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 Cagra.2420s0008.1.p
Organism
Capsella grandiflora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family FAR1
Protein Properties Length: 849aa    MW: 97274.6 Da    PI: 6.6875
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.2420s0008.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR1812.1e-2592194191
                 FAR1   1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekdgkwev 78 
                          +fY+eY++ +GF++ +++s++sk+++e+++++f Cs++g+++e +k+             e+   +r+  +t+Cka+++vk++ dgkw++
  Cagra.2420s0008.1.p  92 SFYQEYSRAIGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDKSfnrprarqskqdPENMAGRRTCAKTDCKASMHVKRRPDGKWVI 181
                          5*******************************************99999999877654444444499999******************** PP

                 FAR1  79 tkleleHnHelap 91 
                          ++++ eHnHel p
  Cagra.2420s0008.1.p 182 HSFVREHNHELLP 194
                          **********975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031012.9E-2392194IPR004330FAR1 DNA binding domain
PfamPF105512.5E-24292384IPR018289MULE transposase domain
PROSITE profilePS509669.26572608IPR007527Zinc finger, SWIM-type
SMARTSM005756.7E-7583610IPR006564Zinc 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
MDIDLRLHSG DLCKGDDEDR GLDNVLQNEH KLHDADEEDM DIGKIEDVSV EVHTDDSVGM  60
GVPTGDLVEY TEGMNLEPLN GMEFESHGEA YSFYQEYSRA IGFNTAIQNS RRSKTTREFI  120
DAKFACSRYG TKREYDKSFN RPRARQSKQD PENMAGRRTC AKTDCKASMH VKRRPDGKWV  180
IHSFVREHNH ELLPAQAVSE QTRKIYAAMA KQFAEYKTVI SLKSDSKSSF EKGRNISVET  240
GDFKILLDFL SRMQTVNSNL FYAVDLGDDQ RVKNVFWVDA KSRHNYGSFC DVVSLDTTYV  300
RNKYKMPLAI FVGVNQHYQY MVLGCALISD ESAATFSWLM ETWLRAMGGE APKVLITELD  360
VVMNSIVPEI FPNTRHCLFL WHVFMKVSEN LGQVIKQHDN FMPKFEKCIY KSCKEEDFAR  420
RWWKNLARFG LKDDQWMHSL YEDRKKWAPT YMTDVLLAGM STSQRAESIN AFFDKYMHKK  480
TSVPEFLKLY ETILQDRCEE EAKADSEMWN KQPTLKSPSP FEKSVSEIYT PAVFKKFQIE  540
VLGAIACSPR EESRDDTGST FRVQDFENNQ DFVVTWNQTK DEVSCICRLF EYKGYLCRHT  600
LNVLQCCHLS SIPRQYILNR WTKDAKSPHF SGEPQQLQTR LLRYNDLCQR ALKLNEEASV  660
SQESYNIAFV AIEGALGNCA GINTSGKSLP DVVTSPTQGL ISVEEENQSR NAGKTSKKKN  720
PTKKRKVNPE PEVMPVAPPE SLQQMDKLSP RTVGIESYYG TQQSVQGMVQ LNLMAPTRDN  780
FYGNHQQTIQ GLRQLNSIAP TYDSYYGAQQ GIHGQGVDFF RPPNFPYDIR DDPNVRTTQL  840
HEDASRHS*
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
PlantRegMapCagra.2420s0008.1.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
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_023641622.10.0protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
SwissprotQ9LIE50.0FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBLR0G3J30.0R0G3J3_9BRAS; Uncharacterized protein
STRINGCagra.2420s0008.1.p0.0(Capsella grandiflora)
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]