PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cotton_A_37559_BGI-A2_v1.0
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family FAR1
Protein Properties Length: 836aa    MW: 95830.2 Da    PI: 7.2531
Description FAR1 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cotton_A_37559_BGI-A2_v1.0genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1FAR185.96.2e-2784186191
                        FAR1   1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkke 71 
                                 +fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+             e++  +r+ ++t+Cka+++vk++
  Cotton_A_37559_BGI-A2_v1.0  84 SFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSfnrprarqskqdPENATGRRSCSKTDCKASMHVKRR 166
                                 5*******************************************9999999988876655555559999************** PP

                        FAR1  72 kdgkwevtkleleHnHelap 91 
                                  dgkw+++++++eHnHel p
  Cotton_A_37559_BGI-A2_v1.0 167 PDGKWVIHSFVKEHNHELLP 186
                                 *****************975 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF031019.6E-2584186IPR004330FAR1 DNA binding domain
PfamPF105518.2E-29285376IPR018289MULE transposase domain
PROSITE profilePS509669.507564600IPR007527Zinc finger, SWIM-type
SMARTSM005751.8E-7575602IPR006564Zinc finger, PMZ-type
PfamPF044348.2E-4575597IPR007527Zinc finger, SWIM-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: 836 aa     Download sequence    Send to blast
MDIDLRLPSG EQCKEDEDAN GIDNMLDGDE SLHNGMVQVV GEDMRAEDGG EMHSSAVDMV  60
TFKEDTNLEP LSGMEFESHG EAYSFYQEYA RSMGFNTAIQ NSRRSKTSRE FIDAKFACSR  120
YGTKREYDKS FNRPRARQSK QDPENATGRR SCSKTDCKAS MHVKRRPDGK WVIHSFVKEH  180
NHELLPAQAV SEQTRRMYAA MARQFAEYKN VVGLKNDPKN PFDKGRNLAL EAADVKILLE  240
FFTHMQSINS NFFYAVDLGE DQRLKSLFWV DSKSRHDYSY FCDAVSFDTT YVTNKYKMPL  300
ALFIGVNHHY QCIPLGCALV SDESAATFSW LMKTWLKAMG GQSPRVLITD QDRTLKSVVA  360
EIFPNTLHCF FLWHVLGKVS ENLGHVIKQH GNLMAKFEKC IYRSWTDEEF GKRWWKILDR  420
FELKDDEWMK SLYEDRKKWV PTYIMNVLLA GMSTVQRAES VNSFFDKYVH KKTTVQDFLK  480
HYEAILQDRY EEEAKANSDS WSKVPALKSP SPFEKSVAGV YTHTLFKKFQ IEVVGAIACH  540
PKPENHDSTC SIFRVQDLEK NQDFIVTLNE MKAEVSCICR LYEYKGYLCR HAMVVLQING  600
HSAIPSQYIL KRWTKEAKSR HFMSEESEQV QSRVQRYNDL FQRGMKLIEE GSLSQESYYI  660
AFRSLEEAFG SCLSANTSNK SLAEAVASPT QGMICIEEDN QSRSTSKMNK KKNPTKKRKG  720
NSEQEVMAVA PTDGLQQMDK LSSRSVALDS YFGAQPSVQG MVQLNLMAPR DNYYGNQQTI  780
QGLLNTIATS HDGYYGTQQA MPGMGPMDFF RSPSFYIRDD PNVRVAQLHD DASRHT
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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_017630678.10.0PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3
SwissprotQ9LIE50.0FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBLA0A0D2PSJ90.0A0A0D2PSJ9_GOSRA; Uncharacterized protein
STRINGGorai.005G134200.10.0(Gossypium raimondii)
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]