PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Thecc1EG013043t1
Common NameTCM_013043
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma
Family FAR1
Protein Properties Length: 844aa    MW: 96662 Da    PI: 7.3737
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG013043t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR185.48.6e-2789191191
              FAR1   1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekdgkwevtkl 81 
                       +fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+             +++  +r+ ++t+Cka+++vk++ dgkw+v+++
  Thecc1EG013043t1  89 SFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSfnrprarqskqdPDNTTGRRSCSKTDCKASMHVKRRPDGKWVVHSF 181
                       5*******************************************9999999987766554444558999************************ PP

              FAR1  82 eleHnHelap 91 
                       ++eHnHel p
  Thecc1EG013043t1 182 VKEHNHELLP 191
                       *******975 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031011.4E-2489191IPR004330FAR1 DNA binding domain
PfamPF105515.4E-29289381IPR018289MULE transposase domain
PROSITE profilePS509669.545569605IPR007527Zinc finger, SWIM-type
PfamPF044345.9E-4579602IPR007527Zinc finger, SWIM-type
SMARTSM005751.8E-7580607IPR006564Zinc 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:0016021Cellular Componentintegral component of membrane
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 844 aa     Download sequence    Send to blast
MDIDLRLPSG EQCKEDEEAN GIDNILDGDE KLHNGVVEAG NIAHVGQDVR PEDGVEMNSS  60
AVDMVTFKED TNLEPLSGME FESHGEAYSF YQEYARSMGF NTAIQNSRRS KTSREFIDAK  120
FACSRYGTKR EYDKSFNRPR ARQSKQDPDN TTGRRSCSKT DCKASMHVKR RPDGKWVVHS  180
FVKEHNHELL PAQAVSEQTR RMYAAMARQF AEYKNVVGLK NDPKNPFDKG RNLALEAGDV  240
KILLEFFTHM QNINSNFFYA IDLGEDQRLK SLFWVDAKSR HDYSYFCDVV SFDTTYVRNK  300
YKMPLALFIG VNHHYQFMPL GCALVSDDSA ATFSWLMQTW LKAMGGQSPR VIITDQDRIV  360
KSVVAEIFPN THHCFFLWHV LGKVSENLGH VIKQHGNFMA KFEKCIYRSW TEEEFAKRWW  420
KILDRFGLKD DEWMKSLYED RRKWVPTYIM DVLLAGMSMV QRSESVNSFF DKYVHKKTTV  480
QEFLKQYEAI LQDRYEEEAK ANSDSWSKLP TLKSPSPFEK SVAGLYTHTV FKKFQVEVVG  540
AIACHPKPEN HDATSSFFRV QDLEKNQDFI VTLNEMKSEV SCICRLYEYK GYLCRHAMVV  600
LQINGHSAIP SQYILKRWTK EAKSRHLMGD ESEQVQSRVQ RYNDLFQRAM KLIEEGSLSQ  660
ESYYIAFRSL EEAFGNCLSA NTSNKSLAEA VTSPTQGMIC IEEDNQSRST SKTNKKKNPT  720
KKRKGNSEQE VMTVPATDGL QQMDKLSSRS VGLDGYFGAQ TSVQGMVQLN LMAPRDNYYG  780
NQQTIQGLGQ LNTIAASHDG YYGPQQTMPG MGQMDFFRAP GFYIRDDTNV RAAQLHDDAS  840
RHA*
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
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_007036967.20.0PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
RefseqXP_017973538.10.0PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
SwissprotQ9LIE50.0FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBLA0A061FWL40.0A0A061FWL4_THECC; Far-red elongated hypocotyls 3 isoform 1
STRINGEOY214710.0(Theobroma cacao)
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. Motamayor JC, et al.
    The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.
    Genome Biol., 2013. 14(6): p. r53
    [PMID:23731509]
  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]