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 Peaxi162Scf00089g00844.1
Organism
Petunia axillaris
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Petunioideae; Petunia
Family C2H2
Protein Properties Length: 1227aa    MW: 137857 Da    PI: 8.9816
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Peaxi162Scf00089g00844.1genomeSGNView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.80.0003711121137123
                                EEET..TTTEEESSHHHHHHHHHH.T CS
                   zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                                y+C    C++sFs+k +L  H ++ +
  Peaxi162Scf00089g00844.1 1112 YQCDleGCSMSFSSKQELLLHKKNvC 1137
                                99*******************99866 PP
2zf-C2H2110.001411361159223
                                EET..TTTEEESSHHHHHHHHHHT CS
                   zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                                +Cp   C+k F ++ +L++H r+H
  Peaxi162Scf00089g00844.1 1136 VCPveGCKKKFFSHKYLVQHRRVH 1159
                                69999*****************99 PP
3zf-C2H212.20.0005411951221123
                                EEET..TTTEEESSHHHHHHHHHH..T CS
                   zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                                y+C+   Cg++F+  s++ rH r+  H
  Peaxi162Scf00089g00844.1 1195 YVCTetGCGQTFRFVSDFSRHKRKtgH 1221
                                99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-141758IPR003349JmjN domain
PROSITE profilePS5118313.3841859IPR003349JmjN domain
PfamPF023758.7E-151952IPR003349JmjN domain
PROSITE profilePS5118421.97186322IPR003347JmjC domain
SMARTSM005581.1E-32186322IPR003347JmjC domain
SuperFamilySSF511971.76E-18200338No hitNo description
PfamPF023732.7E-5219247IPR003347JmjC domain
PfamPF023731.1E-16250305IPR003347JmjC domain
SMARTSM003557.411121134IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.605.0E-511331163IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.01211351159IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.57211351164IPR007087Zinc finger, C2H2
PROSITE patternPS00028011371159IPR007087Zinc finger, C2H2
SuperFamilySSF576673.02E-911511191No hitNo description
Gene3DG3DSA:3.30.160.602.8E-811641189IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001411651189IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74111651194IPR007087Zinc finger, C2H2
PROSITE patternPS00028011671189IPR007087Zinc finger, C2H2
SuperFamilySSF576675.55E-811831217No hitNo description
Gene3DG3DSA:3.30.160.603.5E-911901218IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.1911951221IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.05311951226IPR007087Zinc finger, C2H2
PROSITE patternPS00028011971221IPR007087Zinc 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: 1227 aa     Download sequence    Send to blast
MAEVNIEVFP WLKTLPVAPE YHPTLEEFQD PIAYIFKIEK HASQFGICKI VPPVPPLAKK  60
TILSNLNRSL SARPGSTGPT FTTRQQQIGF CPRKHRPVKK PVWQSGETYT VAEFQGKAKN  120
FEKNYLKKNC FFKKNAALSP LEIETLYWKA TVDKPFSVEY ANDMPGSAFP PKKIGGNGVG  180
GGEGVSLADT EWNMRGVSRA KGSLLKFMKE EIPGVTSPMV YLAMMFSWFA WHVEDHDLHS  240
LNYMHMVTFA TLGEKTTVMS PEVLLSAGIP CCRLVQNAGE FVVTFPRAYH SGFSHGFNCG  300
EAANIATPEW LRFAKEAAIR RASTNCPPMV SHFQLLYDLA LSLCSRVPKN IKIEPRSSRL  360
KDKKRSEGDM LVKELFVEDL NCNNYLLHIL GEGAPVVLLP QDYTGTSNSS YLVAGSQLKV  420
NSRSFPSLSS RDHEVKSLKD SASDDLMLGR KRGMKQLPRS SLEKGKYSSW HAGNRMPDSG  480
RNDDAQSSPE TKRGNLDTAR EMAYKCDTLS EHGLFSCVTC GILCYTCVAI VQPTEEAARH  540
LISSDFRNFN DWTGDVGGVT AIGRDLNAAD SDSSSGWLVK RSPGGLIDVP IESSDRIRKL  600
NNESVGVLSS TKARKETSSL GLLALNYANS SDSDEDEVEA DIPIEACESI HTDSEDEVSL  660
RVIDPYANHR QKRAVSEGRI CQRFDNSIHL ESEHSPSGES NTVSDRLRHH PRSHQVAANC  720
TPFSHKEEMN NNNDVAPFDN MPMQFTSTSD EDSFRMHVFC LQHAVQVEEQ LRQVGGVRIS  780
LLCHPDYPKL EAQAKKVAEE LGSDHFWREI SFREATKEDE EMIQSALEIE EAIHGNGDWT  840
VKLDMNLFYS ANLSRSPLYS KQMPYNFIIY SAFGRSSPDN TPEKSEYTGR GSGKQKRGVV  900
AGKWCGKVWM SSQVHPLLVE RDTDEEQEQN KSIPVQIKPD VKSERPSERA GTRTVATTCK  960
TGRKRKSAAE DRNTSNRKLL IADDLDDSLL SYIPQQHRKT NLRSKRIKYE TPEPQQDVDK  1020
KKRFSTPSDD ELDGGPSTRL RKRIPKPSKE SAAKLVKAKS AIKQHEGTKA EKGSKVKIPS  1080
TNRNTKKDPV MKAPRNNTGN TIKKMKDKEG EYQCDLEGCS MSFSSKQELL LHKKNVCPVE  1140
GCKKKFFSHK YLVQHRRVHM DDRPLKCPWK GCKMTFKWAW ARTEHIRVHT GARPYVCTET  1200
GCGQTFRFVS DFSRHKRKTG HVSKKGR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A2e-641112122523136Lysine-specific demethylase REF6
6a58_A2e-641112122523136Lysine-specific demethylase REF6
6a59_A2e-641112122523136Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1448455GRKRGMKQ
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
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_006351452.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLM1B7Y20.0M1B7Y2_SOLTU; Uncharacterized protein
STRINGPGSC0003DMT4000392240.0(Solanum tuberosum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA49882331
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]