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_011072923.1
Organism
Sesamum indicum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Lamiales; Pedaliaceae; Sesamum
Family C2H2
Protein Properties Length: 1297aa    MW: 144320 Da    PI: 8.5848
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_011072923.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.30.0002512061228323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk F ++ +L++H r+H
  XP_011072923.1 1206 CPvkGCGKKFFSHKYLVQHRRVH 1228
                      9999*****************99 PP
2zf-C2H212.50.0004612641290123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C+   Cg++F+  s++ rH r+  H
  XP_011072923.1 1264 YVCTeaGCGQTFRFVSDFSRHKRKtgH 1290
                      99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.3E-15344IPR003349JmjN domain
PROSITE profilePS5118313.966445IPR003349JmjN domain
PfamPF023751.4E-14538IPR003349JmjN domain
SMARTSM005586.0E-53168337IPR003347JmjC domain
PROSITE profilePS5118433.91168337IPR003347JmjC domain
SuperFamilySSF511971.81E-26186342No hitNo description
PfamPF023736.8E-38201320IPR003347JmjC domain
SMARTSM003552011811203IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.44512041233IPR007087Zinc finger, C2H2
SMARTSM003550.004512041228IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.8E-512051232IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012061228IPR007087Zinc finger, C2H2
SuperFamilySSF576671.74E-912201262No hitNo description
Gene3DG3DSA:3.30.160.603.0E-812331258IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.74112341263IPR007087Zinc finger, C2H2
SMARTSM003550.001412341258IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012361258IPR007087Zinc finger, C2H2
SuperFamilySSF576678.8E-812521286No hitNo description
Gene3DG3DSA:3.30.160.603.0E-912591287IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.34412641295IPR007087Zinc finger, C2H2
SMARTSM003550.1912641290IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012661290IPR007087Zinc 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: 1297 aa     Download sequence    Send to blast
MPVAPEYHPT LAEFQDPIAY IFKIEKEASK YGICKIVPPV PAASKKTVIA NLNKSLLARS  60
TDPESGPTFT TRQQQIGFCP RKHRPVQKPV WQSGEKYTLT EFEVKAKNFE KIYLKKYAKK  120
GLNALEMETV YWNATVDKPF QVEYANDMPG SAFVAQKGCG KKNESTITVG ETEWNMRRVS  180
RENLSLLRFM KEEIPGVTSP MVYVAMMFSW FAWHVEDHDL HSLNYLHMGA GKTWYGVPRE  240
AAVAFEEVIR EHGYGGEINP LVTFATLGEK TTVMSPEVLL SAGVPCCRLV QNAGEFVVTF  300
PRAYHSGFSH GFNCGEAANI ATPEWLRFAK EAAIRRAAIN CPPMVSHFQL LYDLALSLCS  360
GVPKSIAMGP RSSRLKDRKK GEGEMLIKEL FLQDMMQNND MLHSLGKGSS IVLLPQNSLS  420
HSIYNNTSSG FQSTAKSRLF PSLCSPDLEL KTASYDARDE FLLDRKHGIK QPRGHAVNRK  480
SVSSLCSSSE VPSMAPCAEQ IDSEIKRASQ HEQGLFSCVT CGILCFACAA IVQPTEAAAH  540
YLMSADCSKF SYWGTGDDDH NHTRHAKSPN TNLGSGLVLR KKHGPSDVPI SADQIRSVNG  600
ESVGVVSNSK AHKEPSSLGL LALTYGNSSD SEEEETEADL PVDGCGTSKS DSPEDGHACD  660
NIDSKLNCRK EMSSQISDSN AMFGPPIAKC NGGDPQSSNC SDEFPTDNCT VVESNSCTHR  720
SRHRTKSRHD TSNSLTHKTE ATVSTGLTPL EDKNTPFPAR SDEDSYRLHV FCLQHALQVE  780
KRLSQIGGAN VFLVCHPDFP KLESQAKKVA EELESDWLWS EISFREATEE DEEIMRLALE  840
SENAIHGNGD WAVKMGINLF FSANLSRSPL YSKQMHFNFV IYSAFGRSSP IDSSAALDEL  900
EGKCVGRQKK IVVAGKWCGK VWMSSQAHPL LLNKDSQEQE EESEFTAWIK PNLKSERLSQ  960
SSQAAGVASA ICKTSRKRKN NAENSSHVKE KSLEAGKMDE PSIGFPLSNC NKVIKRKRGS  1020
RRLKEENPES EDLDESSEEI QLSNSCNQIK KRHGTKLLKK DTFEADENLD ASSEDFPLSN  1080
SWKQIKSKRG ARKTNKETPE PLKSKKRSKQ QANSLVDDDE LEGGPSTRLR KRTTKACKAS  1140
GPRSTNAKPV LKKQQKDIKT KKVPPVKVPS KAKLKDEEAE YACDMEGCTM SFGSKQELAL  1200
HKKNICPVKG CGKKFFSHKY LVQHRRVHMD DRPLKCPWKG CKMTFKWAWA RTEHIRVHTG  1260
ARPYVCTEAG CGQTFRFVSD FSRHKRKTGH SPKKARG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-75135812353Transcription factor jumonji (Jmj) family protein
6ip4_A2e-75135812353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110141023KRKRGSRRLK
210491059KKRHGTKLLKK
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
PlantRegMapXP_011072923.1
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_011072922.10.0lysine-specific demethylase REF6 isoform X1
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2G9I3H70.0A0A2G9I3H7_9LAMI; [histone H3]-lysine-36 demethylase
STRINGMigut.I00266.1.p0.0(Erythranthe guttata)
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]