PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G25530.1
Common NameFWA, HDG6, HDGL2-6, M7J2.100
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 HD-ZIP
Protein Properties Length: 686aa    MW: 76252.9 Da    PI: 7.3879
Description FLOWERING WAGENINGEN
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G25530.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox52.58.1e-174696656
                 S--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
     Homeobox  6 tftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56
                 + t++q++eLe+++ +n++p++e+r eL ++l++  +qVk+WFqN+R  ek
  AT4G25530.1 46 RRTAYQTQELENFYMENPHPTEEQRYELGQRLNMGVNQVKNWFQNKRNLEK 96
                 5699*******************************************8766 PP

2START196.31.4e-612164362206
                  HHHHHHHHHHHHHHHC-TT-EEEE......EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEEE CS
        START   2 laeeaaqelvkkalaeepgWvkss......esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaetlev 84 
                  la +a++el+++ ++++p+W+ ++       s+++++++++f    v     + +ea+ra+g+v+m++++lv++l+d++ +W + +a     a+t++v
  AT4G25530.1 216 LAITALRELITLGEVDCPFWMIDPivrskgVSKIYEKYRSSFNN--VtkppgQIVEASRAKGLVPMTCVTLVKTLMDTG-KWVNVFApivpVASTHKV 310
                  678999************************************55..4569*****************************.****************** PP

                  ECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SS CS
        START  85 issg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvdlkgr 175
                  +s+g      g lq+++ae+q++splvp R+++f+Ry+++ ++g wv+vd  v+++q+p+   ++ ++++lpSg++i+++sng+s+vtw+e+++++++
  AT4G25530.1 311 LSTGsggtksGSLQQIQAEFQVISPLVPkRKVTFIRYCKEIRQGLWVVVD--VTPTQNPT-LLPYGCSKRLPSGLIIDDLSNGYSQVTWIEQAEYNES 405
                  **************************************************..********.7************************************ PP

                  XXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
        START 176 lphwllrslvksglaegaktwvatlqrqcek 206
                  ++h+l+++l+++g+  gak+w+atlqr+ce+
  AT4G25530.1 406 HIHQLYQPLIGYGIGLGAKRWLATLQRHCES 436
                  *****************************95 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466891.24E-162795IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.603.0E-173192IPR009057Homeodomain-like
PROSITE profilePS5007114.8683898IPR001356Homeobox domain
SMARTSM003898.0E-1739102IPR001356Homeobox domain
CDDcd000862.35E-164299No hitNo description
PfamPF000463.8E-144696IPR001356Homeobox domain
PROSITE profilePS5084836.782206439IPR002913START domain
SuperFamilySSF559613.19E-21211437No hitNo description
CDDcd088759.42E-98211435No hitNo description
SMARTSM002343.1E-69215436IPR002913START domain
PfamPF018521.2E-59216436IPR002913START domain
SuperFamilySSF559611.03E-12459656No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006349Biological Processregulation of gene expression by genetic imprinting
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009911Biological Processpositive regulation of flower development
GO:0031047Biological Processgene silencing by RNA
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008289Molecular Functionlipid binding
GO:0042803Molecular Functionprotein homodimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009009anatomyplant embryo
PO:0009089anatomyendosperm
PO:0020090anatomyembryo sac central cell
PO:0025281anatomypollen
PO:0001185developmental stageplant embryo globular stage
Sequence ? help Back to Top
Protein Sequence    Length: 686 aa     Download sequence    Send to blast
MNGQGDLDAV GNIPKPGEAE GDEIDMINDM SGVNDQDGGR MRRTHRRTAY QTQELENFYM  60
ENPHPTEEQR YELGQRLNMG VNQVKNWFQN KRNLEKINND HLENVTLREE HDRLLATQDQ  120
LRSAMLRSLC NICGKATNCG DTEYEVQKLM AENANLEREI DQFNSRYLSH PKQRMVSTSE  180
QAPSSSSNPG INATPVLDFS GGTRTSEKET SIFLNLAITA LRELITLGEV DCPFWMIDPI  240
VRSKGVSKIY EKYRSSFNNV TKPPGQIVEA SRAKGLVPMT CVTLVKTLMD TGKWVNVFAP  300
IVPVASTHKV LSTGSGGTKS GSLQQIQAEF QVISPLVPKR KVTFIRYCKE IRQGLWVVVD  360
VTPTQNPTLL PYGCSKRLPS GLIIDDLSNG YSQVTWIEQA EYNESHIHQL YQPLIGYGIG  420
LGAKRWLATL QRHCESLSTL SSTNLTEISP GLSAKGATEI VKLAQRMTLN YYRGITSPSV  480
DKWQKIQVEN VAQNMSFMIR KNVNEPGELT GIVLSASTSV WLPVNQHTLF AFISHLSFRH  540
EWDILTNDTT MEETIRIQKA KRHGNIISLL KIVNNGMLVL QEIWNDASGA MVVYAPVETN  600
SIELVKRGEN SDSVKFLPSG FSIVPDGVNG SYHRGNTGGG CLLTFGLQIL VGINPTAALI  660
QGTVKSVETL MAHTIVKIKS ALDLQT
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO135068190.0
Genevisible245239_at0.0
Expression AtlasAT4G25530-
AtGenExpressAT4G25530-
ATTED-IIAT4G25530-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Detected in siliques from 3 days after pollination until maturity of seeds.
