PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Saxifragales; Crassulaceae; Kalanchoe

Family

C2H2

Protein Properties

Length: 1270aa MW: 143110 Da PI: 8.2969

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Kalax.0032s0033.1.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	12.8	0.00036	1153	1178	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C+++F++k +L H r+ + Kalax.0032s0033.1.p 1153 YQCDmeGCTMTFNSKQELLLHKRNiC 1178 99********************9877 PP
2	zf-C2H2	14.3	0.00012	1178	1200	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Kalax.0032s0033.1.p 1178 CPvkGCGKKFISHKYLVQHKRVH 1200 9999*****************99 PP
3	zf-C2H2	11.1	0.0012	1236	1262	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y C Cg++F+ s++ rH r+ H Kalax.0032s0033.1.p 1236 YICAepGCGQTFRFVSDFSRHKRKtgH 1262 789999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	9.8E-14	28	69	IPR003349	JmjN domain
PROSITE profile	PS51183	13.536	29	70	IPR003349	JmjN domain
Pfam	PF02375	2.5E-13	30	63	IPR003349	JmjN domain
SMART	SM00558	1.3E-47	194	363	IPR003347	JmjC domain
PROSITE profile	PS51184	34.584	197	363	IPR003347	JmjC domain
SuperFamily	SSF51197	1.62E-26	212	358	No hit	No description
Pfam	PF02373	2.7E-37	227	346	IPR003347	JmjC domain
SMART	SM00355	7.1	1153	1175	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.528	1176	1205	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.47E-6	1176	1212	No hit	No description
SMART	SM00355	0.0031	1176	1200	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	7.1E-6	1177	1199	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1178	1200	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	9.9E-10	1200	1228	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.554	1206	1235	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0036	1206	1230	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1208	1230	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.76E-9	1216	1260	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.5E-9	1229	1259	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.803	1236	1267	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.79	1236	1262	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1238	1262	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: 1270 aa Download sequence Send to blast
MEKGGAEHQG QGQAGQREVF QWLKTLPQAP EYRPTLAEFH DPVSYIFKIE KEASRYGICK 60 IIPPVPPQLK KTSLANLNRS LAARAPDSAP AFATRQQQIG FCPRKSRPVQ RPVWQSGERY 120 TVQEFEAKAK VFEKNYLKRV GKRAGLSALE METLYWKASL DKPFTVEYAN DMPGSAFVQM 180 KPDRKWRETG DGVNVGETAW NMRGVSRSNL SLLRFLKEEI PGVTSPMLYI AMMFSWFAWH 240 AEDHDMHSLN YLHLGASKTW YGVPKDAAAA FEEVVRVQGY GGEINPLVTF ATLGEKTTIM 300 SPEIFIKAGI PCCRLVQNPG EFVVTFPRAY HTGFSHGFNV GEAANFATPE WLRVAKEAAI 360 RRASVNFPPM LSHAQLLYDL VFALCSRTSS INHGPRSSRL KDKRKSEGET VVKELFVQDV 420 LQNNDQLYLL AQGSCVVTLP ESASGFSISL QSSNRSLIDE KSSLTTGFCS QKEETSASKG 480 VISCGFGRQK SRKSLKNNVN FSVGDNLCSV SERSKPTLNS GESYPASRTS NRWATDQRVF 540 SCVACGILCF PCIAIIQPSE AAKKYIMSAD HSVFHDGIIP SGTTSDGLAV TGKDNINDMN 600 FSSRWREKSP PSSSYEFQEK NESDEVTSEI EEQPEAIGAL GLLASTYANS SDSEDEQFET 660 DSPVLADGPN FSKVSADSDF EFDDAPDHKQ EHDDETNAEH SLSSSKFHIE DEHALLNTVS 720 YQENEQGGPF VDNHHRYTYL DGPNEFPSDS ITKSDSVNHT ASKAKRTGYP RLYHNSSRMH 780 IFCLEHAVEI ESQLQKIGGA HMLLLCHPDY PRIEIEAKMI AEELGLYEHW NDIAFRDATK 840 EDEECIQTVL ENDKGTPRNG DWAVKLGIDL LYSVNLSRSS LYSKQMPFNS IIYNAFGRVP 900 PGEDALTPKM GKRVGNKQKR IKLAGKWCGK VWMSNQVHPL LIPRDQEEPE EDTIINDWPE 960 SDPDDTFNVN PNYACLDEPD TVTDKFGTKR KIVVYSRSNK KAKVSEKMDP IGSPDQAGCS 1020 TQRRPVRMVR SRYMKIEGSE DTKPLDKQKQ GLTQLISHDE DFEVRPRTRI RKRNPKFEED 1080 FEAERPLRKL VYSRKASKTP SRKPPVRSNE ANMKMEPASR SKSIRNEEAP RPRISPNGDA 1140 LRPRKLNGEE AAYQCDMEGC TMTFNSKQEL LLHKRNICPV KGCGKKFISH KYLVQHKRVH 1200 VDDRPLKCPW KGCKMAFKWA WARTEHIRVH TGVRPYICAE PGCGQTFRFV SDFSRHKRKT 1260 GHSTKKVRK*

