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_009149819.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C2H2
Protein Properties Length: 1385aa    MW: 154692 Da    PI: 7.1782
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009149819.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.20.001212681293123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                      y+C    C++sFs+  +L  H r+ +
  XP_009149819.1 1268 YQCDmeGCTMSFSSEKQLSLHKRNiC 1293
                      99********************9877 PP
2zf-C2H215.16.8e-0512931315323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk F ++ +L++H+r+H
  XP_009149819.1 1293 CPvkGCGKNFFSHKYLVQHQRVH 1315
                      9999*****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.1E-171960IPR003349JmjN domain
PROSITE profilePS5118314.2842061IPR003349JmjN domain
PfamPF023751.7E-152154IPR003349JmjN domain
SMARTSM005581.7E-54198367IPR003347JmjC domain
PROSITE profilePS5118434.513201367IPR003347JmjC domain
SuperFamilySSF511971.24E-27213384No hitNo description
PfamPF023732.4E-37231350IPR003347JmjC domain
Gene3DG3DSA:3.30.160.600.00112671290IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003559.412681290IPR015880Zinc finger, C2H2-like
SMARTSM003550.0112911315IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.60912911320IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.1E-712921319IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012931315IPR007087Zinc finger, C2H2
SuperFamilySSF576676.91E-1113071349No hitNo description
Gene3DG3DSA:3.30.160.602.4E-1013201344IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001513211345IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.80113211350IPR007087Zinc finger, C2H2
PROSITE patternPS00028013231345IPR007087Zinc finger, C2H2
SuperFamilySSF576671.95E-813391373No hitNo description
Gene3DG3DSA:3.30.160.607.0E-1013451374IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003551.713511377IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.49213511382IPR007087Zinc finger, C2H2
PROSITE patternPS00028013531377IPR007087Zinc 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: 1385 aa     Download sequence    Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPMAYICKI EEEASRYGIC KIVPPVPPSS  60
KKTAINNLNR SLAARARARA RDGGKPDYDG GPTFTTRQQQ IGFCPRRQRP VQRPVWQSGE  120
RYTFDEFEFK AKNFEKSYLK KCGKKGSVSP LEVETLYWRA SVDKPFSVEY ANDMPGSAFV  180
PLSLAAARRR ESGGDCGTVG ETAWNMRAMA RAEGSLLKFM KEEIPGVTSP MVYIAMMFSW  240
FAWHVEDHDL HSLNYLHMGA GKTWYGVPKD AAMAFEEVVR VHGYGEELNP LVTFSTLGEK  300
TTVMSPEVFV RAGIPCCRLV QNPGDFVITF PGAYHSGFSH GFNFGEASNI ATPQWLRMAK  360
DAAIRRASIN YPPMVSHLQL LYDYALALGS RVPDSIHNKP RSSRLKDKKK SEGEKLTNEL  420
FVQNIIHNNE LLHSLGKGSP IALLPQSSSD VSVCSDVRIG SHLGANQGQT TLLIKSEDLS  480
SDSVMVSLSN GVKEKFTSLC ERNRDHLASK EDETQGTSTD VERRKNNGAV GLSDQRLFSC  540
VTCGVLSFDC VAIIQPKEAA ARYLMSADCS FLNDWTVASG SGNLGQDVVM PPSENTGKQD  600
VGDLYNAPVQ TPYHSTTKTV DQRTSSSSLT KESGALGLLA SAYGDSSDSE EEDHKGLDNP  660
VSDEVACVLE ASSFVTDGND EAGNGLSSAL NSQGLTCEKG KEVDVSHANL SKGGNASSVE  720
ITLPFIPRSD DDFSRLHVFC LEHAAEVEQR LHPIGGINIM LLCHPDYPRI EAEGKVVAKE  780
LGVNHEWNYT EFKNVTREDE ETIQAALANV EAKAGNSDWA VKLGINLSHS AILSRSPLYS  840
KQMPYNSVIY NVFGRTSPAT PQVSGIRSSR QRKYVAGKWC GKVWMSHQVH PFLLEEDFEG  900
EETERSHLRA ALDEDVTVHG NDSRDATTMF GRKYSRKRKA RGKAAPRKKL TSFKREAGVS  960
DDTSEDHSYK QQWRAYGDEE ESYFETGNEV SGDSSNQMSD QQQLKGVESD DDEVSERSLG  1020
QEYTVRREYA SSESSKENGF QVYREDQPMY GDNDMYRHPR GIPRSKRTKV FRDLVSYDSE  1080
DQQRERVFTS DAQTSRMDDE YDSEENSLEE QDFCSSGKRQ TRSIAKRKVK TKIVQSLGDT  1140
GGRTLLQSGS RKKMKELDSY MEGPSTRLRV RTPKPSRGSS ATKPKKTGKK GRNVSFSEVA  1200
SEEEVEENEE ESEEASTRIR VRTLKPPRRS LETKPKKTGK KGSNVSSLSG VASEEEVEED  1260
EQEECLPYQC DMEGCTMSFS SEKQLSLHKR NICPVKGCGK NFFSHKYLVQ HQRVHSDERP  1320
LKCPWKGCKM TFKWAWSRTE HIRVHTGERP YVCAEPGCSQ TFRFVSDFSR HKRKTGHSAK  1380
KIKKK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A7e-741265138520140Lysine-specific demethylase REF6
6a58_A7e-741265138520140Lysine-specific demethylase REF6
6a59_A7e-741265138520140Lysine-specific demethylase REF6
6ip0_A2e-7093904355Transcription factor jumonji (Jmj) family protein
6ip4_A2e-7093904355Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1936948KRKARGKAAPRKK
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
PlantRegMapXP_009149819.1
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_009149819.10.0PREDICTED: lysine-specific demethylase REF6 isoform X1
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A397YY330.0A0A397YY33_BRACM; Uncharacterized protein
TrEMBLM4DNH30.0M4DNH3_BRARP; Uncharacterized protein
STRINGBra018060.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
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]