UniprotTISSUE SPECIFICITY: Expressed in siliques, ovules and germinating seeds. {ECO:0000269|PubMed:17189287}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a homeodomain-containing transcription factor that controls flowering. FWA is silenced in wild type plants and reverse of the imprinted silencing causes a late flowering phenotype. FWA gene contains two tandem repeats around the transcription start site that are necessary and sufficient for silencing via DNA methylation.
UniProtProbable transcription factor involved in the regulation of time of flowering through the photoperiod flowering pathway. May repress FT. {ECO:0000269|PubMed:17189287}.
Function -- GeneRIF ? help Back to Top
  1. The mechanisms of FWA silencing were studied.
    [PMID: 17144899]
  2. Specific interaction of FWA with FT enabled us to use FWA protein as a specific inhibitor of FT protein function
    [PMID: 17189287]
  3. Data show that the expression of FWA was repressed by Arabidopsis relatives of the human lysine-specific Demethylase1 and thus promote the floral transition.
    [PMID: 17921315]
  4. the tandem repeat structure is dispensable for the epigenetic silencing of the FWA gene
    [PMID: 18389059]
  5. Vegetative expression of the A. thaliana FWA gene causes late flowering.
    [PMID: 21457364]
  6. Inflorescence abnormalities in plants overexpressing the Arabidopsis lyrata FT (AlFT) and A. thaliana FWA (AtFWA) genes simultaneously, were studied.
    [PMID: 21889057]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G25530.1
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 AT1G69120(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G25530
IntActSearch Q9FVI6
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G25530
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF2435350.0AF243535.1 Arabidopsis thaliana homeodomain-containing transcription factor FWA (FWA) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_567722.10.0homeobox-leucine zipper protein HDG6
SwissprotQ9FVI60.0FWA_ARATH; Homeobox-leucine zipper protein HDG6
TrEMBLB5BPE60.0B5BPE6_ARATH; Homeodomain-containing transcription factor FWA
TrEMBLB5BQ010.0B5BQ01_ARASU; Homeodomain-containing transcription factor FWA
STRINGAT4G25530.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM2095355
Representative plantOGRP14515136
Publications ? help Back to Top
  1. Page T,Macknight R,Yang CH,Dean C
    Genetic interactions of the Arabidopsis flowering time gene FCA, with genes regulating floral initiation.
    Plant J., 1999. 17(3): p. 231-9
    [PMID:10097382]
  2. Liljegren SJ,Gustafson-Brown C,Pinyopich A,Ditta GS,Yanofsky MF
    Interactions among APETALA1, LEAFY, and TERMINAL FLOWER1 specify meristem fate.
    Plant Cell, 1999. 11(6): p. 1007-18
    [PMID:10368173]
  3. Chou ML,Yang CH
    Late-flowering genes interact with early-flowering genes to regulate flowering time in Arabidopsis thaliana.
    Plant Cell Physiol., 1999. 40(7): p. 702-8
    [PMID:10501030]
  4. Soppe WJ,Bentsink L,Koornneef M
    The early-flowering mutant efs is involved in the autonomous promotion pathway of Arabidopsis thaliana.
    Development, 1999. 126(21): p. 4763-70
    [PMID:10518493]
  5. Kardailsky I, et al.
    Activation tagging of the floral inducer FT.
    Science, 1999. 286(5446): p. 1962-5
    [PMID:10583961]
  6. Rold
    Sucrose availability on the aerial part of the plant promotes morphogenesis and flowering of Arabidopsis in the dark.
    Plant J., 1999. 20(5): p. 581-90
    [PMID:10652130]
  7. Tavares R,Aubourg S,Lecharny A,Kreis M
    Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2.
