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

Kalax.0032s0033.2.p

Organism

Kalanchoe marnieriana

Taxonomic ID

80907

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 1248aa MW: 140784 Da PI: 8.3506

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Kalax.0032s0033.2.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	1131	1156	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C+++F++k +L H r+ + Kalax.0032s0033.2.p 1131 YQCDmeGCTMTFNSKQELLLHKRNiC 1156 99********************9877 PP
2	zf-C2H2	14.4	0.00011	1156	1178	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Kalax.0032s0033.2.p 1156 CPvkGCGKKFISHKYLVQHKRVH 1178 9999*****************99 PP
3	zf-C2H2	11.1	0.0012	1214	1240	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y C Cg++F+ s++ rH r+ H Kalax.0032s0033.2.p 1214 YICAepGCGQTFRFVSDFSRHKRKtgH 1240 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	1.57E-26	212	358	No hit	No description
Pfam	PF02373	2.7E-37	227	346	IPR003347	JmjC domain
SMART	SM00355	7.1	1131	1153	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.528	1154	1183	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0031	1154	1178	IPR015880	Zinc finger, C2H2-like
SuperFamily	SSF57667	2.47E-6	1154	1190	No hit	No description
Gene3D	G3DSA:3.30.160.60	7.0E-6	1155	1177	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1156	1178	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	9.7E-10	1178	1206	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0036	1184	1208	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.554	1184	1213	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1186	1208	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.76E-9	1194	1238	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.4E-9	1207	1237	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.79	1214	1240	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.803	1214	1245	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1216	1240	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: 1248 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 SGWREKSPPS SSYEFQEKNE 600 SDEVTSEIEE QPEAIGALGL LASTYANSSD SEDEQFETDS PVLADGPNFS KVSADSDFEF 660 DDAPDHKQEH DDETNAEHSL SSSKFHIEDE HALLNTVSYQ ENEQGGPFVD NHHRYTYLDG 720 PNEFPSDSIT KSDSVNHTAS KAKRTGYPRL YHNSSRMHIF CLEHAVEIES QLQKIGGAHM 780 LLLCHPDYPR IEIEAKMIAE ELGLYEHWND IAFRDATKED EECIQTVLEN DKGTPRNGDW 840 AVKLGIDLLY SVNLSRSSLY SKQMPFNSII YNAFGRVPPG EDALTPKMGK RVGNKQKRIK 900 LAGKWCGKVW MSNQVHPLLI PRDQEEPEED TIINDWPESD PDDTFNVNPN YACLDEPDTV 960 TDKFGTKRKI VVYSRSNKKA KVSEKMDPIG SPDQAGCSTQ RRPVRMVRSR YMKIEGSEDT 1020 KPLDKQKQGL TQLISHDEDF EVRPRTRIRK RNPKFEEDFE AERPLRKLVY SRKASKTPSR 1080 KPPVRSNEAN MKMEPASRSK SIRNEEAPRP RISPNGDALR PRKLNGEEAA YQCDMEGCTM 1140 TFNSKQELLL HKRNICPVKG CGKKFISHKY LVQHKRVHVD DRPLKCPWKG CKMAFKWAWA 1200 RTEHIRVHTG VRPYICAEPG CGQTFRFVSD FSRHKRKTGH STKKVRK*

Sequence ? help Back to Top

Protein Sequence Length: 1248 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 SGWREKSPPS SSYEFQEKNE  600
SDEVTSEIEE QPEAIGALGL LASTYANSSD SEDEQFETDS PVLADGPNFS KVSADSDFEF  660
DDAPDHKQEH DDETNAEHSL SSSKFHIEDE HALLNTVSYQ ENEQGGPFVD NHHRYTYLDG  720
PNEFPSDSIT KSDSVNHTAS KAKRTGYPRL YHNSSRMHIF CLEHAVEIES QLQKIGGAHM  780
LLLCHPDYPR IEIEAKMIAE ELGLYEHWND IAFRDATKED EECIQTVLEN DKGTPRNGDW  840
AVKLGIDLLY SVNLSRSSLY SKQMPFNSII YNAFGRVPPG EDALTPKMGK RVGNKQKRIK  900
LAGKWCGKVW MSNQVHPLLI PRDQEEPEED TIINDWPESD PDDTFNVNPN YACLDEPDTV  960
TDKFGTKRKI VVYSRSNKKA KVSEKMDPIG SPDQAGCSTQ RRPVRMVRSR YMKIEGSEDT  1020
KPLDKQKQGL TQLISHDEDF EVRPRTRIRK RNPKFEEDFE AERPLRKLVY SRKASKTPSR  1080
KPPVRSNEAN MKMEPASRSK SIRNEEAPRP RISPNGDALR PRKLNGEEAA YQCDMEGCTM  1140
TFNSKQELLL HKRNICPVKG CGKKFISHKY LVQHKRVHVD DRPLKCPWKG CKMAFKWAWA  1200
RTEHIRVHTG VRPYICAEPG CGQTFRFVSD FSRHKRKTGH STKKVRK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	2e-77	20	420	6	383	Transcription factor jumonji (Jmj) family protein
6ip4_A	2e-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.0032s0033.2.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]