PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID PK12630.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Cannabaceae; Cannabis
Family C2H2
Protein Properties Length: 1482aa    MW: 165652 Da    PI: 8.3787
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PK12630.1genomeCCBRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.90.0003313921414323
                 ET..TTTEEESSHHHHHHHHHHT CS
    zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                 Cp   Cgk F ++ +L++H r+H
  PK12630.1 1392 CPvkGCGKKFFSHKYLVQHRRVH 1414
                 9999*****************99 PP

2zf-C2H211.80.0007214501476123
                 EEET..TTTEEESSHHHHHHHHHH..T CS
    zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                 y+C    Cg++F+  s++ rH r+  H
  PK12630.1 1450 YVCAepGCGQTFRFVSDFSRHKRKtgH 1476
                 899999****************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005457.5E-182364IPR003349JmjN domain
PROSITE profilePS5118314.882465IPR003349JmjN domain
PfamPF023753.7E-142558IPR003349JmjN domain
SMARTSM005587.1E-50196365IPR003347JmjC domain
PROSITE profilePS5118432.126199365IPR003347JmjC domain
SuperFamilySSF511972.06E-25210366No hitNo description
PfamPF023735.5E-37229348IPR003347JmjC domain
SMARTSM003552813671389IPR015880Zinc finger, C2H2-like
SMARTSM003550.004513901414IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.44513901419IPR007087Zinc finger, C2H2
SuperFamilySSF576679.34E-613911426No hitNo description
Gene3DG3DSA:3.30.160.601.2E-513921413IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028013921414IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.605.8E-914141442IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.63714201449IPR007087Zinc finger, C2H2
SMARTSM003550.001714201444IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014221444IPR007087Zinc finger, C2H2
SuperFamilySSF576672.81E-914301474No hitNo description
Gene3DG3DSA:3.30.160.602.3E-914431473IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.6214501476IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.03214501481IPR007087Zinc finger, C2H2
PROSITE patternPS00028014521476IPR007087Zinc 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: 1482 aa     Download sequence    Send to blast
MAASTLGSDP SPEVFSWLKT LPLAPEYHPT LAEFQDPISY IFKIEKEASK YGICKIIPPV  60
SPSPKKTVIA NLNKSLAARA GYSEGSNPKT PPTFTTRQQQ IGFCPRKPRP VQRPVWQSGE  120
QYTFQEFETK AKGFEKGFLK KCGKKGGGLS PLEIETLYWK ATVDKPFSVE YANDMPGSAF  180
VPVNAKKSRE AGESVTLGET AWNMRAVSRS KGSLLRFMKE EIPGVTSPMV YVAMLFSWFA  240
WHVEDHDLHS LNYLHMGASK TWYGVPKEAA VAFEEVIRVH GYGAEINPLV TFSILGEKTT  300
VMSPEVFIKE GVPCCRLVQN AGEFVVTFPR AYHTGFSHGF NCAEAANIAT PEWLRVANDA  360
AIRRASINYP PMVSHFQLLY DLALALCSRI PLSIGSEPRS SRLKDKRKGE GETVVKELFV  420
QDVLKNNDLL HVLGKGSPIV LLPRTSSDIP LCSKLRVGSH LRSNTSLSIE EMKSSRSLIS  480
DDLMVDRKQE VDQVKEFYPV KGKLASLCEG SWVPSRGNKR TSGSNFKTPI KSVEVKNNVD  540
SDRLSEQRLF SCVTCGILSF ACVAIVQPKD PAARYLMAAD CSFFNDWVVN AGVASNVFPI  600
SNVDQTESKQ NNYTAWADNC APDSYDGPVP SISNQVQMED QNNEVLSNSE AHEATSALGL  660
LALHYGNSSD SEEDQVREDD SIYENETNME NCSPESKYRC ESSGLSFQNS LSDAAGDDGR  720
SPQELDLGEE RASQNADFHK ENGHNRDDVK YSNRQNVGCS VDASNNVAST ETNCLVGKIR  780
DPMIVSQTCS ADTYDAEATR FCKGIVPMKN EGVPLAPLSD EDSSRMHVFC LEHAVEVEQQ  840
LRQIGGVHIL LLCHPDYPKI ETEAKSIAEE LGINCALNDT TFRDATKDDQ EKIQSALDSE  900
DAMPKNGDWA VKLGINLFYS ANLSRSPLYS KQMPYNSVIY NAFGRTSPTS SSVRSDGFGR  960
RSVKKKVVAG KWCGKVWMSN QVHPLLVKRN PEDEEERGIL AWATPDENLD RNHDTPHRNS  1020
NTMVAKKYVR KRKMKVGNES IKKAKCIKGE DIVSENSMDD DSHEPHRRPF GNNQATRIGG  1080
GSTKKGKQHI QREDAVSDDS MYVSLKQCKR TLRTKVATSV ETDDIVSDDS LGVISNYRNR  1140
KNPRSEKAKH VRDAGIQDVV SDDSLDFESN QRGGRIPKSK QAKFMEEEDS ASDDLPSTNL  1200
YKQQTRIYKS KYAKSIERED DVSDEPVEDY ACDEDKRVLR SKPTKSPMQP KMKQGTGRNV  1260
RQPSSQPVKQ GTRQIMKKET QKTKLHTPRL RNSQCDQDTS HICDDEEEEG GPSTRLRKRT  1320
PKPQKTTGTK KKEQQQQTSN KKAKNVSAGK AQAGRSDTKL KDEEAEYVCD VEGCTMSFGV  1380
KHELVLHKRN ICPVKGCGKK FFSHKYLVQH RRVHMDDRPL RCPWKGCKMT FKWAWARTEH  1440
IRVHTGARPY VCAEPGCGQT FRFVSDFSRH KRKTGHSTKK GR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A7e-76173868353Transcription factor jumonji (Jmj) family protein
6ip4_A7e-76173868353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1959965RRSVKKK
210261032KYVRKRK
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
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010101942.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2P5EIB20.0A0A2P5EIB2_TREOI; TFIIH C1-like domain containing protein
STRINGXP_010101942.10.0(Morus notabilis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF56483250
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]