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 evm_27.model.AmTr_v1.0_scaffold00049.175
Common NameAMTR_s00049p00181100, LOC18441992
Organism
Amborella trichopoda
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella
Family C2H2
Protein Properties Length: 1317aa    MW: 146343 Da    PI: 7.2612
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00049.175genomeTAGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.40.0002312871313123
                                                EEET..TTTEEESSHHHHHHHHHH..T CS
                                   zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                                                y+C+   Cg++F+  s++ rH r+  H
  evm_27.model.AmTr_v1.0_scaffold00049.175 1287 YVCKdnGCGRTFRFVSDFSRHKRKtgH 1313
                                                99********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005453.1E-181556IPR003349JmjN domain
PROSITE profilePS5118314.4091657IPR003349JmjN domain
PfamPF023752.4E-141750IPR003349JmjN domain
SuperFamilySSF511973.3E-26105143No hitNo description
SMARTSM005581.4E-47173342IPR003347JmjC domain
PROSITE profilePS5118434.029173342IPR003347JmjC domain
SuperFamilySSF511973.3E-26191341No hitNo description
PfamPF023731.1E-35206325IPR003347JmjC domain
SMARTSM003551112041226IPR015880Zinc finger, C2H2-like
SuperFamilySSF576675.4E-612261263No hitNo description
SMARTSM003550.04612271251IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.5712271256IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.1E-412281255IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012291251IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.9E-812561281IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.17712571286IPR007087Zinc finger, C2H2
SMARTSM003550.001412571281IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012591281IPR007087Zinc finger, C2H2
SuperFamilySSF576678.97E-1012671309No hitNo description
Gene3DG3DSA:3.30.160.602.4E-912821310IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.2312871313IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.59312871316IPR007087Zinc finger, C2H2
PROSITE patternPS00028012891313IPR007087Zinc 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: 1317 aa     Download sequence    Send to blast
MTDTEVLPWL KSLSLAPEYR PTMAEFQDPI AYIYKIEKEA SSYGICKIIP PLPPSPKKTA  60
IANLNHSLSA LSPSCTFSTR QQQIGFCPRK PRPSATVVQK PVWQSGETYT LEQFEAKAKA  120
FAKSRLKNPN SRPLAIETQF WKATADKPIT VEYANDMPGS AFGDPVEQGV RRVIGESEWN  180
MKVVSRAKGS VLRFMPEEIP GVTSPMVYVA MLFSWFAWHV EDHDLHSLNY LHLGSSKTWY  240
GVPRDAAFAF EEVIRAHGYG GQVNPLVAFA MLGEKTTVMS PQVLIDAGVP CCRLVQNAGE  300
FVVTFPRAYH SGFSHGFNCG EAANIATPEW LRVAKDAAIR RASINYPPMV SHIQLLHALA  360
LSFHSRIPSS ITVEPWSSRL KDKMKGEGEI VVKDLFLQNM IETNDLLHTL SEKGSMCLLL  420
PPSILCETSH VKSKTGLSSN NSEEMSESSN LALRHMTGFD PRKGKAYPLI EGKRVTSIKA  480
RFHKGNHGSY APINRNECLN DSTLSCDLQL DQGLLSCVTC GVLGFACMAV IQPSEAAARN  540
LQSGNCSFLS DQCGGSGLTS DAYPTAEGNA NDSDLNSCSG YTKTDERDDQ DDSQIYSTSH  600
QDCNPPLIKD EKDGQNAYPR TLEKSDPSTA DHNISSLALL ASAYGNASDS EEDEAIQHDI  660
TMHTNEVSPI DTSIACIGTQ QSMPVCAYLP PILRSKDELQ CGDSVLLCSS SPHQNEAANI  720
INHPITNSLS GNEVAAQTSS SFHITNKFSE NSSAKNNNNI PLSRTPNVYQ RRTELVHPDC  780
MPSNCNVPFE QLGCVSNGGP TENVNETAIV NCIDTVRNNR NNSEWQDIDK DSSRMHIFCL  840
EHAMEAEKQL QLMGGANILL LCHSDYPKIE EKAKSIAEEM GVIHSWNGIV FKEASLEDLE  900
RLRVVLEEED DETSHGNGDW AVKLGVNLYH TSNLSRSPLY SKQMPYNSVL YEVLGCNSPD  960
DSSPPGPRPR GRYARQKKIV VAGKWCGKVW MVNQVHPYLS NGKHLKEQHV VLTTKELEND  1020
SKPGERNLDP NQAQKSREDV SEPDEAGTSR DSDPEAVKAS GSLERVSSLD ASLKRKRFTK  1080
RRMSLRRVCS KRPKFCEWGA AGMEGIDPAS EEHDEIGKEP REGETPRSAM KKWNQLDVSP  1140
KGEADEGGPS TRLRQRPRKP QPTSNDETEV PYKRCVRKKR EKKIPESGNK EAREIKAPGD  1200
EDAYQCDIDG CSMGFGTKQE LVIHKRNQCA VKGCGKKFFS HKYLLQHRRV HLDDRPLKCP  1260
WKGCKMTFKW AWARTEHIRV HTGDRPYVCK DNGCGRTFRF VSDFSRHKRK TGHFGK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-8123651355Transcription factor jumonji (Jmj) family protein
6ip4_A1e-8123651355Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110751082KRFTKRRM
211761181RKKREK
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_006852278.10.0lysine-specific demethylase REF6
RefseqXP_020527617.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLW1Q0V70.0W1Q0V7_AMBTC; Uncharacterized protein
STRINGERN137450.0(Amborella trichopoda)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP44011217
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. Amborella Genome Project
    The Amborella genome and the evolution of flowering plants.
    Science, 2013. 342(6165): p. 1241089
    [PMID:24357323]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]