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Basic Information
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CGSNL Gene Symbol
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PHYB
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Gene Symbol Synonym
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phyB, PHYB1, OsPHYB, OsphyB, OsYHB, YHB, OsPHYB/OsYHB
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CGSNL Gene Name
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PHYTOCHROME B
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Gene Name Synonym
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PhytochromeB, Phytochrome B
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Protein Name
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PHYTOCHROME B
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Allele
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phyb, osphyB, phyB-1, phyB-2, phyB-3, phyB-4, phyB-5, phyB-6, osphyB, osphyB-1, osphyB-2, osphyB-N4, phyBT822*
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Chromosome No.
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3
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Explanation
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A2XFW2 (indica), Q10MG9 (japonica). AB109892 (Japonica). JN594127-JN594211 (O. sativa and other wild rice species). CL523988 (phyB-6). MT460250 - MT460374. NCBI Gene Expression Omnibus with an accession number GSE36320. a rice ortholog of Arabidopsis gene for circadian clock component. GO:2000028: regulation of photoperiodism, flowering. GO:1900366: negative regulation of defense response to insect.
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Trait Class
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Biochemical character
Vegetative organ - Leaf
Vegetative organ - Culm
Vegetative organ - Root
Reproductive organ - Heading date
Coloration - Chlorophyll
Tolerance and resistance - Insect 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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AK071993
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MSU ID
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LOC_Os03g19590.1
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RAP ID
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Os03g0309200
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Links
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Oryzabase Chromosome View
(
IRGSP 1.0
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Build5
)
RAP-DB
(
IRGSP 1.0
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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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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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Colleoni P.E., van Es SW., Winkelmolen T., Immink R.G.H., van Esse GW.
J. Exp. Bot. 2024 75(14) 4195-4209
flowering time genes branching out.
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Lei Y., Ma Q., Zhang Y., Li J., Ning X., Wang Y., Ge X., Zhao H., Lin H.
Front Plant Sci 2024 15 1340260
Functional dissection of Phytochrome A in plants.
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Huang J., Qiu Z.Y., He J., Xu H.S., Wang K., Du H.Y., Gao D., Zhao W.N., Sun Q.G., Wang Y.S., Wen P.Z., Li Q., Dong X.O., Xie X.Z., Jiang L., Wang H.Y., Liu Y.Q., Wan J.M.
Plant Physiol. 2023 191(2) 1272-1287
Phytochrome B mediates dim-light-reduced insect resistance by promoting the ethylene pathway in rice.
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Andrade L., Lu Y., Cordeiro A., Costa J.M.F., Wigge P.A., Saibo N.J.M., Jaeger K.E.
Proc. Natl. Acad. Sci. U.S.A. 2022 119(26) e2122582119
The evening complex integrates photoperiod signals to control flowering in rice.
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Lin X., Huang Y., Rao Y., Ouyang L., Zhou D., Zhu C., Fu J., Chen C., Yin J., Bian J., He H., Zou G., Xu J.
BMC Plant Biol. 2022 22(1) 612
A base substitution in OsphyC disturbs its Interaction with OsphyB and affects flowering time and chlorophyll synthesis in rice.
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Pearce S.
Proc. Natl. Acad. Sci. U.S.A. 2022 119(29) e2208745119
Plants change their clocks to flower at the right time.
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Ahn H.R., Kim Y.J., Lim Y.J., Duan S., Eom S.H., Jung K.H.
Plants (Basel) 2021 10(1)
Key Genes in the Melatonin Biosynthesis Pathway with Circadian Rhythm Are Associated with Various Abiotic Stresses.
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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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Cui Y., Wang J., Feng L., Liu S., Li J., Qiao W., Song Y., Zhang Z., Cheng Y., Zhang L., Zheng X., Yang Q.
Front Plant Sci 2020 11 864
A Combination of Long-Day Suppressor Genes Contributes to the Northward Expansion of Rice.
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Hu W., Figueroa-Balderas R., Chi-Ham C., Lagarias J.C.
Plant Direct 2020 4(4) e00210
Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B.
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Cui Y., Zhu M., Xu Z., Xu Q.
Theor. Appl. Genet. 2019 132(6) 1887-1896
Assessment of the effect of ten heading time genes on reproductive transition and yield components in rice using a CRISPR/Cas9 system.
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Tang J., Wang Y., Yin W., Dong G., Sun K., Teng Z., Wu X., Wang S., Qian Y., Pan X., Qian Q., Chu C.
