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 Aqcoe3G132200.1.p
Organism
Aquilegia coerulea
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; stem eudicotyledons; Ranunculales; Ranunculaceae; Thalictroideae; Aquilegia
Family C2H2
Protein Properties Length: 1172aa    MW: 131232 Da    PI: 8.1871
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Aqcoe3G132200.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H214.40.0001110541079123
                         EEET..TTTEEESSHHHHHHHHHH.T CS
            zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                         y+C   +C+++F++k +Lk H r+ +
  Aqcoe3G132200.1.p 1054 YQCDieNCTMVFRSKQDLKLHKRNiC 1079
                         99********************9877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005586.0E-281160IPR003347JmjC domain
PROSITE profilePS5118427.8611187IPR003347JmjC domain
SuperFamilySSF511977.69E-2110143No hitNo description
PfamPF023732.0E-3226138IPR003347JmjC domain
Gene3DG3DSA:3.30.160.607.4E-410491076IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003558.610541076IPR015880Zinc finger, C2H2-like
SMARTSM003550.1410771101IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.26110771106IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.3E-410791100IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028010791101IPR007087Zinc finger, C2H2
SuperFamilySSF576671.06E-910931135No hitNo description
Gene3DG3DSA:3.30.160.601.1E-911011129IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.002711071131IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.53311071136IPR007087Zinc finger, C2H2
PROSITE patternPS00028011091131IPR007087Zinc finger, C2H2
SuperFamilySSF576674.18E-811251159No hitNo description
Gene3DG3DSA:3.30.160.604.8E-911301160IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.2211371163IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.9711371168IPR007087Zinc finger, C2H2
PROSITE patternPS00028011391163IPR007087Zinc 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: 1172 aa     Download sequence    Send to blast
MRGVSRANGS LLKFMKEEIP GVTSPMVYLA MMFSSFAWHV EDYELHSLNY IHLGAAKTWY  60
AVPKDAAVAF EEVVRVHGYG GEVNPLVTCA SLAEKTTLMS PEVLVGAGIP CCRMVQNAGE  120
FVVTFPRAYH SGFSHGDTSG SFTYLFLMYF FNQRNTIFMT GFNCSEAANI ATPEWLMVAK  180
EAAVRRASIN YSPVVSHLQL LYSLALSLCS RIPLSISTEP RSSRLKEKKK SEGETKVKER  240
FVESVIQNNE FLHDLLEQGS SCVLLPKNSL DIICPNVSPG SQVEIYPRFS VGAFSPEEEM  300
ERLENTVLDE IMVDKNTQNR ELNGFRSMKQ YSSCVRKGNR PPSLSVKNPQ NDNADFRTYP  360
SERRNTNTEK ECASQTDGLL DHEMLSCLTC GILSCACVAV VQPREEASKY IVSADCSLFN  420
DWIVASGAPD NEYSNADRFA TTSELNSCSG QVEKSDYNDV NDVTVQCSSY QAEVLNGRVE  480
VNPDIDAQKA ISSLNLLAAA YGNLSDSDDE KAESEMPVSG DENDTVYNQK DRSRSSDETF  540
SSARTFACAS SVDPGHHDDR MKSMFHSSSS IGGESEFSSQ ISWCPSACSR THVRATANGR  600
YEQNLENSLQ NKLASTMPKV SNCLSLERSA CDHADLSTKS TTLDSMPNCY PGLSSARNNC  660
CSLDIPTKDI QIPFKQRSGE DSSKGHMFCL EHAVEIEKQL RTVGGVHVLL VCHPDYPRVE  720
TEAKVLAEEL GINYIWKHIP YREATKDEAA RIRSSLGDKE AVPRNGDWTV KLGINLPYNA  780
SISQSPFYRK KMPYSIVSKV FGCSSPTNSS EKPKIFGKRP GVNNKIVVAG RWCGKVWMSD  840
QVHPYLAQRA CQKEETSARI HSQATSEAKV KIEIKPELSD ESEQTSTSQW KSLRTLTTTV  900
TRKTDKKRKG TLKKGATKKR KCSQPDSPIE AVEDSPTHDS PPRCRKILRT GQANQKTLPI  960
SKKRKCSQPD SPIEAVEDSP THDSPPRCRR NLRTGQAKRK EEAAGGRGKR LKKKSYKLLE  1020
DEDVKPIKQA KKKITKKAST CSEDKIIKDE EQEYQCDIEN CTMVFRSKQD LKLHKRNICL  1080
VEGCDKKFLS HRYLEQHERV HMDDRPLKCP WKGCRMSFKW AWARTEHIRV HTGVRPYECQ  1140
EPGCGQTFRF VTDFSRHRRK TGHSVKKVVD D*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A3e-591054116823137Lysine-specific demethylase REF6
6a58_A3e-591054116823137Lysine-specific demethylase REF6
6a59_A3e-591054116823137Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1906920KRKGTLKKGATKKRK
2911920LKKGATKKRK
39971011KRKEEAAGGRGKRLK
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010250905.10.0PREDICTED: lysine-specific demethylase JMJ705-like
SwissprotQ9STM31e-137REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2G5CHS90.0A0A2G5CHS9_AQUCA; Uncharacterized protein
STRINGAquca_056_00083.10.0(Aquilegia coerulea)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.11e-119relative 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]