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 Tp57577_TGAC_v2_mRNA5306
Organism
Trifolium pratense
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
Family FAR1
Protein Properties Length: 969aa    MW: 110857 Da    PI: 7.5592
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp57577_TGAC_v2_mRNA5306genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR184.81.4e-26215317191
                      FAR1   1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekd 73 
                               +fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+            +e++  +r+ ++t+Cka+++vk++ d
  Tp57577_TGAC_v2_mRNA5306 215 SFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSfnrprarqhkqeSENSTGRRSCSKTDCKASMHVKRRPD 299
                               5********************************************999****99877655555558999**************** PP

                      FAR1  74 gkwevtkleleHnHelap 91 
                               gkw+++++++eHnHel p
  Tp57577_TGAC_v2_mRNA5306 300 GKWVIHSFVKEHNHELLP 317
                               ***************975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031011.7E-24215317IPR004330FAR1 DNA binding domain
PfamPF105519.4E-29414506IPR018289MULE transposase domain
PROSITE profilePS509669.78694730IPR007527Zinc finger, SWIM-type
PfamPF044341.1E-5695728IPR007527Zinc finger, SWIM-type
SMARTSM005752.1E-7705732IPR006564Zinc 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: 969 aa     Download sequence    Send to blast
LELGGGRLEL PEEEKQNKKT RKQQNSTPEK KKARKGRTRI GEEENTCADS DKVVQRADCI  60
LVAPPPPLLV HIVKIKVSDT CEINGEITKS EWIGKRNESN HHHHQHNQFF SFNFSVPLKS  120
SKQVLIMDID LRLPSGEHDK EEEETTTLDN MLEGEEKLHN GDIDGRHMVD AGIELHALNG  180
GDLNSPTVDM VMFKEDTNLE PLFGMEFESH GEAYSFYQEY ARSMGFNTAI QNSRRSKTSR  240
EFIDAKFACS RYGTKREYDK SFNRPRARQH KQESENSTGR RSCSKTDCKA SMHVKRRPDG  300
KWVIHSFVKE HNHELLPAQA VSEQTRKMYA VMARQFAEYK TVVGVKNEKN QFDKGRNLGL  360
EFVEAKLMLD FFIQMQSMNS NFFYAVDLGE DQRLKNLLWI DAKSRHDYIN FCDVVSFDTT  420
YVRNKYKMPL VLFVGVNQHY QFILLGCALI SDESAATFSW LLRTWLKGVG GQVPKVIITD  480
HDMTLKSVIS DVIPSACHCV CLWHILGKVS ENLAHVIKKH VNFMTKFEKC VFRSLTSDDF  540
DNRWEKILDR FELRQDECMQ SLYEDRKLWA PTFMKDVFLG GMSTPQRSES VNSFFDKYVH  600
RKTYIQDFVK QYETILQDRY EEEAKADSDT WNKVATLKTP SPLEKSVAGI FTHTVFKKIQ  660
AEIIGAVACH PKLDRQDETT IVHRVHDMET RKDFFVVVNE VNSELSCICR QFEYKGYLCR  720
HALVVLQYSG HSVFPSQYVL KRWTKDAKIR NVTAEESEHM LARVQRYNDL CHRSLKLSEE  780
GSLSQDSYGI AFHALNEAHK NCVSVNNSSK SPTEAGTSGV HGQLSIEEDT QSRNMGKSNK  840
KKNPTKKKKV NSEAEVMTVG ALDNLQQMDK FSARTAVLEG YYGTQQSVQG MLNLMGPTRD  900
DYYGNQQTLQ GLGPINSIPT SHDGYYGAHQ SMPGLAQLDF LRTGFTYGIR DDPNVRAAQL  960
HEDPSRHA*
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
PlantRegMapTp57577_TGAC_v2_mRNA5306
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
GenBankCT0301920.0CT030192.6 M.truncatula DNA sequence from clone MTH2-16D16 on chromosome 3, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012571076.10.0protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X8
RefseqXP_027190195.10.0protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X4
SwissprotQ9LIE50.0FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBLA0A2K3NNZ10.0A0A2K3NNZ1_TRIPR; Protein far-red impaired response 1-like
STRINGXP_004499738.10.0(Cicer arietinum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF4030530
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]