PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Lamiales; Gesneriaceae; Didymocarpoideae; Trichosporeae; Loxocarpinae; Dorcoceras

Family

C2H2

Protein Properties

Length: 1284aa MW: 143793 Da PI: 8.5854

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KZV21735.1	genome	CNU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15.2	6.2e-05	1193	1215	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H+r+H KZV21735.1 1193 CPvkGCGKKFFSHKYLVQHQRVH 1215 9999*****************99 PP
2	zf-C2H2	12.1	0.00059	1251	1277	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C+ Cg++F+ s++ rH r+ H KZV21735.1 1251 YVCTesGCGQTFRFVSDFSRHKRKtgH 1277 99********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	7.6E-14	22	63	IPR003349	JmjN domain
PROSITE profile	PS51183	13.841	23	64	IPR003349	JmjN domain
Pfam	PF02375	7.7E-15	24	57	IPR003349	JmjN domain
SMART	SM00558	7.4E-47	187	356	IPR003347	JmjC domain
PROSITE profile	PS51184	32.047	190	356	IPR003347	JmjC domain
SuperFamily	SSF51197	5.77E-26	205	355	No hit	No description
Pfam	PF02373	8.1E-38	220	339	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	4.9E-5	1161	1190	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	39	1168	1190	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.57	1191	1220	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0029	1191	1215	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	6.8E-6	1192	1219	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1193	1215	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.2E-9	1207	1249	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.2E-8	1220	1245	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0016	1221	1245	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.824	1221	1250	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1223	1245	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.41E-8	1239	1273	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.9E-9	1246	1274	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.16	1251	1277	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.053	1251	1282	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1253	1277	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: 1284 aa Download sequence Send to blast
MAAEVNSGAT FEVPPWLKSM PVAPEYHPTL AEFQDPIGYI FKIEKEAAKY GICKIVPPVP 60 AGSRKTVIAN FNRSLLARAK EVNPAATFTT RQQQIGFCPR KHRPVKKSVW LSGEKYTLSE 120 FEAKAKSFEK SYLKKYAKKE LNALDMETLF WNATVDKPFS VEYANDMPGS AFVTRRNNGK 180 KNDGVVTVGE TDWNMRGVSR VNVCLLRFMK EEIPGVTSPM VYVAMMFSWF AWHVEDHDFH 240 SLNYLHMGAG KTWYGVPHEA AFAFEDVIRE HGYGGEINPL VTFATLGEKT TVMSPEVLLN 300 AGVPCCRLVQ NAGEFVVTFP RAYHSGFSHG FNCGEAANIA TPEWLRVAKD AAIRRASINC 360 PPMVSHFQLL YDLALSLCSR VPKSIAMKPR SSRLKEKNKD EGEMLIKELF CEDMMQNNSL 420 LHILGKGSSI VLLPQNSLNL MMSPNSQDGF HFTAKFRFPG ICNPNIDSKT SSCNVHDDFT 480 RDGMQAKEML CDVKETPFSL GNSGDTHCMG HTDSDVKKVS QHEQGLFTCV TCGILCFTSV 540 AILQPTKATA LYLKSADCSI FTDWGIAGSY HNPISDVTDP KTNPCTGMVQ KYGLDIAPCT 600 GNQVRAFDDE NLEMDSNNKA SKGPSSLGLL ALAYGNSSDS EQNEDEEEFP AEAKGTGESS 660 YLDDGHACEN TESNISGGKE VYLNSSDSYT NFGLARETGN GTDHHSSDSD KIQTSNCAAI 720 DSNSSIDRLR HKKILDTLNS KYVAHESKAT STGLLSLETT SVSFYPRSDE DSSRLHVFCL 780 QHAMEVEKQL SLIGGAHVFI VCHPDYPRLE SQAKKVAEEL KNDYLWNEIS FRDANVEDEE 840 RIQLALDSEN AIHGNGDWAV KMGINLFYSA NLSRSPLYCK QMPYNSVLYK AFGRRCPVNG 900 SSAESEFEGK GSGRQKKIVV AGKWCGKVWM SSQAHPLLVD QNSEELEQEK GTAARVDWPD 960 LRSEKLSQRY QAAETTSKTS KSRRKRKNMV ENSSNVKAKP LEAENVDEPP QDNGLSKSHK 1020 LVKSRVGSKR LKKEIAKAEN MYESAEEFPL SNCWTQIRSK SRTKRVEKLT KSNFGTRLIE 1080 TREHKKNQEN SEKWSNSLIE DEQNGGPSTR LRKRAAKTHK DIEPRSSKQK IVVKKLRKDT 1140 NTKKRPTMKG TATSPNKVTK ARDEENEHLC DIEGCTMSFG TKHELSMHKR NICPVKGCGK 1200 KFFSHKYLVQ HQRVHLDDRP LKCPWKGCKM SFKWAWARTE HIRVHTGARP YVCTESGCGQ 1260 TFRFVSDFSR HKRKTGHNPK KARG

