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Basic Information
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CGSNL Gene Symbol
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CENH3
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Gene Symbol Synonym
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OsCENH3, CenH3
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CGSNL Gene Name
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CENTROMERIC HISTONE 3C
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Gene Name Synonym
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centromeric histone H3, centromere-specific histone H3, centromere-specific H3 histone, centromere-specific histone H3
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Protein Name
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CENTROMERIC HISTONE 3C
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Allele
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Chromosome No.
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5
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Explanation
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Q6T367. AY438639. GQ849328-GQ849334 (wild rice species). HQ123577-HQ123579 (wild rice species). Oryza alta (D0EKP8, D0EKP9), Oryza australiensis (D0EKQ2), Oryza barthii (A0A0D3G978), Oryza glumipatula (A0A0E0A0Z6), Oryza latifolia (E2GIB7, E2GIB8), Oryza meridonalis (A0A0E0DTC0), Oryza meyeriana vra. Granulata (A0A6G1EGA2), Oryza minuta (DOEKQ0, D0EKQ1), Oryza nivara (A0A0E0HG58), Oryza officianalis (E2GIB6), Oryza punctata (D0EKQ3, A0A0E0L436), Oryza rhizomatis (D0EKQ4), Oryza rufipogon (A0A0E0PP98), Oryza sativa ssp indica (B8AZH6). GO:0080186: developmental vegetative growth. GO:0061458: reproductive system development.
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Trait Class
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Biochemical character
Reproductive organ - Heading date
Reproductive organ - Pollination, fertilization, fertility
Character as QTL - Plant growth activity
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Expression
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Sequence/Locus
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cDNA Accession No.
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AK101975
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MSU ID
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LOC_Os05g41080.1
LOC_Os05g41080.2
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RAP ID
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Os05g0489800
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Links
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Oryzabase Chromosome View
(
IRGSP 1.0
/
Build5
)
RAP-DB
(
IRGSP 1.0
/
Build5
)
Related IDs List (
IRGSP 1.0
/
Build5
)
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INSD Accession List
(Test version)
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Link to INSD Accession List
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Map
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Locate(cM)
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Link map
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Classical linkage map
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References
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Liang S., Jia S., Lu W., Wang J., Huang M., Chen C., Huang C., Zhou D., Guo T., Liu H.
Plant Cell Rep. 2025 44(8) 190
Generation and characterization of rice OsCENH3 mutants for haploid induction.
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Kaur K., Neelam K., Singh J., Malik P., Singh K.
Sci Rep 2023 13(1) 830
Uncovering natural allelic and structural variants of OsCENH3 gene by targeted resequencing and in silico mining in genus Oryza.
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Yi C., Zhang W., Dai X., Li X., Gong Z., Zhou Y., Liang G., Gu M.
Chromosome Res. 2013 21(8) 725-37
Identification and diversity of functional centromere satellites in the wild rice species Oryza brachyantha.
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Zhang T., Talbert P.B., Zhang W., Wu Y., Yang Z., Henikoff J.G., Henikoff S., Jiang J.
Proc. Natl. Acad. Sci. U.S.A. 2013 110(50) E4875-83
The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres.
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Wang M., Tang D., Luo Q., Jin Y., Shen Y., Wang K., Cheng Z.
Plant Cell 2012 24(12) 4961-73
brk1, a Bub1-related kinase, is essential for generating proper tension between homologous kinetochores at metaphase I of rice meiosis.
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Fan C., Walling J.G., Zhang J., Hirsch C.D., Jiang J., Wing R.A.
Plant Cell 2011 23(8) 2821-30
Conservation and purifying selection of transcribed genes located in a rice centromere.
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Wang M. , Tang D. , Wang K. , Shen Y. , Qin B. , Miao C. , Li M. , Cheng Z.
Plant J. 2011 67(4) 583-94
OsSGO1 maintains synaptonemal complex stabilization in addition to protecting centromeric cohesion during rice meiosis.
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Wu Y., Kikuchi S., Yan H., Zhang W., Rosenbaum H., Iniguez A.L., Jiang J.
Plant Cell 2011 23(11) 4054-64
Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription.
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Hui,L., Lu,L., Heng,Y., Qin,R., Xing,Y. and Jin,W.
J Genet Genomics 2010 37(10) 703-711
Expression of CENH3 alleles in synthesized allopolyploid Oryza species
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Hirsch,C.D., Wu,Y., Yan,H. and Jiang,J.
Mol. Biol. Evol. 2009 26(12) 2877-2885
Lineage-specific adaptive evolution of the centromeric protein CENH3 in diploid and allotetraploid Oryza species
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Yan H, Ito H, Nobuta K, Ouyang S, Jin W, Tian S, Lu C, Venu RC, Wang GL, Green PJ, Wing RA, Buell CR, Meyers BC, Jiang J.
Plant Cell 2006 18(9) 2123-33
Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere.
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Lee,H.R., Zhang,W., Langdon,T., Jin,W., Yan,H., Cheng,Z. and Jiang,J.
Proc. Natl. Acad. Sci. U.S.A. 2005 102 (33) 11793-11798
Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species
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Nagaki,K., Cheng,Z., Ouyang,S., Talbert,P.B., Kim,M., Jones,K.M., Henikoff,S., Buell,C.R. and Jiang,J.
Nat Genet 2004 36(2) 138-145
Sequencing of a rice centromere uncovers active genes.
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DB Reference
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Gramene ID
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-
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Ontologies
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Gene Ontology
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chromosome, centromeric region( GO:0000775 )
nucleosome( GO:0000786 )
nucleus( GO:0005634 )
DNA binding( GO:0003677 )
protein binding( GO:0005515 )
nucleosome assembly( GO:0006334 )
double fertilization forming a zygote and endosperm( GO:0009567 )
regulation of chromosome segregation( GO:0051983 )
kinetochore assembly( GO:0051382 )
structural constituent of chromatin( GO:0030527 )
protein heterodimerization activity( GO:0046982 )
kinetochore( GO:0000776 )
photoperiodism, flowering( GO:0048573 )
endosperm development( GO:0009960 )
embryonic development ending in seed dormancy( GO:0009793 )
gamete generation( GO:0007276 )
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Trait Ontology
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pollen fertility( TO:0000421 )
embryo development trait( TO:0000620 )
plant height( TO:0000207 )
flag leaf length( TO:0002757 )
days to heading( TO:0000137 )
flowering time( TO:0002616 )
seed set percent( TO:0000455 )
panicle length( TO:0000040 )
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Plant Ontology
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plant embryo stage( PO:0007631 )
endosperm development stage( PO:0007633 )
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Related Strains
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Phenotype images
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Last updated
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Dec 2, 2025
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Update info.