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

GSVIVT01007564001

Common Name

VIT_17s0000g09980

Organism

Vitis vinifera

Taxonomic ID

29760

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis

Family

C2H2

Protein Properties

Length: 950aa MW: 105704 Da PI: 8.3751

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSVIVT01007564001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.5	0.00045	833	858	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sFs+k +L H ++ + GSVIVT01007564001 833 YQCDmeGCTMSFSSKPELALHKKNiC 858 99*******************99866 PP
2	zf-C2H2	13.6	0.00019	858	880	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H GSVIVT01007564001 858 CPvkGCGKKFFSHKYLVQHRRVH 880 9999*****************99 PP
3	zf-C2H2	11.9	0.00069	916	942	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y C+ Cg++F+ s++ rH r+ H GSVIVT01007564001 916 YICTeaGCGQTFRFVSDFSRHKRKtgH 942 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00558	2.1E-44	1	162	IPR003347	JmjC domain
PROSITE profile	PS51184	33.633	1	162	IPR003347	JmjC domain
SuperFamily	SSF51197	1.92E-26	8	176	No hit	No description
Pfam	PF02373	2.0E-37	26	145	IPR003347	JmjC domain
SMART	SM00355	7.7	833	855	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.383	856	885	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0045	856	880	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.1E-5	857	879	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	858	880	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.56E-9	872	914	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.0E-9	880	908	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.741	886	915	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0014	886	910	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	888	910	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	7.62E-8	904	938	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.5E-9	909	939	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.24	916	942	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.489	916	947	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	918	942	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: 950 aa Download sequence Send to blast
MRGISRAKGS LLRFMKEEIP GVTSPMVYVA MMFSWFAWHV EDHDLHSLNY LHMGAGKTWY 60 GVPREAAVAF EEVVRVHGYG GEINPLVTFA VLGEKTTVMS PEVFVSAGIP CCRLVQNPGE 120 FVVTFPRAYH SGFSHGFNCG EAANIATPEW LRVAKDAAIR RASINYPPMV SHFQLLYDLA 180 LALCSRIPMS ISVEPRSSRL KDKKRGEGET VVKELFVQNI MQNNDLLHIL GKGSSIVLLP 240 KRSSDISVCP NLRVGSSSRV KPRLSLGLCN LEEAMKTSKS ILHLSHGNDN GSALTSQTQN 300 METKIESISH GDGLSDQALF SCVTCGILSF ACVALIQPRE AAARYLMSAD CSFFNDWIVG 360 SGPSGVANED FTGVSGDVHN SELNSCSGWM RKRVPNALFD VPIQSANYQI QTVDQNNEVV 420 SNTGTQKNTS ALGLLALTYA NSSDSEEDQL EPDIPLEADN LASTESNSSE GIFRDPLAIS 480 WATSKYSPVG HDAERAKFSN AIVPVENTNM SFAPRSDEDY SRIHVFCLEH AVEVEQQLRP 540 IGGVNMLLLC HPDYPKVEAE AKLVAEDLGI DYLWNDFVYR DATKEDGEMI QSALDSEECI 600 PGNGDWAVKL GVNLYYSANL SRSPLYIKQM PYNSVIYNVF GRSSANSPTA PDVYGRGPGK 660 QKKIVVAGKW CGKVWMSNQV HPLLAQKDPE EQEEDRNFHV WVKKPDEKPE RKSESSRKAE 720 TSSAPRKSGR KRKMMVENGS TKKANRPERE DPTPRRRNSC EQSAREFDSY VEDELEGGPS 780 TRLRRRNPKP PKELEAKPVV KKQTARKKAK KAPAAKAPGN HNNAKIQDEE EEYQCDMEGC 840 TMSFSSKPEL ALHKKNICPV KGCGKKFFSH KYLVQHRRVH IDDRPLKCPW KGCKMTFKWA 900 WARTEHIRVH TGARPYICTE AGCGQTFRFV SDFSRHKRKT GHSAKKARG*

Sequence ? help Back to Top

Protein Sequence Length: 950 aa Download sequence Send to blast

MRGISRAKGS LLRFMKEEIP GVTSPMVYVA MMFSWFAWHV EDHDLHSLNY LHMGAGKTWY  60
GVPREAAVAF EEVVRVHGYG GEINPLVTFA VLGEKTTVMS PEVFVSAGIP CCRLVQNPGE  120
FVVTFPRAYH SGFSHGFNCG EAANIATPEW LRVAKDAAIR RASINYPPMV SHFQLLYDLA  180
LALCSRIPMS ISVEPRSSRL KDKKRGEGET VVKELFVQNI MQNNDLLHIL GKGSSIVLLP  240
KRSSDISVCP NLRVGSSSRV KPRLSLGLCN LEEAMKTSKS ILHLSHGNDN GSALTSQTQN  300
METKIESISH GDGLSDQALF SCVTCGILSF ACVALIQPRE AAARYLMSAD CSFFNDWIVG  360
SGPSGVANED FTGVSGDVHN SELNSCSGWM RKRVPNALFD VPIQSANYQI QTVDQNNEVV  420
SNTGTQKNTS ALGLLALTYA NSSDSEEDQL EPDIPLEADN LASTESNSSE GIFRDPLAIS  480
WATSKYSPVG HDAERAKFSN AIVPVENTNM SFAPRSDEDY SRIHVFCLEH AVEVEQQLRP  540
IGGVNMLLLC HPDYPKVEAE AKLVAEDLGI DYLWNDFVYR DATKEDGEMI QSALDSEECI  600
PGNGDWAVKL GVNLYYSANL SRSPLYIKQM PYNSVIYNVF GRSSANSPTA PDVYGRGPGK  660
QKKIVVAGKW CGKVWMSNQV HPLLAQKDPE EQEEDRNFHV WVKKPDEKPE RKSESSRKAE  720
TSSAPRKSGR KRKMMVENGS TKKANRPERE DPTPRRRNSC EQSAREFDSY VEDELEGGPS  780
TRLRRRNPKP PKELEAKPVV KKQTARKKAK KAPAAKAPGN HNNAKIQDEE EEYQCDMEGC  840
TMSFSSKPEL ALHKKNICPV KGCGKKFFSH KYLVQHRRVH IDDRPLKCPW KGCKMTFKWA  900
WARTEHIRVH TGARPYICTE AGCGQTFRFV SDFSRHKRKT GHSAKKARG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	9e-68	833	947	23	137	Lysine-specific demethylase REF6
6a58_A	9e-68	833	947	23	137	Lysine-specific demethylase REF6
6a59_A	9e-68	833	947	23	137	Lysine-specific demethylase REF6
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Vvi.29525	0.0	inflorescence

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269\|PubMed:15377760, ECO:0000269\|PubMed:18713399}.

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

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	AM466832	0.0	AM466832.1 Vitis vinifera, whole genome shotgun sequence, contig VV78X011128.17, clone ENTAV 115.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_028116352.1	0.0	LOW QUALITY PROTEIN: lysine-specific demethylase REF6-like
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	F6GTM2	0.0	F6GTM2_VITVI; Uncharacterized protein
STRING	VIT_17s0000g09980.t01	0.0	(Vitis vinifera)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP4401	12	17

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	GSVIVT01007564001

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]