Sequence ? help Back to Top

Protein Sequence Length: 1284 aa Download sequence Send to blast

MAAEVNSGAT FEVPPWLKSM PVAPEYHPTL AEFQDPIGYI FKIEKEAAKY GICKIVPPVP  60
AGSRKTVIAN FNRSLLARAK EVNPAATFTT RQQQIGFCPR KHRPVKKSVW LSGEKYTLSE  120
FEAKAKSFEK SYLKKYAKKE LNALDMETLF WNATVDKPFS VEYANDMPGS AFVTRRNNGK  180
KNDGVVTVGE TDWNMRGVSR VNVCLLRFMK EEIPGVTSPM VYVAMMFSWF AWHVEDHDFH  240
SLNYLHMGAG KTWYGVPHEA AFAFEDVIRE HGYGGEINPL VTFATLGEKT TVMSPEVLLN  300
AGVPCCRLVQ NAGEFVVTFP RAYHSGFSHG FNCGEAANIA TPEWLRVAKD AAIRRASINC  360
PPMVSHFQLL YDLALSLCSR VPKSIAMKPR SSRLKEKNKD EGEMLIKELF CEDMMQNNSL  420
LHILGKGSSI VLLPQNSLNL MMSPNSQDGF HFTAKFRFPG ICNPNIDSKT SSCNVHDDFT  480
RDGMQAKEML CDVKETPFSL GNSGDTHCMG HTDSDVKKVS QHEQGLFTCV TCGILCFTSV  540
AILQPTKATA LYLKSADCSI FTDWGIAGSY HNPISDVTDP KTNPCTGMVQ KYGLDIAPCT  600
GNQVRAFDDE NLEMDSNNKA SKGPSSLGLL ALAYGNSSDS EQNEDEEEFP AEAKGTGESS  660
YLDDGHACEN TESNISGGKE VYLNSSDSYT NFGLARETGN GTDHHSSDSD KIQTSNCAAI  720
DSNSSIDRLR HKKILDTLNS KYVAHESKAT STGLLSLETT SVSFYPRSDE DSSRLHVFCL  780
QHAMEVEKQL SLIGGAHVFI VCHPDYPRLE SQAKKVAEEL KNDYLWNEIS FRDANVEDEE  840
RIQLALDSEN AIHGNGDWAV KMGINLFYSA NLSRSPLYCK QMPYNSVLYK AFGRRCPVNG  900
SSAESEFEGK GSGRQKKIVV AGKWCGKVWM SSQAHPLLVD QNSEELEQEK GTAARVDWPD  960
LRSEKLSQRY QAAETTSKTS KSRRKRKNMV ENSSNVKAKP LEAENVDEPP QDNGLSKSHK  1020
LVKSRVGSKR LKKEIAKAEN MYESAEEFPL SNCWTQIRSK SRTKRVEKLT KSNFGTRLIE  1080
TREHKKNQEN SEKWSNSLIE DEQNGGPSTR LRKRAAKTHK DIEPRSSKQK IVVKKLRKDT  1140
NTKKRPTMKG TATSPNKVTK ARDEENEHLC DIEGCTMSFG TKHELSMHKR NICPVKGCGK  1200
KFFSHKYLVQ HQRVHLDDRP LKCPWKGCKM SFKWAWARTE HIRVHTGARP YVCTESGCGQ  1260
TFRFVSDFSR HKRKTGHNPK KARG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	1e-73	16	377	8	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	1e-73	16	377	8	353	Arabidopsis JMJ13
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	KZV21735.1

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_011072922.1	0.0	lysine-specific demethylase REF6 isoform X1
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A2Z7AIU0	0.0	A0A2Z7AIU0_9LAMI; Uncharacterized protein
STRING	Migut.I00266.1.p	0.0	(Erythranthe guttata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA4988	23	31

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G48430.1	0.0	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]