PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G04240.1
Common NameELF6, F21E1.160, JMJ11, PKDM9B
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: 1340aa    MW: 150072 Da    PI: 6.8943
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G04240.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.90.0003412521275223
                   EET..TTTEEESSHHHHHHHHHHT CS
      zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                   +C+   Cgk F+ + +L+ H+r+H
  AT5G04240.1 1252 RCTheGCGKKFRAHKYLVLHQRVH 1275
                   588889****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.9E-151555IPR003349JmjN domain
PROSITE profilePS5118314.161657IPR003349JmjN domain
PfamPF023757.4E-161750IPR003349JmjN domain
SMARTSM005583.5E-45259428IPR003347JmjC domain
PROSITE profilePS5118434.235262428IPR003347JmjC domain
SuperFamilySSF511971.18E-25263426No hitNo description
PfamPF023732.8E-37292411IPR003347JmjC domain
SMARTSM003556612281250IPR015880Zinc finger, C2H2-like
SMARTSM003550.05712511275IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.31812511280IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.8E-712521280IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012531275IPR007087Zinc finger, C2H2
SuperFamilySSF576673.86E-1012671308No hitNo description
Gene3DG3DSA:3.30.160.602.5E-1012811305IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.003312811305IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.69512811310IPR007087Zinc finger, C2H2
PROSITE patternPS00028012831305IPR007087Zinc finger, C2H2
SuperFamilySSF576677.17E-912991334No hitNo description
Gene3DG3DSA:3.30.160.609.8E-1013061333IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.45213111340IPR007087Zinc finger, C2H2
SMARTSM003550.1113111337IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013131337IPR007087Zinc 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:0033169Biological Processhistone H3-K9 demethylation
GO:0048577Biological Processnegative regulation of short-day photoperiodism, flowering
GO:0048579Biological Processnegative regulation of long-day photoperiodism, flowering
GO:0055114Biological Processoxidation-reduction process
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046872Molecular Functionmetal ion binding
GO:0051213Molecular Functiondioxygenase activity
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:0025281anatomypollen
PO:0001016developmental stageL mature pollen stage
PO:0001017developmental stageM germinated pollen stage
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: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: 1340 aa     Download sequence    Send to blast
MGNVEIPNWL KALPLAPVFR PTDTEFADPI AYISKIEKEA SAFGICKIIP PLPKPSKKYV  60
FYNLNKSLLK CPELVSDVDI SKVCKEDRAV FTTRQQELGQ TVKKNKGEKG KSNSQRSGVK  120
QVWQSGGVYT LDQFEAKSKA FYKTQLGTVK ELAPVVIEAL FWKAALEKPI YIEYANDVPG  180
SAFGEPEDHF RHFRQRKRRG RGFYQRKTEN NDPSGKNGEK SSPEVEKAPL ASTSLSSQDS  240
SKQKNMDIVD EMEGTAGWKL SNSSWNLQMI ARSPGSVTRF MPDDIPGVTS PMVYIGMLFS  300
WFAWHVEDHE LHSMNYLHTG SPKTWYAVPC DYALDFEEVI RKNSYGRNID QLAALTQLGE  360
KTTLVSPEMI VASGIPCCRL VQNPGEFVVT FPRSYHVGFS HGFNCGEAAN FGTPQWLNVA  420
KEAAVRRAAM NYLPMLSHQQ LLYLLTMSFV SRVPRSLLPG GRSSRLRDRQ REEREFLVKR  480
AFVEDILNEN KNLSVLLREP GSRLVMWDPD LLPRHSALAL AAAGVAGASA VSPPAVAKKE  540
LEEGHSELQN KEKTSLLEEL SLFMEKLNDV YYDDDDGLLN DFQVDTGTLP CVACGVLGFP  600
FMSVVQPSEK ALKDLSERQG ETDAQEIMTL SSEKSDCEWK TSSRYIRPRI FCLEHTIELQ  660
RLLQSRGGLK FLVICHKDFQ KFKAHAAIVA EEVKVPFSYD DVLLESASQE ELSLIDLAIE  720
DEEKYEHSVD WTSELGINLR YCVKVRKNSP TKKIQHALSL GGLFSDTSQM LDFTTIRWLQ  780
RKSRSKAKPS STSSFTPCEH LEVKADGKLR DNLDSQTGKK EEKIIQYSRK KKLNPKPSAE  840
QVQELATLAK SKDFDKTCKN FSSRSHLDSA IRSEMNSEIG DSGRVIGVSF SINPCSSSFT  900
VGHGQEHPEI TVKFGSDLDG NVTNSLSMVN GDSADLTLTS ISREQHQGHS MTSNNNGSNS  960
GSHVVASQTI LVSTGDNHDG PRKLSGDYVC SDVSVRGIQE AVEMSDQEFG EPRSTVTNIE  1020
DEQQSQIVKP TQREAVFGDH EQVEGAEAVS TRENLCSEII LHTEHSSAHV GMEIPDINTA  1080
