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 Bostr.18473s0108.1.p
Organism
Boechera stricta
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Boechereae; Boechera
Family C2H2
Protein Properties Length: 135aa    MW: 15676.2 Da    PI: 10.2303
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Bostr.18473s0108.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.60.000887194223
                          EET..TTTEEESSHHHHHHHHHHT CS
               zf-C2H2  2 kCp..dCgksFsrksnLkrHirtH 23
                          kCp   C+++F+   + + Hir+H
  Bostr.18473s0108.1.p 71 KCPwkGCKMTFKWAWSRTEHIRVH 94
                          79********************99 PP
2zf-C2H2163.3e-05100126123
                           EEET..TTTEEESSHHHHHHHHHH..T CS
               zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt..H 23 
                           y+C    Cg++F+  s++ rH r+  H
  Bostr.18473s0108.1.p 100 YVCAepGCGQTFRFVSDFSRHKRKtgH 126
                           899999*****************9777 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.0E-151960IPR003349JmjN domain
PROSITE profilePS5118313.8832061IPR003349JmjN domain
PfamPF023753.5E-152154IPR003349JmjN domain
SuperFamilySSF576674.75E-1555105No hitNo description
Gene3DG3DSA:3.30.160.604.3E-106893IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00157094IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.9287099IPR007087Zinc finger, C2H2
PROSITE patternPS0002807294IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.7E-1194123IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576679.18E-598122No hitNo description
SMARTSM003550.62100126IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.032100131IPR007087Zinc finger, C2H2
PROSITE patternPS000280102126IPR007087Zinc 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: 135 aa     Download sequence    Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPYLVQH  60
QRVHSDDRPL KCPWKGCKMT FKWAWSRTEH IRVHTGARPY VCAEPGCGQT FRFVSDFSRH  120
KRKTGHSVKK TKKR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A5e-535613462140Lysine-specific demethylase REF6
6a58_A5e-535613462140Lysine-specific demethylase REF6
6a59_A5e-535613462140Lysine-specific demethylase REF6
Search in ModeBase
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
PlantRegMapBostr.18473s0108.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAL0496594e-99AL049659.2 Arabidopsis thaliana DNA chromosome 3, BAC clone T29H11.
GenBankAY6644994e-99AY664499.1 Arabidopsis thaliana relative of early flowering 6 (REF6) mRNA, complete cds.
GenBankCP0026864e-99CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002875902.12e-50lysine-specific demethylase REF6 isoform X2
RefseqXP_010503472.12e-50PREDICTED: lysine-specific demethylase REF6-like
SwissprotQ9STM36e-50REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLD7LRW54e-49D7LRW5_ARALL; Uncharacterized protein
STRINGBostr.18473s0108.1.p2e-96(Boechera stricta)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.12e-52relative 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]