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Basic Information
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CGSNL Gene Symbol
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CCA1
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Gene Symbol Synonym
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OsCCA1, OsLHY, LHY, LHY-like_chr.8, COC1, DLN203, OsDLN203, LEM1, OsLEM1, Nhd1, OsNhd1
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CGSNL Gene Name
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CIRCADIAN CLOCK ASSOCIATED 1
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Gene Name Synonym
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LATE ELONGATED HYPOCOTYL, DLN repressor 203, DLN motif protein 203, lvp1 enhancer mutant 1, N-mediated heading date1
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Protein Name
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DLN REPRESSOR 203
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Allele
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oslhy, lem1, oscca1, oscca1-1, oscca1-2, nhd1, nhd1-1, nhd1-2, nhd1-3
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Chromosome No.
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8
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Explanation
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AY885916-AY885946 and DQ374829-DQ374856 (O. sativa and other wild rice species, partial ads). BF889434. a rice ortholog of Arabidopsis gene for circadian clock component. the single ortholog of Arabidopsis LHY/CCA1. a CCA1 ortholog in rice.a conserved MYB domain-containing transcription factor. GO:1902347: response to strigolactone. TO:0000739: shoot axis morphology trait. TO:0000847: panicle inflorescence morphology trait. GO:2000028: regulation of photoperiodism, flowering. GO:1902347: response to strigolactone. GO:1901698: response to nitrogen compound. GO:1904844: response to L-glutamine. GO:0060359: response to ammonium ion. TO:0020093: nitrogen content. GO:0071705: nitrogen compound transport. GO:2000280: regulation of root development. GO:0071941: nitrogen cycle metabolic process. GO:2000904: regulation of starch metabolic process. GO:0090352: regulation of nitrate assimilation. TO:0000934: photoperiod-sensitive flowering time trait.
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Trait Class
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Vegetative organ - Culm
Reproductive organ - Heading date
Reproductive organ - panicle
Heterochrony
Seed
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
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Expression
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Sequence/Locus
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cDNA Accession No.
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AK111893
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MSU ID
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LOC_Os08g06110.2
LOC_Os08g06110.3
LOC_Os08g06110.4
LOC_Os08g06110.5
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RAP ID
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Os08g0157600
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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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Jin Y., Deng L., Wang T., Wang Z., Jing Y., Du M., Li X., Qu H., Ding W., Liu Y., Gu M., Zhang S., Xu G.
Plant Physiol. 2025 198(3)
The Nhd1-myb110-MADS15 transcription factor module regulates flowering time in rice.
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Gawande N.D.
Plant Physiol. 2025 199(1)
Decoding the regulatory trio: The role of Nhd1-OsMYB110-OsMADS15 in rice flowering time.
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Cai L., Hao B., Xu Z., Cui S., Wu Q., Lee J., Hou H., Hu Y., Zhu L., Wang J., Li W., Chang K., Shao W., Zhu S., Gan X., Li C., Jiang L., Tian Y., Liu X., Liu S., Chen L., Wang H., Zhou S., Wan J.
Nat Commun 2025 16(1) 5329
ELD1 mediates photoperiodic flowering via OsCCA1 alternative splicing and interacts with phytochrome signaling in rice.
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Li J., He C., Liu S., Guo Y., Zhang Y., Zhang L., Zhou X., Xu D., Luo X., Liu H., Yang X., Wang Y., Shi J., Yang B., Wang J., Wang P., Deng X., Sun C.
Front Plant Sci 2024 15 1454615
Research progress and application strategies of sugar transport mechanisms in rice.
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Chen K., Su X., Yang H., Peng Y., Wu L., Zhao Z., Lin T., Bai L., Wang L.
Front Plant Sci 2023 14 1155258
Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in <i>Oryza sativa</i>.
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Zhang Q., Xie J., Zhu X., Ma X., Yang T., Khan N.U., Zhang S., Liu M., Li L., Liang Y., Pan Y., Li D., Li J., Li Z., Zhang H., Zhang Z.
Plant Biotechnol. J. 2023 21(5) 1044-1057
Natural variation in tiller number 1 affects its interaction with TIF1 to regulate tillering in rice.
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Hu Z., Guo Y., Ying S., Tang Y., Niu J., Wang T., Huang R., Xie H., Wang W., Peng X.
BMC Plant Biol. 2023 23(1) 502
OsCBL1 modulates rice nitrogen use efficiency via negative regulation of OsNRT2.2 by OsCCA1.
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Li J., Qiu J.X., Zeng Q.H., Yi Zhuang, Zhang N., Xu S.X., Jin J., Dong Z.C., Chen L., Huang W.
