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 AT3G48430.1
Common NameJMJ12, PKDM9A, REF6, T29H11_50
Organism
Arabidopsis thaliana
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 C2H2
Protein Properties Length: 1360aa    MW: 152629 Da    PI: 7.4553
Description relative of early flowering 6
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G48430.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.90.0003312431268123
                   EEET..TTTEEESSHHHHHHHHHH.T CS
      zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                   y+C+   C++sFs+  +L+ H r+ +
  AT3G48430.1 1243 YQCNmeGCTMSFSSEKQLMLHKRNiC 1268
                   99********************9877 PP
2zf-C2H215.26.4e-0512681290323
                   ET..TTTEEESSHHHHHHHHHHT CS
      zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                   Cp   Cgk F ++ +L++H+r+H
  AT3G48430.1 1268 CPikGCGKNFFSHKYLVQHQRVH 1290
                   9999*****************99 PP
3zf-C2H213.60.0001913261352123
                   EEET..TTTEEESSHHHHHHHHHH..T CS
      zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                   y+C   dCg++F+  s++ rH r+  H
  AT3G48430.1 1326 YVCAepDCGQTFRFVSDFSRHKRKtgH 1352
                   899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005457.6E-181960IPR003349JmjN domain
PROSITE profilePS5118313.7442061IPR003349JmjN domain
PfamPF023756.3E-142154IPR003349JmjN domain
SMARTSM005582.2E-54200369IPR003347JmjC domain
PROSITE profilePS5118433.585203369IPR003347JmjC domain
SuperFamilySSF511971.35E-26216387No hitNo description
PfamPF023731.2E-37233352IPR003347JmjC domain
SMARTSM00355812431265IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.17312661295IPR007087Zinc finger, C2H2
SMARTSM003550.008112661290IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012681290IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.3E-612681294IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.79E-1012821324No hitNo description
Gene3DG3DSA:3.30.160.609.6E-912951319IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.92812961325IPR007087Zinc finger, C2H2
SMARTSM003550.001512961320IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012981320IPR007087Zinc finger, C2H2
SuperFamilySSF576675.97E-813141348No hitNo description
Gene3DG3DSA:3.30.160.606.6E-913201349IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.40613261357IPR007087Zinc finger, C2H2
SMARTSM003551.113261352IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013281352IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009741Biological Processresponse to brassinosteroid
GO:0009826Biological Processunidimensional cell growth
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0033169Biological Processhistone H3-K9 demethylation
GO:0035067Biological Processnegative regulation of histone acetylation
GO:0048366Biological Processleaf development
GO:0055114Biological Processoxidation-reduction process
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046872Molecular Functionmetal ion binding
GO:0051213Molecular Functiondioxygenase activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000005anatomycultured plant cell
PO:0000026anatomyprimary root tip
PO:0000027anatomylateral root tip
PO:0000293anatomyguard cell
PO:0003011anatomyroot vascular system
PO:0009025anatomyvascular leaf
PO:0020030anatomycotyledon
