PlantTFDB
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 Solyc07g043270.2.1
Common NameLOC101256896
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family FAR1
Protein Properties Length: 850aa    MW: 97504 Da    PI: 6.7704
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc07g043270.2.1genomeITAGView 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.............tekerrtraetrtgCkaklkvkkekdgkwevt 79 
                         fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+              e++  +ra  +t+Cka+++vk++ dgkw ++
  Solyc07g043270.2.1  91 FYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYEKSanrprsrqgnkqdPENATGRRACAKTDCKASMHVKRRPDGKWIIH 181
                         9***************************************999999899999888776555556699************************ PP

                FAR1  80 kleleHnHelap 91 
                         ++e+eHnHel p
  Solyc07g043270.2.1 182 RFEKEHNHELLP 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
PfamPF105511.4E-27291383IPR018289MULE transposase domain
PROSITE profilePS509669.569571607IPR007527Zinc finger, SWIM-type
PfamPF044342.4E-4579604IPR007527Zinc finger, SWIM-type
SMARTSM005755.4E-6582609IPR006564Zinc 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: 850 aa     Download sequence    Send to blast
MDIDLRLPSQ DHDKEEEEEE QNGIINMLDN EEKIHGDDGM HGMLVIEEKM HAEDRGDMNT  60
PVGTMIDFKE DVNLEPLAGM EFESHGEAYA FYQEYARSMG FNTAIQNSRR SKTSREFIDA  120
KFACSRYGTK REYEKSANRP RSRQGNKQDP ENATGRRACA KTDCKASMHV KRRPDGKWII  180
HRFEKEHNHE LLPAQAVSEQ TRRMYAAMAR QFAEYKNVVG LKSDTKVLFD KGRNSAIEGG  240
DISVLLEFFI QMQNLNSNFF YAVDVGEDQR VKNLFWVDAK ARHDYVNFSD VVSFDTTYVR  300
NKYKMPLALF VGVNQHFQFM LLGCALVSEE SASTFSWVMR TWLKAMGGQA PKTVITDHDL  360
VLKSVISEAL PLSLHYFCLW HILGKVSDTL NHVIKQNEKF MPKFEKCLNR SWTDEEFEKR  420
WRKLVDKFDL REVELVHSLY EDRVKWAPTF IRDVVLAGMS TVQRSESVNS FFDKYVHKKT  480
TIQEFVKQYE SILQDRYEEE AKADSDTWNK QPALRSPSPF EKHLAGLYTH AVFKKFQSEV  540
VGATACGPKR EKQDEIVLTY RVQDFEKTQE FIVTLDEMKS EISCICHLFE YKGYLCRHAL  600
IVLQICAVSS IPPQYILKRW TKDAKSKYSM TDGSEDVQSR FQRYNELCHR AMKLSEEGSL  660
SQESYSFALR ALDDAFGSCV TFNNSNKNML EAGTSSASGL LCIEDDNQSR SMSKTNKKKN  720
NFTKKRKVNS EPDVMAVGAA DSLQQMDKLN SRPVTLDGYF GPQQSVQGMV QLNLMAPTRD  780
NYYANQQTIQ GLGQLNSIAP THDGYYGAQP TMHGLGQMDF FRSPSFSYGI RDEPTVRSSQ  840
LHDDASRHP*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.53250.0callus| flower| fruit| leaf| root
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
PlantRegMapSolyc07g043270.2.1
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
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0137150.0Lycopersicon esculentum clone 132560F, mRNA sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004243646.10.0protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
RefseqXP_019070365.10.0protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
RefseqXP_019070366.10.0protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
SwissprotQ9LIE50.0FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBLA0A3Q7H9910.0A0A3Q7H991_SOLLC; Uncharacterized protein
STRINGSolyc07g043270.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA49621103
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. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]