PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G15090.1
Common Namedl3590w, FAR1, FCAALL.134
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family FAR1
Protein Properties Length: 827aa    MW: 95449.1 Da    PI: 6.6091
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G15090.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR190.72e-2866154291
         FAR1   2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkktekerrtraetrtgCkaklkvkkekdgkwevtkleleHnHelap 91 
                  fY+eYAk++GF++++++s++sk+++ +++++f Cs++g + e++++  +++r++++++t+Cka+++vk++ dgkw +++++++HnHel p
  AT4G15090.1  66 FYQEYAKSMGFTTSIKNSRRSKKTKDFIDAKFACSRYGVTPESESS-GSSSRRSTVKKTDCKASMHVKRRPDGKWIIHEFVKDHNHELLP 154
                  9***************************************999998.9999999*********************************975 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031013.7E-2666154IPR004330FAR1 DNA binding domain
PfamPF105511.1E-25275368IPR018289MULE transposase domain
PROSITE profilePS509668.939555591IPR007527Zinc finger, SWIM-type
PfamPF044349.5E-7557590IPR007527Zinc finger, SWIM-type
SMARTSM005753.1E-7566593IPR006564Zinc 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:0005515Molecular Functionprotein binding
GO:0008270Molecular Functionzinc ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 827 aa     Download sequence    Send to blast
MDLQENLVSD AGDDHMVDIV VEPHSNRDIG IVDEFNIGGD VGFSGDLDLE PRNGIDFDTH  60
EAAYIFYQEY AKSMGFTTSI KNSRRSKKTK DFIDAKFACS RYGVTPESES SGSSSRRSTV  120
KKTDCKASMH VKRRPDGKWI IHEFVKDHNH ELLPALAYHF RIQRNVKLAE KNNIDILHAV  180
SERTKKMYVE MSRQSGGYKN IGSLLQTDVS SQVDKGRYLA LEEGDSQVLL EYFKRIKKEN  240
PKFFYAIDLN EDQRLRNLFW ADAKSRDDYL SFNDVVSFDT TYVKFNDKLP LALFIGVNHH  300
SQPMLLGCAL VADESMETFV WLIKTWLRAM GGRAPKVILT DQDKFLMSAV SELLPNTRHC  360
FALWHVLEKI PEYFSHVMKR HENFLLKFNK CIFRSWTDDE FDMRWWKMVS QFGLENDEWL  420
LWLHEHRQKW VPTFMSDVFL AGMSTSQRSE SVNSFFDKYI HKKITLKEFL RQYGVILQNR  480
YEEESVADFD TCHKQPALKS PSPWEKQMAT TYTHTIFKKF QVEVLGVVAC HPRKEKEDEN  540
MATFRVQDCE KDDDFLVTWS KTKSELCCFC RMFEYKGFLC RHALMILQMC GFASIPPQYI  600
LKRWTKDAKS GVLAGEGADQ IQTRVQRYND LCSRATELSE EGCVSEENYN IALRTLVETL  660
KNCVDMNNAR NNITESNSQL NNGTHEEENQ VMAGVKATKK KTVYRKRKGQ QEASQMLESQ  720
QSLQPMETIS SEAMDMNGYY GPQQNVQGLL NLMEPPHEGY YVDQRTIQGL GQLNSIAPAQ  780
DSFFTNQQAM SGMVGQIDFR PPPNFTYTLQ EEHLSSAQLP GSSSRQL
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.115700.0flower
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2402558480.0
Genevisible245256_at0.0
Expression AtlasAT4G15090-
AtGenExpressAT4G15090-
ATTED-IIAT4G15090-
Functional Description ? help Back to Top
Source Description
TAIREncodes a nuclear localized protein involved in far red light response signaling. Loss of function mutants are defective in far red light responses. Interacts with homologous gene FHY3.
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. Positive regulator of chlorophyll biosynthesis via the activation of HEMB1 gene expression. {ECO:0000269|PubMed:11889039, ECO:0000269|PubMed:12753585, ECO:0000269|PubMed:18033885, ECO:0000269|PubMed:22634759}.
Function -- GeneRIF ? help Back to Top
  1. study shows FHY3 & FAR1, which encode proteins related to Mutator-like transposases, act together to modulate phyA signaling by activating transcription of FHY1 & FHL
    [PMID: 18033885]
  2. Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis.
    [PMID: 22634759]
  3. FHY3 and FAR1 are positive regulators of abscissic acid (ABA) signaling and provide insight into the integration of light and ABA signaling.
