PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Oropetium_20150105_16080A
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Chloridoideae; Cynodonteae; Tripogoninae; Oropetium
Family CO-like
Protein Properties Length: 380aa    MW: 41609.3 Da    PI: 5.4384
Description CO-like family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Oropetium_20150105_16080AgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
                   zf-B_box  4 rkCpeHeekelqlfCedCqqllCedClleeHkg......Htv 39
                               r C  +   +   +C+ +  +lC++C +  H        H++
  Oropetium_20150105_16080A 24 RPCHGCRAAPSVVYCRADAAYLCASCDTRVHAAnhvasrHER 65
                               679***************************955655556665 PP

                   zf-B_box   3 erkCpeHeekelqlfCedCqqllCedClleeHkg......Htvvpl 42 
                                 r+C+ +e+ ++ l C+ +   lC+ C  + H+       H++vp+
                                689*****************************66999999*99986 PP

                        CCT   1 ReaallRYkeKrktRkFeKkirYesRKavAesRpRvKGrFvkqa 44 
                                Rea++lRY++K+++RkFeK+irY++RK++Ae RpR+KGrF+k++
                                9*****************************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003364.8E-62168IPR000315B-box-type zinc finger
CDDcd000211.30E-62468No hitNo description
PROSITE profilePS501199.942668IPR000315B-box-type zinc finger
PROSITE profilePS5011910.53764111IPR000315B-box-type zinc finger
PfamPF006432.7E-666111IPR000315B-box-type zinc finger
CDDcd000213.46E-867111No hitNo description
SMARTSM003364.2E-769111IPR000315B-box-type zinc finger
PROSITE profilePS5101716.222313355IPR010402CCT domain
PfamPF062033.4E-16313355IPR010402CCT domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009658Biological Processchloroplast organization
GO:0009909Biological Processregulation of flower development
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048576Biological Processpositive regulation of short-day photoperiodism, flowering
GO:0048579Biological Processnegative regulation of long-day photoperiodism, flowering
GO:0005622Cellular Componentintracellular
GO:0005515Molecular Functionprotein binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 380 aa     Download sequence    Send to blast
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the regulation of flower development. Required for the promotion of flowering under short day (SD) conditions and the suppression of flowering under long day (LD) conditions. Regulates positively the floral activator HEADING DATE 3a (HD3A) under SD and negatively under LD conditions. {ECO:0000269|PubMed:12700762}.
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Expressed with a circadian rhythm showing a peak at night and then decreasing to reach the lowest levels around the middle of the day in LD conditions. The levels of expression in SD conditions are slightly lower. {ECO:0000269|PubMed:12700762}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012701063.11e-176zinc finger protein HD1 isoform X1
SwissprotQ9FDX81e-152HD1_ORYSJ; Zinc finger protein HD1
TrEMBLM4ZUU10.0M4ZUU1_SETIT; Heading date 1
STRINGPavir.Db01632.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G02380.18e-65CONSTANS-like 2
Publications ? help Back to Top
  1. Luo LG,Zhai HQ,Wan JM
    [Analysis of heading time genotype for a rice male sterile line Zhenshan 97A].
    Yi Chuan Xue Bao, 2001. 28(11): p. 1019-27
  2. Kojima S, et al.
    Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions.
    Plant Cell Physiol., 2002. 43(10): p. 1096-105
  3. Luo LG,Xu JF,Zhai HQ,Wan JM
    [Analysis of photoperiod-sensitivity genes in Minghui63, an restorer line of indica rice(Oryza sativa L.)].
    Yi Chuan Xue Bao, 2003. 30(9): p. 804-10
  4. Shin BS, et al.
    Circadian regulation of rice (Oryza sativa L.) CONSTANS-like gene transcripts.
    Mol. Cells, 2004. 17(1): p. 10-6
  5. Xu JF, et al.
    [Analysis of heading time genotype for a rice photoperiod and thermo--sensitive male sterile line PeiAi64S].
