD, Cotsaftis O, Berthomieu P, Bohnert H, Davenport RJ, Fairbairn, DJ, Horie T, Leigh RA, Lin HX, Luan S, Maser P, Pantoja O, Rodriguez-Navarro A, Schachtman DP, Schroeder JI, Sentenac H, Uozumi N, Very AA, Zhu JK, Dennis ES, Tester M (2006) Nomenclature for HKT transporters, key determinants of plant salinity tolerance. Trends Plant Sci. 11(8):372-4
|
| Rice HKT transporters |
|
|
| Cysteine Rice Peptides |
| Contact: Kevin Silverstein |
| Organization: University of Minnesota |
| Summary: 28 families - 598 members | + Show Details |
|
|
|
| Endo-Beta-Mannanases |
| Contact: Joshua Yuan |
| Organization: University of Tennessee |
| Summary: 1 family - 9 members | + Show Details |
|
| Source:
Yuan JS, Yang X, Lai J, Lin H, Cheng Z-M, Nonogaki H, Chen F (2006) The Endo-Beta-Mannanase gene families in Arabidopsis, rice, and poplar. Funct Integr Genomics 7:1-16
|
| Rice Endo- Beta-Mannanases |
|
|
| Serine Proteases |
| Contact: R. Sowdhamini |
| Organization: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India |
| Summary: 13 families - 222 members | + Show Details |
|
|
|
| Core Replication Machinery Proteins |
| Contact: Randall Shultz |
| Organization: North Carolina State University |
| Summary: 1 family - 58 members | + Show Details |
|
| Source:
Shultz, RW, Tatineni, VM, Hanely-Bowdoin, L, Thompson, WF (2007) Genome-wide Analysis of the Core DNA Replication Machinery in the Higher Plants Arabidopsis thaliana and Oryza sativa. Plant Physiology 144(4):1697-714
|
| Core Replication Machinery Proteins |
|
|
| Glycosyl Hydrolase Family 1 Beta-Glucosidases |
| Contact: James Ketudat Cairns |
| Organization: Suranaree University of Technology, Nakhon Ratachasima, Thailand |
| Summary: 1 family - 38 members | + Show Details |
|
| Source:
Opassiri R, Pomthong B, Onkoksoong T, Akiyama T, Esen A, Ketudat Cairns JR (2006) Analysis of rice glycosyl hydrolase family 1 and expression of Os4bglu12 beta-glucosidase. BMC Plant Biology 6:33
|
| Glycosyl Hydrolase Family 1 Beta-Glucosidases |
|
|
| SBP-Box Proteins |
| Contact: Chenwu Xu |
| Organization: Yangzhou University, Yangzhou, China |
| Summary: 1 family - 19 members | + Show Details |
|
| Source:
Y Yang Z, Wang X, Gu S, Hu Z, Xu H, Xu C. (2007) Comparative study of SBP-box gene family in Arabidopsis and rice. Gene Apr 18; [Epub ahead of print]
|
| SBP-Box Proteins |
|
|
| F-Box Proteins |
| Contact: Jitendra Khurana |
| Organization: University of Delhi, New Dehli, India |
| Summary: 10 families - 687 members | + Show Details |
|
| Source:
Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiology 143(4):1467-83
|
| F-Box Domain Containing Proteins |
| F-Box and Leucine-Rich-Repeats Containing Proteins |
| F-box and Kelch Repeats Containing Proteins |
| F-box and Fibrin-Binding Domain Containing Proteins |
| F-box and TUB Domain Containing Proteins |
| F-box, Leucine-Rich-Repeats and Fibrin-Binding Domain Containing Proteins |
| F-Box and F-Box-Associated-Domain Containing Proteins |
| F-Box and WD40-Repeats Containing Proteins |
| F-Box and Domain of Unknown Function Containing Proteins |
| F-Box and Other Domains Containing Proteins |
|
|
| RCI2 Homologs |
| Contact: Joachin Medina Alcazar |
| Organization: INIA, Madrid, Spain |
| Summary: 1 family - 12 members | + Show Details |
|
| Source:
Medina J, Ballesteros ML and Salinas J (2007) Phylogenetic and functional analysis of Arabidopsis RCI2 genes. J. Exp Bot. In press.
|
| RCI2 Homologs |
|
|
|
