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 Lj0g3v0351959.1
Organism
Lotus japonicus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
Family C2H2
Protein Properties Length: 1558aa    MW: 176500 Da    PI: 8.7566
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lj0g3v0351959.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H210.80.001514421467123
                       EEET..TTTEEESSHHHHHHHHHH.T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                       ++C    C+++F +k +L++H ++ +
  Lj0g3v0351959.1 1442 FQCDieGCTMTFGSKQELTHHKKNiC 1467
                       89*******************99866 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005452.6E-142162IPR003349JmjN domain
PROSITE profilePS5118314.3682263IPR003349JmjN domain
PfamPF023752.7E-132356IPR003349JmjN domain
PROSITE profilePS5118433.22182351IPR003347JmjC domain
SMARTSM005581.3E-49182351IPR003347JmjC domain
SuperFamilySSF511974.39E-25197365No hitNo description
PfamPF023738.6E-37215334IPR003347JmjC domain
Gene3DG3DSA:3.30.160.603.2E-414341463IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003559.114421464IPR015880Zinc finger, C2H2-like
SMARTSM003550.03214651489IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.69714651494IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.2E-414661493IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014671489IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.5E-714941519IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001714951519IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.63714951524IPR007087Zinc finger, C2H2
PROSITE patternPS00028014971519IPR007087Zinc finger, C2H2
SuperFamilySSF576673.73E-915051549No hitNo description
Gene3DG3DSA:3.30.160.603.0E-915201548IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.57215251556IPR007087Zinc finger, C2H2
SMARTSM003551.215251551IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028015271551IPR007087Zinc 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:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1558 aa     Download sequence    Send to blast
MTVSESNGGG DVFPWLKSMP VAPEYRPTAA EFEDPIAYIF KIEKEASKFG ICKIIPPYPA  60
PPRKTAIANL HRSLPGPTFT TRQQQIGFCP RKARPVQRPV WQSGDSYTFQ EFELKAKNFE  120
KTHFKRHGKH HGGAAGCKGP LETETLFWKA TVDKPFSVEY ANDMPGSAFS PKCRRGAGEP  180
ASLAHTGWNM REVSRAGGSL LRFMKEEIPG VTSPMVYVAM MFSWFAWHVE DHDLHSLNYL  240
HMGAGKTWYG VPKDAAVAFE EVVRVHGYGG EINPLVTFSI LGEKNTVMSP EVLVSAGVPC  300
CRLVQNAGEF VVTFPRAYHT GFSHGFNCGE AANIATPEWL RFAKEAAIRR ASINYPPMVS  360
HFQLLYDLAL ALSSRNPGQI SAEPRSSRLK DKKKGEGEAV IKELFVQDVL QNNYILHVFG  420
KESPVVLLPR CSVDISVCSK LRVGCQQLKV NPGFSVNVGI SEGMNSSKDF VSDGVDRNHG  480
IRQEKSFYFV KDKFTTVCEK SRISSFDSNG NTCTSSSKPL QRESETRQED GLSDQRLFSC  540
VTCGVLSFSC VAIVQPREPA ARYLMSADCS FINDWVVGSG VPSNKFTVAN EDANIPEPNM  600
YAGWTKKNAQ GGLYDVPVQS AHDQILNVDQ ILNVDRNYKE AVNTERGKCN TALALLASAY  660
GNSSDSEEDQ GDLDIVVEGH ESNDINSSGK LPSHFRDSHP SLVTELDRQD DIPSTSASYE  720
DYMHHRFESD LSHQSFDHSF ENQDYKITSG AAFINTRAVP DPTSNCSQSD EDSCRMHVFC  780
LEHAAEAEKR LRPIGGANIL LLCHPDYPKI EAEAKLVAED LAIDYMWKDI AYRRATIEDE  840
ERIKSALDSE EAIPGNVDWA VKLGINLFYS ANLSRSPLYS KQMPYNSVIY HAFGRSSPAS  900
SPTKPKVYQR RASKQKKVVA GKWCGKVWMS NQVHPLLVKR DPEDVEDETI LHRRVLPDEK  960
IVRSKNIPKN ETTVKKYGRK RKMTVECRRT RKGSFAEKDV VSDNATEDKP NPKQRRILRS  1020
KKARHVEREG EDLERDYSSP HHRNHISKQT STECGAVSDD LFDGNHDARH RSFDVKKEKF  1080
IDSDVISDDA VEYDSDWQQR GELRSKHAED RERDSISEDS MSIASLQLQR KTSKSKHAQY  1140
IREEDAISDD QMENHCQKQQ KRIPKSRQRK YLAQKDIMIS DDQLELNMRK QWQGNSKSRK  1200
AKYLAEEDSI SDDQLEDNCD KYQSRTPNGR EAECVAGEDV MSDDQLEEAF QKQQRRFPRS  1260
RQRKRIDKEI VDDSAENISH VLHKTPKRKH AKCTDDDGMN SDDEMEDDSH QQQKRTLRTK  1320
QSKPKTLWQM KQPNCLLVKN QTSQPVKRGV ARMLVKSKAP QQVKQSSRLR IKQPGNSREL  1380
NLQVEEEEEG GPSTRLRKRA PKAQESEGKL KVKQTKRRKE KNATAAKVSA GRAKRKNEEA  1440
EFQCDIEGCT MTFGSKQELT HHKKNICPVK GCAKKFFSHK YLVQHRRVHE DDRPLRCPWK  1500
GCKMTFKWAW ARTEHIRVHT GARPYACAEP GCGQTFRFVS DFSRHKRKTG HSAKKSSQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-78113744355Transcription factor jumonji (Jmj) family protein
6ip4_A1e-78113744355Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
113961418RKRAPKAQESEGKLKVKQTKRRK
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}.
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
PlantRegMapLj0g3v0351959.1
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_027339021.10.0lysine-specific demethylase JMJ705-like isoform X1
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLI1JXF40.0I1JXF4_SOYBN; Uncharacterized protein
STRINGGLYMA04G36620.10.0(Glycine max)
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]