    Yi Chuan Xue Bao, 2005. 32(1): p. 57-65
  6. Nakagawa H, et al.
    Flowering response of rice to photoperiod and temperature: a QTL analysis using a phenological model.
    Theor. Appl. Genet., 2005. 110(4): p. 778-86
  7. Murakami M,Matsushika A,Ashikari M,Yamashino T,Mizuno T
    Circadian-associated rice pseudo response regulators (OsPRRs): insight into the control of flowering time.
    Biosci. Biotechnol. Biochem., 2005. 69(2): p. 410-4
  8. Armstead IP, et al.
    Identification of perennial ryegrass (Lolium perenne (L.)) and meadow fescue (Festuca pratensis (Huds.)) candidate orthologous sequences to the rice Hd1(Se1) and barley HvCO1 CONSTANS-like genes through comparative mapping and microsynteny.
    New Phytol., 2005. 167(1): p. 239-47
  9. Ishikawa R, et al.
    Suppression of the floral activator Hd3a is the principal cause of the night break effect in rice.
    Plant Cell, 2005. 17(12): p. 3326-36
  10. Andersen JR,Jensen LB,Asp T,Lübberstedt T
    Vernalization response in perennial ryegrass (Lolium perenne L.) involves orthologues of diploid wheat (Triticum monococcum) VRN1 and rice (Oryza sativa) Hd1.
    Plant Mol. Biol., 2006. 60(4): p. 481-94
  11. Uga Y, et al.
    Accumulation of additive effects generates a strong photoperiod sensitivity in the extremely late-heading rice cultivar 'Nona Bokra'.
    Theor. Appl. Genet., 2007. 114(8): p. 1457-66
  12. Skøt L, et al.
    Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.).
    Genetics, 2007. 177(1): p. 535-47
  13. Kim SL,Lee S,Kim HJ,Nam HG,An G
    OsMADS51 is a short-day flowering promoter that functions upstream of Ehd1, OsMADS14, and Hd3a.
    Plant Physiol., 2007. 145(4): p. 1484-94
  14. Nonoue Y, et al.
    Detection of quantitative trait loci controlling extremely early heading in rice.
    Theor. Appl. Genet., 2008. 116(5): p. 715-22
  15. Armstead IP, et al.
    Identifying genetic components controlling fertility in the outcrossing grass species perennial ryegrass (Lolium perenne) by quantitative trait loci analysis and comparative genetics.
    New Phytol., 2008. 178(3): p. 559-71
  16. Vega-Sánchez ME,Zeng L,Chen S,Leung H,Wang GL
    SPIN1, a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11, is involved in flowering time control in rice.
    Plant Cell, 2008. 20(6): p. 1456-69
  17. Li D, et al.
    Functional characterization of rice OsDof12.
    Planta, 2009. 229(6): p. 1159-69
  18. Takahashi Y,Teshima KM,Yokoi S,Innan H,Shimamoto K
    Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice.
    Proc. Natl. Acad. Sci. U.S.A., 2009. 106(11): p. 4555-60
  19. Luan W, et al.
    The effect of the crosstalk between photoperiod and temperature on the heading-date in rice.
    PLoS ONE, 2009. 4(6): p. e5891
  20. Ishikawa R,Shinomura T,Takano M,Shimamoto K
    Phytochrome dependent quantitative control of Hd3a transcription is the basis of the night break effect in rice flowering.
    Genes Genet. Syst., 2009. 84(2): p. 179-84
  21. Andrés F,Galbraith DW,Talón M,Domingo C
    Analysis of PHOTOPERIOD SENSITIVITY5 sheds light on the role of phytochromes in photoperiodic flowering in rice.
    Plant Physiol., 2009. 151(2): p. 681-90
  22. Higgins JA,Bailey PC,Laurie DA
    Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses.
    PLoS ONE, 2010. 5(4): p. e10065
  23. Sanyal A, et al.
    Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum.
    Mol. Biol. Evol., 2010. 27(11): p. 2487-506
  24. Itoh H,Nonoue Y,Yano M,Izawa T
    A pair of floral regulators sets critical day length for Hd3a florigen expression in rice.