SENLVVDMTH DGEPLESSDI LSSSNGDEAS SNGLQVLNDE LSMESEVSSS ENTEVIEAPN  1140
SMGEAKKKRK IESESETNDN PESSIGFIRS PCEGLRSRGK RKATCETSLK HTETSDEEKK  1200
PIAKRLKKTP KACSGSRQQE VPTTTHPNRC YLEGCKMTFE SKAKLQTHKR NRCTHEGCGK  1260
KFRAHKYLVL HQRVHKDERP FECSWKGCSM TFKWQWARTE HLRLHTGERP YICKVDGCGL  1320
SFRFVSDYSR HRRKTMHYVT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-55242442137346Transcription factor jumonji (Jmj) family protein
6ip4_A5e-55242442137346Arabidopsis JMJ13
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.100920.0flower| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453576210.0
Genevisible245691_at0.0
Expression AtlasAT5G04240-
AtGenExpressAT5G04240-
ATTED-IIAT5G04240-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed at low levels in cotyledons and leaves. Detected in inflorescences, stems, roots and siliques but not in shoot apical meristems or root tips. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}.
Functional Description ? help Back to Top
Source Description
TAIREarly Flowering 6 (ELF6) encodes a Jumonji N/C and zinc finger domain-containing protein that acts as a repressor in the photoperiod pathway. ELF6 interacts with BES1 in a Y2H assay, in vitro, and in Arabidosis protoplasts (based on BiFC). ELF6 may play a role in brassinosteroid signaling by affecting histone methylation in the promoters of BR-responsive genes.
UniProtActs probably as a histone 'Lys-4' (H3K4me) demethylase. Involved in transcriptional gene regulation. Acts as a repressor of the photoperiodic flowering pathway and of FT. Binds around the transcription start site of the FT locus. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:19946624}.
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. AtJmj4 and ELF6 are H3K4 demethylases directly repressing FT chromatin and preventing precocious flowering in Arabidopsis
    [PMID: 19946624]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G04240.1
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 AT5G57560(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDbrassinosteroid
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G19350
IntActSearch Q6BDA0
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Early flowering, but normal development of all organs. Partially redundant with JMJ14. Brassinosteroid-insensitive phenotype. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G04240
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY6645000.0AY664500.1 Arabidopsis thaliana early flowering 6 (ELF6) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_196044.20.0Zinc finger (C2H2 type) family protein / transcription factor jumonji (jmj) family protein
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLA0A178UAR70.0A0A178UAR7_ARATH; ELF6
STRINGAT5G04240.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM115202731
Representative plantOGRP75061114
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. 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]
  3. Hecht V, et al.
    Conservation of Arabidopsis flowering genes in model legumes.
    Plant Physiol., 2005. 137(4): p. 1420-34
    [PMID:15778459]
  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. Jeong JH, et al.
    Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis.
    PLoS ONE, 2009. 4(11): p. e8033
    [PMID:19946624]
  8. Heidari B,Nemie-Feyissa D,Kangasjärvi S,Lillo C
    Antagonistic regulation of flowering time through distinct regulatory subunits of protein phosphatase 2A.
    PLoS ONE, 2013. 8(7): p. e67987
    [PMID:23976921]
  9. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  10. Crevillén P, et al.
    Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state.
    Nature, 2014. 515(7528): p. 587-90
    [PMID:25219852]
  11. 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]
  12. Yang H,Howard M,Dean C
    Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(33): p. 9369-74
    [PMID:27482092]