PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Aqcoe3G132200.2.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: 1147aa    MW: 128248 Da    PI: 8.1881
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Aqcoe3G132200.2.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H214.40.0001110291054123
                         EEET..TTTEEESSHHHHHHHHHH.T CS
            zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                         y+C   +C+++F++k +Lk H r+ +
  Aqcoe3G132200.2.p 1029 YQCDieNCTMVFRSKQDLKLHKRNiC 1054
                         99********************9877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5118430.0411162IPR003347JmjC domain
SMARTSM005581.5E-391162IPR003347JmjC domain
SuperFamilySSF511973.57E-2410154No hitNo description
PfamPF023735.8E-3626145IPR003347JmjC domain
Gene3DG3DSA:3.30.160.607.2E-410241051IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003558.610291051IPR015880Zinc finger, C2H2-like
SMARTSM003550.1410521076IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.26110521081IPR007087Zinc finger, C2H2
PROSITE patternPS00028010541076IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.3E-410591082IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.07E-910681110No hitNo description
SMARTSM003550.002710821106IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.53310821111IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.6E-810831106IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028010841106IPR007087Zinc finger, C2H2
SuperFamilySSF576673.98E-811001134No hitNo description
Gene3DG3DSA:3.30.160.604.9E-911071135IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.2211121138IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.9711121143IPR007087Zinc finger, C2H2
PROSITE patternPS00028011141138IPR007087Zinc 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: 1147 aa     Download sequence    Send to blast
MRGVSRANGS LLKFMKEEIP GVTSPMVYLA MMFSSFAWHV EDYELHSLNY IHLGAAKTWY  60
AVPKDAAVAF EEVVRVHGYG GEVNPLVTCA SLAEKTTLMS PEVLVGAGIP CCRMVQNAGE  120
FVVTFPRAYH SGFSHGFNCS EAANIATPEW LMVAKEAAVR RASINYSPVV SHLQLLYSLA  180
LSLCSRIPLS ISTEPRSSRL KEKKKSEGET KVKERFVESV IQNNEFLHDL LEQGSSCVLL  240
PKNSLDIICP NVSPGSQVEI YPRFSVGAFS PEEEMERLEN TVLDEIMVDK NTQNRELNGF  300
RSMKQYSSCV RKGNRPPSLS VKNPQNDNAD FRTYPSERRN TNTEKECASQ TDGLLDHEML  360
SCLTCGILSC ACVAVVQPRE EASKYIVSAD CSLFNDWIVA SGAPDNEYSN ADRFATTSEL  420
NSCSGQVEKS DYNDVNDVTV QCSSYQAEVL NGRVEVNPDI DAQKAISSLN LLAAAYGNLS  480
DSDDEKAESE MPVSGDENDT VYNQKDRSRS SDETFSSART FACASSVDPG HHDDRMKSMF  540
HSSSSIGGES EFSSQISWCP SACSRTHVRA TANGRYEQNL ENSLQNKLAS TMPKVSNCLS  600
LERSACDHAD LSTKSTTLDS MPNCYPGLSS ARNNCCSLDI PTKDIQIPFK QRSGEDSSKG  660
HMFCLEHAVE IEKQLRTVGG VHVLLVCHPD YPRVETEAKV LAEELGINYI WKHIPYREAT  720
KDEAARIRSS LGDKEAVPRN GDWTVKLGIN LPYNASISQS PFYRKKMPYS IVSKVFGCSS  780
PTNSSEKPKI FGKRPGVNNK IVVAGRWCGK VWMSDQVHPY LAQRACQKEE TSARIHSQAT  840
SEAKVKIEIK PELSDESEQT STSQWKSLRT LTTTVTRKTD KKRKGTLKKG ATKKRKCSQP  900
DSPIEAVEDS PTHDSPPRCR KILRTGQANQ KTLPISKKRK CSQPDSPIEA VEDSPTHDSP  960
PRCRRNLRTG QAKRKEEAAG GRGKRLKKKS YKLLEDEDVK PIKQAKKKIT KKASTCSEDK  1020
IIKDEEQEYQ CDIENCTMVF RSKQDLKLHK RNICLVEGCD KKFLSHRYLE QHERVHMDDR  1080
PLKCPWKGCR MSFKWAWART EHIRVHTGVR PYECQEPGCG QTFRFVTDFS RHRRKTGHSV  1140
KKVVDD*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A3e-591029114323137Lysine-specific demethylase REF6
6a58_A3e-591029114323137Lysine-specific demethylase REF6
6a59_A3e-591029114323137Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1881895KRKGTLKKGATKKRK
2886895LKKGATKKRK
3972986KRKEEAAGGRGKRLK
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-142REF6_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-124relative 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]