PO:0020148anatomyshoot apical meristem
Sequence ? help Back to Top
Protein Sequence    Length: 1360 aa     Download sequence    Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYILKI EEEASRYGIC KILPPLPPPS  60
KKTSISNLNR SLAARAAARV RDGGFGACDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS  120
GEEYSFGEFE FKAKNFEKNY LKKCGKKSQL SALEIETLYW RATVDKPFSV EYANDMPGSA  180
FIPLSLAAAR RRESGGEGGT VGETAWNMRA MSRAEGSLLK FMKEEIPGVT SPMVYVAMMF  240
SWFAWHVEDH DLHSLNYLHM GAGKTWYGVP KDAALAFEEV VRVHGYGEEL NPLVTFSTLG  300
EKTTVMSPEV FVKAGIPCCR LVQNPGEFVV TFPGAYHSGF SHGFNFGEAS NIATPEWLRM  360
AKDAAIRRAA INYPPMVSHL QLLYDFVLAL GSRVPTSINP KPRSSRLKDK ARSEGERLTK  420
KLFVQNIIHN NELLSSLGKG SPVALLPQSS SDISVCSDLR IGSHLITNQE NPIQLKCEDL  480
SSDSVVVDLS NGLKDTVSVK EKFTSLCERS RNHLASTEKD TQETLSDAER RKNDAAVALS  540
DQRLFSCVTC GVLSFDCVAI VQPKEAAARY LMSADCSFFN DWTAASGSAN LGQAARSLHP  600
QSKEKHDVNY FYNVPVQTMD HSVKTGDQKT STTSPTIAHK DNDVLGMLAS AYGDSSDSEE  660
EDQKGLVTPS SKGETKTYDQ EGSDGHEEAR DGRTSDFNCQ RLTSEQNGLS KGGKSSLLEI  720
ALPFIPRSDD DSCRLHVFCL EHAAEVEQQL RPFGGINLML LCHPEYPRIE AEAKIVAEEL  780
VINHEWNDTE FRNVTREDEE TIQAALDNVE AKGGNSDWTV KLGVNLSYSA ILSRSPLYSK  840
QMPYNSIIYK AFGRSSPVAS SPSKPKVSGK RSSRQRKYVV GKWCGKVWMS HQVHPFLLEQ  900
DLEGEESERS CHLRVAMDED ATGKRSFPNN VSRDSTTMFG RKYCRKRKIR AKAVPRKKLT  960
SFKREDGVSD DTSEDHSYKQ QWRASGNEEE SYFETGNTAS GDSSNQMSDP HKGIIRHKGY  1020
KEFESDDEVS DRSLGEEYTV RACAASESSM ENGSQHSMYD HDDDDDDIDR QPRGIPRSQQ  1080
TRVFRNPVSY ESEDNGVYQQ SGRISISNRQ ANRMVGEYDS AENSLEERGF CSTGKRQTRS  1140
TAKRIAKTKT VQSSRDTKGR FLQEFASGKK NEELDSYMEG PSTRLRVRHQ KPSRGSLETK  1200
PKKIGKKRSG NASFSRVATE KDVEEKEEEE EEEENEEEEC AAYQCNMEGC TMSFSSEKQL  1260
MLHKRNICPI KGCGKNFFSH KYLVQHQRVH SDDRPLKCPW KGCKMTFKWA WSRTEHIRVH  1320
TGARPYVCAE PDCGQTFRFV SDFSRHKRKT GHSVKKTNKR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A4e-94122313603140Lysine-specific demethylase REF6
6a58_A4e-94122313603140Lysine-specific demethylase REF6
6a59_A4e-94122313603140Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1945957KRKIRAKAVPRKK
213531359VKKTNKR
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.31690.0flower| root| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO795866970.0
Expression AtlasAT3G48430-
AtGenExpressAT3G48430-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}.
Functional Description ? help Back to Top
Source Description
TAIRRelative of Early Flowering 6 (REF6) encodes a Jumonji N/C and zinc finger domain-containing protein that acts as a positive regulator of flowering in an FLC-dependent pathway. REF6 mutants have hyperacetylation of histone H4 at the FLC locus. REF6 interacts with BES1 in a Y2H assay and in vitro. REF6 may play a role in brassinoteroid signaling by affecting histone methylation in the promoters of BR-responsive genes. It is most closely related to the JHDM3 subfamily of JmjN/C proteins.
UniProtHistone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034). {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:20711170, ECO:0000269|PubMed:21642989, ECO:0000269|PubMed:25105952, ECO:0000269|PubMed:27111034, ECO:0000269|PubMed:27111035}.
Function -- GeneRIF ? help Back to Top
  1. BES1 recruits transcriptional regulators ELF6 and REF6 to regulate target gene expression and coordinate brassinosteroids responses with other developmental processes such as control of flowering time.
