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 Niben101Scf02853g02002.1
Organism
Nicotiana benthamiana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
Family C2H2
Protein Properties Length: 1241aa    MW: 138845 Da    PI: 9.1608
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Niben101Scf02853g02002.1genomeBTI-
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.20.0005512081234123
                                EEET..TTTEEESSHHHHHHHHHH..T CS
                   zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                                y+C+   Cg++F+  s++ rH r+  H
  Niben101Scf02853g02002.1 1208 YVCTetGCGQTFRFVSDFSRHKRKtgH 1234
                                99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005453.6E-161960IPR003349JmjN domain
PROSITE profilePS5118314.9912061IPR003349JmjN domain
PfamPF023752.1E-152154IPR003349JmjN domain
SMARTSM005581.9E-49180349IPR003347JmjC domain
PROSITE profilePS5118431.421180349IPR003347JmjC domain
SuperFamilySSF511974.67E-24194338No hitNo description
PfamPF023732.4E-37213332IPR003347JmjC domain
SMARTSM003552411251147IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.46811481177IPR007087Zinc finger, C2H2
SMARTSM003550.01511481172IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.605.3E-511491176IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028011501172IPR007087Zinc finger, C2H2
SuperFamilySSF576672.89E-911641204No hitNo description
Gene3DG3DSA:3.30.160.602.8E-811771202IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.74111781207IPR007087Zinc finger, C2H2
SMARTSM003550.001411781202IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011801202IPR007087Zinc finger, C2H2
SuperFamilySSF576675.86E-811961230No hitNo description
Gene3DG3DSA:3.30.160.603.7E-912031231IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.1912081234IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.05312081239IPR007087Zinc finger, C2H2
PROSITE patternPS00028012101234IPR007087Zinc 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: 1241 aa     Download sequence    Send to blast
MAEASGNIEV FPWLKTLPVA PEYHPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPVPAPP  60
KKTALSYLNR SLSARSGSNG GPTFTTRQQQ IGFCPRKHRP VKKPVWQSGE NYTVQEFQAK  120
AKAFEKNFLK KNLKKALTSP LEIETLYWKA TVDKPFCVEY ANDMPGSAFA PKKVGNAVTT  180
LADTEWNMRG VSRAKGSLLK FMKEEIPGVT SPMVYLAMMF SWFAWHVEDH DLHSLNYLHM  240
GAGKTWYGVP RDAAVAFEEV IRVHGYAGET NPLVTFATLG EKTTVMSPEV LLSAGIPCCR  300
LVQNAGEFVI TFPRAYHSGF SHGYNCGEAS NIATPGWLIV AKDAAIRRAS INCPPMVSHF  360
QLLYDLALSL CSRVPKNIRI EPRSSRLKDK KKSEGDMLVK ELFVEDLNCN NYLLHILGEG  420
SPVVLLPRHY SGISIGSNSV AGSQLKVNSR FPSLSSPDHE VKSKTDSASD ALMLGRKLRT  480
KQLASVSLEK GKHSSWHAGN RLPESGRDEA ESSPETEGGN LDSARGMTYR CDTLSEHGLF  540
SCVTCGILCY TCVAIIQPTE TAAHHLMSSD YRNFNDWTGN VGGITATSRD ANAAESDSSS  600
GMLVKRAPGG LIDVPIESSD RIRKLNNERV GVLSSTKARK ETSSLGLLAL NYANSSDSDE  660
DEVEANIPVE TCESRHMDFE DEVSLRVIDP YANHRQRRAV SDGRNCQSRD NSIHLESENP  720
PSGESNTLPD RARHQPRSHQ VGANCIPFSH RGEIANSDVV VPFDNGPMQF TSTSDEDSFR  780
IHVFCLQHAV QVEEQLRQVG GVHISLLCHP DYPKLEAQAK KVVEELGRDH FWREISFREA  840
TKEDEEMIQS ALEVEDAIHG NGDWTVKLDI NLFYSSNLSR SPLYSKQMPY NFIIYNAFGR  900
SSPDEKSEYT GTGRGSGKQK RAVVAGKWCG KIWMSSQVHP LLAERRDTDE EQQLNNNSIS  960
ARVKPEVKSE RPCEMTQTIK TVARTGKKRE SRVENKRKSK LLVADDSSVS NVPQQQRKTN  1020
LRSKRIKYET PEPKDEDVDK KKRFDSPIND DPVGGPSTRL RKRMPKPSSE SLVKPRPTPI  1080
KQQNESKKAE KGSKVKIPSA NSNSKKDPVM KANTSKKMKD KEGEYHCDLE GCSMSFNAKQ  1140
ELSLHKKNIC PVEGCKKKFF SHKYLVQHRR VHMDDRPLKC PWKGCKMTFK WAWARTEHIR  1200
VHTGARPYVC TETGCGQTFR FVSDFSRHKR KTGHVSKKGR G
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-71133828366Transcription factor jumonji (Jmj) family protein
6ip4_A5e-71133828366Arabidopsis JMJ13
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00608ChIP-seqTransfer from AT3G48430Download
Motif logo
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_019243504.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A1J6IKD20.0A0A1J6IKD2_NICAT; Lysine-specific demethylase ref6
STRINGXP_009613168.10.0(Nicotiana tomentosiformis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA49882331
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]