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_008239384.1
Organism
Prunus mume
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Amygdaleae; Prunus
Family C2H2
Protein Properties Length: 1485aa    MW: 165717 Da    PI: 8.6788
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_008239384.1genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2130.0003113941416323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk F ++ +L++H r+H
  XP_008239384.1 1394 CPvkGCGKKFFSHKYLVQHRRVH 1416
                      9999*****************99 PP
2zf-C2H211.80.0007214521478123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C    Cg++F+  s++ rH r+  H
  XP_008239384.1 1452 YVCAepGCGQTFRFVSDFSRHKRKtgH 1478
                      899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.8E-172364IPR003349JmjN domain
PROSITE profilePS5118314.6862465IPR003349JmjN domain
PfamPF023752.9E-152558IPR003349JmjN domain
SMARTSM005582.9E-49198367IPR003347JmjC domain
PROSITE profilePS5118432.372201367IPR003347JmjC domain
SuperFamilySSF511977.14E-25212383No hitNo description
PfamPF023736.4E-36231350IPR003347JmjC domain
SMARTSM003554713691391IPR015880Zinc finger, C2H2-like
SuperFamilySSF576671.16E-513901428No hitNo description
PROSITE profilePS5015712.44513921421IPR007087Zinc finger, C2H2
SMARTSM003550.004513921416IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.0E-513931415IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028013941416IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.0E-914161444IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.63714221451IPR007087Zinc finger, C2H2
SMARTSM003550.001714221446IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014241446IPR007087Zinc finger, C2H2
SuperFamilySSF576672.44E-914321476No hitNo description
Gene3DG3DSA:3.30.160.602.2E-914451475IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.46814521483IPR007087Zinc finger, C2H2
SMARTSM003550.6214521478IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014541478IPR007087Zinc 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: 1485 aa     Download sequence    Send to blast
MSASGLAAEP NQEVFSWLKT LPVAPEYHPT WAEFQDPIAY IFKIEKEASK YGICKIVPPV  60
PPSPKKTAIA NLNRSLAARA GPSGVPGTKS QPTFTTRQQQ IGFCPRKPRP VNRPVWQSGE  120
YYTFQQFEAK AKSFEKTYLR KCNKKGGLSP LDIETLYWKA TVDKPFSVEY ANDMPGSAFV  180
PLSARKSSTS RDAGDNVTLG ETAWNMRGVS RSKGSLLRFM KEEIPGVTSP MVYIAMLFSW  240
FAWHVEDHDL HSLNYLHMGA GKTWYGVPRE AAVAFEEVVR VQGYAGEINP LVTFSTLGQK  300
TTVMSPEVFI SSGIPCCRLV QNAGEFVVTF PRAYHTGFSH GFNCGEAANI ATPEWLRVAK  360
DAAIRRASIN YPPMVSHFQL LYDLALALCS RMPARICAEP RSSRLKDKRK GEGEAVVKEL  420
FVQNVIQNND LLHVLGKGSS IVLLPQSSSD LSFCSKLRVG SHLRVNPGFA NGLYDQREEM  480
KPSGSDSDGL MIDRQQGIKQ VKGGYSVKGK LASLSESNRL PSLSGNNDAH ALNSKRLNMS  540
IERESNVEGE GLSDQRLFSC VTCGILSFAC VAIIQPTEAA ARYLMSADRS FFSDWVGSGL  600
AGEVFQVANE DPITSKNDPC TGLVENNAPA GLYDVPVQSA DYQIQRGDQS NKPVSNTEMQ  660
RDTSALGLLA LNYGNSSDSE EDQLAPDVPV CCDETNTTNC SFESRYDYQS ASPSPLRDSY  720
GGTTEAHSPP SPGFDCGNEF PLRSPDHCAR DGRKIANFKD SSYQNFDFSA DCKNNSASTK  780
TNGLVGTSMD PMKLSHSCSP DAHRPQTTEL SKVTLPIETT NTAFPPGCDE DSSRMHVFCL  840
EHAIEVEQQL RSIGGVHIFL LCHPDYPRIE DEAKLMAEEL GISYLWNETT FRDATEEDEK  900
RIQSALDSEE AIAGNGDWAV KLGINLFYSA SLSRSHLYSK QMAYNSVIYN AFGRSSPASS  960
PTRTDVYGRR SGKQKKVVAG KWCGKVWMSN QVHPYLAKRD PEEEEEVVEE EHRSFHAWAM  1020
PDEKLEGQPE STRKTENTLV TKKYARKRKM TAETGTTKKV KCLEKEDAVS DYSVDDNSHQ  1080
QQRRFPKSKQ AEYIESGPTK KAKFVQTEFT LSDDSMQDDS HQPDGRNFRC EQANYIEGND  1140
VSDDSVGVES HQQHRRSAKS KQAKHMERDV VSDDSVEGSS RRQHGRVLRS KTAKGETDNF  1200
HKASSHQERG SISKSKQARF IERDDAAVGE TDNFLQQHKR ILRSKQTQQE TLQKMRRETP  1260
RQVKQGTAPL VKQGTRTLRK QQTAQQMKQQ TPRLRNNQSE QNFDLYADEG AEGGPSTRLR  1320
KRAPKPIKVS GTKPKEQQQT ARKKAKNVSA VKAQAGQNDA KLREEEAEFS CDIDGCTMSL  1380
GSKQELALHK RNICPVKGCG KKFFSHKYLV QHRRVHMDDR PLRCPWKGCK MTFKWAWART  1440
EHIRVHTGAR PYVCAEPGCG QTFRFVSDFS RHKRKTGHSA KKSRG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-75173888353Transcription factor jumonji (Jmj) family protein
6ip4_A2e-75173888353Arabidopsis 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
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_008239384.1
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_008239384.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A251P9670.0A0A251P967_PRUPE; Uncharacterized protein
STRINGXP_008239384.10.0(Prunus mume)
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]