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_08195.1_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: 671aa    MW: 76401.4 Da    PI: 7.7504
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_08195.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.30.00052554579123
                              EEET..TTTEEESSHHHHHHHHHH.T CS
                  zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                              y+C    C++sFs+  +L  H r+ +
  Rsa1.0_08195.1_g00001.1 554 YQCDmeGCTMSFSSEKQLSLHKRNiC 579
                              99********************9877 PP
2zf-C2H216.23e-05579601323
                              ET..TTTEEESSHHHHHHHHHHT CS
                  zf-C2H2   3 Cp..dCgksFsrksnLkrHirtH 23 
                              Cp   Cgk F ++ +L++H+r+H
  Rsa1.0_08195.1_g00001.1 579 CPvkGCGKNFFSHKYLVQHQRVH 601
                              9999*****************99 PP
3zf-C2H2110.0014637663123
                              EEET..TTTEEESSHHHHHHHHHH..T CS
                  zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt..H 23 
                              y+C    C+++F+  s++ rH r+  H
  Rsa1.0_08195.1_g00001.1 637 YVCAepGCSQTFRFVSDFSRHKRKtgH 663
                              899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003559.4554576IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.173577606IPR007087Zinc finger, C2H2
SMARTSM003550.01577601IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.606.5E-7578605IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280579601IPR007087Zinc finger, C2H2
SuperFamilySSF576671.71E-10593634No hitNo description
Gene3DG3DSA:3.30.160.603.2E-10606630IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0015607631IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.801607636IPR007087Zinc finger, C2H2
PROSITE patternPS000280609631IPR007087Zinc finger, C2H2
SuperFamilySSF576677.9E-9625659No hitNo description
Gene3DG3DSA:3.30.160.603.2E-10631660IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.492637668IPR007087Zinc finger, C2H2
SMARTSM003551.7637663IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280639663IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 671 aa     Download sequence    Send to blast
HAAEVEQRLH PIGGINIMLL CHPDYPRIEA EGKIVAKELG VNHEWNDTEF KNVTREDEET  60
IEAALANVET KAGNSDWAVK LGINLSHSAI LSRSPLYSKQ MPYNSVIYNV FGRTSPATSS  120
PTRPQVSGIR SSRQRKYVAG KWCGKVWMSH QVHPFLLEED LEGEETERSH LRVAMDEDVT  180
VHGNDSRDAT TMFGRKYSRK RKARGKAAPR KKLTSFKKEA GVSDDTSEDH SYKQQWRAYG  240
DEEEESYFQT GNSVSGDSSN QTSDQQQRLK RIRGGDKGVK EFESDDDDDE VSERSLGREY  300
AVREYASSES SMENGFQVYR EKQPMYGGDD DDDDDDDNNY RHPGGVPRSK RTKVFRDLVS  360
YDSEENGVYQ QRERVFTSDA QTSRMGVEYD SEENSLEEQD FCSRGGKRKQ TRSIAKRKVK  420
TKIVQSLGDT LLQSGSGKKN QDLDSYMEGP STRLRVRTTK PSRGSSATKP KKTGKKGRNV  480
SFSGVASEEE VEDNEEEEEE SEEASTRIRV RHVKPARRSL ETKPKKSGKK GSNVTLASEE  540
NVEEEDEEEE CLGYQCDMEG CTMSFSSEKQ LSLHKRNICP VKGCGKNFFS HKYLVQHQRV  600
HSDDRPLKCP WKGCKMTFKW AWSRTEHIRV HTGERPYVCA EPGCSQTFRF VSDFSRHKRK  660
TGHSAKKIKK K
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A6e-7855167120140Lysine-specific demethylase REF6
6a58_A6e-7855167120140Lysine-specific demethylase REF6
6a59_A6e-7855167120140Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1199211KRKARGKAAPRKK
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_08195.1_g00001.1
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018439998.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A0D3DRD20.0A0A0D3DRD2_BRAOL; Uncharacterized protein
STRINGBo8g076910.10.0(Brassica oleracea)
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]