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_011072922.1
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: 1316aa    MW: 146234 Da    PI: 8.5474
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_011072922.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.30.0002612251247323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk F ++ +L++H r+H
  XP_011072922.1 1225 CPvkGCGKKFFSHKYLVQHRRVH 1247
                      9999*****************99 PP
2zf-C2H212.40.0004712831309123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C+   Cg++F+  s++ rH r+  H
  XP_011072922.1 1283 YVCTeaGCGQTFRFVSDFSRHKRKtgH 1309
                      99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.3E-152263IPR003349JmjN domain
PROSITE profilePS5118313.9662364IPR003349JmjN domain
PfamPF023751.4E-142457IPR003349JmjN domain
SMARTSM005586.0E-53187356IPR003347JmjC domain
PROSITE profilePS5118433.91187356IPR003347JmjC domain
SuperFamilySSF511971.87E-26205361No hitNo description
PfamPF023736.9E-38220339IPR003347JmjC domain
SMARTSM003552012001222IPR015880Zinc finger, C2H2-like
SMARTSM003550.004512231247IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.44512231252IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.8E-512241251IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012251247IPR007087Zinc finger, C2H2
SuperFamilySSF576671.73E-912391281No hitNo description
Gene3DG3DSA:3.30.160.603.0E-812521277IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001412531277IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74112531282IPR007087Zinc finger, C2H2
PROSITE patternPS00028012551277IPR007087Zinc finger, C2H2
SuperFamilySSF576679.01E-812711305No hitNo description
Gene3DG3DSA:3.30.160.603.0E-912781306IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.1912831309IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.34412831314IPR007087Zinc finger, C2H2
PROSITE patternPS00028012851309IPR007087Zinc 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: 1316 aa     Download sequence    Send to blast
MAAEVSGGGN IEVSPWLKSM PVAPEYHPTL AEFQDPIAYI FKIEKEASKY GICKIVPPVP  60
AASKKTVIAN LNKSLLARST DPESGPTFTT RQQQIGFCPR KHRPVQKPVW QSGEKYTLTE  120
FEVKAKNFEK IYLKKYAKKG LNALEMETVY WNATVDKPFQ VEYANDMPGS AFVAQKGCGK  180
KNESTITVGE TEWNMRRVSR ENLSLLRFMK EEIPGVTSPM VYVAMMFSWF AWHVEDHDLH  240
SLNYLHMGAG KTWYGVPREA AVAFEEVIRE HGYGGEINPL VTFATLGEKT TVMSPEVLLS  300
AGVPCCRLVQ NAGEFVVTFP RAYHSGFSHG FNCGEAANIA TPEWLRFAKE AAIRRAAINC  360
PPMVSHFQLL YDLALSLCSG VPKSIAMGPR SSRLKDRKKG EGEMLIKELF LQDMMQNNDM  420
LHSLGKGSSI VLLPQNSLSH SIYNNTSSGF QSTAKSRLFP SLCSPDLELK TASYDARDEF  480
LLDRKHGIKQ PRGHAVNRKS VSSLCSSSEV PSMAPCAEQI DSEIKRASQH EQGLFSCVTC  540
GILCFACAAI VQPTEAAAHY LMSADCSKFS YWGTGDDDHN HTRHAKSPNT NLGSGLVLRK  600
KHGPSDVPIS ADQIRSVNGE SVGVVSNSKA HKEPSSLGLL ALTYGNSSDS EEEETEADLP  660
VDGCGTSKSD SPEDGHACDN IDSKLNCRKE MSSQISDSNA MFGPPIAKCN GGDPQSSNCS  720
DEFPTDNCTV VESNSCTHRS RHRTKSRHDT SNSLTHKTEA TVSTGLTPLE DKNTPFPARS  780
DEDSYRLHVF CLQHALQVEK RLSQIGGANV FLVCHPDFPK LESQAKKVAE ELESDWLWSE  840
ISFREATEED EEIMRLALES ENAIHGNGDW AVKMGINLFF SANLSRSPLY SKQMHFNFVI  900
YSAFGRSSPI DSSAALDELE GKCVGRQKKI VVAGKWCGKV WMSSQAHPLL LNKDSQEQEE  960
ESEFTAWIKP NLKSERLSQS SQAAGVASAI CKTSRKRKNN AENSSHVKEK SLEAGKMDEP  1020
SIGFPLSNCN KVIKRKRGSR RLKEENPESE DLDESSEEIQ LSNSCNQIKK RHGTKLLKKD  1080
TFEADENLDA SSEDFPLSNS WKQIKSKRGA RKTNKETPEP LKSKKRSKQQ ANSLVDDDEL  1140
EGGPSTRLRK RTTKACKASG PRSTNAKPVL KKQQKDIKTK KVPPVKVPSK AKLKDEEAEY  1200
ACDMEGCTMS FGSKQELALH KKNICPVKGC GKKFFSHKYL VQHRRVHMDD RPLKCPWKGC  1260
KMTFKWAWAR TEHIRVHTGA RPYVCTEAGC GQTFRFVSDF SRHKRKTGHS PKKARG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-76163778353Transcription factor jumonji (Jmj) family protein
6ip4_A1e-76163778353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110331042KRKRGSRRLK
210681078KKRHGTKLLKK
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_011072922.1
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)
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]