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

Phvul.003G207700.1

Common Name

PHAVU_003G207700g

Organism

Phaseolus vulgaris

Taxonomic ID

3885

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 1496aa MW: 170031 Da PI: 9.1831

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Phvul.003G207700.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.4	0.00048	1380	1405	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L +H r+ + Phvul.003G207700.1 1380 YQCDieGCTMSFGSKQELLQHKRNiC 1405 99********************9877 PP
2	zf-C2H2	13	0.00031	1405	1427	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Phvul.003G207700.1 1405 CPvkGCGKNFFSHKYLVQHRRVH 1427 9999*****************99 PP
3	zf-C2H2	11.8	0.00073	1463	1489	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H Phvul.003G207700.1 1463 YVCAepGCGQTFRFVSDFSRHKRKtgH 1489 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	8.7E-19	16	57	IPR003349	JmjN domain
PROSITE profile	PS51183	14.368	17	58	IPR003349	JmjN domain
Pfam	PF02375	4.7E-15	18	51	IPR003349	JmjN domain
SuperFamily	SSF51197	1.92E-26	103	151	No hit	No description
SMART	SM00558	3.5E-48	164	333	IPR003347	JmjC domain
PROSITE profile	PS51184	34.172	164	333	IPR003347	JmjC domain
SuperFamily	SSF51197	1.92E-26	182	338	No hit	No description
Pfam	PF02373	4.2E-36	197	316	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	1.7E-4	1369	1402	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	6.6	1380	1402	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.016	1403	1427	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.549	1403	1432	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	6.35E-6	1403	1439	No hit	No description
PROSITE pattern	PS00028	0	1405	1427	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.6E-5	1405	1431	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
Gene3D	G3DSA:3.30.160.60	2.6E-8	1432	1457	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.824	1433	1462	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0016	1433	1457	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1435	1457	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.73E-9	1443	1487	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.2E-9	1458	1486	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.845	1463	1494	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.62	1463	1489	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1465	1489	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: 1496 aa Download sequence Send to blast
MAGSEEVLPW LKSLPVAPEY RPTTAEFQNP IAYISKIEKE ASQYGICKII PPLPPSPKKT 60 ATANLTRSRP TFTTRQQQIG FCPRRAQPVR RRVWRSGHHY SLREFEAKAK AFHKTYLNKN 120 KPKPLELETL YWKATLDKPF SVEYANDIPG SAFSPLRASR DADYVGDTAW NMRAVSRGSD 180 SLLRFMKEEI PGVTSPMVYV AMLFSWFAWH VEDHDLHSLN YLHFGAPKTW YGVPRDAAVA 240 FEDVVRIHGY GGEINPLVTF AILGEKTTVM SPEVFVGAGI PCCRLVQNAG EFVVTFPRAY 300 HTGFSHGFNC GEAANIATPE WLRFAKDAAI RRASINYPPM VSHFQLLYDL GLAFCSRIPG 360 GIRAEPRSSR LKYKRNGEGE TVIKELFVQD VVENNDLLHT LSKGSAIVLL PRSSSDFSVC 420 SKLRVGSQQL KVNPDFSLNV YDYERMDSPD FISDDLMFNR NHGIKQVKSF YSVKEKFVTL 480 CEKNRILPFS SDGNIYPSSS KTLQGDSEKE TDQGDGLSDQ RLFSCVTCGI LSFSCVAIVQ 540 PREPAATYLM SADCSFFNDW IVGSGVTSNK FANAHEDASI PKPRTYTVTH LVDNAGWTKQ 600 YAQHDSNGVP VQSEALNSGR DKGNTALALL ASAYGNSSDS EEDQGRLDIA LDGDELNVIN 660 HPSTNGSQEM SSMPSHFKDP HASPMVRVIG LDKEDDIHSR RMDNYEYYMH KRVEHIMTPF 720 DYSVKSEDLD NTSGVAFRNT RAVPHLSLNR SQDTHTDEDS SRMHIFCLEH AVEAEQQLRP 780 IGGAHILLLC HPDYPKIEAE AKIVAEELRI GYTWKNTIYR QANREDEVRI QSALDSEEAI 840 PGNGDWAVKL GINLFYSANL SRSALYVKQI PYNSVIYKAF GQSSPASSPT EPKVYQRRTN 900 KQKKVVAGKW CGKVWMSNQV HPLLAKRDFE DVENETSLHG WPLPDDEKIE RSVSNHKSNT 960 STRKSGKKWK KSVQKGGTWE ESFSERDWLS DNSIEEKSNK YRRRILGSKQ TRHIERDDTT 1020 SQGDYSPLPH HKKPISKHSE SSGNDAVSDD SCIQHRRKAN TNEAKFVGGD VFSDDTMDYG 1080 SDRLHRGELS NGQDAISDNS LGTCSLQLRR KTPKGKYDKY IIEEDMISDD QSEVCFWKQR 1140 GNISKGRQRS LSAKNKDNRE HHRQKQQQRN LRSRQDKHLA FIGEEDVMSD DQLKDHFQKP 1200 QRSTRRSRQN KYNDKDLMDD LAKNNFYMLY RTRKRKQAKD MDEDSIDSDD LIEDIFHLQH 1260 KRTLQSKQSK SQILQPKKQT NPLHLRNKTS RPVKQGAPTL MKSKAARQAK NQSGNSKDLT 1320 LHVEEEEDGG PRTRLRKRVL EKESEGNLKE KRIKREKAKN TTAAKVSVGH AKTKDEESEY 1380 QCDIEGCTMS FGSKQELLQH KRNICPVKGC GKNFFSHKYL VQHRRVHEDD RPLKCPWKGC 1440 KMSFKWAWAR TEHIRVHTGA RPYVCAEPGC GQTFRFVSDF SRHKRKTGHA TKKNC*

