PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G22170.1
Common NameCPD45, FHY3, MKA23.12
Organism
Arabidopsis thaliana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family FAR1
Protein Properties Length: 839aa    MW: 95996.3 Da    PI: 7.0309
Description far-red elongated hypocotyls 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G22170.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR181.61.3e-2584186191
         FAR1   1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekdgkwevtkleleHn 86 
                  +fY+eY++ +GF++ +++s++sk+++e+++++f Cs++g+++e +k+             e+   +r+  +t+Cka+++vk++ dgkw++++++ eHn
  AT3G22170.1  84 SFYQEYSRAMGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDKSfnrprarqskqdPENMAGRRTCAKTDCKASMHVKRRPDGKWVIHSFVREHN 181
                  5*******************************************99999999877654444444499999**************************** PP

         FAR1  87 Helap 91 
                  Hel p
  AT3G22170.1 182 HELLP 186
                  **975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031011.9E-2384186IPR004330FAR1 DNA binding domain
PfamPF105514.8E-24284376IPR018289MULE transposase domain
PROSITE patternPS005910343353IPR031158Glycosyl hydrolases family 10, active site
PROSITE profilePS509669.223564600IPR007527Zinc finger, SWIM-type
SMARTSM005756.7E-7575602IPR006564Zinc finger, PMZ-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009585Biological Processred, far-red light phototransduction
GO:0010018Biological Processfar-red light signaling pathway
GO:0010218Biological Processresponse to far red light
GO:0042753Biological Processpositive regulation of circadian rhythm
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008270Molecular Functionzinc ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025195anatomypollen tube cell
PO:0025281anatomypollen
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 839 aa     Download sequence    Send to blast
MDIDLRLHSG DLCKGDDEDR GLDNVLHNEE DMDIGKIEDV SVEVNTDDSV GMGVPTGELV  60
EYTEGMNLEP LNGMEFESHG EAYSFYQEYS RAMGFNTAIQ NSRRSKTTRE FIDAKFACSR  120
YGTKREYDKS FNRPRARQSK QDPENMAGRR TCAKTDCKAS MHVKRRPDGK WVIHSFVREH  180
NHELLPAQAV SEQTRKIYAA MAKQFAEYKT VISLKSDSKS SFEKGRTLSV ETGDFKILLD  240
FLSRMQSLNS NFFYAVDLGD DQRVKNVFWV DAKSRHNYGS FCDVVSLDTT YVRNKYKMPL  300
AIFVGVNQHY QYMVLGCALI SDESAATYSW LMETWLRAIG GQAPKVLITE LDVVMNSIVP  360
EIFPNTRHCL FLWHVLMKVS ENLGQVVKQH DNFMPKFEKC IYKSGKDEDF ARKWYKNLAR  420
FGLKDDQWMI SLYEDRKKWA PTYMTDVLLA GMSTSQRADS INAFFDKYMH KKTSVQEFVK  480
VYDTVLQDRC EEEAKADSEM WNKQPAMKSP SPFEKSVSEV YTPAVFKKFQ IEVLGAIACS  540
PREENRDATC STFRVQDFEN NQDFMVTWNQ TKAEVSCICR LFEYKGYLCR HTLNVLQCCH  600
LSSIPSQYIL KRWTKDAKSR HFSGEPQQLQ TRLLRYNDLC ERALKLNEEA SLSQESYNIA  660
FLAIEGAIGN CAGINTSGRS LPDVVTSPTQ GLISVEEDNH SRSAGKTSKK KNPTKKRKVN  720
PEQDVMPVAA PESLQQMDKL SPRTVGIESY YGTQQSVQGM VQLNLMGPTR DNFYGNQQTM  780
QGLRQLNSIA PSYDSYYGPQ QGIHGQGVDF FRPANFSYDI RDDPNVRTTQ LHEDASRHS
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.277250.0floral meristem| flower| seed| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible256820_at1e-170
Expression AtlasAT3G22170-
AtGenExpressAT3G22170-
ATTED-IIAT3G22170-
Functional Description ? help Back to Top
Source Description
TAIRA component of the PHYA signaling network, mediates the FR-HIR response to far-red light in concert with FAR1.
