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 Rsa1.0_09451.1_g00001.1
Organism
Raphanus sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family C2H2
Protein Properties Length: 1311aa    MW: 146216 Da    PI: 7.442
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_09451.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.20.0005511941219123
                               EEET..TTTEEESSHHHHHHHHHH.T CS
                  zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                               ykC    C++sFs+  +L  H r+ +
  Rsa1.0_09451.1_g00001.1 1194 YKCDieGCTMSFSSEKQLSMHKRNiC 1219
                               99********************9877 PP
2zf-C2H214.97.6e-0512191241323
                               ET..TTTEEESSHHHHHHHHHHT CS
                  zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                               Cp   CgksF ++ +L++H r+H
  Rsa1.0_09451.1_g00001.1 1219 CPvkGCGKSFFSHKYLVQHRRVH 1241
                               9999*****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-161758IPR003349JmjN domain
PROSITE profilePS5118313.6891859IPR003349JmjN domain
PfamPF023757.4E-141952IPR003349JmjN domain
SuperFamilySSF511971.43E-26125176No hitNo description
SMARTSM005581.4E-53198367IPR003347JmjC domain
PROSITE profilePS5118434.235201367IPR003347JmjC domain
SuperFamilySSF511971.43E-26216382No hitNo description
PfamPF023733.8E-38231350IPR003347JmjC domain
Gene3DG3DSA:3.30.160.606.8E-411931216IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003557.111941216IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.21412171246IPR007087Zinc finger, C2H2
SMARTSM003550.002712171241IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.2E-612181245IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012191241IPR007087Zinc finger, C2H2
SuperFamilySSF576673.02E-1012331275No hitNo description
Gene3DG3DSA:3.30.160.608.1E-1012461270IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.80112471276IPR007087Zinc finger, C2H2
SMARTSM003550.001512471271IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012491271IPR007087Zinc finger, C2H2
SuperFamilySSF576671.34E-812651299No hitNo description
Gene3DG3DSA:3.30.160.601.9E-912711299IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.15712771308IPR007087Zinc finger, C2H2
SMARTSM003551.212771303IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012791303IPR007087Zinc 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: 1311 aa     Download sequence    Send to blast
MSEQSTDVFP WLKSLPVAPE FRPTLAEFQD PIAYIFKIEE EASRYGICKI LPPLPPPSKK  60
TTVSNLNRSL AARASAHDGA CDYDGSPAFA TRQQQVGFCP RRQRPVQRPV WQSGERYSFG  120
EFEAKAKTFE KSYLKRCCGG GRKSQQLSAL EIETLYWRAT VDKPFTVEYA NDMPGSAFIP  180
LSLAAARRRE YGGSDGGTVG ESAWNMRAMA RAEGSLLRFM KEEIPGVTSP MVYVAMMFSW  240
FAWHVEDHDL HSLNYLHMGA GKTWYGVPKD AALAFEEVVR DHGYGGELNP LVTFSTLGEK  300
TTVMSPEVFV KAGIPCCRLV QNPGEFVVTF PRAYHSGFSH GFNCGEASNI ATPEWLRVAK  360
EAAIRRAAIS YPPMVSHLQL LYDYALALGS RVPASIHAKP RSSRLKDKKR SEGEKLSKEL  420
FAQNVIHNNE LFCSLGKGSP VALLPQSSSD VSVCSDLRIG SHLSANQEKP IQPKSEDFSP  480
ESSTACLNSG FKETVSVKEK FTSLCGRNIN QETMPEAERK ENDGAVGLSD QRLFSCVTCG  540
IICFDCVAIV QPKEAAARYL SSADFSFFSD WTVSSGSANP GQDERSLVVE PHSQSMGKRN  600
VGCIYSAPVQ STDHSVMKGD QRTSTASGAL GLLASAYGDS SDSEEENHKG IDAGISQNGA  660
SSYEAPAFGT DGNEEATDGR TSDHSSQRLP CGKGVGVAEG PNGGSASVLE VTLPFVSSSE  720
DDSSRLHVFC LEHAAEVEQQ LRPFGGVNIM LLCHPEYPRI EAEGKVIAEE LGVNHEWNDT  780
EFRNVTREDE ETIQAALVNV EAKAGNSDWT VKLSINLSYS AILSRSPLYS KQMPYNSVIY  840
NMFGRSSPST SSPTQHQVAG KRCSRQRKYV VGKWCGKVWM SHQVHPFLLQ EDLEGEESDV  900
SGERLLPCNV SRDATTMFGR KYSRKRKMRA KAVPRKKLTS FKREDGVSDD TSEDHSYKQQ  960
WRRAFGNEEE MSDDSSNPMS DHLKGIRRDK GVREFESDDE VSDRSLGEEY AARECADSDS  1020
SMDRYALEDS VYDVHNDDSI YRHPRSKRAK VIRIPVYQQR GNIQASRIGG DYDSEDDSVE  1080
EQEGFSTRKR QTRSTAKRKV KTEIVESPRD TRGRRTLQQS GYRKKIQDLD PYMEGPSTRL  1140
RVRILKPSRV SSETKPKRGS SNASFSRGLS EEELEEDGDE EEEEEERPAA ASAYKCDIEG  1200
CTMSFSSEKQ LSMHKRNICP VKGCGKSFFS HKYLVQHRRV HSDDRPLKCP WKGCKMTFKW  1260
AWSRTEHIRV HTGERPYHCA EPGCGQTFRF VSDFSRHKKK TGHSAKKTKK R
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-7563903355Transcription factor jumonji (Jmj) family protein
6ip4_A2e-7563903355Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1922927SRKRKM
2924936KRKMRAKAVPRKK
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
PlantRegMapRsa1.0_09451.1_g00001.1
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_018458318.10.0PREDICTED: lysine-specific demethylase REF6-like isoform X2
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLV4M0K30.0V4M0K3_EUTSA; Uncharacterized protein
STRINGXP_006404260.10.0(Eutrema salsugineum)
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]