Cell Rep 2023 42(7) 112765
OsTOC1 plays dual roles in the regulation of plant circadian clock by functioning as a direct transcription activator or repressor.
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Li K., Tang S., Zhang S., Tian Y., Qu H., Gu M., Xu G.
J. Exp. Bot. 2023 74(5) 1460-1474
Rice circadian clock regulator nhd1 controls the expression of the sucrose transporter gene OsSUT1 and impacts carbon-nitrogen balance.
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Sun C., Liu S., He C., Zhong C., Liu H., Luo X., Li K., Zhang K., Wang Q., Chen C., Tang Y., Yang B., Chen X., Xu P., Zou T., Li S., Qin P., Wang P., Chu C., Deng X.
Int J Mol Sci 2022 23(12)
Crosstalk between the Circadian Clock and Histone Methylation.
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Li J., Wang D., Sun S., Sun L., Zong J., Lei Y., Yu J., Liang W., Zhang D.
Plant Physiol. 2022 189(2) 955-971
The regulatory role of CARBON STARVED ANTHER-mediated photoperiod-dependent male fertility in rice.
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Cai Z., Zhang Y., Tang W., Chen X., Lin C., Liu Y., Ye Y., Wu W., Duan Y.
Front Plant Sci 2022 13 853042
LUX ARRHYTHMO Interacts With ELF3a and ELF4a to Coordinate Vegetative Growth and Photoperiodic Flowering in Rice.
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Zhang S., Zhang Y., Li K., Yan M., Zhang J., Yu M., Tang S., Wang L., Qu H., Luo L., Xuan W., Xu G.
Curr. Biol. 2021 31(4) 671-683.e5
Nitrogen Mediates flowering time and Nitrogen Use Efficiency via Floral Regulators in Rice.
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Wei H., Wang X., He Y., Xu H., Wang L.
EMBO J. 2021 40(3) e105086
Clock component OsPRR73 positively regulates rice salt tolerance by modulating OsHKT2;1-mediated sodium homeostasis.
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Liang L., Zhang Z., Cheng N., Liu H., Song S., Hu Y., Zhou X., Zhang J., Xing Y.
Plant Cell Environ. 2021 44(3) 842-855
The transcriptional repressor OsPRR73 links circadian clock and photoperiod pathway to control heading date in rice.
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Sun C., Zhang K., Zhou Y., Xiang L., He C., Zhong C., Li K., Wang Q., Yang C., Wang Q., Chen C., Chen D., Wang Y., Liu C., Yang B., Wu H., Chen X., Li W., Wang J., Xu P., Wang P., Fang J., Chu C., Deng X.
Plant Biotechnol. J. 2021 19(8) 1644-1657
Dual function of clock component OsLHY sets critical day length for photoperiodic flowering in rice.
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Yoo Y.H., Jiang X., Jung K.H.
Plants (Basel) 2020 9(9)
An Abiotic Stress Responsive U-Box E3 Ubiquitin Ligase Is Involved in OsGI-Mediating Diurnal Rhythm Regulating Mechanism.
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Wang F., Han T., Song Q., Ye W., Song X., Chu J., Li J., Chen Z.J.
Plant Cell 2020 32(10) 3124-3138
The Rice Circadian Clock Regulates Tiller Growth and Panicle Development Through Strigolactone Signaling and Sugar Sensing.
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Strable J.
Plant Cell 2020 32(10) 3043-3044
Sugars Inform the Circadian Clock How to Shape Rice Shoots via the Strigolactone Pathway.
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Singh P., Mathew I.E., Verma A., Tyagi A.K., Agarwal P.
Int J Mol Sci 2019 20(7)
Analysis of Rice Proteins with DLN repressor Motif/S.
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Zhu C., Peng Q., Fu D., Zhuang D., Yu Y., Duan M., Xie W., Cai Y., Ouyang Y., Lian X., Wu C.
Plant Cell 2018 30(10) 2352-2367
The E3 Ubiquitin Ligase HAF1 Modulates Circadian Accumulation of EARLY FLOWERING3 to Control heading date in Rice under Long-Day Conditions.
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Bai B., Zhao J., Li Y., Zhang F., Zhou J., Chen F., Xie X.
Plant Sci. 2016 247 25-34
OsBBX14 delays heading date by repressing florigen gene expression under long and short-day conditions in rice.
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Matsuzaki J., Kawahara Y., Izawa T.
Plant Cell 2015 27(3) 633-48
Punctual Transcriptional Regulation by the Rice Circadian Clock under Fluctuating Field Conditions.
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Yang Y., Peng Q., Chen G.X., Li X.H., Wu C.Y.