UniProtTranscription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'. Activates the expression of FHY1 and FHL involved in light responses. When associated with PHYA, protects it from being recognized and degraded by the COP1/SPA complex. Positive regulator of chlorophyll biosynthesis via the activation of HEMB1 gene expression. {ECO:0000269|PubMed:11889039, ECO:0000269|PubMed:12753585, ECO:0000269|PubMed:17012604, ECO:0000269|PubMed:18033885, ECO:0000269|PubMed:18715961, ECO:0000269|PubMed:22634759}.
Function -- GeneRIF ? help Back to Top
  1. FHY3 appears to be a novel gating factor, specifically in gating red light signaling to the clock during daytime
    [PMID: 17012604]
  2. study shows FHY3 & FAR1, which encode proteins related to Mutator-like transposases, act together to modulate phyA signaling by activating transcription of FHY1 & FHL
    [PMID: 18033885]
  3. The zinc finger domain is essential for direct DNA binding of FHY3 in mediating light signaling. The central core transposase domain and C-terminal SWIM domain are essential for the transcriptional regulatory activity of FHY3.
    [PMID: 18715961]
  4. phyA associations with FHY3 and FHY1 protect underphosphorylated phyA from being recognized by the COP1/SPA complex.
    [PMID: 18722184]
  5. Data suggest that FHY3 regulates multiple facets of plant development, thus providing insights into its functions beyond light and circadian pathways.
    [PMID: 21803941]
  6. The fhy3 phenotypes of axillary bud outgrowth suppression and of stress-induced leaf growth retardation both required the AUXIN-RESISTANT1 gene, and are independent of phyA.
    [PMID: 22540368]
  7. Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis.
    [PMID: 22634759]
  8. COP1 gene expression in response to photomorphogenic UV-B is controlled by a combinatorial regulation of FHY3 and HY5, and this UV-B-specific working mode of FHY3 and HY5 is distinct from that in far-red light and circadian conditions.
    [PMID: 23150635]
  9. FRS4/CPD25 and FHY3/CPD45 function as a heterodimer that cooperatively activates ARC5.
    [PMID: 23662592]
  10. FHY3 and FAR1 are positive regulators of abscissic acid (ABA) signaling and provide insight into the integration of light and ABA signaling.
    [PMID: 23946351]
  11. domestication of FHY3/FAR1 may enable angiosperms to better integrate various endogenous and exogenous signals for coordinated regulation of growth and development, thus enhancing their fitness and adaptation
    [PMID: 25956482]
  12. this study demonstrates an important role of FHY3 and FAR1 in regulating plant immunity, through integrating chlorophyll biosynthesis and the salicylic acid signaling pathway.
    [PMID: 25989254]
  13. FHY3 and FAR1 directly bind the promoter of MIPS1 to activate its expression and thereby promote inositol biosynthesis to prevent
    [PMID: 26714049]
  14. In shoot apical meristem, FHY3 directly represses CLV3, which consequently regulates WUS to maintain the stem cell pool.
    [PMID: 27469166]
  15. the light-signaling proteins FHY3 and FAR1 influence starch synthesis and starch granule formation through transcriptional activation of ISA2.
    [PMID: 27859295]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00078ChIP-seq26531826Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G22170.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated after exposure to far-red light. Subject to a negative feedback regulation by PHYA signaling. Up-regulated by white light. {ECO:0000269|PubMed:11889039, ECO:0000269|PubMed:18033885, ECO:0000269|PubMed:22634759}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT4G15090 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT2G37678(A), AT2G40080(A), AT5G02200(A)
Interaction -- BIND ? help Back to Top
Source Intact With Description
BINDAT4G15090FAR1 interacts with FHY3.
