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 XP_016481998.1
Organism
Nicotiana tabacum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
Family FAR1
Protein Properties Length: 849aa    MW: 97284.8 Da    PI: 6.704
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_016481998.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR185.39.8e-2791193291
            FAR1   2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk.............tekerrtraetrtgCkaklkvkkekdgkwevtklel 83 
                     fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+              e++  +ra  +t+Cka+++vk++ dgkw ++++e+
  XP_016481998.1  91 FYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYEKSanrprsrqgnkqdPENATGRRACAKTDCKASMHVKRRPDGKWIIHRFEK 185
                     9***************************************999999899999888776555556699**************************** PP

            FAR1  84 eHnHelap 91 
                     eHnHel p
  XP_016481998.1 186 EHNHELLP 193
                     *****975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031011.2E-2491193IPR004330FAR1 DNA binding domain
PfamPF105511.3E-29291383IPR018289MULE transposase domain
PROSITE profilePS509669.557571607IPR007527Zinc finger, SWIM-type
PfamPF044346.6E-6572605IPR007527Zinc finger, SWIM-type
SMARTSM005751.1E-6582609IPR006564Zinc finger, PMZ-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009585Biological Processred, far-red light phototransduction
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
Sequence ? help Back to Top
Protein Sequence    Length: 849 aa     Download sequence    Send to blast
MDIDLRLPSR DHDKEEEEEQ NGIINMLDNE EKMHSDDGMH GMLVVVEEKM HAEDGGDMNT  60
PVENIIEFKE DVNLEPLAGM EFESHGEAYA FYQEYARSMG FNTAIQNSRR SKTSREFIDA  120
KFACSRYGTK REYEKSANRP RSRQGNKQDP ENATGRRACA KTDCKASMHV KRRPDGKWII  180
HRFEKEHNHE LLPAQAVSEQ TRRMYAAMAR QFAEYKNVVG LKSDSKGPFE KGRNSAMEGG  240
DINVLLEFFI QMQSLNSNFF YAADVGEDQR VKNLFWVDAK ARHDYANFSD VVSFDTTYIR  300
NKYKMPLALF VGVNQHYQFM LLGCALVSDE SATTFSWVMR TWLKAMGGQA PKTVITDHDQ  360
VLKSVISEAL PSSLHYFCMW HILGKVSETL NHVIKQNEKF MAKFEKCIYR SSTDEEFEKR  420
WRKLVDRFDL REAELIHLLY EDRVKWIPMF MRDAFLAGMS TVQRSESVNS FFDKYVHKKT  480
TVPEFVKQYE TILQDRYEEE AKADSDTWNK QPALKSPSPF EKHVAGLYTH AVFKKFQAEV  540
LGAVACIPKR EQQDETTITF GVKDYEKDQD FIVTLNEVKS EISCVCHLFE FKGYLCRHAL  600
IVLQICGVSS IPLHYILKRW TKDAKSKYSM TDGSEDVQSR VQRYNELCYR AMKLSEEGSL  660
SQESYSFALR ALDDAFGSCV TFNNSNKNIL EAGTSSAPGL LCVEDDNQSR SMSKTNKKKN  720
SFTKKRKVNS EPDVMAVGAA DSLQQMDKLN SRPVTLDGYF GPQQSVQGMV QLNLMAPTRD  780
NYYGNQQTIQ GLGQLNSIAP THDGYYGAQP TMHGLGQMDF FRAPSFPYGI RDEPNVRSAQ  840
LHDEASRHP
Functional Description ? help Back to Top
Source Description
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00078ChIP-seqTransfer from AT3G22170Download
Motif logo
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
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0137150.0BT013715.1 Lycopersicon esculentum clone 132560F, mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009804948.10.0PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X3
RefseqXP_009804949.10.0PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X3
RefseqXP_016481998.10.0PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3-like isoform X3
RefseqXP_016481999.10.0PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3-like isoform X3
SwissprotQ9LIE50.0FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBLA0A1S4AZK20.0A0A1S4AZK2_TOBAC; protein FAR-RED ELONGATED HYPOCOTYL 3-like isoform X3
TrEMBLA0A1U7YPD60.0A0A1U7YPD6_NICSY; protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X3
STRINGXP_009804946.10.0(Nicotiana sylvestris)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G22170.20.0far-red elongated hypocotyls 3
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]