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 Glyma.04G124300.1.p
Common NameGLYMA_04G124300, LOC100810223
Organism
Glycine max
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja
Family FAR1
Protein Properties Length: 844aa    MW: 96226.3 Da    PI: 7.3019
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Glyma.04G124300.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR185.86.8e-2789191191
                 FAR1   1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekdgkwev 78 
                          +fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+            +e++  +r+ ++t+Cka+++vk+++dgkw++
  Glyma.04G124300.1.p  89 SFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSfnrprarqnkqdSENSTGRRSCSKTDCKASMHVKRRSDGKWVI 178
                          5*******************************************9999***999887665556669999********************* PP

                 FAR1  79 tkleleHnHelap 91 
                          +++++eHnHel p
  Glyma.04G124300.1.p 179 HSFVKEHNHELLP 191
                          **********975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031019.3E-2589191IPR004330FAR1 DNA binding domain
PfamPF105517.2E-29288380IPR018289MULE transposase domain
PROSITE profilePS509669.507568604IPR007527Zinc finger, SWIM-type
PfamPF044348.8E-6576602IPR007527Zinc finger, SWIM-type
SMARTSM005755.0E-6579606IPR006564Zinc 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: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: 844 aa     Download sequence    Send to blast
MDIDLRLPSG EHDKEDEETT TIDNMLDSEE KLHNGGIDGR NIVDTGIEVH ALNGGDLNSP  60
TVDIVMFKED TNLEPLSGME FESHGEAYSF YQEYARSMGF NTAIQNSRRS KTSREFIDAK  120
FACSRYGTKR EYDKSFNRPR ARQNKQDSEN STGRRSCSKT DCKASMHVKR RSDGKWVIHS  180
FVKEHNHELL PAQAVSEQTR RMYAAMARQF AEYKTVVGLK NEKNPFDKGR NLGLESGEAR  240
LMLDFFIQMQ NMNSNFFYAV DLGEDQRLKN LLWIDAKSRN DYINFCDVVS FDTAYVRNKY  300
KMPLALFVGV NQHYQFTLLG CALISDESAA TFSWLFRTWL KGVGGQVPKV IITDHDKTLK  360
SVISDIFPNS SHCVCLWHIL GKVSENLSPV IKKHENFMAK FEKCIYRSLT SDDFEKRWWK  420
IVDKFELRED ECMQSLYEDR KLWAPTFMKD VFLGGMSTVQ RSESVNSFFD KYVHKKTSVQ  480
DFVKQYEAIL QDRYEEEAKA DSDTWNKVAT LKTPSPLEKS VAGIFSHAVF KKIQTEVVGA  540
VACHPKADRQ DDTTIVHRVH DMETNKDFFV VVNQVKSELS CICRLFEYRG YLCRHALFVL  600
QYSGQSVFPS QYILKRWTKD AKVRNIMGEE SEHMLTRVQR YNDLCQRALK LSEEGSLSQE  660
SYGIAFHALH EAHKSCVSVN NSSKSSPTEA GTPGAHGQLS TEEDTQSRNM GKSNKKKHPT  720
KKKKVNSEAE VITVGALDNL QQMDKFSTRA VTLEGYYGTQ QSVQGMLNLM GPTRDDYYGN  780
QQTLQGLGPI SSIPTSHDGY YGTHQGMPGL AQLDFLRTGF TYGIRDDPNV RATQLHEDPS  840
RHA*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Gma.50560.0cotyledon| epicotyl| leaf| stem
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
Cis-element ? help Back to Top
SourceLink
PlantRegMapGlyma.04G124300.1.p
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
GenBankKM5877010.0KM587701.1 Glycine max clone GmFHY3 FHY3 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006578386.10.0protein FAR-RED ELONGATED HYPOCOTYL 3-like isoform X1
RefseqXP_025983872.10.0protein FAR-RED ELONGATED HYPOCOTYL 3-like isoform X1
RefseqXP_025983873.10.0protein FAR-RED ELONGATED HYPOCOTYL 3-like isoform X1
RefseqXP_025983874.10.0protein FAR-RED ELONGATED HYPOCOTYL 3-like isoform X1
RefseqXP_025983875.10.0protein FAR-RED ELONGATED HYPOCOTYL 3-like isoform X1
SwissprotQ9LIE50.0FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBLI1JVW10.0I1JVW1_SOYBN; Uncharacterized protein
STRINGGLYMA04G14850.10.0(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF4030530
Representative plantOGRP1057657
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]