PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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

Family

C2H2

Protein Properties

Length: 1566aa MW: 177452 Da PI: 8.7387

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.06G174000.1.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	11.9	0.00068	1449	1474	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L++H ++ + Glyma.06G174000.1.p 1449 YQCDidGCTMSFGSKQELMHHKKNiC 1474 99*******************99866 PP
2	zf-C2H2	12.9	0.00034	1474	1496	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Glyma.06G174000.1.p 1474 CPvkGCGKKFFSHKYLVQHRRVH 1496 9999*****************99 PP
3	zf-C2H2	13.4	0.00023	1532	1558	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C dCg++F+ s++ rH r+ H Glyma.06G174000.1.p 1532 YVCAepDCGQTFRFVSDFSRHKRKtgH 1558 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	2.0E-15	20	61	IPR003349	JmjN domain
PROSITE profile	PS51183	13.813	21	62	IPR003349	JmjN domain
Pfam	PF02375	1.4E-13	22	55	IPR003349	JmjN domain
SuperFamily	SSF51197	4.39E-26	176	367	No hit	No description
PROSITE profile	PS51184	33.894	180	349	IPR003347	JmjC domain
SMART	SM00558	9.6E-49	180	349	IPR003347	JmjC domain
Pfam	PF02373	2.3E-35	213	332	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	5.4E-4	1438	1471	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.45E-5	1445	1501	No hit	No description
SMART	SM00355	8.1	1449	1471	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.944	1472	1501	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0045	1472	1496	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.8E-6	1473	1495	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1474	1496	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	4.18E-9	1488	1530	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.7E-10	1496	1524	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1502	1526	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1502	1531	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1504	1526	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	7.04E-8	1520	1554	No hit	No description
Gene3D	G3DSA:3.30.160.60	8.6E-9	1525	1555	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.697	1532	1563	IPR007087	Zinc finger, C2H2
SMART	SM00355	1.1	1532	1558	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1534	1558	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: 1566 aa Download sequence Send to blast
MGVVSEGNGD VLPWLKSMPV APEYRPSAAE FQDPISYIFK IEKEASKYGI CKIIPPFPPS 60 SRKTAIANLN RSLAETGSTF TTRQQQIGFC PRRPRPVQRP VWQSGDRYTF TEFESKAKSF 120 EKTYLKRHAK KASGLGPGPL ETETLFWKAT LDKPFSVEYA NDMPGSAFSP KCRRVGDPSS 180 LADTQWNMRA VSRAKGSLLQ FMKEEIPGVT SPMVYVAMLF SWFAWHVEDH DLHSLNYLHM 240 GAGKTWYGVP RDAAVAFEEV VRVHGYGGEI NPLVTFAILG EKTTVMSPEV FISAGVPCCR 300 LVQNAGEFVV TFPRAYHTGF SHGFNCGEAA NIATPEWLRF AKDAAIRRAS LNYPPMVSHF 360 QLLYDLALAL CSRIPAGISA EPRSSRLKDK KKGEGETVIK ELFVQDVLQN NDLLHFLGQG 420 SAVVLLPHSS VDISVCSKLR VGSQQSINLS NSEGMHSSKG FVSDDLAFNR SHGIKQGKSF 480 YFVKDKFTTL CERNMISSFD VNGNISISSF NPLQRDTERE TCQGDGLSDQ RLFSCVTCGI 540 LCFSCVAIVQ PREPAARYLM SADCSFFNDW VVGSGVSNNK FTIAREEATI PESNMYTGWM 600 KKNVQDGIHD VPFQSSQVAL NTVSENGNTA LALLASAYGN SSDSEEDQIA VDSHESNVIN 660 SASESLLSDT RDSHASRTAL DRGDYIPSKS SSYEDFIHRR LECFENTRTV PNSTSNCSQD 720 AYDAKRSLSS KSMVPFDYKK ALMVLQSDED SSRMHVFCLE HAAEAEQQLR SIGGADILLL 780 CHPDYPKIEA EAKMVAEDLG IDYVLKNIVY RHASTEDEER IQSALDNEEA IPGNGDWAVK 840 LGINLFYSAN LSRSPLYSKQ MPYNSVIYSA FGCSSPASSL VEPKVYQRRV NKQKKIVAGK 900 WCGKVWMSNQ VHPLLAKRDS EDIEDEKLLQ GLTLPDEKIE RSESTPKREA ISRKSGKKRK 960 KTAENGRFRK GSYAKKNILS DDSTEDKPNS QPRRILRSKK ARHVERDCAA LKRDYSPPYH 1020 HRKPTSHQTN FTESDAVSDD SLDDDDHMRQ RRNVKVEKAK FMDNDVVSND TMDYDSDCLQ 1080 REEHSSKQVE DMERDANSED FLDVGSLQLQ RKISRAMHVK SIREEDIISD DQMESPFQKR 1140 QKRIPKSRQG KYLTGKDIIS DDQLELKMQK RQQTNPKSRQ AKYLNKEDIA SDDQLEDHYR 1200 RYQRNPKGRQ ATCVAGEDEM SDDHLENHCQ KQQTNFSRKR QNKDVVREVK NEMCDDQLED 1260 HFLKQHRRFP KSRQNKHTEK EIMDDLAENN SHLLHRTPKR KQAKCMEEDD MNSDDEMEDD 1320 QPLRRALRSK QAKPKTLLKQ ANSFQAKKQA SRPIKQGSRL LVKSKAPQQI KQPAHLRNKQ 1380 SNNTQEFSLY MEEEEDGGPS TRLRKRATKA QESEGKLKDK QTKRKKVKNA AAAKVSVGHA 1440 KMKDGEAEYQ CDIDGCTMSF GSKQELMHHK KNICPVKGCG KKFFSHKYLV QHRRVHEDER 1500 PLKCPWKGCK MTFKWAWART EHIRVHTGAR PYVCAEPDCG QTFRFVSDFS RHKRKTGHSA 1560 KKNCQ*

