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

KFK34139.1

Organism

Arabis alpina

Taxonomic ID

50452

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Arabideae; Arabis

Family

C2H2

Protein Properties

Length: 1352aa MW: 152071 Da PI: 8.5922

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KFK34139.1	genome	MPIPBR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.5	0.00044	1235	1260	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 ++C C++sF++ +L +H r+ + KFK34139.1 1235 FQCDleGCTMSFNSEKELAVHKRNiC 1260 89********************9877 PP
2	zf-C2H2	11.8	0.00075	1260	1282	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L +H r+H KFK34139.1 1260 CPvkGCGKNFFSHKYLLQHRRVH 1282 9999*****************99 PP
3	zf-C2H2	12	0.00065	1318	1344	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H KFK34139.1 1318 YVCAepGCGQTFRFVSDFSRHKRKtgH 1344 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	1.0E-15	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	13.786	20	61	IPR003349	JmjN domain
Pfam	PF02375	7.7E-14	21	54	IPR003349	JmjN domain
SMART	SM00558	2.2E-51	200	369	IPR003347	JmjC domain
PROSITE profile	PS51184	33.823	203	369	IPR003347	JmjC domain
SuperFamily	SSF51197	4.39E-27	218	387	No hit	No description
Pfam	PF02373	1.7E-37	234	352	IPR003347	JmjC domain
SMART	SM00355	12	1235	1257	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.902	1258	1287	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.02	1258	1282	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1260	1282	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	9.0E-6	1260	1286	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	6.87E-10	1274	1316	No hit	No description
Gene3D	G3DSA:3.30.160.60	9.6E-9	1287	1311	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0015	1288	1312	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.928	1288	1317	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1290	1312	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.04E-8	1306	1340	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.8E-9	1312	1341	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.62	1318	1344	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.032	1318	1349	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1320	1344	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: 1352 aa Download sequence Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPVPPPS 60 KKTAISNLNR SLAARAAARV RDGGGSAFDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS 120 GEHYSFGEFE YKAKTFEKNY LKKCSKKSQL SALEMETLYW KATVDKPFSV EYANDMPGSA 180 FIPLSLAAAR RREYGGDGGT VGETAWNMRA MARAEGSLLK FMKEEIPGVT SPMIYIAMMF 240 SWFAWHVEDH DLHSLNYLHM GASKTWYGVP KDAAVAFEEV VRVHGYGGEL NPLVTFSTLG 300 EKTTVMSPEV FVKAGIPCCR LVQNPGDFVV TFPRAYHSGF SHGFNCGEAS NIATPEWLRM 360 AKDAAIRRAA ISYRPIVSHL QLLYDFALAL GSRVPTSIHT KPRSSRLKDK KRSEGEKLTK 420 ELFVQNIIHN NELLHSLGKG SPIALLPQSS SDKSVCSDQR KSLHLYXXXX MVSLSNGVKD 480 TVSVKEKFTS LCERNRNHLE KETQGTLTDA ERRKNVRLSD QRLFSCVTCG ILSFDCVAIV 540 QPKEAAARYL MSADCSFFND WTVASGSANL GQVARSLHPQ SMEKHDADYF YDVPIEIMDQ 600 RTSSTSLTKA QKDNDALGLL ASAYGDSSDS EEEDHKGIDI PISEGAFKAS SVDTDGKEEA 660 RDGRSSDFNS QRLSCGKGKE VEVSHATSTC STLSCTSKQN KLSKGDNTSL VEIALPFVPR 720 SDDDSSRLHV FCLEHAAEVE EQLRPIGGIH IMLLCHPEYP RIEAEAKIVA EELGVNQEWN 780 DTEFRNVTQE DEETIQAALD NVGTKAGNSD WAVKLGINLS YSAILSRSPL YSKQMPYNSI 840 IYNAFGRSSP ATSSPSKLEI SGKRSSRQRK YVVGKWCGKV WMSHQVHPFL LQQDLEGEES 900 DRSHHLRVAL DEDVTGKRLF PGNNSRDATT MFGRKYSRKR KMRAKAVPRK KLTSFKREDG 960 VSDDTSEDHS YKQQWRASDN EEESYFEIGN TGSGDSSNHM SDHQQLKGSR RHKGLKEFES 1020 GDEASDRSLG EEYAVRDYAV SESSMENSFE LYREKQSRYD HEDDDLYRYP RGIPRNKRAK 1080 VFRNPVSYDS EENGAYQQRR RVSTSKQARR MGGEYDSAEN SLEEQNFSVT GKRQTRSTAK 1140 RKAKIEAVQS PSDTEGCGLQ GFASGKKNRE LDSYMEGPST RLRVRNLKPS RGSKVTKPKK 1200 TGRKGISIAT FSRAASEEEL EEDEGENEEE ERTAFQCDLE GCTMSFNSEK ELAVHKRNIC 1260 PVKGCGKNFF SHKYLLQHRR VHSDDRPLKC PWKGCKMTFK WAWSRTEHIR VHTGARPYVC 1320 AEPGCGQTFR FVSDFSRHKR KTGHSVKKTK KR

