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

Vun009318

Organism

Vigna unguiculata

Taxonomic ID

3917

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna

Family

C2H2

Protein Properties

Length: 234aa MW: 27108.3 Da PI: 10.9643

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PUT-167a-Vigna_unguiculata-28909	PU_ref	plantGDB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15.2	6e-05	119	144	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L +H r+ + Vun009318 119 YQCDmeGCTMSFGSKQELLQHKRNiC 144 99********************9877 PP
2	zf-C2H2	15.9	3.7e-05	144	166	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Vun009318 144 CPvkGCGKKFFSHKYLVQHRRVH 166 9999*****************99 PP
3	zf-C2H2	14.9	7.6e-05	202	228	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H Vun009318 202 YVCAepGCGQTFRFVSDFSRHKRKtgH 228 899999*****************9777 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.0E-4	115	141	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	7.8	119	141	IPR015880	Zinc finger, C2H2-like
SuperFamily	SSF57667	5.69E-7	142	179	No hit	No description
PROSITE profile	PS50157	12.508	142	171	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0045	142	166	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.1E-6	143	165	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	144	166	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.4E-6	166	178	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.824	172	201	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0016	172	196	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	174	196	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.6E-4	179	194	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.12E-10	182	226	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.0E-10	195	225	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.845	202	233	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.62	202	228	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	204	228	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 234 aa Download sequence Send to blast
ALQSKQSKAQ ILQQTKTNPL HARNKTSRPV KQKQGAHTLM KSKAARQAKK QSGNSKDLTL 60 HVEEDEDGGP RTRLRKRVLE KEAEGKVKEK RTKREKERNK TAAKVLFAIP KQRMRESEYQ 120 CDMEGCTMSF GSKQELLQHK RNICPVKGCG KKFFSHKYLV QHRRVHEDDR PLKCPWKGCK 180 MSFKWAWART EHIRVHTGAR PYVCAEPGCG QTFRFVSDFS RHKRKTGHAT KKNC

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	2e-75	117	233	21	137	Lysine-specific demethylase REF6
6a58_A	2e-75	117	233	21	137	Lysine-specific demethylase REF6
6a59_A	2e-75	117	233	21	137	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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027921852.1	1e-152	lysine-specific demethylase REF6-like
Swissprot	Q9STM3	1e-71	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A4D6KW38	1e-151	A0A4D6KW38_VIGUN; Histone demethylase JARID1
STRING	XP_007155510.1	1e-136	(Phaseolus vulgaris)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G48430.1	8e-72	relative of early flowering 6

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]