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 Aqcoe0015s0011.1.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: 1330aa    MW: 148566 Da    PI: 8.2681
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Aqcoe0015s0011.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.30.0002612281253123
                          EEET..TTTEEESSHHHHHHHHHH.T CS
             zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                          y+C   +C+++F++k +Lk H r+ +
  Aqcoe0015s0011.1.p 1228 YQCDieNCTMVFRSKQDLKLHKRNiC 1253
                          99********************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.5E-162162IPR003349JmjN domain
PROSITE profilePS5118313.552263IPR003349JmjN domain
PfamPF023751.4E-142356IPR003349JmjN domain
SMARTSM005582.3E-45192361IPR003347JmjC domain
PROSITE profilePS5118430.445192361IPR003347JmjC domain
SuperFamilySSF511971.76E-24207354No hitNo description
PfamPF023731.1E-35225344IPR003347JmjC domain
Gene3DG3DSA:3.30.160.608.5E-412231250IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.1712281255IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.40612281264IPR007087Zinc finger, C2H2
SuperFamilySSF576672.73E-1212511302No hitNo description
Gene3DG3DSA:3.30.160.601.1E-812551287IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.002712651289IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.53312651294IPR007087Zinc finger, C2H2
PROSITE patternPS00028012671289IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.7E-912881318IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.2212951321IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.9712951326IPR007087Zinc finger, C2H2
PROSITE patternPS00028012971321IPR007087Zinc 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: 1330 aa     Download sequence    Send to blast
MEELRTESVL QVDQCLKSLP LAPTYYPTLV EFQDPISYIF KIEKEASQYG ICKIVPPLPP  60
ASKITSITNF NRSLSQTNSS SDSKTLSTFT TQEQQFGFSQ GKSKLVKMNL LQSRDSCSFK  120
QFEAKAKEFE KSILKKSGKK KKKDFSELEI ETLYWKACFD KPLLIECANC IPGSGFVPIN  180
GKKLREAGEA STVGETPWNM RGVSRANGSL LKFMKEEIPG VTSPMVYLAM MFSSFAWHVE  240
DYELHSLNYI HLGAAKTWYA VPKDAAVAFE EVVRVHGYGG EVNPLVTCAS LAEKTTLMSP  300
EVLVGAGIPC CRLVQNAGEF VVTFPRAYHS GFSHGFNCSE AANIATPEWL MVAKEAAVRR  360
ASINYSPVVS HLQLLYSLAL SFCSRIPLSI STEPRSSRLK EKKKSEGETK VKERFVESVI  420
QNNEFLHDLL EQGSSCVLLP KNSLDIICPN VSPGSQVEIY PRFSVGAFSP EEEMERLENT  480
VLDEIMVDKN TQNRELNGFR SMKQYSSCVR KGNRPPSLSV KNPQNDNADF RTYPSERRNT  540
NTEKECASQT DGLLDHEMLS CLTCGILSCA CVAVVQPREE ASKYIVSADC SLFNDWIVAS  600
GAPDNEYSNA DRFANTSELN SCSGQVEKSD YNDVNDVTVQ CSSYQAEVLN GRVEVNPDID  660
AQKAISSLNL LAAAYGNLSD SDDEKAESEM PVSGDENDTV YNQKDRSRSS DETFSSARTF  720
ACASSVDPGH HDDRMKSMFH SSSSIGGGSE FSSQISWCPS ACSRTHVRAT ANGRYEQNLE  780
NSLQNKLVST IPKVSNCLSL ERSACDHADL STKSTTLDSM PNCYPGLSSA RNNCCSLDIP  840
TKDIQIPFKQ RSGEDSSKGH MFCLEHAVEI EKQLRTVGGV HVLLVCHPDY PRVETEAKVL  900
AEELGINYIW KHIPYREATK DEAARIQSSL GDKEAVPRNG DWTVKLGINL PYNASISQSP  960
FYRKKMPYSI VSKVFGCSSP TNSSEKPKIF GKRPGVNNKI VVAGRWCGKV WMSDQVHPYL  1020
AQRACQKEET SASIHSQATS EAKVKIEIKP ELSDESEQTS TSQWKSLRTL TTTVTRKTDK  1080
KRKGTLKKGA TKKRKCSQPD SPIEAVEDSP THDSPPRCRR ILRTGQANQK TLPISKKRKC  1140
SQPDSPIEAV EDSPTHDSPP RCRRNLRTGQ AKRKEEAAGG RGKRLKKKSY KLLEDEDVKP  1200
IKQAKKKITK KASTCSEDKI IKDEEQEYQC DIENCTMVFR SKQDLKLHKR NICLHERVHM  1260
DDRPLKCPWK GCRMSFKWAW ARTEHIRVHT GVRPYECQEP GCGQTFRFVT DFSRHRRKTG  1320
HSVKKVVDD*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-641944812412Transcription factor jumonji (Jmj) family protein
6ip4_A2e-641944812412Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110801094KRKGTLKKGATKKRK
210851094LKKGATKKRK
311711185KRKEEAAGGRGKRLK
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
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2G5F8950.0A0A2G5F895_AQUCA; Uncharacterized protein
STRINGAquca_001_00004.10.0(Aquilegia coerulea)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.11e-176relative 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]