PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Alismatales; Zosteraceae; Zostera

Family

C2H2

Protein Properties

Length: 1150aa MW: 129023 Da PI: 8.0266

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Zosma72g00070.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	10.8	0.0016	1033	1058	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF++ +L H + + Zosma72g00070.1 1033 YQCDmdGCTMSFTSLQDLSIHKANiC 1058 99*******************87655 PP
2	zf-C2H2	15	7e-05	1058	1080	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp dCgk F ++ +L++H r+H Zosma72g00070.1 1058 CPvkDCGKKFFSHKYLVQHRRVH 1080 9999*****************99 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	6.1E-15	27	68	IPR003349	JmjN domain
PROSITE profile	PS51183	14.049	28	69	IPR003349	JmjN domain
Pfam	PF02375	4.8E-14	29	62	IPR003349	JmjN domain
SuperFamily	SSF51197	1.81E-25	194	390	No hit	No description
PROSITE profile	PS51184	32.951	201	380	IPR003347	JmjC domain
SMART	SM00558	1.0E-42	211	380	IPR003347	JmjC domain
Pfam	PF02373	5.8E-35	244	363	IPR003347	JmjC domain
SMART	SM00355	21	1033	1055	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0084	1056	1080	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.736	1056	1085	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	4.2E-5	1057	1084	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1058	1080	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	9.67E-10	1072	1114	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.5E-8	1085	1110	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.261	1086	1115	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0016	1086	1110	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1088	1110	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	4.7E-8	1104	1138	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.8E-9	1111	1139	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.55	1116	1142	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.346	1116	1147	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1118	1142	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:0040010	Biological Process	positive regulation of growth rate
GO:0045815	Biological Process	positive regulation of gene expression, epigenetic
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
GO:0071558	Molecular Function	histone demethylase activity (H3-K27 specific)

Sequence ? help Back to Top
Protein Sequence Length: 1150 aa Download sequence Send to blast
MVTSSTTAAT VDAHPLDILP WLKTLPLAPE YHPTVAEFQD PIAYILKIEK EASTYGICKI 60 VPPIPAPPRK TVITNLNRLF SSRSSVSDGG GGGGSKKKPL PTFSTRQQQI GFCPRKSRPA 120 KKPVWHSGEQ YTLQQFEVKA KQFEKTQLKR CGRKGPNVGF SALEVETLFW KASMDKPLMI 180 EYANDMPGSG FIPLPLTTMA KKWREEDNLC NVGDTTWNMR GVSRAKGSLL KFMKEDIPGV 240 SSPMVYIAMM FSWFAWHVED HELHSLNYMH MGASKTWYGV PRDAGLAFEE VIRIHGYGGE 300 VNPLVTFSIL SEKTTVMSPE ELTGAKIPCC RLVQNAGDFV VTFPGSYHCG FSHGFNCGEA 360 ANIATPEWLK VAKEAAVRRA SINYPPMISH FQLLYELALS LSSRVIPSSS YTTEPRSSRL 420 KDKMKGEGEV MVKDLFVEDI IQTNTLLHVL LNKGGSSSCV VVLPHTTNNN SSSSSSLNST 480 MKLKQQRISN GLCSTSSSVS NTFRNNHLGK CSRIRNGGSG LLSNSCDAED DDTSSIIGKE 540 MSSGFGNEGL LDQGLLSCVA CGILSSACVA IIQPTPEAAL RLMSANENSL DNQSYEPTAW 600 STPDVIKNNQ EEVNRRSGYL DKGPSGLDLL ASAYGNSSSD SEEEDNIDKV ENNGERISAH 660 SFNIPNSSNL MMIDSRSFIC REENRDSSRM HIFCLEHAQD VERQLSPIGG VQMMIVCYPE 720 YPKLQTEAKL MAGEMRKEYT WKDMDFKEAT EEDCERIQSA LDDEQVIPTN SDWAVKIHVN 780 LYYSSNLSKS SLYSKQLPYN AIIYKAFGRN LSSSSEGPPE QQQIKVFRRR RGRQKKIVVA 840 GKWCGKVWMS NQVHPLLSSN HKNDYEEHND NGDFQGEFSD HKPAADENDD EYDVKDEEET 900 TLMVASGRRK KKLVGNRLIG KKTKNTSKLA KSAPEVEDGE EDLINNSEKS KRVLRERKKT 960 VRSCLNHDSP GEDEDDEEEE VSLTTRLRRK RPAPKKNNKV EKKLKKSNTK KKEEEAPLNV 1020 TVKEDDEDDS EEYQCDMDGC TMSFTSLQDL SIHKANICPV KDCGKKFFSH KYLVQHRRVH 1080 LDDRPLKCPW KGCKMSFKWA WARTEHIRVH TGDRPYICME RGCGQTFRFV SDFSRHKRKT 1140 GHVTKKGRR*