    [PMID: 18467490]
  2. Genome-wide analyses showed that REF6 colocalizes with BRM at many genomic sites with the CTCTGYTY motif. Loss of REF6 results in decreased BRM occupancy at BRM-REF6 co-targets
    [PMID: 27111034]
  3. Genome-wide analyses showed that REF6 colocalizes with BRM at many genomic sites with the CTCTGYTY motif. Loss of REF6 results in decreased BRM occupancy at BRM-REF6 co-targets
    [PMID: 27111035]
  4. demonstrate that H3K27me3 REF6 methylation represents an epigenetic mechanism prohibiting the premature transcriptional activation of key developmentally up-regulated senescence regulatory as well as functional genes
    [PMID: 30969965]
  5. Study shows that in Arabidopsis non-CG methylation in CTCTGYTY motifs is one way to prevent REF6 targeting. Structural analysis demonstrates that CHG methylation is unfavorable for REF6 binding and attenuates REF6-binding affinity. Results reveal a mechanism for a transcriptional-activating histone-modifying enzyme in avoiding heterochromatic binding through its intrinsic DNA methylation unfavorable DNA-binding activity.
    [PMID: 31048693]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00608ChIP-seqSRX1184290Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G48430.1
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 AT5G10140(R), AT5G57560(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDbrassinosteroid
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G18960, AT1G19350, AT1G24260, AT1G69120
IntActSearch Q9STM3
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Late-flowering in both long and short days. Brassinosteroid-insensitive phenotype. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G48430
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY6644990.0AY664499.1 Arabidopsis thaliana relative of early flowering 6 (REF6) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_680116.20.0relative of early flowering 6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A178VKP40.0A0A178VKP4_ARATH; REF6
STRINGAT3G48430.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
Representative plantOGRP44011217
Publications ? help Back to Top
  1. Noh B, et al.
    Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time.
    Plant Cell, 2004. 16(10): p. 2601-13
    [PMID:15377760]
  2. Hecht V, et al.
    Conservation of Arabidopsis flowering genes in model legumes.
    Plant Physiol., 2005. 137(4): p. 1420-34
    [PMID:15778459]
  3. Alexandre CM,Hennig L
    FLC or not FLC: the other side of vernalization.
    J. Exp. Bot., 2008. 59(6): p. 1127-35
    [PMID:18390846]
  4. Yu X, et al.
    Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2008. 105(21): p. 7618-23
    [PMID:18467490]
  5. Lu F, et al.
    Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice.
    J Integr Plant Biol, 2008. 50(7): p. 886-96
    [PMID:18713399]
  6. Zhou X,Ma H
    Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence.
    BMC Evol. Biol., 2008. 8: p. 294
    [PMID:18950507]
  7. Reiland S, et al.
    Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks.
    Plant Physiol., 2009. 150(2): p. 889-903
    [PMID:19376835]
  8. Ko JH, et al.
    Growth habit determination by the balance of histone methylation activities in Arabidopsis.
    EMBO J., 2010. 29(18): p. 3208-15
    [PMID:20711170]
  9. Lu F,Cui X,Zhang S,Jenuwein T,Cao X
    Arabidopsis REF6 is a histone H3 lysine 27 demethylase.
    Nat. Genet., 2011. 43(7): p. 715-9
    [PMID:21642989]
  10. Bienvenut WV, et al.
    Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-α-acetylation features.
    Mol. Cell Proteomics, 2012. 11(6): p. M111.015131
    [PMID:22223895]
  11. Smaczniak C, et al.
    Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(5): p. 1560-5
    [PMID:22238427]
  12. Stroud H,Greenberg MV,Feng S,Bernatavichute YV,Jacobsen SE
    Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.
    Cell, 2013. 152(1-2): p. 352-64
    [PMID:23313553]
  13. 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]
  14. Li C, et al.
    Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 687-93
    [PMID:27111034]
  15. Cui X, et al.
    REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 694-9
    [PMID:27111035]
  16. Hyun Y, et al.
    Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem.
    Dev. Cell, 2016. 37(3): p. 254-66
    [PMID:27134142]
  17. Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE
    Research progress on the autonomous flowering time pathway in Arabidopsis.
    Physiol Mol Biol Plants, 2017. 23(3): p. 477-485
    [PMID:28878488]
  18. Li C, et al.
    Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis.
    Plant Biotechnol. J., 2018. 16(8): p. 1446-1451
    [PMID:29331085]
  19. Wang X, et al.
    The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis.
    PLoS Genet., 2019. 15(4): p. e1008068
    [PMID:30969965]
  20. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]