BINDAT3G22170FHY3 interacts with another molecule of FHY3.
Interaction ? help Back to Top
Source Intact With
BioGRIDAT3G22170, AT4G15090, AT5G11260, AT1G01060
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Reduced protochlorophyllide levels in darkness and less photobleaching in the light. {ECO:0000269|PubMed:22634759}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G22170
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0013060.0AP001306.1 Arabidopsis thaliana genomic DNA, chromosome 3, P1 clone:MKA23.
GenBankCP0026860.0CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001118673.10.0far-red elongated hypocotyls 3
RefseqNP_188856.20.0far-red elongated hypocotyls 3
SwissprotQ9LIE50.0FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBLA0A178VJL50.0A0A178VJL5_ARATH; FHY3
STRINGAT3G22170.20.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM11826253
Representative plantOGRP1057657
Publications ? help Back to Top
  1. Desnos T,Puente P,Whitelam GC,Harberd NP
    FHY1: a phytochrome A-specific signal transducer.
    Genes Dev., 2001. 15(22): p. 2980-90
    [PMID:11711433]
  2. Wang H,Deng XW
    Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1.
    EMBO J., 2002. 21(6): p. 1339-49
    [PMID:11889039]
  3. Hudson ME,Lisch DR,Quail PH
    The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway.
    Plant J., 2003. 34(4): p. 453-71
    [PMID:12753585]
  4. Lin R,Wang H
    Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development.
    Plant Physiol., 2004. 136(4): p. 4010-22
    [PMID:15591448]
  5. Zhou Q, et al.
    FHL is required for full phytochrome A signaling and shares overlapping functions with FHY1.
    Plant J., 2005. 43(3): p. 356-70
    [PMID:16045472]
  6. Allen T, et al.
    Arabidopsis FHY3 specifically gates phytochrome signaling to the circadian clock.
    Plant Cell, 2006. 18(10): p. 2506-16
    [PMID:17012604]
  7. Lin R, et al.
    Transposase-derived transcription factors regulate light signaling in Arabidopsis.
    Science, 2007. 318(5854): p. 1302-5
    [PMID:18033885]
  8. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
    [PMID:18650403]
  9. Genoud T, et al.
    FHY1 mediates nuclear import of the light-activated phytochrome A photoreceptor.
    PLoS Genet., 2008. 4(8): p. e1000143
    [PMID:18670649]
  10. Lin R, et al.
    Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction.
    Plant Physiol., 2008. 148(2): p. 981-92
    [PMID:18715961]
  11. Saijo Y, et al.
    Arabidopsis COP1/SPA1 complex and FHY1/FHY3 associate with distinct phosphorylated forms of phytochrome A in balancing light signaling.
    Mol. Cell, 2008. 31(4): p. 607-13
    [PMID:18722184]
  12. Wang Y, et al.
    Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis.
    Plant Physiol., 2008. 148(3): p. 1201-11
    [PMID:18775970]
  13. Stephenson PG,Terry MJ
    Light signalling pathways regulating the Mg-chelatase branchpoint of chlorophyll synthesis during de-etiolation in Arabidopsis thaliana.
    Photochem. Photobiol. Sci., 2008. 7(10): p. 1243-52
    [PMID:18846290]
  14. Shen Y, et al.
    Phytochrome A mediates rapid red light-induced phosphorylation of Arabidopsis FAR-RED ELONGATED HYPOCOTYL1 in a low fluence response.
    Plant Cell, 2009. 21(2): p. 494-506
    [PMID:19208901]
  15. Reiland S, et al.
    Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks.
    Plant Physiol., 2009. 150(2): p. 889-903
    [PMID:19376835]
  16. Li J, et al.
    Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome A signaling.
    Plant Cell, 2010. 22(11): p. 3634-49
    [PMID:21097709]
  17. Li G, et al.
    Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis.
    Nat. Cell Biol., 2011. 13(5): p. 616-22
    [PMID:21499259]
  18. Ouyang X, et al.
    Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development.
