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 EcC054602.20
Organism
Eucalyptus camaldulensis
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: 1402aa    MW: 157118 Da    PI: 9.331
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
EcC054602.20genomeECGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H210.80.001612871312123
                    EEET..TTTEEESSHHHHHHHHHH.T CS
       zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                    ykC    C++sF +k +L+ H ++ +
  EcC054602.20 1287 YKCDleGCTMSFGSKQELTLHKKNvC 1312
                    99*******************99866 PP
2zf-C2H213.40.0002313111334223
                    EET..TTTEEESSHHHHHHHHHHT CS
       zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                    +Cp   Cgk F ++ +L++H r+H
  EcC054602.20 1311 VCPvkGCGKKFFSHKYLVQHRRVH 1334
                    69999*****************99 PP
3zf-C2H210.90.001413701396123
                    EEET..TTTEEESSHHHHHHHHHH..T CS
       zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                    y C    Cg++F+  s++ rH r+  H
  EcC054602.20 1370 YICAepGCGQTFRFVSDFSRHKRKtgH 1396
                    789999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.8E-162061IPR003349JmjN domain
PROSITE profilePS5118314.342162IPR003349JmjN domain
PfamPF023751.5E-142255IPR003349JmjN domain
SMARTSM005584.3E-46193362IPR003347JmjC domain
PROSITE profilePS5118433.213196362IPR003347JmjC domain
SuperFamilySSF511971.57E-25207377No hitNo description
PfamPF023731.3E-36226345IPR003347JmjC domain
SMARTSM003551112871309IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.46613101339IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.3E-513101338IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.003713101334IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013121334IPR007087Zinc finger, C2H2
SuperFamilySSF576671.94E-913261368No hitNo description
Gene3DG3DSA:3.30.160.604.1E-813391364IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001413401364IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74113401369IPR007087Zinc finger, C2H2
PROSITE patternPS00028013421364IPR007087Zinc finger, C2H2
SuperFamilySSF576674.32E-813581392No hitNo description
Gene3DG3DSA:3.30.160.603.4E-913651393IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.7913701396IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.88913701401IPR007087Zinc finger, C2H2
PROSITE patternPS00028013721396IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006165Biological Processnucleoside diphosphate phosphorylation
GO:0006183Biological ProcessGTP biosynthetic process
GO:0006228Biological ProcessUTP biosynthetic process
GO:0006241Biological ProcessCTP biosynthetic process
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:0004550Molecular Functionnucleoside diphosphate kinase activity
GO:0005515Molecular Functionprotein binding
GO:0016747Molecular Functiontransferase activity, transferring acyl groups other than amino-acyl groups
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1402 aa     Download sequence    Send to blast
MAAATEPSQE VFSWLKNLPL APEYHPTLAE FQDPIAYIFK IEKEASKYGI CKIVPPVPPG  60
PKKSAITNLN RSLAARASSS ERPNSKSSPT FTTRQQQIGF CPRKPCPVKK PVWQSGENYT  120
FQDFETKAKS FERVYLRKFY KKGSPSALEI ETLYWKAAVD KPFSVEYAND IPGSAFPPIR  180
SKKGRETGEG MLTVGETNWN MRGVSRSKGS LLRFMKEEIP GVTSPMVYVA MMFSWFAWHV  240
EDHDLHSLNY LHMGAGKTWY GVPRDAAVAF EEVVRVQGYG GEVNPLITFA VLGEKTTVMS  300
PEVLVGAGVP CCRLVQNAGE FVVTFPRAYH SGFSHGFNCG EAANIATPEW LLFAKEAAIR  360
RASINYPPMV SHFQLLYDLA LAFCSRVPTC INTGPRSSRL KDKKKGEGES MVKEQFVQNC  420
IENNKLLHIL GKDSTVVRLP ESSSDISVCS NLRVGSHLRV NRSLSEDTMT SHGGLVSDNL  480
IADRKQTIDL VDDLYSMKSF SSFYERKRIL SMYGAGDIQP PRDGDGDSKA QGDRLSDQRL  540
FSCVTCGILT FACAAIVQPR EPAARYLMSA DCSFFNDWTV NPGVPTKGFN VSAGADIIAY  600
KRRTQAGSVE KSRAAALYDV SPLQSTNYQI QEAHQSSEAF SNSDKLKGTS ALGLLALNYG  660
NSSDSEEDQI DSDAPNETTS RPQYGNNNLP DSALPPFLPE HHSGPNGSSP HNCCPEIGYR  720
GANFVDKSHQ TFKYSANFRA DETRSSEKHG STGFPKSDED SSRMHIFCLE HAIEVDQRLR  780
PIGGVYIYLV CHPDYPRVEA EAKLLAEELG IDHSWNEIAF RDAMGEDKER IQSALDSEEA  840
IAGYGDWAVK LGINLFYSAN LCSSPLYSKQ MPYNSVIYNA FGRESSSSPA KLDDFGRRPS  900
KQKKSVAGKW CGKVWMSNQV HPFLAPKDAE EVEEERSFHA SMTSDDKLER QSGLNRETTL  960
ATRKFSRKRK MARESGPSKK KSVSRKEEVS DDALAEDSEK LMSIPKHKTA KSFRREDPVS  1020
DDQVDEISCL QHQTIPRRKQ KKFVKRGYAS SDDDSLEDKF KALRGKNFRK ATNFTSSGDM  1080
LSDDSLEEDS QQQGRILTGK KTKHYERDDV MSDDSEGNYN KLQHPRIRKK TPANAKFEGA  1140
DSDSSPEDAF PQRQRSLRNR KVNRDTLRIK NQGNLLEKLK KRGIPRVTKE VGARHLKQES  1200
SRSRSNKYER SVEQSDESDE EDPEGGGPST RLRKRTAKPT KERKADKPPP GKKQANNGKK  1260
NVKAGPTVKR PVGRNDARME KFEEAEYKCD LEGCTMSFGS KQELTLHKKN VCPVKGCGKK  1320
FFSHKYLVQH RRVHLDDRPL KCPWKGCKMT FKWAWARTEH IRVHTGARPY ICAEPGCGQT  1380
FRFVSDFSRH KRKTGHSVKG KG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-78144588421Transcription factor jumonji (Jmj) family protein
6ip4_A1e-78144588421Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1965970SRKRKM
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
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]