Community Annotation of Rice Gene Families

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 the Rice Genome Annotation Project. The community annotations are displayed in a tabular format on this page and also can be viewed along our Rice Genome Annotation as a track in the Rice Genome Browser.

If you would like to contribute rice community annotation to the Rice Genome Annotation Project web site, please go to the 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

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
ATP-dependent metalloprotease family
Contact: Steven Rodermel
Organization: Iowa State University
Summary: 1 family - 9 members+ Show Details
Source: Yu, F., Park, S., and Rodermel, S.R. (2005) Functional redundancy of AtFtsH metalloproteases in thylakoid membrane complexes. Plant Physiology 138:1957-1966.
ATP-dependent metalloprotease family (Homology to Filamentation temperature sensitive from E. coli)
Bric-A-Brac/Tramtrack/Broad Complex (BTB) Proteins
Contact: Derek Gingerich
Organization: University of Wisconsin-Eau Claire
Summary: 18 families - 146 members+ Show Details
Source: Gingerich DJ, Hanada K, Shiu SH, Vierstra RD (2007) Large-scale, lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice. Plant Cell 19(8):2329-48
BTB proteins with Meprin adn TRAF Homology (MATH) domain
BTB proteins with MATH domain
BTB proteins with A3 subfamily conserved domain
Armadillo repeats with a BTB domain
BTB proteins with tetratricopeptide repeats
BTB proteins with pentapeptide repeats
BTB proteins with B4 subfamily conserved domain
BTB proteins with TAZ zinc finger and calmodulin-binding domain
BTB proteins with C2 subfamily conserved domain
BTB proteins with C3 subfamily conserved domain
BTB proteins
Ankyrin repeat region with 2 BTB domains
BTB proteins with E1 subfamily conserved sequence
Protein with two BTB domains and a F5/8 type C (discoidin) domain
BTB protein with Ankyrin repeat region
BTB proteins with NPH3 domains
BTB Proteins with MATH domain
BTB proteins with H family conserved sequence
C2H2 zinc finger proteins
Contact: Sanjay Kapoor
Organization: University of Delhi, South Campus
Summary: 1 family - 179 members+ Show Details
Source: Agarwal P, Arora R, Ray S, Singh AK, Singh VP, Takatsuji H, Kapoor S, Tyagi AK (2007) Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis. Plant Mol. Biol. 65(4):467-85
C2H2 zinc finger proteins
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
Source: Boonburapong B and Buaboocha T (2007) Genome-wide identification and analysis of the rice camodulin and related potential calcium sensor proteins. BMC Plant Biology 7:4.
Rice calmodulins
Calmodulin-related sensor proteins
Cellulose Synthase Gene Family
Contact: Jonathan Walton
Organization: Michigan State University
Summary: 2 families - 45 members+ Show Details
Cellulose Synthase Family
Cellulose Synthase-like Family
Conserved peptide uORF-containing transcripts
Contact: Celine Hayden
Organization: University of Arizona
Summary: 1 family - 40 members+ Show Details
Source: Hayden CA and Jorgensen RA (2007) Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes. BMC Biology 5:32
Conserved peptide uORF-containing transcripts
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
Cysteine Rice Peptides
Contact: Kevin Silverstein
Organization: University of Minnesota
Summary: 28 families - 598 members+ Show Details
Source: Silverstein KAT, Moskal WA Jr, Wu H, Underwood BA, Graham MA, Town CD, and VandenBosch KA (2007) Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. Plant J. 51(2):262-80
Kazal-type serine protease inhibitor precursor
Kunitz-type trypsin inhibitor precursor
Antimicrobial peptide MBP-1 family protein precursor
Bowman-Birk type brain trypsin inhibitor
Chitinase family protein precursor
Cysteine-rich family protein precursor
Cysteine-rich protein with CXXC and CXXXC motifs precursor
Cysteine-rich protein with paired CXXXC motifs precursor
Defensin and defensin-like family
ECA1 gametogenesis related family protein precursor
Gibberellin-regulated GASA/GAST/Snakin family protein precursor
Glycine and cysteine rich family protein precursor
Hevein family protein precursor
Anther specific LEM1 family protein precursor
MTN26 protein family
Proteinase inhibitor II family protein precursor
Seed allergenic protein RA5/RA14/RA17
Root cap and late embryogenesis related protein family
Ripening-related family protein precursor
2S albumin seed storage family protein precursor
Stigma specific Stig1 family protein precursor
Wound induced protein precursor
Maternally expressed gene (MEG) family protein precursor
Prolamin precursor
Rapid alkalinization factor (RAFL) family protein precursor
Plant thionin family protein precursor
Pollen Ole e I allergen and extensin family protein precursor
Protease inhibitor/Seed storage/LTP family protein precursor
Early Auxin-responsive Aux/IAA Gene Family
Contact: Jitendra Khurana
Organization: University of Delhi
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
Early Auxin-responsive GH3 Gene Family
Contact: Jitendra Khurana
Organization: University of Delhi
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
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
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
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
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
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
Indole-3-acetic-acid synthetase family
Contact: Javier Terol
Organization: Centro de Genomica IVIA
Summary: 1 family - 13 members+ Show Details
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
LIM domain proteins
Contact: Dominique Arnaud
Organization: INRA-Orléans
Summary: 1 family - 6 members+ Show Details
Source: Arnaud D, Déjardin A, Leplé J-C, Lesage-Descauses M-C, and Pilate G (2007) Genome-wide analysis of LIM gene family in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa. DNA Research 14:103-116.
LIM domain proteins
Lipocalin Gene Family
Contact: Fathey Sarhan
Organization: University of Quebec at Montreal
Summary: 2 families - 3 members+ Show Details
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
MADS-box family
Contact: Sanjay Kapoor
Organization: University of Delhi, South Campus
Summary: 1 family - 75 members+ Show Details
MADS-box family
Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, Kapoor S. (2007) MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8:242.
MAP kinases with altered expression upon Magnaporthe grisea inoculation
Contact: Yinong Yang
Organization: Pennsylvania State University
Summary: 1 family - 17 members+ Show Details
Source: Reyna NS and Yang Y (2006) Molecular analysis of the rice MAP kinase gene family in relation to Magnaporthe grisea infection. Molecular Plant Microbe Interactions 19(5):530-540.
Rice MAP kinases with altered expression upon Magnaporthe grisea infection
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)
Phosphatidylethanolamine Binding Protein (PEBP) Gene Family
Contact: Fabien Chardon
Organization: INRA
Summary: 3 families - 18 members+ Show Details
Source: Chardon, F., Damerval, C. (2005) Phylogenomic analysis of the PEBP gene family in cereals. Journal of Molecular Evolution 61:579-590
Rice homologs of the Arabidopsis Flowering Locus T (FT)
Rice homologs of Mother of FT and TFL1 gene (MFT)
Rice CENTRORADIALIS-like homologs to the Arabidopsis TFL1 gene
Protein Disulfide Isomerase Superfamily
Contact: Norma Houston
Organization:North Carolina State University
Summary: 3 families - 19 members+ Show Details
Source: Norma L. Houston, Chuanzhu Fan, Qiu-Yun Xiang, Jan-Michael Schulze, Rudolf Jung, and Rebecca S. Boston (2005) Phylogenetic Analyses Identify 10 Classes of the Protein Disulfide Isomerase Family in Plants, Including Single-Domain Protein Disulfide Isomerase-Related Proteins. Plant Physiology 137: 762-778.
Protein Disulfide Isomerase Family
Adenylyl Sulfate Reductase Like Family
Quiesin-sulfhydryl Oxidase Family
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
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
Red Pericarp Gene of Rice
Contact: Susan McCouch
Organization: Cornell University
Summary: 1 family - 1 member+ 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
Rice Kinase Interactome
Contact: Pamela C. Ronald
Organization: University of California, Davis
Summary: 1 family - 150 members+ Show Details
Source: Ding X, Richter T, Chen M, Fujii H, Seo YS, Xie M, Zheng X, Kanrar S, Stevenson RA, Dardick C, Li Y, Jiang H, Zhang Y, Yu F, Bartley LE, Chern M, Bart R, Chen X, Zhu L, Farmerie WG, Gribskov M, Zhu JK, Fromm ME, Ronald PC, Song WY. (2009) A rice kinase-protein interaction map. Plant Physiol. 149(3):1478-92.