    Plant Mol. Biol., 2000. 42(5): p. 703-17
    [PMID:10809443]
  8. Onouchi H,Ige
    Mutagenesis of plants overexpressing CONSTANS demonstrates novel interactions among Arabidopsis flowering-time genes.
    Plant Cell, 2000. 12(6): p. 885-900
    [PMID:10852935]
  9. Soppe WJ, et al.
    The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene.
    Mol. Cell, 2000. 6(4): p. 791-802
    [PMID:11090618]
  10. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  11. Chou ML,Haung MD,Yang CH
    EMF genes interact with late-flowering genes in regulating floral initiation genes during shoot development in Arabidopsis thaliana.
    Plant Cell Physiol., 2001. 42(5): p. 499-507
    [PMID:11382816]
  12. Cao X,Jacobsen SE
    Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing.
    Curr. Biol., 2002. 12(13): p. 1138-44
    [PMID:12121623]
  13. Halliday KJ,Koornneef M,Whitelam GC
    Phytochrome B and at Least One Other Phytochrome Mediate the Accelerated Flowering Response of Arabidopsis thaliana L. to Low Red/Far-Red Ratio.
    Plant Physiol., 1994. 104(4): p. 1311-1315
    [PMID:12232170]
  14. Genger RK,Peacock WJ,Dennis ES,Finnegan EJ
    Opposing effects of reduced DNA methylation on flowering time in Arabidopsis thaliana.
    Planta, 2003. 216(3): p. 461-6
    [PMID:12520338]
  15. Kankel MW, et al.
    Arabidopsis MET1 cytosine methyltransferase mutants.
    Genetics, 2003. 163(3): p. 1109-22
    [PMID:12663548]
  16. Hsu HF,Huang CH,Chou LT,Yang CH
    Ectopic expression of an orchid (Oncidium Gower Ramsey) AGL6-like gene promotes flowering by activating flowering time genes in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(8): p. 783-94
    [PMID:12941870]
  17. Suh SS,Choi KR,Lee I
    Revisiting phase transition during flowering in Arabidopsis.
    Plant Cell Physiol., 2003. 44(8): p. 836-43
    [PMID:12941876]
  18. Tzeng TY,Hsiao CC,Chi PJ,Yang CH
    Two lily SEPALLATA-like genes cause different effects on floral formation and floral transition in Arabidopsis.
    Plant Physiol., 2003. 133(3): p. 1091-101
    [PMID:14526112]
  19. Kinoshita T, et al.
    One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation.
    Science, 2004. 303(5657): p. 521-3
    [PMID:14631047]
  20. Zilberman D, et al.
    Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats.
    Curr. Biol., 2004. 14(13): p. 1214-20
    [PMID:15242620]
  21. Lippman Z, et al.
    Role of transposable elements in heterochromatin and epigenetic control.
    Nature, 2004. 430(6998): p. 471-6
    [PMID:15269773]
  22. Zhang WW,Cao SX,Jiang L,Zhu SS,Wan JM
    [Genomic imprinting and seed development].
    Yi Chuan, 2005. 27(4): p. 665-70
    [PMID:16120596]
  23. Pischke MS,Huttlin EL,Hegeman AD,Sussman MR
    A transcriptome-based characterization of habituation in plant tissue culture.
    Plant Physiol., 2006. 140(4): p. 1255-78
    [PMID:16489130]
  24. Jullien PE,Katz A,Oliva M,Ohad N,Berger F
    Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis.
    Curr. Biol., 2006. 16(5): p. 486-92
    [PMID:16527743]
  25. Jullien PE,Kinoshita T,Ohad N,Berger F
    Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting.
    Plant Cell, 2006. 18(6): p. 1360-72
    [PMID:16648367]
  26. Nakamura M, et al.
    Characterization of the class IV homeodomain-Leucine Zipper gene family in Arabidopsis.
    Plant Physiol., 2006. 141(4): p. 1363-75
    [PMID:16778018]
  27. Chan SW,Zhang X,Bernatavichute YV,Jacobsen SE
    Two-step recruitment of RNA-directed DNA methylation to tandem repeats.
    PLoS Biol., 2006. 4(11): p. e363
    [PMID:17105345]
  28. Kinoshita Y, et al.
    Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats.
    Plant J., 2007. 49(1): p. 38-45
    [PMID:17144899]
  29. Ikeda Y,Kobayashi Y,Yamaguchi A,Abe M,Araki T
    Molecular basis of late-flowering phenotype caused by dominant epi-alleles of the FWA locus in Arabidopsis.
    Plant Cell Physiol., 2007. 48(2): p. 205-20
    [PMID:17189287]
  30. Jiang D,Yang W,He Y,Amasino RM
    Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition.