Plant Physiol. 2019 181(3) 1295-1313
Mutation of a Nucleotide-Binding Leucine-Rich Repeat Immune Receptor-Type Protein Disrupts Immunity to Bacterial Blight.
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Zheng T., Sun J., Zhou S., Chen S., Lu J., Cui S., Tian Y., Zhang H., Cai M., Zhu S., Wu M., Wang Y., Jiang L., Zhai H., Wang H., Wan J.
New Phytol. 2019 224(1) 306-320
Post-transcriptional regulation of Ghd7 protein stability by phytochrome and OsGI in photoperiodic control of flowering in rice.
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Xie C., Zhang G., An L., Chen X., Fang R.
Planta 2019 250(1) 105-114
Phytochrome-interacting factor-like protein OsPIL15 integrates light and gravitropism to regulate tiller angle in rice.
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Mao C., Lu S., Lv B., Zhang B., Shen J., He J., Luo L., Xi D., Chen X., Ming F.
Plant Physiol. 2017 174(3) 1747-1763
A Rice NAC Transcription Factor Promotes leaf senescence via ABA Biosynthesis.
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Yoo Y.H., Nalini Chandran AK., Park J.C., Gho Y.S., Lee S.W., An G., Jung K.H.
Front Plant Sci 2017 8 580
OsPhyB-Mediating Novel Regulatory Pathway for drought tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies.
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Cordeiro A.M., Figueiredo D.D., Tepperman J., Borba A.R., Lourenço T., Abreu I.A., Ouwerkerk P.B., Quail P.H., Margarida Oliveira M., Saibo N.J.
Biochim. Biophys. Acta 2016 1859(2) 393-404
Rice Phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of Phytochrome B.
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Sheng P., Wu F., Tan J., Zhang H., Ma W., Chen L., Wang J., Wang J., Zhu S., Guo X., Wang J., Zhang X., Cheng Z., Bao Y., Wu C., Liu X., Wan J.
Plant Mol. Biol. 2016 92(1-2) 209-22
A CONSTANS-like transcriptional activator, OsCOL13, functions as a negative regulator of flowering downstream of OsphyB and upstream of Ehd1 in rice.
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Inagaki N., Kinoshita K., Kagawa T., Tanaka A., Ueno O., Shimada H., Takano M.
PLoS ONE 2015 10(8) e0135408
Phytochrome B Mediates the Regulation of Chlorophyll Biosynthesis through Transcriptional Regulation of ChlH and GUN4 in Rice Seedlings.
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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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Gao H., Jin M., Zheng X.M., Chen J., Yuan D., Xin Y., Wang M., Huang D., Zhang Z., Zhou K., Sheng P., Ma J., Ma W., Deng H., Jiang L., Liu S., Wang H., Wu C., Yuan L., Wan J.
Proc. Natl. Acad. Sci. U.S.A. 2014
Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice.
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Zhao,D.-S., Zhang,C.-Q., Gu,M.-H. and Liu,Q.-Q.
Zuo Wu Xue Bao 2013 39(10) 1799-1805
Genetic and Expression Anaylses of Ef7-1, a Novel Ef7 Allele, in Rice
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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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Hirose F., Inagaki N., Takano M.
Plant Signal Behav 2013 8(3)
Differences and similarities in the photoregulation of gibberellin metabolism between rice and dicots.
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Huang,C.L., Hung,C.Y., Chiang,Y.C., Hwang,C.C., Hsu,T.W., Huang,C.C., Hung,K.H., Tsai,K.C., Wang,K.H., Osada,N., Schaal,B.A. and Chiang,T.Y.
Plant J. 2012 70(5) 769-782
Footprints of natural and artificial selection for photoperiod pathway genes in Oryza
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Ishikawa R. , Aoki M. , Kurotani K. , Yokoi S. , Shinomura T. , Takano M. , Shimamoto K.
Mol. Genet. Genomics 2011 285(6) 461-70
Phytochrome B regulates Heading date 1 (Hd1)-mediated expression of rice florigen Hd3a and critical day length in rice.
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Osugi A., Itoh H., Ikeda-Kawakatsu K., Takano M., Izawa T.
Plant Physiol. 2011 157(3) 1128-37
Molecular dissection of the roles of phytochrome in photoperiodic flowering in rice.
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Lee Y.-S., Jeong D.-H., Lee D.-Y., Yi J., Ryu C.-H., Kim S.L., Jeong H.J., Choi S.C., Jin P., Yang J., Cho L.-H., Choi H., An G.
Plant Journal 2010 63(1) 18-30
OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB.
