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 mrna09903.1-v1.0-hybrid
Organism
Fragaria vesca
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria
Family C2H2
Protein Properties Length: 1493aa    MW: 165633 Da    PI: 9.4815
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
mrna09903.1-v1.0-hybridgenomeGDRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2110.001313731398123
                               EEET..TTTEEESSHHHHHHHHHH.T CS
                  zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                               ++C    C++sF +k++L+ H ++ +
  mrna09903.1-v1.0-hybrid 1373 FVCDieGCTMSFGTKHELNLHKKNvC 1398
                               899999***************99866 PP
2zf-C2H213.50.0002213971420223
                               EET..TTTEEESSHHHHHHHHHHT CS
                  zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                               +Cp   Cgk F ++ +L++H r+H
  mrna09903.1-v1.0-hybrid 1397 VCPvkGCGKKFFSHKYLVQHRRVH 1420
                               69999*****************99 PP
3zf-C2H211.80.0007314561482123
                               EEET..TTTEEESSHHHHHHHHHH..T CS
                  zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                               y+C    Cg++F+  s++ rH r+  H
  mrna09903.1-v1.0-hybrid 1456 YVCAepGCGQTFRFVSDFSRHKRKtgH 1482
                               899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.8E-162061IPR003349JmjN domain
PROSITE profilePS5118314.2432162IPR003349JmjN domain
PfamPF023753.7E-152255IPR003349JmjN domain
SuperFamilySSF511971.54E-24115174No hitNo description
PROSITE profilePS5118432.547187366IPR003347JmjC domain
SMARTSM005585.8E-46197366IPR003347JmjC domain
SuperFamilySSF511971.54E-24215365No hitNo description
PfamPF023733.5E-36230349IPR003347JmjC domain
Gene3DG3DSA:3.30.160.607.9E-413691394IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003551413731395IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.61213961425IPR007087Zinc finger, C2H2
SMARTSM003550.003713961420IPR015880Zinc finger, C2H2-like
SuperFamilySSF576671.33E-513961432No hitNo description
Gene3DG3DSA:3.30.160.607.7E-613961419IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028013981420IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.604.2E-914201448IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.63714261455IPR007087Zinc finger, C2H2
SMARTSM003550.001714261450IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014281450IPR007087Zinc finger, C2H2
SuperFamilySSF576672.27E-914361480No hitNo description
Gene3DG3DSA:3.30.160.602.1E-914491479IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.6214561482IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.80314561487IPR007087Zinc finger, C2H2
PROSITE patternPS00028014581482IPR007087Zinc 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: 1493 aa     Download sequence    Send to blast
MAAPPEQPPE VLPWLRALPV APEYHPTWAE FQDPIAYIFK IEKEASQYGI CKIVPPVPPA  60
PKKTAIANLN KSLILRNGPV TGKGPKAQPT FTTRQQQIGF CPRKARPVQR PVWQSGEHYT  120
FSQFEAKAKS FEKSYLKKQR KKGGLSALDI ETLYWKATVD KPFSVEYAND MPGSAFVPLS  180
SKKSGGSTSR EAGDGVTLGE TAWNMRGVSR SRGSLLRFMK EEIPGVTCPM VYVAMMFSWF  240
AWHVEDHDLH SLNYLHMGAG KTWYGVPREA AVAFEEVVRV QGYGGEINPL VTFATLGEKT  300
TVMSPEVFIS SGIPCCRLVQ NAGEFVVTFP RAYHTGFSHG FNCGEAANIA TPEWLRVAND  360
AAVRRASINY PPMVSHFQLL YDLALALCSR TPVHSSAEPR SSRLKDKKKG EGETVVKGLF  420
VKNVIQNNEL LHVLGKGSSI VLLPQSSSDI SVCSKLRVGS QLRVNPDDLI IDGNRGIKQV  480
SVKGKLASLC ESSRHLSLNG NDSAATPSKM LNMSAKRESN VEGEGLSDQR LFSCVTCGIL  540
SFSCVAIIQP REAAARYLMS ADCSFFNDWA VDCEPIQGAN GDPNSSKKGP CTETGLKQKS  600
APDSLYDAPF QSADNQNQIT DPSNEVDSNT ENQRDTNALG LLALTYGVSS DSEEDQANQD  660
VPVCGDKSNL SDCSLEGRYE YQSASPPLRA SYGGTAGVRS PTSPGFDCGI GLPTIDGNGL  720
PTIDVYVENR PEATNFKDKG HQYSVDLDTN NLALTKTNGL VGTSIDPMKV SYSGSPDAFD  780
VQPTGFGQVT LRKDSTGTSF APGFDHDSSR MHVFCLEHAV EVEQQLRSFG GAHILLLCHP  840
DYPRIVDEAK EIAEELGVNY PWNDLVFRNA TRADEQRIQS ALDSEEAIAG NGDWAVKMGI  900
NLFYSASLSR SHLYSKQMPY NSVIYNAFGR SSPATSPAGP EVCGRRPAKQ KKVVVGKWCG  960
KVWMSNQVHP FLIKREHEEK KVEQERRRFQ ESPIPDEKLH GNTESTHKTE KTVVTKQYSR  1020
KRKMTVDGET TKKAKRTDAV SAQSVDDDSH LQQMRFLKNK QGKHIESGPT KKSKIEKEDA  1080
VSSDSMEDDF RQQNRRTLRS KQAKHSVGDD DVSDDSMGVD SQQQQTRIAK SKQAKHSAKD  1140
FSVVSDDSVG VDSDHQQKRV AESNTREFSA VSDDSLDESI HQLHRRSLRR NKGKSIGREN  1200
FTSQNLYGVS SRQKQKKTSK SKQAKIVERE EAALDETTDD NAALQHKIVR GKQIKPETLQ  1260
QMKRETPHRV RQGSRRLQES QQQTPRIRNT TDVHAEEPEG GPSTRLRKRP PKEQPETSRK  1320
KAKVQPETGR KKAKEQQQTG RIKVNTASAV KTKNASARKT KNASGARVEE AEFVCDIEGC  1380
TMSFGTKHEL NLHKKNVCPV KGCGKKFFSH KYLVQHRRVH EDDRPLRCPW KGCKMTFKWA  1440
WARTEHIRVH TGARPYVCAE PGCGQTFRFV SDFSRHKRKT GHSVKKGKGR SR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-73123876353Transcription factor jumonji (Jmj) family protein
6ip4_A2e-73123876353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110181023SRKRKM
213181331RKKAKVQPETGRKK
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
PlantRegMapmrna09903.1-v1.0-hybrid
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_004301036.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2P6P5A50.0A0A2P6P5A5_ROSCH; Putative [histone H3]-lysine-36 demethylase
STRINGXP_004301036.10.0(Fragaria vesca)
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]