Sequence ? help Back to Top

Protein Sequence Length: 1150 aa Download sequence Send to blast

MVTSSTTAAT VDAHPLDILP WLKTLPLAPE YHPTVAEFQD PIAYILKIEK EASTYGICKI  60
VPPIPAPPRK TVITNLNRLF SSRSSVSDGG GGGGSKKKPL PTFSTRQQQI GFCPRKSRPA  120
KKPVWHSGEQ YTLQQFEVKA KQFEKTQLKR CGRKGPNVGF SALEVETLFW KASMDKPLMI  180
EYANDMPGSG FIPLPLTTMA KKWREEDNLC NVGDTTWNMR GVSRAKGSLL KFMKEDIPGV  240
SSPMVYIAMM FSWFAWHVED HELHSLNYMH MGASKTWYGV PRDAGLAFEE VIRIHGYGGE  300
VNPLVTFSIL SEKTTVMSPE ELTGAKIPCC RLVQNAGDFV VTFPGSYHCG FSHGFNCGEA  360
ANIATPEWLK VAKEAAVRRA SINYPPMISH FQLLYELALS LSSRVIPSSS YTTEPRSSRL  420
KDKMKGEGEV MVKDLFVEDI IQTNTLLHVL LNKGGSSSCV VVLPHTTNNN SSSSSSLNST  480
MKLKQQRISN GLCSTSSSVS NTFRNNHLGK CSRIRNGGSG LLSNSCDAED DDTSSIIGKE  540
MSSGFGNEGL LDQGLLSCVA CGILSSACVA IIQPTPEAAL RLMSANENSL DNQSYEPTAW  600
STPDVIKNNQ EEVNRRSGYL DKGPSGLDLL ASAYGNSSSD SEEEDNIDKV ENNGERISAH  660
SFNIPNSSNL MMIDSRSFIC REENRDSSRM HIFCLEHAQD VERQLSPIGG VQMMIVCYPE  720
YPKLQTEAKL MAGEMRKEYT WKDMDFKEAT EEDCERIQSA LDDEQVIPTN SDWAVKIHVN  780
LYYSSNLSKS SLYSKQLPYN AIIYKAFGRN LSSSSEGPPE QQQIKVFRRR RGRQKKIVVA  840
GKWCGKVWMS NQVHPLLSSN HKNDYEEHND NGDFQGEFSD HKPAADENDD EYDVKDEEET  900
TLMVASGRRK KKLVGNRLIG KKTKNTSKLA KSAPEVEDGE EDLINNSEKS KRVLRERKKT  960
VRSCLNHDSP GEDEDDEEEE VSLTTRLRRK RPAPKKNNKV EKKLKKSNTK KKEEEAPLNV  1020
TVKEDDEDDS EEYQCDMDGC TMSFTSLQDL SIHKANICPV KDCGKKFFSH KYLVQHRRVH  1080
LDDRPLKCPW KGCKMSFKWA WARTEHIRVH TGDRPYICME RGCGQTFRFV SDFSRHKRKT  1140
GHVTKKGRR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	2e-70	17	403	4	355	Transcription factor jumonji (Jmj) family protein
6ip4_A	2e-70	17	403	4	355	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	907	912	RRKKKL
2	990	999	RPAPKKNNKV

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_020106930.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A0K9NS69	0.0	A0A0K9NS69_ZOSMR; Zinc finger protein
STRING	VIT_17s0000g09980.t01	0.0	(Vitis vinifera)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP5346	32	46

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	Zosma72g00070.1

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]