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 PEQU_38228
Organism
Phalaenopsis equestris
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; Asparagales; Orchidaceae; Epidendroideae; Vandeae; Aeridinae; Phalaenopsis
Family C2H2
Protein Properties Length: 1359aa    MW: 150871 Da    PI: 8.9859
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PEQU_38228genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H210.90.001412421265122
                  EEET..TTTEEESSHHHHHHHHHH CS
     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt 22  
                  y+C    C+ sFs+k +L  H r 
  PEQU_38228 1242 YTCDieGCSLSFSTKQELSLHKRD 1265
                  99*******************985 PP
2zf-C2H210.70.001713251351123
                  EEET..TTTEEESSHHHHHHHHHH..T CS
     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                  y C    Cg++F+  s++ rH r+  H
  PEQU_38228 1325 YICRepGCGQTFRFVSDFSRHKRKtnH 1351
                  889999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005455.5E-171960IPR003349JmjN domain
PROSITE profilePS5118314.1182061IPR003349JmjN domain
PfamPF023754.2E-142154IPR003349JmjN domain
PROSITE profilePS5118433.411229408IPR003347JmjC domain
SMARTSM005585.3E-46239408IPR003347JmjC domain
SuperFamilySSF511972.58E-24253421No hitNo description
PfamPF023736.7E-36272391IPR003347JmjC domain
Gene3DG3DSA:3.30.160.603.5E-412371264IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003551112421264IPR015880Zinc finger, C2H2-like
SMARTSM003558.112651289IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.22112651294IPR007087Zinc finger, C2H2
PROSITE patternPS00028012671289IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.1E-812841317IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.09412951324IPR007087Zinc finger, C2H2
SMARTSM003550.001412951319IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012971319IPR007087Zinc finger, C2H2
SuperFamilySSF576677.77E-1013051355No hitNo description
Gene3DG3DSA:3.30.160.601.5E-913181347IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.30213251356IPR007087Zinc finger, C2H2
SMARTSM003550.1313251351IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013271351IPR007087Zinc 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: 1359 aa     Download sequence    Send to blast
MGVEPPLVEI LPWLKSLPVA PEYHPTLSEF QDPIAYILKI EKEASAYGIC KIVPPLPAAP  60
RKTVFANLNK SFAARPQNPN SSPSTNPSSN SNSKRSPTFS TRQQQIGFCP RRPRPVQKPV  120
WQSGDCYTLS QFEAKAKLFE LSYLSKSAPA SATAASAAAT SSGSSSRKKK KIKLKKRQKK  180
SSKLFSSYLS ALEVETLYWK ACADKPFSVE YANDIPGSGF PPIGSPTGKR WREEEAASNV  240
GETAWNMRGV SRAKGSLLRF MKEEIPGVTS PMLYVAMMFS WFAWHVEDHE LHSLNYLHLG  300
AGKTWYGVPR DAALAFEDVV RIHGYCGEVN PLMTFTLLGE KTTVMSPEVL IDAGIPCCRL  360
VQNAGEFVVT FPGSYHCGFS HGFNCGEAAN IATPGWLRVA KEAAIRRAST NYPPMVSHFQ  420
LLYALALSLC SRMPICGNNE PRSSRLKDKL QGEGELMVKK TFVQSVAETN ELLSCLLEKG  480
SSCIVLPQNT SDSPLSSNSL VRSKVKLKPR LSLGLCSREE ALKASRALPC DDVMQERNTG  540
MKHLSGFGSL KGNSVAVYHR KKHSAASNNK SVTTEAASSM LELQNLKEEK DSNLEGDGLL  600
DQGLLSCVTC GILSFACVAV VEPREAASRY LTSSGCSSLF DQSFGSGEIN DVALDTKLQR  660
SDDCLGRKDG DVKDTLVEKM DHSTRYSTQD SVPIEVGSEN SKQNGLSALD LLASAYGGES  720
SDSDDERLPH EMPACTHENF ANEFLLSYRL DNDRVATKHP DLWFGKVPFA EMEQELVGAK  780
CQNAVAAENF CRTTSNDPNY LSQSADDRYL LKLDSRCYKP EHKKSLAPHS MKDSSCSSIW  840
SLGGSINSSR MEFRSSYHNS GTQDVHETNM KMQVTTPCSD DFSLCIAPCY GSDLPSENSN  900
GATQLISYHS DMKKAAVSAI QRSDKDSSRK HVFCLQHAME VEKKLCSIGG VHIMLLCHPD  960
YPKIEAEAKA LAEELGINYA WNKIDFMEAT EKDHERIQAA LKDEESIPTN SDWAVKLGIN  1020
LYYSASLSKS PLYSKQMPYN EVIYKSFSCN SPNSSMVKTK GSGKRQGRQK KIVVAGKWCG  1080
KVWMSNQVHP YLAQRKDAQD EESEEGPFAQ GGMTNPSSIN GSESNGSSAN GSSLASKKSK  1140
KRKKRPMLKS NGKRRRFNQS NDILEVIEDD DKVSQTDKGR ILRSKNRLKH KTDSEGGPSS  1200
RLRQRPMKSE DTKLVKPSFK KQNEKRAKGG QPPKSYDDEG EYTCDIEGCS LSFSTKQELS  1260
LHKRDICPVK GCGKKLFSHK YMMQHRKVHM DDRPLQCPWK GCKMTFKWAW ARTEHIRVHT  1320
GDRPYICREP GCGQTFRFVS DFSRHKRKTN HSAKKFRRS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A3e-66114976413Transcription factor jumonji (Jmj) family protein
6ip4_A3e-66114976413Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
111361144KKSKKRKKR
211391143KKRKK
311411155RKKRPMLKSNGKRRR
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_020599580.10.0lysine-specific demethylase JMJ705-like
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2I0W8110.0A0A2I0W811_9ASPA; Lysine-specific demethylase REF6
STRINGXP_008797141.10.0(Phoenix dactylifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP53463246
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]