PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Araha.17006s0006.1.p

Organism

Arabidopsis halleri

Taxonomic ID

81970

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

C2H2

Protein Properties

Length: 1011aa MW: 113257 Da PI: 6.6516

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Araha.17006s0006.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.9	0.00034	893	918	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sFs+ +L+ H r+ + Araha.17006s0006.1.p 893 YQCDmeGCTMSFSSEKQLTLHKRNiC 918 99********************9877 PP
2	zf-C2H2	15.5	4.8e-05	918	940	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H+r+H Araha.17006s0006.1.p 918 CPvkGCGKNFFSHKYLVQHQRVH 940 9999*****************99 PP
3	zf-C2H2	12.4	0.00047	976	1002	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H Araha.17006s0006.1.p 976 YVCAepGCGQTFRFVSDFSRHKRKtgH 1002 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51184	16.888	1	91	IPR003347	JmjC domain
Pfam	PF02373	5.6E-17	19	74	IPR003347	JmjC domain
SuperFamily	SSF51197	1.87E-11	22	110	No hit	No description
SMART	SM00355	7.5	893	915	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	13.173	916	945	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.01	916	940	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	8.3E-7	917	944	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	918	940	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.26E-10	933	974	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.9E-9	945	969	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0015	946	970	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.928	946	975	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	948	970	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.27E-8	964	998	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.3E-9	970	999	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.62	976	1002	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.032	976	1007	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	978	1002	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009741	Biological Process	response to brassinosteroid
GO:0009826	Biological Process	unidimensional cell growth
GO:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0033169	Biological Process	histone H3-K9 demethylation
GO:0035067	Biological Process	negative regulation of histone acetylation
GO:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 1011 aa Download sequence Send to blast
EVVRVHGYGG ELNPLVTFST LGEKTTVMSP EVFVKAGIPC CRLVQNPGDF VVTFPGAYHS 60 GFSHGFNFGE ASNIATPEWL RMAKDAAIRR AAINYPPMVS HLQLLYDFAL ALGSRVPTSI 120 NAKPRSSRLK DKLRSEGERL TKKLFVQNII HNNELLYSLG KGSPVALLPQ SSSDISVCSD 180 LRIGSHLITN QENPIQLKSE DLSSDSVMVG LSNGLKDTVS VKEKFTSLCE RSRNHLASRE 240 KDTQEILSDA ERRKNDGAVA LSDQRLFSCV TCGVLSFDCV AIVQPKEAVA RYLMSADCSF 300 FNDWTAASGS ANLGQAARSL HPLSTEKHDV NYFYNVPVQT MDHSMKTGDQ RTSTTSLTMA 360 HKDNGALGLL ASAYGDSSDS EEEGQKGLDV PTSEGETKKY DKEDPDGNEE ARDGRTSDFN 420 SQRLTSEQNR LSKGGNSSLL EIALPFIPRS DDDSCRLHVF CLEHAAEVEQ QLRPFGGIHI 480 MLLCHPEYPR IEAEAKIVAE ELVINHEWND TEFRNVTRED EETIQAALDN VEAKGGNSDW 540 TVKLGINLSY SAILSRSPLY SKQMPYNSVI YNAFGRSSPS TSSPLKPEVS GKRSSRQRKY 600 VVGKWCGKVW MSHQREDGVS DDTSEDHSYK QQWRASGNEE ESYFETGNTV SGDSSNQMSD 660 QQLKGIRRHR GVKEFESDDE VSDRSLGEEY TVRGCAASES SMENGFQQSM YDDDDDDDDD 720 DINRHPRGVP RSERITVFRN PVSYDSEENG IYHQRGRVSR SNRQANRMGG EYDSEENSLE 780 EQDFCSTGKR QTRSTAKRKV KIETVRSPRD TKGRTLQEFA SGKKNEELDS YMEGPSTRLR 840 VRNLKPLRAA SETKPKKIGK KRSGNASFSR VATEEDVEED EEAENEEEEC AAYQCDMEGC 900 TMSFSSEKQL TLHKRNICPV KGCGKNFFSH KYLVQHQRVH SDDRPLKCPW KGCKMTFKWA 960 WSRTEHIRVH TGARPYVCAE PGCGQTFRFV SDFSRHKRKT GHSVKKTKKR *

