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 Peinf101Scf02778g00033.1
Organism
Petunia inflata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Petunioideae; Petunia; Petunia integrifolia
Family C2H2
Protein Properties Length: 1261aa    MW: 141559 Da    PI: 8.9635
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Peinf101Scf02778g00033.1genomeSGNView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.70.0003811451170123
                                EEET..TTTEEESSHHHHHHHHHH.T CS
                   zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                                y+C    C++sFs+k +L  H ++ +
  Peinf101Scf02778g00033.1 1145 YQCDleGCSMSFSSKQELLLHKKNvC 1170
                                99*******************99866 PP
2zf-C2H210.90.001411691192223
                                EET..TTTEEESSHHHHHHHHHHT CS
                   zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                                +Cp   C+k F ++ +L++H r+H
  Peinf101Scf02778g00033.1 1169 VCPveGCKKKFFSHKYLVQHRRVH 1192
                                69999*****************99 PP
3zf-C2H212.20.0005612281254123
                                EEET..TTTEEESSHHHHHHHHHH..T CS
                   zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                                y+C+   Cg++F+  s++ rH r+  H
  Peinf101Scf02778g00033.1 1228 YVCTetGCGQTFRFVSDFSRHKRKtgH 1254
                                99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-141758IPR003349JmjN domain
PROSITE profilePS5118313.3841859IPR003349JmjN domain
PfamPF023759.0E-151952IPR003349JmjN domain
PROSITE profilePS5118431.429186359IPR003347JmjC domain
SMARTSM005582.0E-49186359IPR003347JmjC domain
SuperFamilySSF511976.59E-26200375No hitNo description
PfamPF023734.8E-36219342IPR003347JmjC domain
SMARTSM003557.411451167IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.605.9E-511661196IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.57211681197IPR007087Zinc finger, C2H2
SuperFamilySSF576671.72E-511681205No hitNo description
SMARTSM003550.01211681192IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011701192IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.2E-911971222IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.61411981227IPR007087Zinc finger, C2H2
SMARTSM003550.001411981222IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012001222IPR007087Zinc finger, C2H2
SuperFamilySSF576675.45E-1012081250No hitNo description
Gene3DG3DSA:3.30.160.603.8E-1012231250IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.05312281259IPR007087Zinc finger, C2H2
SMARTSM003550.1912281254IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012301254IPR007087Zinc 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: 1261 aa     Download sequence    Send to blast
MAEVNIEVFP WLKTLPVAPE YHPTLEEFQD PIAYIFKIEK HASQFGICKI VPPVPPLAKK  60
TILSNLNRSL SARPGSTGPT FTTRQQQIGF CPRKHRPVKK PVWQSGETYT VAEFQGKAKN  120
FEKNYLKKNC FLKKTAALSP LEIETLYWKA TVDKPFSVEY ANDMPGSAFP PKKIGGNGGG  180
GGEGVSLADT EWNMRGVSRA KGSLLKFMKE EIPGVTSPMV YLAMMFSWFA WHVEDHDLHS  240
LNYMHMGAGK TWYGVPRDAA VAFEEFIVKQ YKALFYNVRE YSTITFATLG EKTTVMSPEV  300
LLSAGIPCCR LVQNAGEFVV TFPRAYHSGF SHGFNCGEAA NIATPEWLRF AKEAAIRRAS  360
TNCPPMVSHF QLLYDLALSL CSRVPKNIKI EPRSSRLKDK KRSEGDMLVK ELFVEDLNCN  420
NYLLHILGEG SPVVLLPQDY TGTSNSSYLV AGSQLKVNSR SFPSLSSRDH EVKSLKDSAS  480
DGLMLGRKRG MKQLPRGSLE KGKYSSWHAG NRMPDSGRND DAQSSPETKR GNLDTAREMA  540
YKCDTLSEHG LFSCVTCGIL CYTCVAIVQP TEEAAHHLIS SDFRNFNDWT GDVGGVTAIG  600
RDLNAADSDS SSGWLVKRSP GGLIDVPIES SDRIRKLNNE SVGVLSSTKA RKETSSLGLL  660
ALNYANSSDS DEDEVEADIP VEACESIHTD SEDEVSLRVI DPYANHRQKR AVSEGRICQR  720
FDNPSEYSPS GESNTVSDRL RHHPRSHQVA ANCTPFSHKE EMNNNNDVAP FDNMPMQFTS  780
TSDEDSFRIH VFCLQHAVQV EEQLRQVGGV RISLLCHPDY PKLEAQAKKV AEELGSDHFW  840
REISFREATK EDEEMIQSAL EIEEAIHGNG DWTVKLDMNL FYSANLSRSP LYSKQMPYNF  900
IIYSAFGRSS PDNTPEKSEY TGRGSGKQKR GVVAGKWCGK VWMSSQVHPL LVERDTDEEQ  960
EQNKSIPVQI KPDVKSERPS ERAGTRTVAT TCKTGRKRKS AAEDRNTSNH KLLIADDLDD  1020
SLLSYIPQQH RKTNLRSKRI KYETPEPQQD VDKKKRFSTP SDDELDGGPS TRLRKRIPKP  1080
SKESAAKLVK AKSAIKQHEG MKAEKGSKVK IPSTNRNTKK DPVMKAPRSN TGNTIKKMKD  1140
KEGEYQCDLE GCSMSFSSKQ ELLLHKKNVC PVEGCKKKFF SHKYLVQHRR VHMDDRPLKC  1200
PWKGCKMTFK WAWARTEHIR VHTGERPYVC TETGCGQTFR FVSDFSRHKR KTGHVSKKGR  1260
G
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-71113928366Transcription factor jumonji (Jmj) family protein
6ip4_A5e-71113928366Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1485492GRKRGMKQ
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006351452.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2G3CCS70.0A0A2G3CCS7_CAPCH; Lysine-specific demethylase REF6
STRINGPGSC0003DMT4000392240.0(Solanum tuberosum)
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]