    Nat. Genet., 2010. 42(7): p. 635-8
  25. Saito H, et al.
    Complete loss of photoperiodic response in the rice mutant line X61 is caused by deficiency of phytochrome chromophore biosynthesis gene.
    Theor. Appl. Genet., 2011. 122(1): p. 109-18
  26. Matsubara K, et al.
    Ehd3, encoding a plant homeodomain finger-containing protein, is a critical promoter of rice flowering.
    Plant J., 2011. 66(4): p. 603-12
  27. Zhao XL,Shi ZY,Peng LT,Shen GZ,Zhang JL
    An atypical HLH protein OsLF in rice regulates flowering time and interacts with OsPIL13 and OsPIL15.
    N Biotechnol, 2011. 28(6): p. 788-97
  28. Tanaka N, et al.
    The COP1 ortholog PPS regulates the juvenile-adult and vegetative-reproductive phase changes in rice.
    Plant Cell, 2011. 23(6): p. 2143-54
  29. Li C,Huang L,Xu C,Zhao Y,Zhou DX
    Altered levels of histone deacetylase OsHDT1 affect differential gene expression patterns in hybrid rice.
    PLoS ONE, 2011. 6(7): p. e21789
  30. Shibaya T, et al.
    Genetic interactions involved in the inhibition of heading by heading date QTL, Hd2 in rice under long-day conditions.
    Theor. Appl. Genet., 2011. 123(7): p. 1133-43
  31. Bai XF,Luo LJ,Yan WH,Kovi MR,Xing YZ
    Quantitative trait loci for rice yield-related traits using recombinant inbred lines derived from two diverse cultivars.
    J. Genet., 2011. 90(2): p. 209-15
  32. Wang W, et al.
    Comparative transcriptomes profiling of photoperiod-sensitive male sterile rice Nongken 58S during the male sterility transition between short-day and long-day.
    BMC Genomics, 2011. 12: p. 462
  33. Matsubara K, et al.
    Natural variation in Hd17, a homolog of Arabidopsis ELF3 that is involved in rice photoperiodic flowering.
    Plant Cell Physiol., 2012. 53(4): p. 709-16
  34. Song Y,Gao Z,Luan W
    Interaction between temperature and photoperiod in regulation of flowering time in rice.
    Sci China Life Sci, 2012. 55(3): p. 241-9
  35. Wang J,Hu J,Qian Q,Xue HW
    LC2 and OsVIL2 promote rice flowering by photoperoid-induced epigenetic silencing of OsLF.
    Mol Plant, 2013. 6(2): p. 514-27
  36. Zhang ZH, et al.
    Pleiotropism of the photoperiod-insensitive allele of Hd1 on heading date, plant height and yield traits in rice.
    PLoS ONE, 2012. 7(12): p. e52538
  37. Wu W, et al.
    Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia.
    Proc. Natl. Acad. Sci. U.S.A., 2013. 110(8): p. 2775-80
  38. Kovi MR, et al.
    Expression patterns of photoperiod and temperature regulated heading date genes in Oryza sativa.
    Comput Biol Chem, 2013. 45: p. 36-41
  39. Hori K, et al.
    Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response.
    Plant J., 2013. 76(1): p. 36-46
  40. Ogiso-Tanaka E, et al.
    Natural variation of the RICE FLOWERING LOCUS T 1 contributes to flowering time divergence in rice.
    PLoS ONE, 2013. 8(10): p. e75959
  41. Duan M, et al.
    Genetic analysis of an elite super-hybrid rice parent using high-density SNP markers.
    Rice (N Y), 2013. 6(1): p. 21
  42. Hu S, et al.
    A point mutation in the zinc finger motif of RID1/EHD2/OsID1 protein leads to outstanding yield-related traits in japonica rice variety Wuyunjing 7.
    Rice (N Y), 2013. 6(1): p. 24
  43. Piao R, et al.
    Isolation and characterization of a dominant dwarf gene, d-h, in rice.