Sequence ? help Back to Top

Protein Sequence Length: 1270 aa Download sequence Send to blast

MEKGGAEHQG QGQAGQREVF QWLKTLPQAP EYRPTLAEFH DPVSYIFKIE KEASRYGICK  60
IIPPVPPQLK KTSLANLNRS LAARAPDSAP AFATRQQQIG FCPRKSRPVQ RPVWQSGERY  120
TVQEFEAKAK VFEKNYLKRV GKRAGLSALE METLYWKASL DKPFTVEYAN DMPGSAFVQM  180
KPDRKWRETG DGVNVGETAW NMRGVSRSNL SLLRFLKEEI PGVTSPMLYI AMMFSWFAWH  240
AEDHDMHSLN YLHLGASKTW YGVPKDAAAA FEEVVRVQGY GGEINPLVTF ATLGEKTTIM  300
SPEIFIKAGI PCCRLVQNPG EFVVTFPRAY HTGFSHGFNV GEAANFATPE WLRVAKEAAI  360
RRASVNFPPM LSHAQLLYDL VFALCSRTSS INHGPRSSRL KDKRKSEGET VVKELFVQDV  420
LQNNDQLYLL AQGSCVVTLP ESASGFSISL QSSNRSLIDE KSSLTTGFCS QKEETSASKG  480
VISCGFGRQK SRKSLKNNVN FSVGDNLCSV SERSKPTLNS GESYPASRTS NRWATDQRVF  540
SCVACGILCF PCIAIIQPSE AAKKYIMSAD HSVFHDGIIP SGTTSDGLAV TGKDNINDMN  600
FSSRWREKSP PSSSYEFQEK NESDEVTSEI EEQPEAIGAL GLLASTYANS SDSEDEQFET  660
DSPVLADGPN FSKVSADSDF EFDDAPDHKQ EHDDETNAEH SLSSSKFHIE DEHALLNTVS  720
YQENEQGGPF VDNHHRYTYL DGPNEFPSDS ITKSDSVNHT ASKAKRTGYP RLYHNSSRMH  780
IFCLEHAVEI ESQLQKIGGA HMLLLCHPDY PRIEIEAKMI AEELGLYEHW NDIAFRDATK  840
EDEECIQTVL ENDKGTPRNG DWAVKLGIDL LYSVNLSRSS LYSKQMPFNS IIYNAFGRVP  900
PGEDALTPKM GKRVGNKQKR IKLAGKWCGK VWMSNQVHPL LIPRDQEEPE EDTIINDWPE  960
SDPDDTFNVN PNYACLDEPD TVTDKFGTKR KIVVYSRSNK KAKVSEKMDP IGSPDQAGCS  1020
TQRRPVRMVR SRYMKIEGSE DTKPLDKQKQ GLTQLISHDE DFEVRPRTRI RKRNPKFEED  1080
FEAERPLRKL VYSRKASKTP SRKPPVRSNE ANMKMEPASR SKSIRNEEAP RPRISPNGDA  1140
LRPRKLNGEE AAYQCDMEGC TMTFNSKQEL LLHKRNICPV KGCGKKFISH KYLVQHKRVH  1200
VDDRPLKCPW KGCKMAFKWA WARTEHIRVH TGVRPYICAE PGCGQTFRFV SDFSRHKRKT  1260
GHSTKKVRK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	1e-77	20	420	6	383	Transcription factor jumonji (Jmj) family protein
6ip4_A	1e-77	20	420	6	383	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}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010663055.1	0.0	PREDICTED: lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	F6GTM2	0.0	F6GTM2_VITVI; Uncharacterized protein
STRING	VIT_17s0000g09980.t01	0.0	(Vitis vinifera)

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	Kalax.0032s0033.1.p

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]