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Takano M,Inagaki N,Xie X,Kiyota S,Baba-Kasai A,Tanabata T,Shinomura T
Proc. Natl. Acad. Sci. U.S.A. 2009 106(34) 14705-10
Phytochromes are the sole photoreceptors for perceiving red/far-red light in rice.
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Komiya R., Yokoi S., Shimamoto K.
Development 2009 136(20) 3443-50
A gene network for long-day flowering activates RFT1 encoding a mobile flowering signal in rice.
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Pareek A, Singh A, Kumar M, Kushwaha HR, Lynn AM, Singla-Pareek SL.
Plant Physiol. 2006 142(2) 380-97
Whole-genome analysis of Oryza sativa reveals similar architecture of two-component signaling machinery with Arabidopsis.
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Ishikawa R., Tamaki S., Yokoi S., Inagaki N., Shinomura T., Takano M., Shimamoto K.
Plant Cell 2005 17(12) 3326-36
Suppression of the floral activator Hd3a is the principal cause of the night break effect in rice.
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Takano,M., Inagaki,N., Xie,X., Yuzurihara,N., Hihara,F., Ishizuka,T., Yano,M., Nishimura,M., Miyao,A., Hirochika,H. and Shinomura,T.
Plant Cell 2005 17(12) 3311-3325
Distinct and cooperative functions of phytochromes a, B, and C in the control of deetiolation and flowering in rice.
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Basu,D., Dehesh,K., Schneider-Poetsch,H.J., Harrington,S.E., McCouch,S.R. and Quail,P.H.
Plant Mol. Biol. 2000 44(1) 27-42
Rice PHYC gene: structure, expression, map position and evolution.
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Mathews,S. and Sharrock,R.A.
Mol. Biol. Evol. 1996 13(8) 1141-1150
The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms.
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Dehesh,K., Tepperman,J., Christensen,A.H. and Quail,P.H.
Mol. Gen. Genet. 1991 225(2) 305-313
phyB is evolutionarily conserved and constitutively expressed in rice seedling shoots.
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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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two-component sensor activity( GO:0000155 )
protein-chromophore linkage( GO:0018298 )
protein homodimerization activity( GO:0042803 )
protein-tetrapyrrole linkage( GO:0017006 )
ATP binding( GO:0005524 )
G-protein coupled photoreceptor activity( GO:0008020 )
membrane( GO:0016020 )
peptidyl-histidine phosphorylation( GO:0018106 )
transcription( GO:0006350 )
regulation of transcription, DNA-dependent( GO:0006355 )
sensory perception( GO:0007600 )
red, far-red light phototransduction( GO:0009585 )
circadian rhythm( GO:0007623 )
photoperiodism, flowering( GO:0048573 )
regulation of chlorophyll biosynthetic process( GO:0010380 )
response to water deprivation( GO:0009414 )
hydrogen peroxide catabolic process( GO:0042744 )
photomorphogenesis( GO:0009640 )
response to red light( GO:0010114 )
photoreceptor activity( GO:0009881 )
response to deep water( GO:0030912 )
chloroplast organization( GO:0009658 )
response to low light intensity stimulus( GO:0009645 )
defense response to insect( GO:0002213 )
ethylene mediated signaling pathway( GO:0009873 )
regulation of ethylene mediated signaling pathway( GO:0010104 )
positive regulation of ethylene biosynthetic process( GO:0010365 )
regulation of nuclear mRNA splicing, via spliceosome( GO:0048024 )
regulation of alternative nuclear mRNA splicing, via spliceosome( GO:0000381 )
negative regulation of long-day photoperiodism, flowering( GO:0048579 )
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Trait Ontology
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days to heading( TO:0000137 )
chlorophyll content( TO:0000495 )
chlorophyll ratio( TO:0000298 )
leaf color( TO:0000326 )
flowering time( TO:0002616 )
drought tolerance( TO:0000276 )
hydrogen peroxide content( TO:0000605 )
stomatal frequency( TO:0000566 )
filled grain number( TO:0000447 )
seed set percent( TO:0000455 )
red light sensitivity( TO:0000158 )
leaf length( TO:0000135 )
seminal root length( TO:0000586 )
crown root number( TO:0002685 )
root shape( TO:0002710 )
submergence tolerance( TO:0000524 )
tiller number( TO:0000346 )
chloroplast development trait( TO:0002715 )
plant height( TO:0000207 )
light intensity sensitivity( TO:0000460 )
brown planthopper resistance( TO:0000424 )
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Plant Ontology
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Related Strains
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Phenotype images
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Last updated
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Oct 9, 2025
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Update info.