    PLoS ONE, 2014. 9(2): p. e86210
  44. Naranjo L,Talón M,Domingo C
    Diversity of floral regulatory genes of japonica rice cultivated at northern latitudes.
    BMC Genomics, 2014. 15: p. 101
  45. Chen J, et al.
    Characterization of epistatic interaction of QTLs LH8 and EH3 controlling heading date in rice.
    Sci Rep, 2014. 4: p. 4263
  46. Ryu EH,Yang EJ,Woo ER,Chang HC
    Purification and characterization of antifungal compounds from Lactobacillus plantarum HD1 isolated from kimchi.
    Food Microbiol., 2014. 41: p. 19-26
  47. Yang S,Weers BD,Morishige DT,Mullet JE
    CONSTANS is a photoperiod regulated activator of flowering in sorghum.
    BMC Plant Biol., 2014. 14: p. 148
  48. Cai Y, et al.
    Dlf1, a WRKY transcription factor, is involved in the control of flowering time and plant height in rice.
    PLoS ONE, 2014. 9(7): p. e102529
  49. Chen JY, et al.
    Fine mapping of qHd1, a minor heading date QTL with pleiotropism for yield traits in rice (Oryza sativa L.).
    Theor. Appl. Genet., 2014. 127(11): p. 2515-24
  50. Liu X, et al.
    The rice enhancer of zeste [E(z)] genes SDG711 and SDG718 are respectively involved in long day and short day signaling to mediate the accurate photoperiod control of flowering time.
    Front Plant Sci, 2014. 5: p. 591
  51. Kwon CT,Koo BH,Kim D,Yoo SC,Paek NC
    Casein kinases I and 2α phosphorylate oryza sativa pseudo-response regulator 37 (OsPRR37) in photoperiodic flowering in rice.
    Mol. Cells, 2015. 38(1): p. 81-8
  52. Li X, et al.
    Combinations of Hd2 and Hd4 genes determine rice adaptability to Heilongjiang Province, northern limit of China.
    J Integr Plant Biol, 2015. 57(8): p. 698-707
  53. Yoshitake Y, et al.
    The effects of phytochrome-mediated light signals on the developmental acquisition of photoperiod sensitivity in rice.
    Sci Rep, 2015. 5: p. 7709
  54. Liu T,Zhu S,Tang Q,Tang S
    Identification of a CONSTANS homologous gene with distinct diurnal expression patterns in varied photoperiods in ramie (Boehmeria nivea L. Gaud).
    Gene, 2015. 560(1): p. 63-70
  55. Tamaki S, et al.
    FT-like proteins induce transposon silencing in the shoot apex during floral induction in rice.
    Proc. Natl. Acad. Sci. U.S.A., 2015. 112(8): p. E901-10
  56. Gómez-Ariza J, et al.
    Loss of floral repressor function adapts rice to higher latitudes in Europe.
    J. Exp. Bot., 2015. 66(7): p. 2027-39
  57. Tsuji H, et al.
    Hd3a promotes lateral branching in rice.
    Plant J., 2015. 82(2): p. 256-66
  58. Jin J, et al.
    MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice.
    Plant Physiol., 2015. 168(4): p. 1275-85
  59. Hori K, et al.
    Genetic architecture of variation in heading date among Asian rice accessions.
    BMC Plant Biol., 2015. 15: p. 115
  60. Zhao J, et al.
    Genetic interactions between diverged alleles of Early heading date 1 (Ehd1) and Heading date 3a (Hd3a)/ RICE FLOWERING LOCUS T1 (RFT1) control differential heading and contribute to regional adaptation in rice (Oryza sativa).
    New Phytol., 2015. 208(3): p. 936-48
  61. Liu H, et al.
    Parallel Domestication of the Heading Date 1 Gene in Cereals.
    Mol. Biol. Evol., 2015. 32(10): p. 2726-37
  62. Zhang J, et al.
    Combinations of the Ghd7, Ghd8 and Hd1 genes largely define the ecogeographical adaptation and yield potential of cultivated rice.