Sequence ? help Back to Top

Protein Sequence Length: 1352 aa Download sequence Send to blast

MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPVPPPS  60
KKTAISNLNR SLAARAAARV RDGGGSAFDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS  120
GEHYSFGEFE YKAKTFEKNY LKKCSKKSQL SALEMETLYW KATVDKPFSV EYANDMPGSA  180
FIPLSLAAAR RREYGGDGGT VGETAWNMRA MARAEGSLLK FMKEEIPGVT SPMIYIAMMF  240
SWFAWHVEDH DLHSLNYLHM GASKTWYGVP KDAAVAFEEV VRVHGYGGEL NPLVTFSTLG  300
EKTTVMSPEV FVKAGIPCCR LVQNPGDFVV TFPRAYHSGF SHGFNCGEAS NIATPEWLRM  360
AKDAAIRRAA ISYRPIVSHL QLLYDFALAL GSRVPTSIHT KPRSSRLKDK KRSEGEKLTK  420
ELFVQNIIHN NELLHSLGKG SPIALLPQSS SDKSVCSDQR KSLHLYXXXX MVSLSNGVKD  480
TVSVKEKFTS LCERNRNHLE KETQGTLTDA ERRKNVRLSD QRLFSCVTCG ILSFDCVAIV  540
QPKEAAARYL MSADCSFFND WTVASGSANL GQVARSLHPQ SMEKHDADYF YDVPIEIMDQ  600
RTSSTSLTKA QKDNDALGLL ASAYGDSSDS EEEDHKGIDI PISEGAFKAS SVDTDGKEEA  660
RDGRSSDFNS QRLSCGKGKE VEVSHATSTC STLSCTSKQN KLSKGDNTSL VEIALPFVPR  720
SDDDSSRLHV FCLEHAAEVE EQLRPIGGIH IMLLCHPEYP RIEAEAKIVA EELGVNQEWN  780
DTEFRNVTQE DEETIQAALD NVGTKAGNSD WAVKLGINLS YSAILSRSPL YSKQMPYNSI  840
IYNAFGRSSP ATSSPSKLEI SGKRSSRQRK YVVGKWCGKV WMSHQVHPFL LQQDLEGEES  900
DRSHHLRVAL DEDVTGKRLF PGNNSRDATT MFGRKYSRKR KMRAKAVPRK KLTSFKREDG  960
VSDDTSEDHS YKQQWRASDN EEESYFEIGN TGSGDSSNHM SDHQQLKGSR RHKGLKEFES  1020
GDEASDRSLG EEYAVRDYAV SESSMENSFE LYREKQSRYD HEDDDLYRYP RGIPRNKRAK  1080
VFRNPVSYDS EENGAYQQRR RVSTSKQARR MGGEYDSAEN SLEEQNFSVT GKRQTRSTAK  1140
RKAKIEAVQS PSDTEGCGLQ GFASGKKNRE LDSYMEGPST RLRVRNLKPS RGSKVTKPKK  1200
TGRKGISIAT FSRAASEEEL EEDEGENEEE ERTAFQCDLE GCTMSFNSEK ELAVHKRNIC  1260
PVKGCGKNFF SHKYLLQHRR VHSDDRPLKC PWKGCKMTFK WAWSRTEHIR VHTGARPYVC  1320
AEPGCGQTFR FVSDFSRHKR KTGHSVKKTK KR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	3e-74	1234	1352	22	140	Lysine-specific demethylase REF6
6a58_A	3e-74	1234	1352	22	140	Lysine-specific demethylase REF6
6a59_A	3e-74	1234	1352	22	140	Lysine-specific demethylase REF6
6ip0_A	5e-73	9	465	4	421	Transcription factor jumonji (Jmj) family protein
6ip4_A	5e-73	9	465	4	421	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	936	941	SRKRKM
2	938	950	KRKMRAKAVPRKK

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	KFK34139.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY664499	0.0	AY664499.1 Arabidopsis thaliana relative of early flowering 6 (REF6) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006404261.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A087GW87	0.0	A0A087GW87_ARAAL; Uncharacterized protein
STRING	A0A087GW86	0.0	(Arabis alpina)

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]