    [PMID: 23946351]
  4. domestication of FHY3/FAR1 may enable angiosperms to better integrate various endogenous and exogenous signals for coordinated regulation of growth and development, thus enhancing their fitness and adaptation
    [PMID: 25956482]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00434DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G15090.1
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. {ECO:0000269|PubMed:18033885}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT2G37678(A), AT2G40080(A), AT3G22170(A), AT5G02200(A)
Interaction -- BIND ? help Back to Top
Source Intact With Description
BINDAT4G15090FAR1 interacts with another molecule of FAR1.
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G15090, AT5G11260
IntActSearch Q9SWG3
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Elongated hypocotyls and reduced expansion of cotyledons under continuous far-red light. Reduced protochlorophyllide levels in darkness and less photobleaching in the light. {ECO:0000269|PubMed:10444599, ECO:0000269|PubMed:22634759}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G15090
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1595870.0AF159587.1 Arabidopsis thaliana far-red impaired response protein (FAR1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_567455.40.0protein FAR-RED IMPAIRED RESPONSE 1
SwissprotQ9SWG30.0FAR1_ARATH; Protein FAR-RED IMPAIRED RESPONSE 1
TrEMBLV4MHH40.0V4MHH4_EUTSA; Uncharacterized protein
STRINGAT4G15090.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP3012351
MalvidsOGEM11826253
Publications ? help Back to Top
  1. Hudson M,Ringli C,Boylan MT,Quail PH
    The FAR1 locus encodes a novel nuclear protein specific to phytochrome A signaling.
    Genes Dev., 1999. 13(15): p. 2017-27
    [PMID:10444599]
  2. Wang H,Deng XW
    Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1.
    EMBO J., 2002. 21(6): p. 1339-49
    [PMID:11889039]
  3. McCormac AC,Terry MJ
    Light-signalling pathways leading to the co-ordinated expression of HEMA1 and Lhcb during chloroplast development in Arabidopsis thaliana.
    Plant J., 2002. 32(4): p. 549-59
    [PMID:12445126]
  4. Wang H, et al.
    Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis.
    Plant J., 2002. 32(5): p. 723-33
    [PMID:12472688]
  5. Hudson ME,Lisch DR,Quail PH
    The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway.
    Plant J., 2003. 34(4): p. 453-71
    [PMID:12753585]
  6. Lin R,Wang H
    Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development.
    Plant Physiol., 2004. 136(4): p. 4010-22
    [PMID:15591448]
  7. Lin R, et al.
    Transposase-derived transcription factors regulate light signaling in Arabidopsis.
    Science, 2007. 318(5854): p. 1302-5
    [PMID:18033885]
  8. Genoud T, et al.
    FHY1 mediates nuclear import of the light-activated phytochrome A photoreceptor.
    PLoS Genet., 2008. 4(8): p. e1000143
    [PMID:18670649]
  9. Lin R, et al.
    Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction.
    Plant Physiol., 2008. 148(2): p. 981-92
    [PMID:18715961]
  10. Shen Y, et al.
    Phytochrome A mediates rapid red light-induced phosphorylation of Arabidopsis FAR-RED ELONGATED HYPOCOTYL1 in a low fluence response.
    Plant Cell, 2009. 21(2): p. 494-506
    [PMID:19208901]
  11. Li J, et al.
    Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome A signaling.
    Plant Cell, 2010. 22(11): p. 3634-49
    [PMID:21097709]
  12. Li G, et al.
    Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis.
    Nat. Cell Biol., 2011. 13(5): p. 616-22
    [PMID:21499259]
  13. Ouyang X, et al.
    Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development.
    Plant Cell, 2011. 23(7): p. 2514-35
    [PMID:21803941]
  14. Tang W, et al.
    Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis.
    Plant Cell, 2012. 24(5): p. 1984-2000
    [PMID:22634759]
  15. Tang W, et al.
    FAR-RED ELONGATED HYPOCOTYL3 and FAR-RED IMPAIRED RESPONSE1 transcription factors integrate light and abscisic acid signaling in Arabidopsis.
    Plant Physiol., 2013. 163(2): p. 857-66
    [PMID:23946351]
  16. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  17. Wang H,Wang H
    Multifaceted roles of FHY3 and FAR1 in light signaling and beyond.
    Trends Plant Sci., 2015. 20(7): p. 453-61
    [PMID:25956482]