    New Phytol., 2015. 208(4): p. 1056-66
  63. Zheng XM, et al.
    Nonfunctional alleles of long-day suppressor genes independently regulate flowering time.
    J Integr Plant Biol, 2016. 58(6): p. 540-8
  64. Yang Y, et al.
    The RING-Finger Ubiquitin Ligase HAF1 Mediates Heading date 1 Degradation during Photoperiodic Flowering in Rice.
    Plant Cell, 2015. 27(9): p. 2455-68
  65. Liu X, et al.
    Brassinosteroid (BR) biosynthetic gene lhdd10 controls late heading and plant height in rice (Oryza sativa L.).
    Plant Cell Rep., 2016. 35(2): p. 357-68
  66. Su L,Shan JX,Gao JP,Lin HX
    OsHAL3, a Blue Light-Responsive Protein, Interacts with the Floral Regulator Hd1 to Activate Flowering in Rice.
    Mol Plant, 2016. 9(2): p. 233-244
  67. Kim SK, et al.
    OsNF-YC2 and OsNF-YC4 proteins inhibit flowering under long-day conditions in rice.
    Planta, 2016. 243(3): p. 563-76
  68. Wei FJ, et al.
    Both Hd1 and Ehd1 are important for artificial selection of flowering time in cultivated rice.
    Plant Sci., 2016. 242: p. 187-194
  69. Liu B, et al.
    SET DOMAIN GROUP 708, a histone H3 lysine 36-specific methyltransferase, controls flowering time in rice (Oryza sativa).
    New Phytol., 2016. 210(2): p. 577-88
  70. Jeong HJ,Yang J,Cho LH,An G
    OsVIL1 controls flowering time in rice by suppressing OsLF under short days and by inducing Ghd7 under long days.
    Plant Cell Rep., 2016. 35(4): p. 905-20
  71. Sun X, et al.
    The Oryza sativa Regulator HDR1 Associates with the Kinase OsK4 to Control Photoperiodic Flowering.
    PLoS Genet., 2016. 12(3): p. e1005927
  72. Nemoto Y,Nonoue Y,Yano M,Izawa T
    Hd1,a CONSTANS ortholog in rice, functions as an Ehd1 repressor through interaction with monocot-specific CCT-domain protein Ghd7.
    Plant J., 2016. 86(3): p. 221-33
  73. Lee YS,Yi J,An G
    OsPhyA modulates rice flowering time mainly through OsGI under short days and Ghd7 under long days in the absence of phytochrome B.
    Plant Mol. Biol., 2016. 91(4-5): p. 413-27
  74. Bai B, et al.
    OsBBX14 delays heading date by repressing florigen gene expression under long and short-day conditions in rice.
    Plant Sci., 2016. 247: p. 25-34
  75. Galbiati F, et al.
    Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice.
    Plant Cell Environ., 2016. 39(9): p. 1982-93
  76. Shibaya T, et al.
    Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice.
    Plant Cell Physiol., 2016. 57(9): p. 1828-38
  77. Sheng P, et al.
    A CONSTANS-like transcriptional activator, OsCOL13, functions as a negative regulator of flowering downstream of OsphyB and upstream of Ehd1 in rice.
    Plant Mol. Biol., 2016. 92(1-2): p. 209-22
  78. Wang J, et al.
    Overexpression of OsMYB1R1-VP64 fusion protein increases grain yield in rice by delaying flowering time.
    FEBS Lett., 2016. 590(19): p. 3385-3396
  79. Kong DY, et al.
    Research progress of photoperiod regulated genes on flowering time in rice.
    Yi Chuan, 2016. 38(6): p. 532-542
  80. Sun B, et al.
    Fine mapping and candidate gene analysis of qHD5, a novel major QTL with pleiotropism for yield-related traits in rice (Oryza sativa L.).
    Theor. Appl. Genet., 2017. 130(1): p. 247-258
  81. Hori K,Matsubara K,Yano M
    Genetic control of flowering time in rice: integration of Mendelian genetics and genomics.
    Theor. Appl. Genet., 2016. 129(12): p. 2241-2252