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

Kaladp0091s0061.2.p

Organism

Kalanchoe laxiflora

Taxonomic ID

1670617

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: 1197aa MW: 134901 Da PI: 8.2632

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Kaladp0091s0061.2.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	12.9	0.00034	1080	1105	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C+++F++k +L H r+ + Kaladp0091s0061.2.p 1080 YQCDmeGCTMTFNSKQELLLHKRNiC 1105 99********************9877 PP
2	zf-C2H2	14.4	0.00011	1105	1127	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Kaladp0091s0061.2.p 1105 CPvkGCGKKFISHKYLVQHKRVH 1127 9999*****************99 PP
3	zf-C2H2	11.2	0.0012	1163	1189	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y C Cg++F+ s++ rH r+ H Kaladp0091s0061.2.p 1163 YICAepGCGQTFRFVSDFSRHKRKtgH 1189 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	2.4E-13	30	63	IPR003349	JmjN domain
SMART	SM00558	5.1E-11	194	337	IPR003347	JmjC domain
PROSITE profile	PS51184	19.219	197	339	IPR003347	JmjC domain
SuperFamily	SSF51197	5.77E-11	212	281	No hit	No description
Pfam	PF02373	7.1E-20	227	315	IPR003347	JmjC domain
SMART	SM00355	7.1	1080	1102	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.528	1103	1132	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.28E-6	1103	1139	No hit	No description
SMART	SM00355	0.0031	1103	1127	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	6.6E-6	1104	1126	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1105	1127	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	9.2E-10	1127	1155	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.554	1133	1162	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0036	1133	1157	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1135	1157	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.65E-9	1143	1187	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.1E-9	1156	1186	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.803	1163	1194	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.79	1163	1189	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1165	1189	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: 1197 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 PCCRTSSINH GPRSSRLKDK RKSEGETVVK ELFIQDVLQN NDQLYLLAQG 360 SCVVTLPESA SGFSISLQSS NRSLIDEKSS LTTGFCSQKE ETSASKGVIS CGFGRQKSRK 420 SLKNNVNFSV GGNLCSVSER SKPTLNSGES YPSSHTSNRW VTDQRVFSCV ACGILCFPCI 480 AIIQPSEAAK KYIMSADHSV FHDGIIPSGT TSDGLAVTGK DNINDMNFSS RWREKSPRSS 540 SYEFQEKNES DEVTSEIEEQ PEAIGALGLL ASTYANSSDS EHEQFETDSP VLADGPNFSK 600 VSADSDFEFD DAPDHKQEHD DETNAEHSLS SSKFHIEDEH ALLNTVSYQE NEQGGSFVDN 660 HHRYTYLDGP NEFPSDSITK SDSVNHIASK AKRTGYPRLY HNSSRMHIFC LEHAVEIESQ 720 LQKIGGAHML LLCHPDYPRI EIEAKMIAEE LGLYEHWNDI AFRDATKEDE ECIQTVLEND 780 KGTPRNGDWA VKLGIDLLYS VNLSRSSLYS KQMPFNSIIY NAFGRVPPGE DALTPKMGKG 840 VGNKQKRIKL AGKWCGKVWM SNQVHPLLIP RDQEEPEEDT IINDWPESDP DDTFNVNPNY 900 ACLDEPDTVT DKFGTKRKIV VYSRSNKRAK VAEKMDPIGS PDQAGCSTQR RPVRMVRSRY 960 MKIEGSEDTK PLDKQKQGLT QLISHDEDFE VGPRTRIRKR NPKFEEDFEA ERPLRKLVYS 1020 RKASKTPSQK RPVRSNEANM KMEPASRSKS IRNEEAPRPR ISPNGDALRP RKLNGEEAAY 1080 QCDMEGCTMT FNSKQELLLH KRNICPVKGC GKKFISHKYL VQHKRVHVDD RPLKCPWKGC 1140 KMAFKWAWAR TEHIRVHTGV RPYICAEPGC GQTFRFVSDF SRHKRKTGHS TKKVRK*

Sequence ? help Back to Top

Protein Sequence Length: 1197 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 PCCRTSSINH GPRSSRLKDK RKSEGETVVK ELFIQDVLQN NDQLYLLAQG  360
SCVVTLPESA SGFSISLQSS NRSLIDEKSS LTTGFCSQKE ETSASKGVIS CGFGRQKSRK  420
SLKNNVNFSV GGNLCSVSER SKPTLNSGES YPSSHTSNRW VTDQRVFSCV ACGILCFPCI  480
AIIQPSEAAK KYIMSADHSV FHDGIIPSGT TSDGLAVTGK DNINDMNFSS RWREKSPRSS  540
SYEFQEKNES DEVTSEIEEQ PEAIGALGLL ASTYANSSDS EHEQFETDSP VLADGPNFSK  600
VSADSDFEFD DAPDHKQEHD DETNAEHSLS SSKFHIEDEH ALLNTVSYQE NEQGGSFVDN  660
HHRYTYLDGP NEFPSDSITK SDSVNHIASK AKRTGYPRLY HNSSRMHIFC LEHAVEIESQ  720
LQKIGGAHML LLCHPDYPRI EIEAKMIAEE LGLYEHWNDI AFRDATKEDE ECIQTVLEND  780
KGTPRNGDWA VKLGIDLLYS VNLSRSSLYS KQMPFNSIIY NAFGRVPPGE DALTPKMGKG  840
VGNKQKRIKL AGKWCGKVWM SNQVHPLLIP RDQEEPEEDT IINDWPESDP DDTFNVNPNY  900
ACLDEPDTVT DKFGTKRKIV VYSRSNKRAK VAEKMDPIGS PDQAGCSTQR RPVRMVRSRY  960
MKIEGSEDTK PLDKQKQGLT QLISHDEDFE VGPRTRIRKR NPKFEEDFEA ERPLRKLVYS  1020
RKASKTPSQK RPVRSNEANM KMEPASRSKS IRNEEAPRPR ISPNGDALRP RKLNGEEAAY  1080
QCDMEGCTMT FNSKQELLLH KRNICPVKGC GKKFISHKYL VQHKRVHVDD RPLKCPWKGC  1140
KMAFKWAWAR TEHIRVHTGV RPYICAEPGC GQTFRFVSDF SRHKRKTGHS TKKVRK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	4e-69	1078	1196	21	139	Lysine-specific demethylase REF6
6a58_A	4e-69	1078	1196	21	139	Lysine-specific demethylase REF6
6a59_A	4e-69	1078	1196	21	139	Lysine-specific demethylase REF6
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	1e-156	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	1e-147	relative of early flowering 6

Link Out ? help Back to Top
Phytozome	Kaladp0091s0061.2.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]