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 Ote100006770191
Organism
Ocimum tenuiflorum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Ocimeae; Ocimum
Family C2H2
Protein Properties Length: 1285aa    MW: 143336 Da    PI: 8.629
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ote100006770191genomeOteDB-
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.30.0002611691194123
                                    EEET..TTTEEESSHHHHHHHHHH.T CS
                       zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                                    y C    C++sFs+k +L+ H r+ +
  Ote100006770191|100006770191 1169 YACDmeGCTMSFSSKQELTLHKRNiC 1194
                                    789999****************9877 PP
2zf-C2H213.30.0002511941216323
                                    ET..TTTEEESSHHHHHHHHHHT CS
                       zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                                    Cp   Cgk F ++ +L++H r+H
  Ote100006770191|100006770191 1194 CPvkGCGKKFFSHKYLVQHRRVH 1216
                                    9999*****************99 PP
3zf-C2H212.20.0005712521278123
                                    EEET..TTTEEESSHHHHHHHHHH..T CS
                       zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                                    y+C+   Cg++F+  s++ rH r+  H
  Ote100006770191|100006770191 1252 YVCTetGCGQTFRFVSDFSRHKRKtgH 1278
                                    99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005453.8E-152263IPR003349JmjN domain
PROSITE profilePS5118314.0352364IPR003349JmjN domain
PfamPF023756.7E-142457IPR003349JmjN domain
SuperFamilySSF511977.69E-26109129No hitNo description
SMARTSM005584.8E-50170339IPR003347JmjC domain
PROSITE profilePS5118433.331173339IPR003347JmjC domain
SuperFamilySSF511977.69E-26188344No hitNo description
PfamPF023731.7E-37203322IPR003347JmjC domain
Gene3DG3DSA:3.30.160.604.1E-411641191IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003551111691191IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.36211921221IPR007087Zinc finger, C2H2
SMARTSM003550.004511921216IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.3E-511931220IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028011941216IPR007087Zinc finger, C2H2
SuperFamilySSF576672.23E-912081250No hitNo description
Gene3DG3DSA:3.30.160.602.9E-812211246IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.74112221251IPR007087Zinc finger, C2H2
SMARTSM003550.001412221246IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012241246IPR007087Zinc finger, C2H2
SuperFamilySSF576675.97E-812401274No hitNo description
Gene3DG3DSA:3.30.160.603.4E-912471274IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.07412521283IPR007087Zinc finger, C2H2
SMARTSM003550.1912521278IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012541278IPR007087Zinc 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: 1285 aa     Download sequence    Send to blast
MAAEVSGGGN IEVPPWLKSM AVAPEYHPTL AEFQDPIAYI FKIEKEASSY GICKIVPPVP  60
TAPRKTVVSN LNKSLLARSN ETGPTFTTRQ QQIGFCPRKH RPVQKPVWQS GERYTLAEFE  120
AKAKGFEKNY LKKYAKKALS SLEIETLYWN AMVDKPLSVD GGKKNEGGLT VGETEWNMRT  180
LSRENLSLLK FMKEEIPGVT SPMVYVAMMF SWFAWHVEDH DLHSMNYLHL GSGKTWYGVP  240
RAAAVAFEEV IREHGYGGEI NPLVTFATLG EKTTVMSPEV LLNAGVPCCR LVQNAGEFVV  300
TFPRAYHSGF SHGFNCGEAA NIATPEWLRV AKEAAIRRAA INCPPMVSHF QLLYDLALSL  360
CSRVPKSIAT EPRSSRLKDR KRGEGDKLIK ELFYQDMMQN NDMLNVLGKG SSIVLLPQNY  420
LNHSFSSNPM TGFQSTKSKL FPSLCSLGLE LKNACDNASD DFTLDKKQGL KQAKGSVAKR  480
TFSALFGIDI HSPAHAGETH CELKKASPCE QGLFSCVTCG ILCFACVAIV QPTEATAQYL  540
MSADCSTLSN LEESDNDLTH ICDPKASNEN LPSVFVLRSQ NGLSADQHID GGNVCSASDS  600
KAHKEPSSLG LLALAYGNFS DSEEEDSEAI VPAEGCGTSK SDDFRNEDAN VNTDPKADCT  660
TEISLLTSDS SAKFDPALAT SKDGEALYPE FSDGCNKSTS TLIKSNSLTC RFSRHQTEPQ  720
LDIPNSLSRK AVGTPITGLA PQEPSTFPFS SRLDEDSSRL HVFCLQHAMQ VRRRLSQFGG  780
ADVFLVCHPD YPKLESEAKK VAEELESNYI WSEVSFREAT DEDEEIIRRA LESENAIHGN  840
RDWAVKLGIN LFYSANLSRS PLYSKQMHYN FVVYNAFGRS SPTDSSASEG EREGGGLGRQ  900
KKITVAGKWC GKVWMSNQAH PLLLNKDSQQ HEQDFAVASW TKPDVKYVRR TERRPAAGLL  960
SAARKMSRKK KNDPESSSLM RGKSLEAEKL DESRDFSLSN NKIKRKRTSR MVKEENPESE  1020
NVVESSEESQ LSDSCKESES RRGIKRSRKE NCEAEEDSFE EERPLSKSWK QIKRKQRAKR  1080
REKETPDTAK NQKKSKKHEL NTLVEEEMEG GPSTRLRKRT TKPSTDSGAR LSKPKPVVKA  1140
QQRDAKTTKK SSASKSPSVG KIRDEEAEYA CDMEGCTMSF SSKQELTLHK RNICPVKGCG  1200
KKFFSHKYLV QHRRVHMEDR PLKCPWKGCK MTFKWAWART EHIRVHTGAR PYVCTETGCG  1260
QTFRFVSDFS RHKRKTGHAP KKARG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A6e-69163608353Transcription factor jumonji (Jmj) family protein
6ip4_A6e-69163608353Arabidopsis 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_011072922.10.0lysine-specific demethylase REF6 isoform X1
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A4D9ALJ00.0A0A4D9ALJ0_SALSN; Uncharacterized protein
STRINGMigut.I00266.1.p0.0(Erythranthe guttata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA49882331
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]