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 AA96G00099
Organism
Aethionema arabicum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Aethionemeae; Aethionema
Family C2H2
Protein Properties Length: 1327aa    MW: 149880 Da    PI: 7.458
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AA96G00099genomeVEGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H214.69.4e-0512101235123
                  EEET..TTTEEESSHHHHHHHHHH.T CS
     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                  y+C    Cg+sF++k +L  H ++ +
  AA96G00099 1210 YVCDmeGCGMSFRSKKELALHKKNiC 1235
                  99*******************99866 PP
2zf-C2H214.79e-0512351257323
                  ET..TTTEEESSHHHHHHHHHHT CS
     zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                  Cp  dCgk F ++ +L++H r+H
  AA96G00099 1235 CPvkDCGKKFFSHKYLVQHRRVH 1257
                  9999*****************99 PP
3zf-C2H212.70.0003912931319123
                  EEET..TTTEEESSHHHHHHHHHH..T CS
     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                  y+C+   Cg++F+  s++ rH r+  H
  AA96G00099 1293 YVCGepGCGQTFRFVSDFSRHKRKtgH 1319
                  89********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005458.1E-171960IPR003349JmjN domain
PROSITE profilePS5118314.7282061IPR003349JmjN domain
PfamPF023758.1E-152154IPR003349JmjN domain
SuperFamilySSF511973.84E-28115177No hitNo description
SMARTSM005584.0E-52197366IPR003347JmjC domain
PROSITE profilePS5118434.029200366IPR003347JmjC domain
SuperFamilySSF511973.84E-28215385No hitNo description
PfamPF023737.7E-38230349IPR003347JmjC domain
SMARTSM003556.312101232IPR015880Zinc finger, C2H2-like
SMARTSM003550.008412331257IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.73612331262IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.605.1E-512341256IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012351257IPR007087Zinc finger, C2H2
SuperFamilySSF576671.98E-912491291No hitNo description
Gene3DG3DSA:3.30.160.609.4E-612571270IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.46812631292IPR007087Zinc finger, C2H2
SMARTSM003550.001112631287IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012651287IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.3E-412711285IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.43E-812811315No hitNo description
Gene3DG3DSA:3.30.160.604.4E-912861316IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.5412931319IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.90712931324IPR007087Zinc finger, C2H2
PROSITE patternPS00028012951319IPR007087Zinc 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:0040010Biological Processpositive regulation of growth rate
GO:0045815Biological Processpositive regulation of gene expression, epigenetic
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
GO:0071558Molecular Functionhistone demethylase activity (H3-K27 specific)
Sequence ? help Back to Top
Protein Sequence    Length: 1327 aa     Download sequence    Send to blast
MAVSEQSQDV FPWLKSLPLA PEFRPTLSEF QDPIAYIFKI EEEASKYGIC KIVPPVAVSS  60
KKSAISNLNR SLVARAASRV CKGGACDYDN GPTFTTRQQQ IGFCPRKQRP VQRPVWQSGE  120
HYSFGEFEAK AKNFERNYLK KSGKKSQLSP LEIETLYWRA TVDKPFSVEY ANDMPGSAFI  180
PLSTAAARRR ESGDGGTVGE TNWNMRAVAR ADGSLLKFMK EEIPGVTSPM VYIAMMFSWF  240
AWHVEDHDLH SLNYLHMGAG KTWYGVPKDA AAAFEEVVRV HGYGEELNPL VTFSTLGEKT  300
TVMSPEVFVK AGIPCCRLVQ NPGEFVVTFP RAYHSGFSHG FNCGEASNIA TPEWLKMAKD  360
AAIRRAAIKY PPMVSHLQLL YDFALALGSK VSTSMNTKPR SSRLKDKKRS EGERLTKELF  420
VRNVIHNNQL LHSLGKGSPV ALLPLSSSDI SVCSELRIGA QLGTNQEKIG EFNKDVMKSE  480
DLSSDMIGLS NGYTDSVSVK EKFTSLCEKS RSYKTEENLD RGVGLSDQRL FSCVTCGILS  540
YDCVAIVQPK EGAARYLMSA DCSFFNDWSG SSNLIQDSEG KEKRDNESLY NVKIGDERVA  600
TTFLTNSRKE DGALGLLASA YGDSSDSEDE NKALSVDVCA VSCDIELKQA RDCGNSDGFV  660
EVSHGSSSYS TISCKNTSVL EIGLPFVSRS DDDSSRLHVF CLEHAAEVEQ QLRPIGGIHL  720
TLLCHPEYPR IEAEAKSVAE ELGISHEWND TEFRNVNRED EERIQKALNN VEAKTGNSDW  780
AVKLGINLSY SAVLSRSPLY SKQMPYNSVI YNAFGRNSST NSPANPEGSS RRSSRQRKFV  840
VGKWCGKVWM SHQVHPFMLE EDLEEEEPEK PEKSLHLRAV LDEEDTEKKR PCNIFRNSVT  900
MVAKKYSRKR KMRAKTSTRK KVLKIENGVS DDTSEDHSYK QQWRASGNEE EDVYFETGNT  960
VSGDSYDQQL KNFRRNKRSS CRDQEIESDD EVSDRSLGEE YAVRECAASE SSMENSFQLY  1020
KEKQSINNKK AFGNSIYDQD QEDETLYRSQ SKGIPRSKRT KVFRNPISYD SEENGSFTRS  1080
IKQIRQAGNE YDSADEEDDR EGRDSPQDRD FIGTTKRVCK SRQTRANRKT KAETIQSLEE  1140
IKGRSFQKNQ ETDSCIDGPS TRLRMRKQKP LRGLEIKPRR IAVSEEEVEE EEEEVEEEED  1200
DIEEGESSGY VCDMEGCGMS FRSKKELALH KKNICPVKDC GKKFFSHKYL VQHRRVHLDD  1260
RPLKCPWKGC KRTFKWAWAR TEHIRVHTGA RPYVCGEPGC GQTFRFVSDF SRHKRKTGHS  1320
VKKTKKK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A3e-7594324387Transcription factor jumonji (Jmj) family protein
6ip4_A3e-7594324387Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1906911SRKRKM
2908920KRKMRAKTSTRKK
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
PlantRegMapAA96G00099
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_006404260.10.0lysine-specific demethylase REF6
RefseqXP_024013589.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A1J3JIY40.0A0A1J3JIY4_NOCCA; Lysine-specific demethylase REF6
STRINGXP_006404260.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
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]