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

485204

Common Name

ARALYDRAFT_485204

Organism

Arabidopsis lyrata

Taxonomic ID

81972

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 1358aa MW: 152229 Da PI: 7.2982

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
485204	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.4	0.00048	1240	1265	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sFs+ +L+ H r+ + 485204 1240 YQCDmeGCTMSFSSEKQLTLHKRNiC 1265 99********************9877 PP
2	zf-C2H2	15.1	6.7e-05	1265	1287	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H+r+H 485204 1265 CPvkGCGKNFFSHKYLVQHQRVH 1287 9999*****************99 PP
3	zf-C2H2	12	0.00065	1323	1349	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H 485204 1323 YVCAepGCGQTFRFVSDFSRHKRKtgH 1349 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	7.6E-18	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	13.744	20	61	IPR003349	JmjN domain
Pfam	PF02375	6.3E-14	21	54	IPR003349	JmjN domain
SMART	SM00558	6.2E-53	200	369	IPR003347	JmjC domain
PROSITE profile	PS51184	33.99	203	369	IPR003347	JmjC domain
SuperFamily	SSF51197	8.79E-28	216	387	No hit	No description
Pfam	PF02373	1.4E-37	233	352	IPR003347	JmjC domain
SMART	SM00355	7.5	1240	1262	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.01	1263	1287	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	13.173	1263	1292	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.4E-6	1265	1291	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1265	1287	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.82E-10	1279	1321	No hit	No description
Gene3D	G3DSA:3.30.160.60	9.6E-9	1292	1316	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0015	1293	1317	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.928	1293	1322	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1295	1317	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.04E-8	1311	1345	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.9E-9	1317	1346	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.62	1323	1349	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.032	1323	1354	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1325	1349	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: 1358 aa Download sequence Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYILKI EEEASRYGIC KILPPLPPPS 60 KKTSISNLNR SLAARAAARV RDGGFGACDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS 120 GEEYSFGEFE FKAKNFEKNY LKKCGKKSQL SALEIETLYW RATVDKPFSV EYANDMPGSA 180 FIPLSLAAAR RRESGGEGGT VGETAWNMRA MSRAEGSLLK FMKEEIPGVT SPMVYIAMMF 240 SWFAWHVEDH DLHSLNYLHM GAGKTWYGVP KDAAVAFEEV VRVHGYGGEL NPLVTFSTLG 300 EKTTVMSPEV FVKAGIPCCR LVQNPGDFVV TFPGAYHSGF SHGFNFGEAS NIATPEWLRM 360 AKDAAIRRAA INYPPMVSHL QLLYDFALAL GSRVPTSINA KPRSSRLKDK LRSEGERLTK 420 KLFVQNIIHN NELLSSLGKG SPVALLPQSS SDISVCSDLR IGSHLITNQE NPILLKSEDL 480 SSDSVMVGLS NGLKDTVSVK EKFTSLCERS RNHLASREKD TQETLSDAER RKNDGAVALS 540 DQRLFSCVTC GVLSFDCVAI VQPKEAAARY LMSADCSFFN DWTAASGSAN LGQAARSLHP 600 QSTEKHDVNY FYNDPVQTMD HSMKTGDQRT STTSLTMAHK DNGALGLLAS AYGDSSDSEE 660 EGQKGLDVPT SEGETKKYDQ EDADGNEEAR DGRTSDFNSQ RLTSEQNRLS KGGNSSLLEI 720 ALPFIPRSDD DSCRLHVFCL EHAAEVEQQL RPFGGIHIML LCHPEYPRIE AEAKIVAEEL 780 VINHEWNDTE FRNVTREDEE TIQAALDNVE PKGGNSDWTV KLGINLSYSA ILSRSPLYSK 840 QMPYNSVIYN AFGRSSPATS SPLKPEVSGK RSSRQRKYVV GKWCGKVWMS HQVHPFLLEQ 900 DLEGEESERN CHLRGALVED VTRTGLLPCN VSRDATTMFG RKYCRKRKVR AKAVPRKKLT 960 SFKREDGVSD DTSEDHSYKQ QWRASGNEEE SYFETGNTVS GDSSNQMSDQ QLKGIRRHRG 1020 VKEFESDNEV SDRSLGEEYT VRGCAASESS MENGFQQSMY DDDDDDDDID RHPRGIPRSE 1080 RIAVFRNPVS YDSEENGIYH QRGRVSRSNR QANRMGGEYD SEENSLEEQD FCSTGKRQTR 1140 STAKRKVKIE TVRSPRDTKG RTLQEFASGK KNEELDSYME GPSTRLRVRN LKPLRAASET 1200 KPKKIGKKRS GNASFSRVAT EEDMEEDEEA ENEEEECAAY QCDMEGCTMS FSSEKQLTLH 1260 KRNICPVKGC GKNFFSHKYL VQHQRVHSDD RPLKCPWKGC KMTFKWAWSR TEHIRVHTGA 1320 RPYVCAEPGC GQTFRFVSDF SRHKRKTGHS VKKTKKR*

