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 XP_015882347.1
Organism
Ziziphus jujuba
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rhamnaceae; Paliureae; Ziziphus
Family C2H2
Protein Properties Length: 1454aa    MW: 162472 Da    PI: 8.8928
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_015882347.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.60.000213631386223
                      EET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                      +Cp   Cgk F ++ +L++H r+H
  XP_015882347.1 1363 VCPvkGCGKKFFSHKYLVQHRRVH 1386
                      69999*****************99 PP
2zf-C2H211.90.0007114221448123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C    Cg++F+  s++ rH r+  H
  XP_015882347.1 1422 YVCAepGCGQTFRFVSDFSRHKRKtgH 1448
                      899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005459.8E-172061IPR003349JmjN domain
PROSITE profilePS5118314.6032162IPR003349JmjN domain
PfamPF023752.6E-142255IPR003349JmjN domain
PROSITE profilePS5118433.982192361IPR003347JmjC domain
SMARTSM005582.0E-49192361IPR003347JmjC domain
SuperFamilySSF511972.17E-27206375No hitNo description
PfamPF023731.2E-36225344IPR003347JmjC domain
SMARTSM003552813391361IPR015880Zinc finger, C2H2-like
SMARTSM003550.003713621386IPR015880Zinc finger, C2H2-like
SuperFamilySSF576675.88E-613621398No hitNo description
PROSITE profilePS5015712.54913621391IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.608.4E-613631385IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028013641386IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.605.3E-913861414IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001713921416IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.63713921421IPR007087Zinc finger, C2H2
PROSITE patternPS00028013941416IPR007087Zinc finger, C2H2
SuperFamilySSF576672.57E-914021446No hitNo description
Gene3DG3DSA:3.30.160.602.3E-914151445IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.6214221448IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.2414221453IPR007087Zinc finger, C2H2
PROSITE patternPS00028014241448IPR007087Zinc 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: 1454 aa     Download sequence    Send to blast
MAASAEPPQE VFSWLKTLPS APEYHPTLAE FQDPISYIFK IEKEASKYGI CKIVPPVPPS  60
PRKTAMANLH KSLAARSAFS DSSNPKSQPT FTTRQQQIGF CPRKPRPVQR PVWQSGEYYT  120
FSQFETRAKN FEKTFLKKCT KKGGLSPLEI ETLYWKATVD KPFSVEYAND MPGSAFVPVS  180
TKKSREAGEG VTLGETAWNM RAVSRAKGSL LRFMKEEIPG VTSPMVYIAM MFSWFAWHVE  240
DHDLHSLNYL HMGAGKTWYG VPREAAVAFE EVVRVHGYGG EVNPLVTFAI LGEKTTVMSP  300
EVFISAGIPC CRLVQNPGEF VVTFPRAYHT GFSHGFNCGE AANIATPEWL GVAKDAAIRR  360
ASINYPPMVS HYQLLYDLAL ALCSRVPASI TAEPRSSRLK DKKKGEGETV VKEQFVQDVI  420
HNNDLLHVLG KGSPIVLLPR SSLDISVCSK LRVGSQLRVN TTFPVGLCNS GGEMKSSGSL  480
ISDDLMMMDT KQEIKQVKGF YLVKGKFASL CEGSRIPSLS GNDSQFSLNA KSVGIEGENN  540
SGNDGLSDQR LFSCVTCGIL SFSCVAIIQP REPAARYLMS ADCSFFNDWV VGSGVASDVF  600
TVANADPIAQ NTCTGLVEKN GPDSLYDVPV QSVNEDKSNE VVSNAEKHEP ASALGLLALN  660
YGNSSDSEDD QVDPNVSVYG AETILPNRAS GIYQYDHSSS TLQDRHVDAS GLQGQSSCRL  720
YSGGGLASLN VDLNMDNCTV DVDSDNLAST KSNGLVGQFR DPMNVLHACS SGSYDAETTK  780
FGKGITPVKN ANMPFAPRCD EESSRMHVFC LDHAVEVEQQ LRQIGGVDIL LLCHPDYPKI  840
EAEAKVIAED LGIGCLWNAH TFRKATKEDE ERIQAALDSE EAIPKNGDWA VKLGINLFYS  900
ASLSRSPLYS KQMPYNSVIY NAFGRSSPAV SPTRSDGYVR RSGKQKKVVA GKWCGKVWMS  960
SQVHPFLAKR DPEEEEDEER GFHTWPIPDE RLERKPDTSR RNDSTMITRK YVRKRKMAVE  1020
SGLNKKAKCI QKEDAVSGNS MNDDSHQQQR RLPRSKEVCI KRGSTKKIKC IETEEAVSDD  1080
SIDDNSDEQH KRTHRRNQAN YIERDDIVSD DSLGVDSHHQ NKQIFRGKQA KHTGREDVVS  1140
DDSLDSNSCL LNRRIPRSKQ SKFFGREDSV SDDFYGDNAQ QQQRRIQSKQ AKSMEREDEI  1200
LDEPVEDNSH QQHKRILRNK RTKSAIQQQK MKRETSRNVK QAISKPVKQG TRRQEKMKQQ  1260
TPRLRNNPSE QNMFYTNAEE ELEGGPSTRL RKRIPKPLKV AGAKRKEQQQ PKSKKKVKKA  1320
STGKAQGGHN DARDEEAEYL CDLEGCTMSF GTKQELVLHK RNVCPVKGCG KKFFSHKYLV  1380
QHRRVHMDDR PLRCPWKGCK MTFKWAWART EHIRVHTGAR PYVCAEPGCG QTFRFVSDFS  1440
RHKRKTGHSA KKGR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A6e-78143828353Transcription factor jumonji (Jmj) family protein
6ip4_A6e-78143828353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110091015KYVRKRK
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
PlantRegMapXP_015882347.1
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_015882347.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2P5BA480.0A0A2P5BA48_PARAD; TFIIH C1-like domain containing protein
STRINGXP_010101942.10.0(Morus notabilis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF56483250
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]