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 XP_016435656.1
Organism
Nicotiana tabacum
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: 1242aa    MW: 138799 Da    PI: 9.2589
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_016435656.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H210.80.001611261151123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                      y C    C++sFs+k +L  H ++ +
  XP_016435656.1 1126 YHCDleGCSMSFSTKQELSLHKKNvC 1151
                      889999***************99866 PP
2zf-C2H2110.001311501173223
                      EET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                      +Cp   C+k F ++ +L++H r+H
  XP_016435656.1 1150 VCPveGCKKKFFSHKYLVQHRRVH 1173
                      69999*****************99 PP
3zf-C2H212.20.0005512091235123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C+   Cg++F+  s++ rH r+  H
  XP_016435656.1 1209 YVCTetGCGQTFRFVSDFSRHKRKtgH 1235
                      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
PROSITE profilePS5118431.698180349IPR003347JmjC domain
SMARTSM005581.8E-49180349IPR003347JmjC domain
SuperFamilySSF511971.07E-24194338No hitNo description
PfamPF023733.0E-37213332IPR003347JmjC domain
SMARTSM003551111261148IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.606.6E-511471177IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.57211491178IPR007087Zinc finger, C2H2
SMARTSM003550.01211491173IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011511173IPR007087Zinc finger, C2H2
SuperFamilySSF576673.41E-911651205No hitNo description
Gene3DG3DSA:3.30.160.602.8E-811781203IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001411791203IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74111791208IPR007087Zinc finger, C2H2
PROSITE patternPS00028011811203IPR007087Zinc finger, C2H2
SuperFamilySSF576675.76E-811971231No hitNo description
Gene3DG3DSA:3.30.160.603.7E-912041232IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.90712091240IPR007087Zinc finger, C2H2
SMARTSM003550.1912091235IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012111235IPR007087Zinc 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: 1242 aa     Download sequence    Send to blast
MAEASGNIEV FPWLKTLPVA PEYHPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPVPAPP  60
KKTALAYLNR SLSARSGSNG GPTFTTRQQQ IGFCPRKHRP VKKPVWQSGE NYTVQEFQAK  120
AKAFEKNYLK KNFKKALTSP LEIETLFWKA TVDKPFSVEY ANDMPGSAFA PKKVGNVVTT  180
LADTEWNMRG VSRAKGSLLK FMKEEIPGVT SPMVYLAMMF SWFAWHVEDH DLHSLNYLHM  240
GAGKTWYGVP RDAAVAFEEV IRVHGYAGET NPLVTFATLG EKTTVMSPEV LLSAGIPCCR  300
LVQNAGDFVI TFPRAYHSGF SHGFNCGEAS NIATPGWLIV AKDAAIRRAS INCPPMVSHF  360
QLLYDLALSL CSRVPKNIRI EPRSSRLKDK KKSEGDMLVK ELFVEDLNCN NYLLHILGEG  420
SPVVLLPRHY SGISIGSNSV AGSQLKVNSR FPSLSSPDHE VKSKTDSASD ALMLGRKQRM  480
KQLASVSLEK GKHSSWHTGN RLPESGRDEA ESSPETEREN LDPERGMTYR CDTLSEHGLF  540
SCVTCGILCY TCVAIIQPTE AAAHHLMSSD YRNFNDWTGN VGGVTANSRD ANAAESDSSS  600
GWLVKRAPGG LINVPIESSD RIRKLNNESV GVLSSTKARK ETSSLGLLAL NYANSSDSDE  660
DEVEANIPVE ACESRQMDFE DEVSLRVIDP YANHRQRRAV SGGRNCQSLD NSVHLESGNL  720
PSGESNTLPD RSRHQLRSHQ VGANCIPFAH RGEIANSDGV APFDNGPMQF TSTSDEDSFR  780
IHVFCLQHAV QVEEQLRQVG GVHISLLCHP ADYPKLEAQA KKVAEELGRD HFWREISFRE  840
ATKEDEEMIQ SALEVEEAIH GNGDWTVKLD INLFYSANLS RSPLYSKQMP CNFIIYNAFG  900
RSSPDEKSEY TGTGRGSGKQ RRAVVAGKWC GKVWMSSQVH PLLAERRDTD EEQQQNNNSI  960
SARVKPEVKS ERPCEMTPTV KIVARTGKKR KSRVENKRNS KLLIADDSSV SNVPQQQRKT  1020
NLRSKRIKYE TPEPKEEDVD KKKRFGSPIN DDPDGGPSTR LRKRMPKPSK ESLVKPKPAP  1080
IKQQNESKKA EKGSKVKIPS SNSNSKKDPV MKANTSKKMK DKEGEYHCDL EGCSMSFSTK  1140
QELSLHKKNV CPVEGCKKKF FSHKYLVQHR RVHMDDRPLK CPWKGCKMTF KWAWARTEHI  1200
RVHTGARPYV CTETGCGQTF RFVSDFSRHK RKTGHISKKG RG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A4e-72133828366Transcription factor jumonji (Jmj) family protein
6ip4_A4e-72133828366Arabidopsis 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
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9754420.0HG975442.1 Solanum pennellii chromosome ch03, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009613168.10.0PREDICTED: lysine-specific demethylase REF6 isoform X1
RefseqXP_016435656.10.0PREDICTED: lysine-specific demethylase REF6-like isoform X1
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A1S3X7130.0A0A1S3X713_TOBAC; lysine-specific demethylase REF6-like isoform X1
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]