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 678292906
Organism
Utricularia gibba
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Lamiales; Lentibulariaceae; Utricularia
Family C2H2
Protein Properties Length: 1191aa    MW: 133610 Da    PI: 8.1374
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
678292906genomeUGSPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.90.0001611581184123
                 EEET..TTTEEESSHHHHHHHHHH..T CS
    zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                 y+C+   Cgk+F+  s++ rH r+  H
  678292906 1158 YVCTqsGCGKTFRFVSDFSRHKRKtgH 1184
                 99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005455.7E-172263IPR003349JmjN domain
PROSITE profilePS5118314.2982364IPR003349JmjN domain
PfamPF023751.7E-132457IPR003349JmjN domain
SuperFamilySSF511977.42E-27109170No hitNo description
SMARTSM005583.2E-49187356IPR003347JmjC domain
PROSITE profilePS5118433.53187356IPR003347JmjC domain
SuperFamilySSF511977.42E-27205354No hitNo description
PfamPF023732.4E-37220339IPR003347JmjC domain
SMARTSM003553310751097IPR015880Zinc finger, C2H2-like
SuperFamilySSF576677.32E-610961134No hitNo description
PROSITE profilePS5015712.07110981127IPR007087Zinc finger, C2H2
SMARTSM003550.06110981122IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.607.4E-510991126IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028011001122IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.0E-911271152IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.61411281157IPR007087Zinc finger, C2H2
SMARTSM003550.001411281152IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011301152IPR007087Zinc finger, C2H2
SuperFamilySSF576674.64E-1111381181No hitNo description
Gene3DG3DSA:3.30.160.603.7E-1111531181IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.5111581189IPR007087Zinc finger, C2H2
SMARTSM003550.0711581184IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011601184IPR007087Zinc 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: 1191 aa     Download sequence    Send to blast
MAAEVTGTGS IEVAPFLRCM PEAPEYHPTL LEFQDPVAYI FKIEKEASKY GICKIVPPLP  60
ASPRKTVFSN FNKSILARTN DPASIPTFTT RQQQIGFCPR KHRPVQKSVW QSGERYTLNE  120
FEAKAKNFEK NYLRKNAKKG FNALEMETLF WNAMLDKPFN VEYANDMPGS AFMVGKTGAK  180
RSEGAVSVGE SDWNMRRVSR ENLSLLRFMK EEIAGVTSPM VYVAMMFSWF AWHVEDHDFH  240
SLNYLHMGSS KTWYGVPREA SVAFEEVIRE HGYGGEINPM VTFATLGKKT TVMSPEVLLN  300
AGVPCCRLVQ NAGDFVVTFP RAYHSGFSHG FNCGEAANIA TPEWLRVAKE AAIRRAAINC  360
PPMVSHYQLH YDLVLSLCSS VPNRPGREPK SSRLKDRMKG EGEKLIKELF LEDMLQNNDM  420
LRSLGKGSSI VLLPQKSLCH VVSSDSPAGF RSKSSMFDIF LTADNNLKMA SSINLLGESE  480
HDAKQNTDKH GSNSVNGQKD SCFGSSEVKR APPRDLGLYS CVSCGVICYA CVAIVQPTEA  540
AARYISSADL SLFNCSDNAL DDTGDSKYHN TSFVSGGLIS SDDDFHLTPE VGMIENRLEI  600
DRVPINAVAK GPSSLGLLAL TYDDLSDSEE EDTSAILPEG CGTNKSDDTC DGHTASPKID  660
NSMAEIPVQV ADFDGQSVQP PIAVREDREP QNSWAMPSTK AKLLDSLDKA DEDSTRLHVF  720
CLEHALQVER RLIQLGGARV FLACHPDYPT FESQAKKLAE ELEHDATWNK ISFRDASEED  780
EKILEQALES ENGTMHGHGD WAVKLGINLF YSANLSYSPL YSKQMHYNTN IYAALGRTCP  840
TEEKGFSRQK RVAVAGKWCG KVWMSNQVHP LLVNRGLQDE QPEPEPAPWA SPRSVPDAGK  900
FSLFSMVDRK MKDSSRSLPV VEHKRTRSSI KRKRRVTEEF LESRSFDDSE VLESCKSKFR  960
SGNDRKTDTS EDENQDESSE DFPLSNTWKR IKDEQHAGKL RVKDMLLQAK RKEITKEDQE  1020
GSYSTRLRKR PEKRNKDASA AKAGVGTTKG KSSSKKPEKK THARDVKVRD EEGEYPCDVE  1080
GCSMSLGSKH ELVLHKRNIC PVKGCGKKFF LHKYLLQHRR VHMDDRPLKC PWKGCKMTFK  1140
WAWARTEHIR VHTGERPYVC TQSGCGKTFR FVSDFSRHKR KTGHVPKKTR G
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-722036912345Transcription factor jumonji (Jmj) family protein
6ip4_A1e-722036912345Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110281035KRPEKRNK
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
PlantRegMap678292906
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_011072922.10.0lysine-specific demethylase REF6 isoform X1
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2G9I3H70.0A0A2G9I3H7_9LAMI; [histone H3]-lysine-36 demethylase
STRINGMigut.I00266.1.p0.0(Erythranthe guttata)
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]