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 676740286
Organism
Sisymbrium irio
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Sisymbrieae; Sisymbrium
Family FAR1
Protein Properties Length: 865aa    MW: 98831.1 Da    PI: 6.8368
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
676740286genomeVEGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR180.43.2e-25100203191
       FAR1   1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk.............tekerrtraetrtgCkaklkvkkekdgkwevtkleleHnH 87 
                +fY+eY++ +GF++ +++s++sk+++e+++++f Cs++g+++e +k+             +++   +r+  +t+Cka+++vk++ dgkw++++++ +HnH
  676740286 100 SFYQEYSRAIGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDKTfnrprarqskqepENNMAGRRTCAKTDCKASMHVKRRPDGKWVIHSFVRDHNH 199
                5********************************************999***99887655544444599999***************************** PP

       FAR1  88 elap 91 
                el p
  676740286 200 ELLP 203
                *975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031014.2E-23100203IPR004330FAR1 DNA binding domain
PfamPF105518.5E-26301392IPR018289MULE transposase domain
PROSITE profilePS509669.137581617IPR007527Zinc finger, SWIM-type
SMARTSM005751.3E-6592619IPR006564Zinc 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: 865 aa     Download sequence    Send to blast
VMDIDLRLHS GDLCKQGDEE SRGLDNVSHN EHKLQAAASA GGGEEDLDIG KIEDVTVEVH  60
TEDDSAGMAV PTGELVEYTE GMNLEPLNGM EFESHGEAYS FYQEYSRAIG FNTAIQNSRR  120
SKTTREFIDA KFACSRYGTK REYDKTFNRP RARQSKQEPE NNMAGRRTCA KTDCKASMHV  180
KRRPDGKWVI HSFVRDHNHE LLPAQAVSEQ TRKIYAAMAK QFAEYKTVIS LKTDSKSSFE  240
KGRSLSVETG DFKVLLDFVS RMQILNSNFF YAVDLGDDQR VKNVFWVDAK SRHNYVSFCD  300
VVSLDTTYVR NKYKMPLAVF VGVNQHYQYM VLGCALLSDE SAATFSWLME TWLRAMGGQA  360
PKVLITEQDV VMNSIVPEVF PNTQHCLFLW HVLIKVSEHL GQVAKQHENF TAKFEKCIYK  420
SWKEEDFARR WWKILARFGL KDDHWMQSLY EDRRKWAPTY MTDVLLAGMS TSQRADSINA  480
FFDKYLHRKT SVQEFVKLYD TILQDRCEEE AKADSETWNK PPAMKSPSPF EKSVSEVYTP  540
AVFKKFQIEV LGAIACSPRE ENRDATCSTF RVQDFENNQD FVVTWNQAKA EVSCICRLFE  600
FKGYLCRHTL NVLQCCHLSS IPSQYILKRW TKDAKSRHFS GEPQQLQTRL QRYNDLCQRA  660
LKLAEDASIS QESYNIAFLA IEESLGNCAG VNTSGRSLPD VVTSPTQGLI SVEEDNQSRS  720
AGKTSKKKNP TKKRKSYDPD YGLQVNSEQD VMPVAAPESL QQMDKLSPRT VGIESYYGTQ  780
QSVQNMVQLN LMAPTRDSFY GNQQTIQGLR QLNSIAPSYD SYYTAQQGIH GQGVDFFRPP  840
NFPYDIRDDP NVRTTQLHED ASRHT
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
PlantRegMap676740286
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
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
RefseqXP_006406203.10.0protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
RefseqXP_006406204.10.0protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
SwissprotQ9LIE50.0FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBLV4LYQ90.0V4LYQ9_EUTSA; Uncharacterized protein
STRINGXP_006406203.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM11826253
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]