Sequence ? help Back to Top

Protein Sequence Length: 1496 aa Download sequence Send to blast

MAGSEEVLPW LKSLPVAPEY RPTTAEFQNP IAYISKIEKE ASQYGICKII PPLPPSPKKT  60
ATANLTRSRP TFTTRQQQIG FCPRRAQPVR RRVWRSGHHY SLREFEAKAK AFHKTYLNKN  120
KPKPLELETL YWKATLDKPF SVEYANDIPG SAFSPLRASR DADYVGDTAW NMRAVSRGSD  180
SLLRFMKEEI PGVTSPMVYV AMLFSWFAWH VEDHDLHSLN YLHFGAPKTW YGVPRDAAVA  240
FEDVVRIHGY GGEINPLVTF AILGEKTTVM SPEVFVGAGI PCCRLVQNAG EFVVTFPRAY  300
HTGFSHGFNC GEAANIATPE WLRFAKDAAI RRASINYPPM VSHFQLLYDL GLAFCSRIPG  360
GIRAEPRSSR LKYKRNGEGE TVIKELFVQD VVENNDLLHT LSKGSAIVLL PRSSSDFSVC  420
SKLRVGSQQL KVNPDFSLNV YDYERMDSPD FISDDLMFNR NHGIKQVKSF YSVKEKFVTL  480
CEKNRILPFS SDGNIYPSSS KTLQGDSEKE TDQGDGLSDQ RLFSCVTCGI LSFSCVAIVQ  540
PREPAATYLM SADCSFFNDW IVGSGVTSNK FANAHEDASI PKPRTYTVTH LVDNAGWTKQ  600
YAQHDSNGVP VQSEALNSGR DKGNTALALL ASAYGNSSDS EEDQGRLDIA LDGDELNVIN  660
HPSTNGSQEM SSMPSHFKDP HASPMVRVIG LDKEDDIHSR RMDNYEYYMH KRVEHIMTPF  720
DYSVKSEDLD NTSGVAFRNT RAVPHLSLNR SQDTHTDEDS SRMHIFCLEH AVEAEQQLRP  780
IGGAHILLLC HPDYPKIEAE AKIVAEELRI GYTWKNTIYR QANREDEVRI QSALDSEEAI  840
PGNGDWAVKL GINLFYSANL SRSALYVKQI PYNSVIYKAF GQSSPASSPT EPKVYQRRTN  900
KQKKVVAGKW CGKVWMSNQV HPLLAKRDFE DVENETSLHG WPLPDDEKIE RSVSNHKSNT  960
STRKSGKKWK KSVQKGGTWE ESFSERDWLS DNSIEEKSNK YRRRILGSKQ TRHIERDDTT  1020
SQGDYSPLPH HKKPISKHSE SSGNDAVSDD SCIQHRRKAN TNEAKFVGGD VFSDDTMDYG  1080
SDRLHRGELS NGQDAISDNS LGTCSLQLRR KTPKGKYDKY IIEEDMISDD QSEVCFWKQR  1140
GNISKGRQRS LSAKNKDNRE HHRQKQQQRN LRSRQDKHLA FIGEEDVMSD DQLKDHFQKP  1200
QRSTRRSRQN KYNDKDLMDD LAKNNFYMLY RTRKRKQAKD MDEDSIDSDD LIEDIFHLQH  1260
KRTLQSKQSK SQILQPKKQT NPLHLRNKTS RPVKQGAPTL MKSKAARQAK NQSGNSKDLT  1320
LHVEEEEDGG PRTRLRKRVL EKESEGNLKE KRIKREKAKN TTAAKVSVGH AKTKDEESEY  1380
QCDIEGCTMS FGSKQELLQH KRNICPVKGC GKNFFSHKYL VQHRRVHEDD RPLKCPWKGC  1440
KMSFKWAWAR TEHIRVHTGA RPYVCAEPGC GQTFRFVSDF SRHKRKTGHA TKKNC*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	4e-81	8	347	6	346	Transcription factor jumonji (Jmj) family protein
6ip4_A	4e-81	8	347	6	346	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1231	1236	TRKRKQ

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	Phvul.003G207700.1

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	AP015034	0.0	AP015034.1 Vigna angularis var. angularis DNA, chromosome 1, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_007155510.1	0.0	hypothetical protein PHAVU_003G207700g
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	V7CBG9	0.0	V7CBG9_PHAVU; Uncharacterized protein
STRING	XP_007155510.1	0.0	(Phaseolus vulgaris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF5648	32	50

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	Phvul.003G207700.1
Entrez Gene	18635557

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]