    Plant Cell, 2011. 23(7): p. 2514-35
    [PMID:21803941]
  19. Stirnberg P,Zhao S,Williamson L,Ward S,Leyser O
    FHY3 promotes shoot branching and stress tolerance in Arabidopsis in an AXR1-dependent manner.
    Plant J., 2012. 71(6): p. 907-20
    [PMID:22540368]
  20. Tang W, et al.
    Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis.
    Plant Cell, 2012. 24(5): p. 1984-2000
    [PMID:22634759]
  21. Huang X, et al.
    Arabidopsis FHY3 and HY5 positively mediate induction of COP1 transcription in response to photomorphogenic UV-B light.
    Plant Cell, 2012. 24(11): p. 4590-606
    [PMID:23150635]
  22. Gao Y, et al.
    Arabidopsis FRS4/CPD25 and FHY3/CPD45 work cooperatively to promote the expression of the chloroplast division gene ARC5 and chloroplast division.
    Plant J., 2013. 75(5): p. 795-807
    [PMID:23662592]
  23. Tilbrook K, et al.
    The UVR8 UV-B Photoreceptor: Perception, Signaling and Response.
    Arabidopsis Book, 2013. 11: p. e0164
    [PMID:23864838]
  24. Tang W, et al.
    FAR-RED ELONGATED HYPOCOTYL3 and FAR-RED IMPAIRED RESPONSE1 transcription factors integrate light and abscisic acid signaling in Arabidopsis.
    Plant Physiol., 2013. 163(2): p. 857-66
    [PMID:23946351]
  25. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  26. Chang N,Gao Y,Zhao L,Liu X,Gao H
    Arabidopsis FHY3/CPD45 regulates far-red light signaling and chloroplast division in parallel.
    Sci Rep, 2015. 5: p. 9612
    [PMID:25872642]
  27. Wang C, et al.
    SCAB3 Is Required for Reorganization of Actin Filaments during Light Quality Changes.
    J Genet Genomics, 2015. 42(4): p. 161-8
    [PMID:25953354]
  28. Wang H,Wang H
    Multifaceted roles of FHY3 and FAR1 in light signaling and beyond.
    Trends Plant Sci., 2015. 20(7): p. 453-61
    [PMID:25956482]
  29. Wang W, et al.
    A pair of light signaling factors FHY3 and FAR1 regulates plant immunity by modulating chlorophyll biosynthesis.
    J Integr Plant Biol, 2016. 58(1): p. 91-103
    [PMID:25989254]
  30. Ma L, et al.
    Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1.
    Mol Plant, 2016. 9(4): p. 541-57
    [PMID:26714049]
  31. Siddiqui H,Khan S,Rhodes BM,Devlin PF
    FHY3 and FAR1 Act Downstream of Light Stable Phytochromes.
    Front Plant Sci, 2016. 7: p. 175
    [PMID:26941752]
  32. Li D, et al.
    FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(33): p. 9375-80
    [PMID:27469166]
  33. Liu L,Li B,Liu X
    FAR-RED ELONGATED HYPOCOTYL3 promotes floral meristem determinacy in Arabidopsis.
    Plant Signal Behav, 2016. 11(10): p. e1238545
    [PMID:27660915]
  34. Ma L,Xue N,Fu X,Zhang H,Li G
    Arabidopsis thaliana FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1) modulate starch synthesis in response to light and sugar.
    New Phytol., 2017. 213(4): p. 1682-1696
    [PMID:27859295]
  35. Liu Y, et al.
    Light and Ethylene Coordinately Regulate the Phosphate Starvation Response through Transcriptional Regulation of PHOSPHATE STARVATION RESPONSE1.
    Plant Cell, 2017. 29(9): p. 2269-2284
    [PMID:28842534]
  36. Joly-Lopez Z, et al.
    Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements.
    Front Plant Sci, 2017. 8: p. 2027
    [PMID:29250089]