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 Achn274201
Organism
Actinidia chinensis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; Ericales; Actinidiaceae; Actinidia
Family C2H2
Protein Properties Length: 1065aa    MW: 117927 Da    PI: 8.8503
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Achn274201genomeIKGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H210.70.0017977995523
                 TTTEEESSHHHHHHHHHHT CS
     zf-C2H2   5 dCgksFsrksnLkrHirtH 23 
                  Cgk F ++ +L++H r+H
  Achn274201 977 GCGKKFFSHKYLVQHRRVH 995
                 7****************99 PP
2zf-C2H212.30.0005210311057123
                  EEET..TTTEEESSHHHHHHHHHH..T CS
     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                  y+C    Cg++F+  s++ rH r+  H
  Achn274201 1031 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1057
                  89********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005455.9E-132667IPR003349JmjN domain
PROSITE profilePS5118313.7862768IPR003349JmjN domain
PfamPF023757.7E-142861IPR003349JmjN domain
PROSITE profilePS5118432.57196365IPR003347JmjC domain
SMARTSM005581.0E-47196365IPR003347JmjC domain
SuperFamilySSF511977.69E-26210370No hitNo description
PfamPF023735.0E-36230348IPR003347JmjC domain
SMARTSM0035526974995IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.3E-49781001IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.4719781000IPR007087Zinc finger, C2H2
SuperFamilySSF576671.14E-99871029No hitNo description
PROSITE profilePS5015710.82410011030IPR007087Zinc finger, C2H2
SMARTSM003550.003610011025IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.6E-810021025IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028010031025IPR007087Zinc finger, C2H2
SuperFamilySSF576673.24E-810191053No hitNo description
Gene3DG3DSA:3.30.160.601.8E-910261054IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.8510311057IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.03210311062IPR007087Zinc finger, C2H2
PROSITE patternPS00028010331057IPR007087Zinc 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: 1065 aa     Download sequence    Send to blast
MASSSAPVAA EQPTTEVFPW LKTLPLAPEY HPTLAEFEDP IAYIFKIETE ASKYGICKIV  60
PPVAAPTKKI AIANLNRSLL ARSTTANPKS PPTFTTRQQQ IGFCPRKHRP VQKPVWQSGE  120
NYTFPQFEAK AKSFERNYLK KFPKKGLSAL EVETLYWKAF GDKPFSVEYA NDMPGSAFAP  180
VSARKKGRET GEAVTNVGET AWNMRGVSRA KGSLLRFMKE EIPGVTSPMA YLAMMFSWFA  240
WHVEDHDLHS LNYMHMGAGK TWYGVPREAA VAFEEVIRVH GYGGEINPLV TLAILGEKTT  300
VMSPEVLVGA GIPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PGWLRVAKDA  360
AIRRAAINCP PMVSHFQLLY DLALSLCSRI PKSIDSEPRS SRLKHKRRGE GETLIKKLFA  420
EDVMKNNDLL HILAEGSSIV LLPHNSFDDS VYSNSRIASR FKGNSSFPLG LCNPEEEFKA  480
SEKFSSACDD QGLFSCVTCG ILSFACVAIV QPKDSAAHYL MSADCGIFND GDVVPRVTSD  540
GFTVAAGAAI LSRLDSRSGW VGKSTPDGLF DVPIQSADHI QTVDRSPELL SDTEIQKGTS  600
ALGLLALAYS SSDSEDEEVE ADIPLETHNI ASTESNSVGG RLTHQMKLST AASNDSPVAH  660
NALTSRSNTY VPMENTSMSF APKSGDDSYR PHVFCLQHAA EVEQQLRPIG GSHILLLCHP  720
DYPELEAEAK LVAEELAINY FWNDIAFREA TKEDEERIQT ALESEEGTHG NGDWAVKLGI  780
NLFYSANLGR SPLYSKQMPY NSIIYKAFGR TSLTNSPTKP KFHGKGSGRK KKIVVAGKWC  840
GKVWMSNQVH PLLVERDAEE GEDDNTSFRG WAKPEVKRER LSERARLAET NFEIKKIGKK  900
RKNTTQKEGG AIKKSKSAKV EDSSPQTQRS SDCNKSRFDS FIEDELEGGP STRLRKRTSK  960
LPAEDKLVLK KHTSIKGCGK KFFSHKYLVQ HRRVHMDDRP LKCPWKGCKM AFKWAWARTE  1020
HIRVHTGARP YVCAEEGCGQ TFRFVSDFSR HKRKTGHSTK KGRG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A3e-74153863353Transcription factor jumonji (Jmj) family protein
6ip4_A3e-74153863353Arabidopsis 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
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_009613169.10.0PREDICTED: lysine-specific demethylase REF6 isoform X2
RefseqXP_016435657.10.0PREDICTED: lysine-specific demethylase REF6-like isoform X2
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLF6GTM20.0F6GTM2_VITVI; Uncharacterized protein
STRINGVIT_17s0000g09980.t010.0(Vitis vinifera)
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]