    Plant Cell, 2007. 19(10): p. 2975-87
    [PMID:17921315]
  31. Ohr H,Bui AQ,Le BH,Fischer RL,Choi Y
    Identification of putative Arabidopsis DEMETER target genes by GeneChip analysis.
    Biochem. Biophys. Res. Commun., 2007. 364(4): p. 856-60
    [PMID:17964287]
  32. Lavrov SA,Kibanov MV
    Noncoding RNAs and chromatin structure.
    Biochemistry Mosc., 2007. 72(13): p. 1422-38
    [PMID:18282134]
  33. Fujimoto R, et al.
    Evolution and control of imprinted FWA genes in the genus Arabidopsis.
    PLoS Genet., 2008. 4(4): p. e1000048
    [PMID:18389059]
  34. Manzano C,Abraham Z,L
    Identification of ubiquitinated proteins in Arabidopsis.
    Plant Mol. Biol., 2008. 68(1-2): p. 145-58
    [PMID:18535787]
  35. Kraft E,Bostick M,Jacobsen SE,Callis J
    ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases.
    Plant J., 2008. 56(5): p. 704-15
    [PMID:18643997]
  36. Jullien PE, et al.
    Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis.
    PLoS Biol., 2008. 6(8): p. e194
    [PMID:18700816]
  37. Koornneef M,Hanhart CJ,van der Veen JH
    A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana.
    Mol. Gen. Genet., 1991. 229(1): p. 57-66
    [PMID:1896021]
  38. Wuest SE, et al.
    Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes.
    Curr. Biol., 2010. 20(6): p. 506-12
    [PMID:20226671]
  39. Jullien PE,Berger F
    Parental genome dosage imbalance deregulates imprinting in Arabidopsis.
    PLoS Genet., 2010. 6(3): p. e1000885
    [PMID:20333248]
  40. Hanada K, et al.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2011. 28(1): p. 377-82
    [PMID:20736450]
  41. Shin R,Jez JM,Basra A,Zhang B,Schachtman DP
    14-3-3 proteins fine-tune plant nutrient metabolism.
    FEBS Lett., 2011. 585(1): p. 143-7
    [PMID:21094157]
  42. Greenberg MV, et al.
    Identification of genes required for de novo DNA methylation in Arabidopsis.
    Epigenetics, 2011. 6(3): p. 344-54
    [PMID:21150311]
  43. Fujimoto R, et al.
    Epigenetic variation in the FWA gene within the genus Arabidopsis.
    Plant J., 2011. 66(5): p. 831-43
    [PMID:21457364]
  44. Schoft VK, et al.
    Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte.
    Proc. Natl. Acad. Sci. U.S.A., 2011. 108(19): p. 8042-7
    [PMID:21518889]
  45. Kawanabe T,Fujimoto R
    Inflorescence abnormalities occur with overexpression of Arabidopsis lyrata FT in the fwa mutant of Arabidopsis thaliana.
    Plant Sci., 2011. 181(4): p. 496-503
    [PMID:21889057]
  46. Rea M, et al.
    Histone H1 affects gene imprinting and DNA methylation in Arabidopsis.
    Plant J., 2012. 71(5): p. 776-86
    [PMID:22519754]
  47. Ouyang B, et al.
    Transcriptome profiling and methyl homeostasis of an Arabidopsis mutant deficient in S-adenosylhomocysteine hydrolase1 (SAHH1).
    Plant Mol. Biol., 2012. 79(4-5): p. 315-31
    [PMID:22555436]
  48. Meinke DW
    A survey of dominant mutations in Arabidopsis thaliana.
    Trends Plant Sci., 2013. 18(2): p. 84-91
    [PMID:22995285]
  49. 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]
  50. Sanda SL,Amasino RM
    Interaction of FLC and late-flowering mutations in Arabidopsis thaliana.
    Mol. Gen. Genet., 1996. 251(1): p. 69-74
    [PMID:8628249]
  51. Ruiz-GarcĂ­a L, et al.
    Different roles of flowering-time genes in the activation of floral initiation genes in Arabidopsis.
    Plant Cell, 1997. 9(11): p. 1921-34
    [PMID:9401118]
  52. Kakutani T
    Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana.
    Plant J., 1997. 12(6): p. 1447-51
    [PMID:9450349]
  53. Haung MD,Yang CH
    EMF genes interact with late-flowering genes to regulate Arabidopsis shoot development.
    Plant Cell Physiol., 1998. 39(4): p. 382-93
    [PMID:9615462]