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_013604508.1
Organism
Brassica oleracea
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: 1376aa    MW: 153430 Da    PI: 7.1694
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013604508.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.20.001212591284123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                      y+C    C++sFs+  +L  H r+ +
  XP_013604508.1 1259 YQCDmeGCTMSFSSEKQLSLHKRNiC 1284
                      99********************9877 PP
2zf-C2H216.42.5e-0512841306323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk+F ++ +L++H+r+H
  XP_013604508.1 1284 CPvkGCGKTFFSHKYLVQHQRVH 1306
                      9999*****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005458.3E-171960IPR003349JmjN domain
PROSITE profilePS5118314.2432061IPR003349JmjN domain
PfamPF023754.1E-152154IPR003349JmjN domain
SMARTSM005583.0E-53202371IPR003347JmjC domain
PROSITE profilePS5118433.783205371IPR003347JmjC domain
SuperFamilySSF511971.25E-27217388No hitNo description
PfamPF023731.8E-37235354IPR003347JmjC domain
Gene3DG3DSA:3.30.160.600.00112581281IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003559.412591281IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.33912821311IPR007087Zinc finger, C2H2
SMARTSM003550.001512821306IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.607.2E-712831310IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012841306IPR007087Zinc finger, C2H2
SuperFamilySSF576674.3E-1012981339No hitNo description
Gene3DG3DSA:3.30.160.609.4E-1013111335IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.80113121341IPR007087Zinc finger, C2H2
SMARTSM003550.001513121336IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013141336IPR007087Zinc finger, C2H2
SuperFamilySSF576672.43E-813301364No hitNo description
Gene3DG3DSA:3.30.160.601.3E-913361365IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.38813421373IPR007087Zinc finger, C2H2
SMARTSM003552.213421368IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013441368IPR007087Zinc 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: 1376 aa     Download sequence    Send to blast
MAVSEQSQDV FPWLKSLPVA PEFKPTLAEF QDPMAYICKI EEEASRYGIC KIVPPVPPSS  60
KKTAINNLNR SLAARARARA RDGNGNGGKS DYDDGPTFTT RQQQIGFCPR RQRPVQRPVW  120
QSGERYTFDE FEFKAKNFEK SYLKKCGKKG SVSPLEVETL YWRASVDKPF SVEYANDMPG  180
SAFVPLSLAA ARRRESGGDC GTVGETAWNM RAMARAEGSL LKFMKEEIPG VTSPMVYIAM  240
MFSWFAWHVE DHDLHSLNYL HMGAAKTWYG VPKDAAMAFE EVVRVHGYGE ELNPLVTFST  300
LGEKTTVMSP EVFVRAGIPC CRLVQNPGDF VITFPGAYHS GFSHGFNFGE ASNIATPQWL  360
RMAKDAAIRR ASINYPPMVS HLQLLYDYAL ALGSRVPDSI HNKPRSSRLK DKKKSEGEKL  420
TNELFVQNVI HNNELLHSLG KGSPIALLPQ SSSDVSVCSD VRIGSHLGAN QGQTTLLIKS  480
EDLSSDSVMA SLSNGVKEKF TSLCERNRAD ETQGTSTDGE KRKNNGAVGL SDQRLFSCVT  540
CGVLSFDCVA IIQPKEAAAR YLMSADCSSL NDWTVASGSA NLGQDVVMPP SGKQDVGDLY  600
NAPVQTPYHS TTKTVDQRTS SSSLTKENGA LGLLASAYGD SSDSEEEDHK GLDNPVSDEV  660
EASSFVTDGN DEAGNGLSSA LNSQGLTCEK GKEVDVSHAN LSKGGNTSSV EITLPFIPRS  720
DDDFSRLHVF CLEHAAEVEQ RLHPIGGINI MLLCHPDYPR IEAEGKVVAK ELGVNHEWND  780
TEFKNVTRED EETIQAALAN VEAKAGNSDW AVKLGINLSH SAILSRSPLY SKQMPYNSVI  840
YNVFGRTSPA TPQVSGIRSS RQRKYVAGKW CGKVWMSHQV HPFLLEEDLE GEETERSHLR  900
AALDEDVTVH GNDSRDATTM FGRKYSRKRK ARGKAAPRKK LTSFKREAGV SDDTTSEDHS  960
YKQQWRAYGD EEESYFETGN EVSGDSSNQM SDQQQLKVVE SDDDEVSERS LGQEYAVRRE  1020
YASSESSMEN GFQVYREDQP MYGDDDMYRH PRGIPRNKRT KVFRDLVSYD SEDQQRERVF  1080
TSDAQTSRMG DEYDSEENSL EEQDFCSSGK RQTRSIAKRK VKTKIVQSLG DTGGRTLLQS  1140
GSRKKMKELD SYMEGPSTRL RVRTPKPSRG SSATKPKKTG KKGRNVSFSE VASEEEVEEN  1200
EEESEEASTR IRVRTLKPPR RSLETKPKKT GKKGSNVSLS GVASEEEVEE NEQEECLPYQ  1260
CDMEGCTMSF SSEKQLSLHK RNICPVKGCG KTFFSHKYLV QHQRVHSDDR PLKCPWKGCK  1320
MTFKWAWSRT EHIRVHTGER PYICAEPGCS QTFRFVSDFS RHKRKTGHSA KKIKKK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A1e-731256137620140Lysine-specific demethylase REF6
6a58_A1e-731256137620140Lysine-specific demethylase REF6
6a59_A1e-731256137620140Lysine-specific demethylase REF6
6ip0_A6e-7093944355Transcription factor jumonji (Jmj) family protein
6ip4_A6e-7093944355Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1927939KRKARGKAAPRKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bol.107920.0leaf
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_013604508.1
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_013604508.10.0PREDICTED: lysine-specific demethylase REF6 isoform X2
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A0D3DRD20.0A0A0D3DRD2_BRAOL; Uncharacterized protein
STRINGBo8g076910.10.0(Brassica oleracea)
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]