Sequence ? help Back to Top

Protein Sequence Length: 1358 aa Download sequence Send to blast

MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYILKI EEEASRYGIC KILPPLPPPS  60
KKTSISNLNR SLAARAAARV RDGGFGACDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS  120
GEEYSFGEFE FKAKNFEKNY LKKCGKKSQL SALEIETLYW RATVDKPFSV EYANDMPGSA  180
FIPLSLAAAR RRESGGEGGT VGETAWNMRA MSRAEGSLLK FMKEEIPGVT SPMVYIAMMF  240
SWFAWHVEDH DLHSLNYLHM GAGKTWYGVP KDAAVAFEEV VRVHGYGGEL NPLVTFSTLG  300
EKTTVMSPEV FVKAGIPCCR LVQNPGDFVV TFPGAYHSGF SHGFNFGEAS NIATPEWLRM  360
AKDAAIRRAA INYPPMVSHL QLLYDFALAL GSRVPTSINA KPRSSRLKDK LRSEGERLTK  420
KLFVQNIIHN NELLSSLGKG SPVALLPQSS SDISVCSDLR IGSHLITNQE NPILLKSEDL  480
SSDSVMVGLS NGLKDTVSVK EKFTSLCERS RNHLASREKD TQETLSDAER RKNDGAVALS  540
DQRLFSCVTC GVLSFDCVAI VQPKEAAARY LMSADCSFFN DWTAASGSAN LGQAARSLHP  600
QSTEKHDVNY FYNDPVQTMD HSMKTGDQRT STTSLTMAHK DNGALGLLAS AYGDSSDSEE  660
EGQKGLDVPT SEGETKKYDQ EDADGNEEAR DGRTSDFNSQ RLTSEQNRLS KGGNSSLLEI  720
ALPFIPRSDD DSCRLHVFCL EHAAEVEQQL RPFGGIHIML LCHPEYPRIE AEAKIVAEEL  780
VINHEWNDTE FRNVTREDEE TIQAALDNVE PKGGNSDWTV KLGINLSYSA ILSRSPLYSK  840
QMPYNSVIYN AFGRSSPATS SPLKPEVSGK RSSRQRKYVV GKWCGKVWMS HQVHPFLLEQ  900
DLEGEESERN CHLRGALVED VTRTGLLPCN VSRDATTMFG RKYCRKRKVR AKAVPRKKLT  960
SFKREDGVSD DTSEDHSYKQ QWRASGNEEE SYFETGNTVS GDSSNQMSDQ QLKGIRRHRG  1020
VKEFESDNEV SDRSLGEEYT VRGCAASESS MENGFQQSMY DDDDDDDDID RHPRGIPRSE  1080
RIAVFRNPVS YDSEENGIYH QRGRVSRSNR QANRMGGEYD SEENSLEEQD FCSTGKRQTR  1140
STAKRKVKIE TVRSPRDTKG RTLQEFASGK KNEELDSYME GPSTRLRVRN LKPLRAASET  1200
KPKKIGKKRS GNASFSRVAT EEDMEEDEEA ENEEEECAAY QCDMEGCTMS FSSEKQLTLH  1260
KRNICPVKGC GKNFFSHKYL VQHQRVHSDD RPLKCPWKGC KMTFKWAWSR TEHIRVHTGA  1320
RPYVCAEPGC GQTFRFVSDF SRHKRKTGHS VKKTKKR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	4e-79	1237	1357	20	140	Lysine-specific demethylase REF6
6a58_A	4e-79	1237	1357	20	140	Lysine-specific demethylase REF6
6a59_A	4e-79	1237	1357	20	140	Lysine-specific demethylase REF6
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	945	957	KRKVRAKAVPRKK

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	485204

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_002875902.1	0.0	lysine-specific demethylase REF6 isoform X2
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	D7LRW5	0.0	D7LRW5_ARALL; Uncharacterized protein
STRING	fgenesh2_kg.5__1196__AT3G48430.1	0.0	(Arabidopsis lyrata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5259	28	43

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	485204
Entrez Gene	9311970

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]