Gene - Detail

Detail of Gene

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Basic Information
CGSNL Gene Symbol CCA1
Gene Symbol Synonym OsCCA1, OsLHY, LHY, LHY-like_chr.8, COC1, DLN203, OsDLN203, LEM1, OsLEM1, Nhd1, OsNhd1
Gene Name Synonym LATE ELONGATED HYPOCOTYL, DLN repressor 203, DLN motif protein 203, lvp1 enhancer mutant 1, N-mediated heading date1
Protein Name
Allele oslhy, lem1, oscca1, oscca1-1, oscca1-2, nhd1, nhd1-1, nhd1-2, nhd1-3
Chromosome No. 8
Explanation a rice ortholog of Arabidopsis gene for circadian clock component. the single ortholog of Arabidopsis LHY/CCA1. BF889434. AY885916-AY885946 and DQ374829-DQ374856 (O. sativa and other wild rice species, partial ads). a CCA1 ortholog in rice. 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.
Trait Class Vegetative organ - Culm
Reproductive organ - Heading date
Reproductive organ - panicle
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
cDNA Accession No. AK111893
MSU ID LOC_Os08g06110.2
RAP ID Os08g0157600
Links Oryzabase Chromosome View ( IRGSP 1.0 / Build5 )
RAP-DB ( IRGSP 1.0 / Build5 )
Related IDs List ( IRGSP 1.0 / Build5 )
INSD Accession List
(Test version)
Link to INSD Accession List
Link map Classical linkage map
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Strable J.
Plant Cell 2020  32(10)  3043-3044
Sugars Inform the Circadian Clock How to Shape Rice Shoots via the Strigolactone Pathway.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
TextPresso Search Search textpresso for CCA1 ( Recent references may be retrievable, but without any warranty )
DB Reference
Gramene ID -
Gene Ontology positive regulation of long-day photoperiodism, flowering( GO:0048578 )
negative regulation of short-day photoperiodism, flowering( GO:0048577 )
nitrogen utilization( GO:0019740 )
vegetative to reproductive phase transition( GO:0010228 )
regulation of transcription, DNA-dependent( GO:0006355 )
inflorescence development( GO:0010229 )
seed development( GO:0048316 )
photoperiodism, flowering( GO:0048573 )
detection of carbohydrate stimulus( GO:0009730 )
response to carbohydrate stimulus( GO:0009743 )
DNA binding( GO:0003677 )
defense response to fungus( GO:0050832 )
circadian rhythm( GO:0007623 )
regulation of circadian rhythm( GO:0042752 )
Trait Ontology 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 )
Plant Ontology leaf( PO:0025034 )
seed development stage( PO:0001170 )
inflorescence development stage( PO:0001083 )
root( PO:0009005 )
bud( PO:0000055 )
shoot system( PO:0009006 )
inflorescence( PO:0009049 )
plant embryo( PO:0009009 )
endosperm( PO:0009089 )
seed( PO:0009010 )
shoot apical meristem( PO:0020148 )
Related Strains
Phenotype images
Last updated
Dec 26, 2023