Mol Plant 2013 6(1) 202-15
OsELF3 is Involved in Circadian Clock Regulation for Promoting Flowering under Long-Day Conditions in Rice.
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Zhao J., Huang X., Ouyang X., Chen W., Du A., Zhu L., Wang S., Deng X.W., Li S.
PLoS ONE 2012 7(8) e43705
OsELF3-1, an Ortholog of Arabidopsis EARLY FLOWERING 3, Regulates Rice Circadian Rhythm and Photoperiodic Flowering.
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Wang W., Liu Z., Guo Z., Song G., Cheng Q., Jiang D., Zhu Y., Yang D.
BMC Genomics 2011 12 462
Comparative transcriptomes profiling of photoperiod-sensitive male sterile rice Nongken 58S during the male sterility transition between short-day and long-day.
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Ogiso E,Takahashi Y,Sasaki T,Yano M,Izawa T
Plant Physiol. 2010 152(2) 808-20
The role of casein kinase II in flowering time regulation has diversified during evolution.
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Murakami M, Tago Y, Yamashino T, Mizuno T.
Plant Cell Physiol. 2007 48(1) 110-21
Comparative Overviews of Clock-Associated Genes of Arabidopsis thaliana and Oryza sativa.
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Tang,T., Lu,J., Huang,J., He,J., McCouch,S.R., Shen,Y., Kai,Z., Purugganan,M.D., Shi,S. and Wu,C.-I.
PLoS Genet. 2 (11), e199 REMARK Publication Status: Online-Only 2006 2(11)
Genomic Variation in Rice: Genesis of Highly Polymorphic Linkage Blocks during Domestication
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L Xiong, M W Lee, M Qi, Y Yang
Mol. Plant Microbe Interact. 2001 14(5) 685-92
Identification of defense-related rice genes by suppression subtractive hybridization and differential screening.
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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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DNA binding( GO:0003677 )
defense response to fungus( GO:0050832 )
circadian rhythm( GO:0007623 )
regulation of circadian rhythm( GO:0042752 )
response to carbohydrate stimulus( GO:0009743 )
detection of carbohydrate stimulus( GO:0009730 )
photoperiodism, flowering( GO:0048573 )
seed development( GO:0048316 )
inflorescence development( GO:0010229 )
regulation of transcription, DNA-dependent( GO:0006355 )
vegetative to reproductive phase transition( GO:0010228 )
nitrogen utilization( GO:0019740 )
negative regulation of short-day photoperiodism, flowering( GO:0048577 )
positive regulation of long-day photoperiodism, flowering( GO:0048578 )
glutamate biosynthetic process( GO:0006537 )
glutamine biosynthetic process( GO:0006542 )
regulation of nitrogen utilization( GO:0006808 )
response to herbicide( GO:0009635 )
phloem transport( GO:0010233 )
phloem loading( GO:0009915 )
root development( GO:0048364 )
starch metabolic process( GO:0005982 )
sucrose metabolic process( GO:0005985 )
regulation of cellular amino acid metabolic process( GO:0006521 )
response to photoperiod, red light( GO:0009907 )
response to nutrient levels( GO:0031667 )
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Trait Ontology
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blast disease( TO:0000074 )
shoot branching( TO:0002639 )
tillering ability( TO:0000329 )
yield trait( TO:0000371 )
flowering time( TO:0002616 )
days to heading( TO:0000137 )
tiller number( TO:0000346 )
seed development trait( TO:0000653 )
inflorescence development trait( TO:0000621 )
nitrogen sensitivity( TO:0000011 )
photosynthetic rate( TO:0001015 )
sucrose content( TO:0000328 )
amino acid content( TO:0002673 )
plant height( TO:0000207 )
shoot dry weight( TO:0000552 )
chlorophyll content( TO:0000495 )
chlorophyll-a content( TO:0000293 )
chlorophyll-b content( TO:0000295 )
root development trait( TO:0000656 )
herbicide sensitivity( TO:0000058 )
red light sensitivity( TO:0000158 )
phosphorus sensitivity( TO:0000102 )
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Plant Ontology
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shoot apical meristem( PO:0020148 )
seed( PO:0009010 )
endosperm( PO:0009089 )
plant embryo( PO:0009009 )
inflorescence( PO:0009049 )
shoot system( PO:0009006 )
bud( PO:0000055 )
root( PO:0009005 )
inflorescence development stage( PO:0001083 )
seed development stage( PO:0001170 )
leaf( PO:0025034 )
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Related Strains
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Phenotype images
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Last updated
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Jan 11, 2026
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Update info.