PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Araha.17006s0007.1.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family C2H2
Protein Properties Length: 958aa    MW: 107104 Da    PI: 6.7057
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.17006s0007.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.20.00054840865123
                           EEET..TTTEEESSHHHHHHHHHH.T CS
               zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                           y+C    C++sF++  +L+ H r+ +
  Araha.17006s0007.1.p 840 YQCDmeGCTMSFRSEKQLTLHKRNiC 865
                           99********************9877 PP

2zf-C2H215.64.5e-05865887323
                           ET..TTTEEESSHHHHHHHHHHT CS
               zf-C2H2   3 Cp..dCgksFsrksnLkrHirtH 23 
                           Cp   Cgk F ++ +L++H+r+H
  Araha.17006s0007.1.p 865 CPvkGCGKNFFSHKYLVQHQRVH 887
                           9999*****************99 PP

3zf-C2H212.50.00044923949123
                           EEET..TTTEEESSHHHHHHHHHH..T CS
               zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt..H 23 
                           y+C    Cg++F+  s++ rH r+  H
  Araha.17006s0007.1.p 923 YVCAepGCGQTFRFVSDFSRHKRKtgH 949
                           899999****************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5118415.6271107IPR003347JmjC domain
SMARTSM005580.00368107IPR003347JmjC domain
PfamPF023734.0E-173590IPR003347JmjC domain
SuperFamilySSF511974.39E-1037126No hitNo description
SMARTSM003557.7840862IPR015880Zinc finger, C2H2-like
SMARTSM003550.01863887IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.173863892IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.607.8E-7864891IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280865887IPR007087Zinc finger, C2H2
SuperFamilySSF576671.47E-10879921No hitNo description
Gene3DG3DSA:3.30.160.603.5E-9892916IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.24893922IPR007087Zinc finger, C2H2
SMARTSM003557.0E-4893917IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280895917IPR007087Zinc finger, C2H2
SuperFamilySSF576672.02E-8911945No hitNo description
Gene3DG3DSA:3.30.160.601.2E-9917946IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.62923949IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.032923954IPR007087Zinc finger, C2H2
PROSITE patternPS000280925949IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 958 aa     Download sequence    Send to blast
MEVVRVHGYG GELNPLVDQE EDVNDSIAVF SVTISTLGEK TTVMSPEVFV KAGIPCCRLV  60
QNPGEFVVTF PRAYHSGFSH GFNCGEASNI ATPEWLRVAK DAAIRRAAIN YPPMVSHLQL  120
LYDYALALGS RMPTSINTKP RSSRLKDKKR SEGERLTKKL FVQNIIHNNE LLSSLGKGSP  180
VALLPQSSSD LSVCSDLRIG SNLITNQEKP IQLKSEDLSS DSVMVGLNNG LKDTVSVKEK  240
FTSLCERNRN HLASSEKETQ ETLSDAERRK NDGAVALSDQ RLFSCVTCGV LSFDCVAIVQ  300
PTEAAARYLM SADCSFFNDW TVVSGSANLE STEKHDVDYF YNVPSQTTDH SMNTGDQKTS  360
TASLTTAHKK DGALSLLASA YGDSSDSEEE DHKVLNAILS EDRKYDQSGS CAYEASSFDT  420
DGKEEARDGR SSDSNRQRLV CRKETGVVEG SNATSTCSTL SWTTEHSRLS KGSNTSLPFV  480
PRSDDDSSRL HVFCLEHAAE VEQKLRPIGG IHLMLLCHPE AEAKIVAEEL VIDHEWNDTE  540
FRNVTREDEE TIQAALDNVE AKGGNSDWTV KLGINLSYSA ILSHSPLYSK QMPYNSVIYN  600
AFGRSSPAKS SPLKPEVFGR RSSRQRKYVV GKWCEFESDD EVSDRSLGEE YAVRERAVSE  660
SSTENSFQLH GHSIDENALE DSVYGHDDDK LYRHPKGLPR SKRTKVFRNP VSYDSEENDV  720
YQRRGNIQAS RIGGEYESEE DSLEELDFCS TRKRQTRSTA KRNVKTEIVQ GPRETNQEFD  780
SYMEGPSTRL RVRIPKPSRV SSETKPKKIG KKGSRNASFS RVATEEDVEE DEEGEECAAY  840
QCDMEGCTMS FRSEKQLTLH KRNICPVKGC GKNFFSHKYL VQHQRVHSDD RPLKCPWKGC  900
NMTFKWAWSR TEHIRVHTGA RPYVCAEPGC GQTFRFVSDF SRHKRKTGHS VKKTKKR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A2e-7983795720140Lysine-specific demethylase REF6
6a58_A2e-7983795720140Lysine-specific demethylase REF6
6a59_A2e-7983795720140Lysine-specific demethylase REF6
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapAraha.17006s0007.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY6644990.0AY664499.1 Arabidopsis thaliana relative of early flowering 6 (REF6) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020880349.10.0lysine-specific demethylase REF6 isoform X1
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLD7LRW60.0D7LRW6_ARALL; Uncharacterized protein
STRINGscaffold_501791.10.0(Arabidopsis lyrata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
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]