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 Prupe.5G159200.1.p
Organism
Prunus persica
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: 1487aa    MW: 165801 Da    PI: 8.5796
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Prupe.5G159200.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2130.0003113951417323
                          ET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                          Cp   Cgk F ++ +L++H r+H
  Prupe.5G159200.1.p 1395 CPvkGCGKKFFSHKYLVQHRRVH 1417
                          9999*****************99 PP
2zf-C2H211.80.0007214531479123
                          EEET..TTTEEESSHHHHHHHHHH..T CS
             zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                          y+C    Cg++F+  s++ rH r+  H
  Prupe.5G159200.1.p 1453 YVCAepGCGQTFRFVSDFSRHKRKtgH 1479
                          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
SuperFamilySSF511976.87E-25212383No hitNo description
PfamPF023736.4E-36231350IPR003347JmjC domain
SMARTSM003554713701392IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.15213931422IPR007087Zinc finger, C2H2
SMARTSM003550.004513931417IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.9E-713941416IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028013951417IPR007087Zinc finger, C2H2
SuperFamilySSF576671.61E-914091451No hitNo description
Gene3DG3DSA:3.30.160.605.2E-1014171445IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.63714231452IPR007087Zinc finger, C2H2
SMARTSM003550.001714231447IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014251447IPR007087Zinc finger, C2H2
SuperFamilySSF576673.64E-814411475No hitNo description
Gene3DG3DSA:3.30.160.602.2E-914461476IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.6214531479IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.46814531484IPR007087Zinc finger, C2H2
PROSITE patternPS00028014551479IPR007087Zinc 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: 1487 aa     Download sequence    Send to blast
MSASGLAAEP NQEVFSWLKT LPVAPEYHPT WAEFQDPIAY IFKIEKEASK YGICKIVPPV  60
PPSPKKTAIA NLNRSLAARA GPSGAPGTKS QPTFTTRQQQ IGFCPRKPRP VNRPVWQSGE  120
YYTFQQFEAK AKSFEKTYLR KCNKKGGLSP LDIETLYWKA TVDKPFSVEY ANDMPGSAFV  180
PVSARKSSTS 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
KSSGSDSDGL LIDRQHGIKQ VKGGYSVKGK LASLCESNRL PSLSGNNDAH ALNSKRLNMN  540
IERESNVEGE GLSDQRLFSC VTCGILSFAC VAIIQPTEAA ARYLMSADRS FFSDWVVGSG  600
LAGEVFQVAN EDPITSKDDP CTGLVENNAP AGLYDVPVQS ADYQIQRGDQ SNKPVSNTEM  660
QRDTSALGLL ALNYGNSSDS EEDQLAPDVP VCCDETNTTN CSFESRYDYQ SASPSPLRDS  720
YGGTTEAHSP PSPGFDCGNE LPLQSPDHYA RDGRKIANFK DSSYQNFDFS ADFKNNSAST  780
KTNGLVGTSM DPMKLSHSCS PDAHRPQTTE LSKVTLPIET TNTAFPPGCD EDSSRMHVFC  840
LEHAIEVEQQ LRSIGGVHIF LLCHPDYPRI EDEAKLMAEE LGISYLWNET TFRDATEEDE  900
KRIQSALDSE EAIAGNGDWA VKLGINLFYS ASLSRSHLYS KQMAYNSVIY NAFGRSSPAS  960
SPTRTDVYGR RSGKQKKVVA GKWCGKVWMS NQVHPYLAKR DPEEEEEVVE EEHRSFHAWA  1020
MPDEKLEGQP ESTRKTENTL VTKKYARKRK MTAETGTTKK VKCLEKEDAV SDYSVDDNSH  1080
QQQRRFPKSK QAEYIESGPT KKAKFVQTEF TLSDDSMQDD SHQPDGRNFR CEQANYIEGN  1140
DVSDDSVGVE SHQQHRRSAK SKQAKHMERD VVSDDSVEGS SRQQHGRVLR SKTAKGETDN  1200
FHKASSHQER GSISKSKQAR FIERDDAAVG ETDNFLQQHK RILRSKQTQQ ETLQKMRRET  1260
PRQVKQGTAL LVKQGTRTLR KQQTGQQMKQ QTPRLRNNQS EQNFDLYADE GAEGGPSTRL  1320
RKRAPKPIKV SGTKPKEQQQ TARKKAKNVS AVKSQAGQND AKLREEEAEF SCDIDGCTMS  1380
LGSKQELALH KRNICPVKGC GKKFFSHKYL VQHRRVHTDD RPLRCPWKGC KMTFKWAWAR  1440
TEHIRVHTGA RPYVCAEPGC GQTFRFVSDF SRHKRKTGHS AKKSRG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-75173888353Transcription factor jumonji (Jmj) family protein
6ip4_A1e-75173888353Arabidopsis JMJ13
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}.
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
PlantRegMapPrupe.5G159200.1.p
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_020419346.10.0lysine-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]