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 Eucgr.K02763.1.p
Common NameEUGRSUZ_K02763
Organism
Eucalyptus grandis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Myrtales; Myrtaceae; Myrtoideae; Eucalypteae; Eucalyptus
Family C2H2
Protein Properties Length: 1213aa    MW: 135846 Da    PI: 9.0799
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Eucgr.K02763.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2110.001310971122123
                        EEET..TTTEEESSHHHHHHHHHH.T CS
           zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                        ykC    C++sF +k +L+ H ++ +
  Eucgr.K02763.1.p 1097 YKCDleGCTMSFGSKQELTLHKKNvC 1122
                        99*******************99866 PP
2zf-C2H213.70.0001911211144223
                        EET..TTTEEESSHHHHHHHHHHT CS
           zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                        +Cp   Cgk F ++ +L++H r+H
  Eucgr.K02763.1.p 1121 VCPvkGCGKKFFSHKYLVQHRRVH 1144
                        69999*****************99 PP
3zf-C2H211.20.001211801206123
                        EEET..TTTEEESSHHHHHHHHHH..T CS
           zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                        y C    Cg++F+  s++ rH r+  H
  Eucgr.K02763.1.p 1180 YICAepGCGQTFRFVSDFSRHKRKtgH 1206
                        789999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005584.3E-463172IPR003347JmjC domain
PROSITE profilePS5118433.2136172IPR003347JmjC domain
SuperFamilySSF511975.77E-2518187No hitNo description
PfamPF023731.1E-3636155IPR003347JmjC domain
SMARTSM003551110971119IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.1E-511201148IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.003711201144IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.46611201149IPR007087Zinc finger, C2H2
PROSITE patternPS00028011221144IPR007087Zinc finger, C2H2
SuperFamilySSF576671.62E-911361178No hitNo description
Gene3DG3DSA:3.30.160.603.5E-811491174IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001411501174IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74111501179IPR007087Zinc finger, C2H2
PROSITE patternPS00028011521174IPR007087Zinc finger, C2H2
SuperFamilySSF576673.71E-811681202No hitNo description
Gene3DG3DSA:3.30.160.602.9E-911751203IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.7911801206IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.88911801211IPR007087Zinc finger, C2H2
PROSITE patternPS00028011821206IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
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:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1213 aa     Download sequence    Send to blast
MLTVGETNWN MRGVSRSKGS LLRFMKEEIP GVTSPMVYVA MMFSWFAWHV EDHDLHSLNY  60
LHMGAGKTWY GVPRDAAVAF EEVVRVQGYG GEVNPLITFA VLGEKTTVMS PEVLVGAGVP  120
CCRLVQNAGE FVVTFPRAYH SGFSHGFNCG EAANIATPEW LLFAKEAAIR RASINYPPMV  180
SHFQLLYDLA LAFCSRVPTC INTGPRSSRL KDKKKGEGES MVKEQFVQNC IENNKLLHIL  240
GKDSTVVRLP ESSSDISVCS NLRVGSHLRV NRSLSEDTMM SHGGLVSDNL IADRKQTIDL  300
VDDLYSMKAF SSFYERKRIL SMYGAGDIHP PRDGEGDSKA QGDRLSDQRL FSCVTCGILT  360
FACAAIVQPR EPAARYLMSA DCSFFNDWTV NPGVPTKGFN VSAGADIIAY KRRTQAGSVE  420
KSRAAALYDV SPLQSTNYPI QEAHQSSEAF SNSDKLKGTS ALGLLALNYG NSSDSEEDQI  480
DSDAPNETTS RPQYGNNNLP DSALPPFLPE HHSGPNGGSP HNCCPEIGYR GANFVDKSHQ  540
TFKYSANFRA DETRSSEKHG STGFPKSDED SSRMHIFCLE HAIEVDQRLR PIGGVYIYLA  600
CHPDYPRVEA EAKLLAEELG IDHSWNEIAF RDAMGEDKER IQSALDSEEA IAGYGDWAVK  660
LGINLFYSAN LCSSPLYSKQ MPYNSVIYNA FGRESSSSPA KLDDFGRRPS KQKKSVAGKW  720
CGKVWMSNQV HPFLAPKDAE EVEEERSFHA SMTSDDKLER QSGLNRETTL ATRKFSRKRK  780
MARESGPSKK KSVSRKEEVS DDALAEDSEK LMSIPKHKTA KSFRREDPVS DDQVDEISCL  840
QHQTIPRRKQ KKFVKRGYAS SDDDSLEDKF KALRGKNFRK ATNFTSSGDM LSDDSLEEDS  900
QQQGRILTGK KTKHYERDDV MSDDSEGNYN KLQHPRIRKK TPANAKFEGA DSDSSPEDAF  960
PQRQRSLRNR KVNRDTLRIK NQGNLLEKLK KRGIPRVTKE VSARHLKQES SRPRSNKYER  1020
SVEQSDESDE EDQEGGGPST RLRKRTAKPT KERKADKPPP GKKQANNGKK NVKAGPTVKR  1080
PVGRNDARME KFEEAEYKCD LEGCTMSFGS KQELTLHKKN VCPVKGCGKK FFSHKYLVQH  1140
RRVHLDDRPL KCPWKGCKMT FKWAWARTEH IRVHTGARPY ICAEPGCGQT FRFVSDFSRH  1200
KRKTGHSVKG KG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A3e-681095120921135Lysine-specific demethylase REF6
6a58_A3e-681095120921135Lysine-specific demethylase REF6
6a59_A3e-681095120921135Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1775780SRKRKM
Functional Description ? help Back to Top
Source Description
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00608ChIP-seqTransfer from AT3G48430Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapEucgr.K02763.1.p
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_010037473.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A059A5S00.0A0A059A5S0_EUCGR; Uncharacterized protein
STRINGXP_010037473.10.0(Eucalyptus grandis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.10.0relative of early flowering 6
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]