Rohila JS, Chen M, Chen S, Chen J, Cerny R, Dardick C, Canlas P, Xu X, Gribskov M, Kanrar S, Zhu JK, Ronald P, Fromm ME. (2006) Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice. Plant J. 46(1):1-13.

Rohila JS, Chen M, Chen S, Chen J, Cerny R, Dardick C, Canlas P, Fuji H, Gribskov M, Kanrar S, Knoflicek L, Stevenson B, Xie M, Xu X,Zheng X, Zhu J-K, Ronald P and Fromm ME. (2008) Protein-Protein Interactions of TAP-Tagged Protein Kinases in Rice. Under Revision for Molecular and Cellular Biology.
Rice Kinase Interactome
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
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
Source: Tripathi, LP and Sowdhamini R (2006) Cross genome comparisons of serine proteases in Arabidopsis and rice. BMC Genomics 7:200
Prolyl oligopeptidases
Serine carboxypeptidases
Serine beta-lactamases
Clp proteases
Lon proteases
Signal peptidases
Lysosomal Pro-x carboxypeptidases
C-terminal processing peptidases
Proteases IV
Rhomboid proteases
Nucleoporin autopeptidases
Small auxin-up gene family
Contact: Jitendra Khurana
Organization: University of Delhi
Summary: 1 family - 58 members+ Show Details
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
Topoisomerase 6 homologs
Contact: Jitendra Khurana
Organization: University of Delhi
Summary: 1 family - 4 members+ Show Details
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
Type-A Response Regulators
Contact: Jitendra Khurana
Organization: University of Delhi
Summary: 1 family - 10 members+ Show Details
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
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
WRKY Gene Superfamily
Contact: Jeff Shen
Organization: University of Nevada - Las Vegas
Summary: 1 family - 83 members+ Show Details
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

NSF Logo This work is supported by grants (DBI-0321538/DBI-0834043) from the National Science Foundation.