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 Sp_185680_rszf.t1
Common NameSOVF_185680
Organism
Spinacia oleracea
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Chenopodiaceae; Chenopodioideae; Anserineae; Spinacia
Family C2H2
Protein Properties Length: 1377aa    MW: 154117 Da    PI: 8.3893
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sp_185680_rszf.t1genomeTBVRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.70.0001912861308323
                         ET..TTTEEESSHHHHHHHHHHT CS
            zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                         Cp   Cgk F ++ +L++H r+H
  Sp_185680_rszf.t1 1286 CPvkGCGKKFFSHKYLVQHRRVH 1308
                         9999*****************99 PP
2zf-C2H212.80.0003513441370123
                         EEET..TTTEEESSHHHHHHHHHH..T CS
            zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                         y+C+   Cg++F+  s++ rH r+  H
  Sp_185680_rszf.t1 1344 YVCNepGCGQTFRFVSDFSRHKRKtgH 1370
                         99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-162566IPR003349JmjN domain
PROSITE profilePS5118313.912667IPR003349JmjN domain
PfamPF023757.0E-142760IPR003349JmjN domain
SMARTSM005583.6E-49195364IPR003347JmjC domain
PROSITE profilePS5118433.561198364IPR003347JmjC domain
SuperFamilySSF511977.42E-25211378No hitNo description
PfamPF023731.3E-36228347IPR003347JmjC domain
SuperFamilySSF576671.9E-612821321No hitNo description
PROSITE profilePS5015712.44512841313IPR007087Zinc finger, C2H2
SMARTSM003550.004512841308IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.607.8E-612851307IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012861308IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.2E-913081336IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.7213141343IPR007087Zinc finger, C2H2
SMARTSM003550.002313141338IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013161338IPR007087Zinc finger, C2H2
SuperFamilySSF576671.56E-913241367No hitNo description
Gene3DG3DSA:3.30.160.601.5E-913371367IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.1413441370IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.36513441375IPR007087Zinc finger, C2H2
PROSITE patternPS00028013461370IPR007087Zinc 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:0040010Biological Processpositive regulation of growth rate
GO:0045815Biological Processpositive regulation of gene expression, epigenetic
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
GO:0071558Molecular Functionhistone demethylase activity (H3-K27 specific)
Sequence ? help Back to Top
Protein Sequence    Length: 1377 aa     Download sequence    Send to blast
MGSSSIVTAE HSSPEVFPWL KTLPVAPEYH PTIQEFQDPI AYIFKIEKEA SKFGICKIVP  60
PVPPQSKKSV ISNLNQSLLN SSKNPSNPQP TFTTRQQQVG FCPRKQRPIQ KSVWQSGECY  120
TLQQFEAKAK AFEKNYLKNR AKKAVSPLEV ETLYWKANGD RPFSVEYAND MPGSGFMPMK  180
ERKRTGEIVA GAAANVGETA WNMRGVAREN GSLLRFMKEE IPGVTSPMVY VAMMFSWFAW  240
HVEDHDLHSL NYLHLGAGKT WYGVPKDAAS AFEEVIRVYG FGEEINPLVT FAQLGEKTTV  300
MSPEVLINAG VPCCRLVQNA GEFVVTFPRA YHSGFSHGFN CGEASNIATP EWLRFAKDAA  360
IRRASINYPP MVSHFQLLYD LALAICSRAS IGNSAEPRSS RLKDKKKGEG EMLVKQMFVQ  420
DVIQNNELLY TLGQGSEVVL LPHNSSEIFV WSNLRVGSKY KVKPGLPFSL YSSEEAIKAS  480
DDIMLARDDR KQKAFSSVKT KSGGCMSTTP HEIQHSETEK GGGAAGDGFS DRGLFSCVKC  540
GIWTFACVAI VQPTESAAQY LMSADCNSFN DWIAGSGVSS HGMDPIDGEA NISDPNSFSG  600
SMEKHPPDGA YDIPVHSTDY HAQSISNTSK LKSNTAEIVE VGSHTETKRE SSALGLLAMT  660
YGNSSDSDED DVQPNSPVIS EDNLSGDGSW GARFHQDDSA SPVFEQGYDS GAERGPSQIS  720
SRSECEDEDS SQRSDFYEHC GHRRVNGDDN EYDSHNCSAK FTEEDILTSE QNYSPIADEH  780
DTAKISCAID PVGKPNLSFA HRCDEDSSRM HVFCLEHAVE VEKQLRPIGG VHILLLCHPD  840
YPNVEVEAKK AAEELEMDYG WKDIAFSMAT KEDEERIHMA LQSEESTPKN GDWAVKLGIN  900
LFYSAILSRS PLYNKQMPYN SIIYNAFGCT SPSKSSPEEA KVRGKGFGRQ KKLVMAGKWC  960
GKVWMSNQVH PLLLHRDPDE EERNFNACMK SDEKVGRKSE TSHKAQTTYT NRKVGKKRRS  1020
MPESTKVKKM KFEATEFADT DPEDSVDDKP EVETRRSVRK SKTQCRSIKR VKHQEEEEIL  1080
DGMSEDSQDE IKSLKSGRVL KLGTKQILKT KGRRSAAAIL SYSDDDSLDD RSHQHGLRSC  1140
NRKLKSTRMV RSQPKEIVDS ESEGSPSNES EIEEHQRRNI RSPGSSQRRV PVHRQFESVT  1200
DDDDDEMAGG PSTRLRKRIS RPIQERKEIK PTVKRQVQKP KGKKAAPLTK NIIPARKGPK  1260
MRLPVSRGPA MKGSKQELAL HKRNICPVKG CGKKFFSHKY LVQHRRVHMD DRPLKCPWKG  1320
CRMTFKWAWA RTEHIRVHTG ARPYVCNEPG CGQTFRFVSD FSRHKRKTGH AAKKARK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A3e-72194228383Transcription factor jumonji (Jmj) family protein
6ip4_A3e-72194228383Arabidopsis JMJ13
Search in ModeBase
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_021855215.10.0lysine-specific demethylase REF6 isoform X1
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A0K9QF770.0A0A0K9QF77_SPIOL; Uncharacterized protein
STRINGXP_010667395.10.0(Beta vulgaris)
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]