Sequence ? help Back to Top

Protein Sequence Length: 1566 aa Download sequence Send to blast

MGVVSEGNGD VLPWLKSMPV APEYRPSAAE FQDPISYIFK IEKEASKYGI CKIIPPFPPS  60
SRKTAIANLN RSLAETGSTF TTRQQQIGFC PRRPRPVQRP VWQSGDRYTF TEFESKAKSF  120
EKTYLKRHAK KASGLGPGPL ETETLFWKAT LDKPFSVEYA NDMPGSAFSP KCRRVGDPSS  180
LADTQWNMRA VSRAKGSLLQ FMKEEIPGVT SPMVYVAMLF SWFAWHVEDH DLHSLNYLHM  240
GAGKTWYGVP RDAAVAFEEV VRVHGYGGEI NPLVTFAILG EKTTVMSPEV FISAGVPCCR  300
LVQNAGEFVV TFPRAYHTGF SHGFNCGEAA NIATPEWLRF AKDAAIRRAS LNYPPMVSHF  360
QLLYDLALAL CSRIPAGISA EPRSSRLKDK KKGEGETVIK ELFVQDVLQN NDLLHFLGQG  420
SAVVLLPHSS VDISVCSKLR VGSQQSINLS NSEGMHSSKG FVSDDLAFNR SHGIKQGKSF  480
YFVKDKFTTL CERNMISSFD VNGNISISSF NPLQRDTERE TCQGDGLSDQ RLFSCVTCGI  540
LCFSCVAIVQ PREPAARYLM SADCSFFNDW VVGSGVSNNK FTIAREEATI PESNMYTGWM  600
KKNVQDGIHD VPFQSSQVAL NTVSENGNTA LALLASAYGN SSDSEEDQIA VDSHESNVIN  660
SASESLLSDT RDSHASRTAL DRGDYIPSKS SSYEDFIHRR LECFENTRTV PNSTSNCSQD  720
AYDAKRSLSS KSMVPFDYKK ALMVLQSDED SSRMHVFCLE HAAEAEQQLR SIGGADILLL  780
CHPDYPKIEA EAKMVAEDLG IDYVLKNIVY RHASTEDEER IQSALDNEEA IPGNGDWAVK  840
LGINLFYSAN LSRSPLYSKQ MPYNSVIYSA FGCSSPASSL VEPKVYQRRV NKQKKIVAGK  900
WCGKVWMSNQ VHPLLAKRDS EDIEDEKLLQ GLTLPDEKIE RSESTPKREA ISRKSGKKRK  960
KTAENGRFRK GSYAKKNILS DDSTEDKPNS QPRRILRSKK ARHVERDCAA LKRDYSPPYH  1020
HRKPTSHQTN FTESDAVSDD SLDDDDHMRQ RRNVKVEKAK FMDNDVVSND TMDYDSDCLQ  1080
REEHSSKQVE DMERDANSED FLDVGSLQLQ RKISRAMHVK SIREEDIISD DQMESPFQKR  1140
QKRIPKSRQG KYLTGKDIIS DDQLELKMQK RQQTNPKSRQ AKYLNKEDIA SDDQLEDHYR  1200
RYQRNPKGRQ ATCVAGEDEM SDDHLENHCQ KQQTNFSRKR QNKDVVREVK NEMCDDQLED  1260
HFLKQHRRFP KSRQNKHTEK EIMDDLAENN SHLLHRTPKR KQAKCMEEDD MNSDDEMEDD  1320
QPLRRALRSK QAKPKTLLKQ ANSFQAKKQA SRPIKQGSRL LVKSKAPQQI KQPAHLRNKQ  1380
SNNTQEFSLY MEEEEDGGPS TRLRKRATKA QESEGKLKDK QTKRKKVKNA AAAKVSVGHA  1440
KMKDGEAEYQ CDIDGCTMSF GSKQELMHHK KNICPVKGCG KKFFSHKYLV QHRRVHEDER  1500
PLKCPWKGCK MTFKWAWART EHIRVHTGAR PYVCAEPDCG QTFRFVSDFS RHKRKTGHSA  1560
KKNCQ*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	4e-80	10	370	4	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	4e-80	10	370	4	353	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	956	960	KKRKK
2	1403	1425	RKRATKAQESEGKLKDKQTKRKK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Gma.36465	0.0	leaf\| somatic embryo

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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Glyma.06G174000.1.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	AC235340	0.0	AC235340.1 Glycine max strain Williams 82 clone GM_WBb0086A04, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003528125.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	I1KC81	0.0	I1KC81_SOYBN; Uncharacterized protein
STRING	GLYMA06G18300.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF5648	32	50
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	Glyma.06G174000.1.p
Entrez Gene	100810972

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]