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 Vradi07g14630.1
Organism
Vigna radiata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
Family C2H2
Protein Properties Length: 1517aa    MW: 172491 Da    PI: 9.0566
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Vradi07g14630.1genomeSNUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.40.0004814011426123
                       EEET..TTTEEESSHHHHHHHHHH.T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                       y+C    C++sF +k +L +H r+ +
  Vradi07g14630.1 1401 YQCDieGCTMSFGSKQELLQHKRNiC 1426
                       99********************9877 PP
2zf-C2H212.90.0003414261448323
                       ET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                       Cp   Cgk F ++ +L++H r+H
  Vradi07g14630.1 1426 CPvkGCGKKFFSHKYLVQHRRVH 1448
                       9999*****************99 PP
3zf-C2H211.80.0007414841510123
                       EEET..TTTEEESSHHHHHHHHHH..T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                       y+C    Cg++F+  s++ rH r+  H
  Vradi07g14630.1 1484 YVCAepGCGQTFRFVSDFSRHKRKtgH 1510
                       899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.0E-171657IPR003349JmjN domain
PROSITE profilePS5118314.0631758IPR003349JmjN domain
PfamPF023754.0E-141851IPR003349JmjN domain
SuperFamilySSF511977.42E-2696338No hitNo description
SMARTSM005585.4E-49166335IPR003347JmjC domain
PROSITE profilePS5118434.489166335IPR003347JmjC domain
PfamPF023731.5E-36199318IPR003347JmjC domain
Gene3DG3DSA:3.30.160.605.7E-513881423IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003556.614011423IPR015880Zinc finger, C2H2-like
SuperFamilySSF576677.59E-614241460No hitNo description
PROSITE profilePS5015712.50814241453IPR007087Zinc finger, C2H2
SMARTSM003550.004514241448IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014261448IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.5E-514261452IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
Gene3DG3DSA:3.30.160.602.6E-814531478IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001614541478IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.82414541483IPR007087Zinc finger, C2H2
PROSITE patternPS00028014561478IPR007087Zinc finger, C2H2
SuperFamilySSF576672.73E-914641508No hitNo description
Gene3DG3DSA:3.30.160.602.4E-914791507IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.84514841515IPR007087Zinc finger, C2H2
SMARTSM003550.6214841510IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014861510IPR007087Zinc 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: 1517 aa     Download sequence    Send to blast
MTASEEVLPW LKSLPVAPEY RPTEAEFQNP IAYIFKIEKE ASQYGICKII PPLPPSPKKT  60
ATANLTRSHP TFTTRQQQIG FCPRRPQPVR RRVWYSGHHY SLREFEAKAK AFHKTYLKKS  120
KPKPSPLELE TLYWKATLDK SFSVEYANDI PGSAFSPLRA LRDADYVGDT PWNMRVVSRG  180
SDSLLRFMKE EIPGVTSPMV YVAMLFSWFA WHVEDHDLHS LNYLHFGAPK TWYGVPKDAA  240
VAFEEVVRVH GYGGEINPLV TFAILGEKTT VMSPEVFVGA GVPCCRLVQN AGEFVVTFPR  300
AYHTGFSHGF NCGEAANIAT PEWLRFAKDA AIRRASINYP PMVSHFQLLY DLGLALCSRI  360
PGGIRAEPRS SRLKYKRNGE GETVIKELFV QDVVENNDLL HTLSKGSAIV LLPRSSSDFS  420
VCSKLRVGSR QLKVNPDFSL NVYNYEGMDS SDFISNDLMF NRNHGIKQVK SFYSVKEKFV  480
TLCERNRVLP LSSNGNIYTS SSKTDSKKET DKGDGLSDHR LFSCVTCGIL SFSCVAIVQP  540
REPAATYLMS ADCSFFNDWI VGSGVTSNKF SIAHEDASIP KPRTYTGSDN LFHNAGWTKQ  600
NAQHDSNGVP IQSVEHHAQI ADQNFEEALN SGREKGNTAL ALLASAYGNS SDSEEDQGGL  660
DIALDGDELN AVNHSASNGS QEMSSMPSHF QDPHTSPMVR VIRLNKGDDI HSRRIDNYEY  720
YMHKRLEQIM TPLNYSVKSE DHDNTSGVAF RNTRAVPHPT LNCSQDTHTD EDSSRMHIFY  780
YPKIEAEAKF VAEELGIGYT WKNTVYRQAN REDEERIQSA LDSEEAIPGN GDWAVKLGIN  840
LFYSANLSRS ALYSKQIPYN SVIYKAFGQN SPASSPTEPK VYQRRTNKQK KVVAGKWCGK  900
VWMSNQVHPL LAKRDSEDVE DETSLHGWPL PDEKIQRSES NHKSNTSTRK SGKKWKKSVE  960
KGGIWEESFV ERDSLSDNSI EDKFNKYQRR IIGGKRSRHI ERDDTASEGD YSPLPLHRKP  1020
ITKHSESSEN DGMSDDLLDD DSCIQHRRRA NTNEAKLIDS DVFSDDTMDY GSDWLRRGEL  1080
SNEQDAISDD SLSAGSLELH GKIPKGNYDK YITEEDVISD DQREVCLWKQ RGKISKGRQR  1140
SLSAKSGDGL KHHRQKQQQR NLRSRQDKHF AVENITSDDQ MEGRSFKCQR RIPKNKQVKF  1200
IEVEDVMSDD QLKGDFQKPQ RSTRRSRQNK YNDKDVMNDL AENNFHILHR TRKRKQVKGM  1260
DEDNIDSDDQ MDDILHQRHK RTLQSKQSKA EILQQTKQTN PHHARNKTSH PAKQKQGAHT  1320
KMKSRAARQT KNQSGNSKDL TLHVEEEEDG GPRTRLRKRV LEKESEGKLK EKRTKREKEK  1380
NTTAAKVLVG HAKTKDEESE YQCDIEGCTM SFGSKQELLQ HKRNICPVKG CGKKFFSHKY  1440
LVQHRRVHED DRPLKCPWKG CKMSFKWAWA RTEHIRVHTG ARPYVCAEPG CGQTFRFVSD  1500
FSRHKRKTGH ATKKNC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-8083496346Transcription factor jumonji (Jmj) family protein
6ip4_A2e-8083496346Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
112501255TRKRKQ
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
PlantRegMapVradi07g14630.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0150340.0AP015034.1 Vigna angularis var. angularis DNA, chromosome 1, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_014508868.10.0lysine-specific demethylase REF6-like
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A1S3US050.0A0A1S3US05_VIGRR; lysine-specific demethylase REF6-like
STRINGXP_007155510.10.0(Phaseolus vulgaris)
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]