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 Spipo4G0034800
Organism
Spirodela polyrhiza
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Alismatales; Araceae; Lemnoideae; Spirodela
Family C2H2
Protein Properties Length: 1072aa    MW: 118203 Da    PI: 9.2689
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Spipo4G0034800genomeMIPS/IBISView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.45.4e-05955980123
                     EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                     y+C+   C++sF++k +L +H r+ +
  Spipo4G0034800 955 YPCNveGCSMSFRSKQDLAVHKRNiC 980
                     89********************9877 PP
2zf-C2H213.40.000239801002323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk F ++ +L++H+r+H
  Spipo4G0034800  980 CPvkGCGKKFFSHKYLVHHQRVH 1002
                      9999*****************99 PP
3zf-C2H213.10.0002910381064123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C+   Cg++F+  s++ rH r+  H
  Spipo4G0034800 1038 YVCKepGCGQTFRFVSDFSRHKRKtgH 1064
                      99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.3E-172465IPR003349JmjN domain
PROSITE profilePS5118314.3952566IPR003349JmjN domain
PfamPF023753.1E-152659IPR003349JmjN domain
SMARTSM005583.4E-48216385IPR003347JmjC domain
PROSITE profilePS5118433.815216385IPR003347JmjC domain
SuperFamilySSF511971.84E-25230384No hitNo description
PfamPF023731.1E-36249368IPR003347JmjC domain
SMARTSM003558.5955977IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.5089781007IPR007087Zinc finger, C2H2
SMARTSM003550.0099781002IPR015880Zinc finger, C2H2-like
SuperFamilySSF576674.53E-69791015No hitNo description
Gene3DG3DSA:3.30.160.603.6E-59791006IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS0002809801002IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.4E-810071032IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001410081032IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74110081037IPR007087Zinc finger, C2H2
PROSITE patternPS00028010101032IPR007087Zinc finger, C2H2
SuperFamilySSF576671.71E-910181060No hitNo description
Gene3DG3DSA:3.30.160.601.0E-910331061IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.1410381064IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.88710381069IPR007087Zinc finger, C2H2
PROSITE patternPS00028010401064IPR007087Zinc 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: 1072 aa     Download sequence    Send to blast
MASPSSSVEH PPLEVLSWLK TLPLAPEYHP TLAEFQDPIA YIHKIEKEAS QYGICKIVPP  60
VPPAPKKTTI ANLNRSFAAL QKNCFGSGGG GATPKKGAPT FTTRQQQIGF CPRRPRPVQK  120
PVWQSGEQYT LQQFENKAKQ FERAHIKRTV GGGSGARKSG GGGNAGGPLS PLEVETLFWK  180
ACADKPFSVE YANDMPGSGF GLPLVGKKWR DGEAGSVGET AWNMRGVSRA KGSLLKFMKE  240
DIPGVTSPMV YVAMMFSWFA WHVEDHELHS LNYLHMGAGK TWYGVPRDAG LAFEDVIRLH  300
GYGGEVNSLV TFAILGEKTT VMSPEVLIEA GIPCCRLVQN AGDFVVTFPG SYHSGFSLGF  360
NCGEAANIAT PEWLRVAKEA AVRRASINYP PMVSHYQLLY ELALSLSSRD TTNNSSEPRS  420
YRLKDRMKSE GEQMIKELFV ENVLETNWRL HSLLDKGSSC IVLPHNAFDI SVAPYSRVIS  480
QIKVKPRLSL SFYNQEEALN ASRSLFPSED TLERNSGLRY LSGFSSMNGR FISSAEAKRF  540
PAEKCSKTDV STSYTIADSQ ETGPEKEVTL RSDGLLDQGV LSCVTCGILS FTCVAIVRPT  600
DIAARCLMSA DCSSFNDLYA GSGETSDTVI FGNANAHNYN FLARPDYPKI ENEARSLAEE  660
LGMECSWEEI CFMEASKEDQ QKICGAIEDE EAVPTNSDWA VKLGINLFYS ANLSKSPLYS  720
KQLPYNPVIY RAFGRSASGS SPGRAGVNGK RRSKQKRIVV AGKWCGKVWM TSQVHPFLAH  780
KNEIHEQYEA AAAAAAALAE EAKIEGDADC QREALPGKRE RPDDGMETET ERRSEPKGKN  840
KKKKMKNSSK KPASKKPKCL SLAEAAAVEV AAAVESLTES FSARRQRSGR LRRPISRPSL  900
DQEEEQRHYA VEEERPTAAK SAAAENKKKK TAAAAAPAVK KKKKHPDAGE DGGDYPCNVE  960
GCSMSFRSKQ DLAVHKRNIC PVKGCGKKFF SHKYLVHHQR VHVDDRPLKC PWKGCKMTFK  1020
WAWARTEHIR VHTGARPYVC KEPGCGQTFR FVSDFSRHKR KTGHVSRKGR S*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-71164736412Transcription factor jumonji (Jmj) family protein
6ip4_A1e-71164736412Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1750756RRSKQKR
2840850KKKKMKNSSKK
3927943KKKTAAAAAPAVKKKKK
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_008797141.10.0LOW QUALITY PROTEIN: lysine-specific demethylase JMJ705-like
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A1D6G6Q70.0A0A1D6G6Q7_MAIZE; 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]