Sequence ? help Back to Top

Protein Sequence Length: 1011 aa Download sequence Send to blast

EVVRVHGYGG ELNPLVTFST LGEKTTVMSP EVFVKAGIPC CRLVQNPGDF VVTFPGAYHS  60
GFSHGFNFGE ASNIATPEWL RMAKDAAIRR AAINYPPMVS HLQLLYDFAL ALGSRVPTSI  120
NAKPRSSRLK DKLRSEGERL TKKLFVQNII HNNELLYSLG KGSPVALLPQ SSSDISVCSD  180
LRIGSHLITN QENPIQLKSE DLSSDSVMVG LSNGLKDTVS VKEKFTSLCE RSRNHLASRE  240
KDTQEILSDA ERRKNDGAVA LSDQRLFSCV TCGVLSFDCV AIVQPKEAVA RYLMSADCSF  300
FNDWTAASGS ANLGQAARSL HPLSTEKHDV NYFYNVPVQT MDHSMKTGDQ RTSTTSLTMA  360
HKDNGALGLL ASAYGDSSDS EEEGQKGLDV PTSEGETKKY DKEDPDGNEE ARDGRTSDFN  420
SQRLTSEQNR LSKGGNSSLL EIALPFIPRS DDDSCRLHVF CLEHAAEVEQ QLRPFGGIHI  480
MLLCHPEYPR IEAEAKIVAE ELVINHEWND TEFRNVTRED EETIQAALDN VEAKGGNSDW  540
TVKLGINLSY SAILSRSPLY SKQMPYNSVI YNAFGRSSPS TSSPLKPEVS GKRSSRQRKY  600
VVGKWCGKVW MSHQREDGVS DDTSEDHSYK QQWRASGNEE ESYFETGNTV SGDSSNQMSD  660
QQLKGIRRHR GVKEFESDDE VSDRSLGEEY TVRGCAASES SMENGFQQSM YDDDDDDDDD  720
DINRHPRGVP RSERITVFRN PVSYDSEENG IYHQRGRVSR SNRQANRMGG EYDSEENSLE  780
EQDFCSTGKR QTRSTAKRKV KIETVRSPRD TKGRTLQEFA SGKKNEELDS YMEGPSTRLR  840
VRNLKPLRAA SETKPKKIGK KRSGNASFSR VATEEDVEED EEAENEEEEC AAYQCDMEGC  900
TMSFSSEKQL TLHKRNICPV KGCGKNFFSH KYLVQHQRVH SDDRPLKCPW KGCKMTFKWA  960
WSRTEHIRVH TGARPYVCAE PGCGQTFRFV SDFSRHKRKT GHSVKKTKKR *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	2e-80	890	1010	20	140	Lysine-specific demethylase REF6
6a58_A	2e-80	890	1010	20	140	Lysine-specific demethylase REF6
6a59_A	2e-80	890	1010	20	140	Lysine-specific demethylase REF6
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Histone 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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00608	ChIP-seq	Transfer from AT3G48430	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Araha.17006s0006.1.p

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY664499	0.0	AY664499.1 Arabidopsis thaliana relative of early flowering 6 (REF6) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002875902.1	0.0	lysine-specific demethylase REF6 isoform X2
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	D7LRW5	0.0	D7LRW5_ARALL; Uncharacterized protein
STRING	fgenesh2_kg.5__1196__AT3G48430.1	0.0	(Arabidopsis lyrata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5259	28	43

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G48430.1	0.0	relative of early flowering 6

Link Out ? help Back to Top
Phytozome	Araha.17006s0006.1.p

Publications ? help Back to Top
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] 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] 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] 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] 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] 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] Qiu Q, et al. DNA methylation repels targeting of Arabidopsis REF6. Nat Commun, 2019. 10(1): p. 2063 [PMID:31048693]