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

906087

Common Name

ARALYDRAFT_906087

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: 1379aa MW: 154908 Da PI: 7.7631

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
906087	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	0.00049	1261	1286	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sFs+ +L+ H r+ + 906087 1261 YQCDmeGCTMSFSSEKQLTLHKRNiC 1286 99********************9877 PP
2	zf-C2H2	15.1	6.8e-05	1286	1308	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H+r+H 906087 1286 CPvkGCGKNFFSHKYLVQHQRVH 1308 9999*****************99 PP
3	zf-C2H2	11.9	0.00067	1344	1370	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H 906087 1344 YVCAepGCGQTFRFVSDFSRHKRKtgH 1370 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	1.1E-16	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	13.689	20	61	IPR003349	JmjN domain
Pfam	PF02375	7.8E-14	21	54	IPR003349	JmjN domain
SuperFamily	SSF51197	2.22E-26	118	179	No hit	No description
SMART	SM00558	1.7E-50	200	369	IPR003347	JmjC domain
PROSITE profile	PS51184	32.65	203	369	IPR003347	JmjC domain
SuperFamily	SSF51197	2.22E-26	218	386	No hit	No description
Pfam	PF02373	2.7E-37	233	352	IPR003347	JmjC domain
SMART	SM00355	7.5	1261	1283	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.01	1284	1308	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	13.173	1284	1313	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1286	1308	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.4E-6	1286	1312	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.61E-10	1300	1342	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.3E-9	1313	1337	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.24	1314	1343	IPR007087	Zinc finger, C2H2
SMART	SM00355	7.0E-4	1314	1338	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1316	1338	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.04E-8	1332	1366	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.9E-9	1338	1367	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.032	1344	1375	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.62	1344	1370	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1346	1370	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0040010	Biological Process	positive regulation of growth rate
GO:0045815	Biological Process	positive regulation of gene expression, epigenetic
GO:0005634	Cellular Component	nucleus
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding
GO:0071558	Molecular Function	histone demethylase activity (H3-K27 specific)

Sequence ? help Back to Top
Protein Sequence Length: 1379 aa Download sequence Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPLPPPS 60 KKTSISNLNR SLAARAAARV RDGGESSFDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS 120 GEHYSFGEFE AKAKTFEKNY LKKCGKKSQL SALEIETLYW RATVDKPFSV EYANDMPGSA 180 FIPLSLAAAR RREYGGDGGT VGETAWNMRA MSRAEGSLLK FMKEEIPGVT SPMVYIAMMF 240 SWFAWHVEDH DLHSLNYLHM GAGKTWYGVP KDAAVAFEEV VRVHGYGGEL NPLVTISTLG 300 EKTTVMSPEV FVKAGIPCCR LVQNPGEFVV TFPRAYHSGF SHGFNCGEAS NIATPEWLRV 360 AKDAAIRRAA INYPPMVSHL QLLYDYALAL GSRVPTSINT KPRSSRLKDK KRSEGERLTK 420 KLFVQNIIHN NELLSSLGKG SPVALLPQSS SDISVCSDLR IGSNLITNQE NPIQLKSEDL 480 SSHSVMVGLN NGLKNTVSVK EKFTSLCERN RNHLASSEKE TQETLSDAER RKNDRAVALS 540 DQRLFSCVTC GVLSFDCVAI VQPKEAAARY LMSADCSFFN DWTVVSGSAN LGQAARSLHL 600 QSTEKHDMDF FYNVPSQTTD HSMNTGDQKT STVSLTTAHK KDGALSLLAS AYGDSSDSEE 660 EGHKVLDAFV SEDRKYDQSG SCAYEASSFD TDGKEEARDG QSSDSNRQRL VCRKETGVVQ 720 GSNATSTCST LSCTTEHSRL RKGSNTSLPF VPRSDNDSSR LHVFCLEHAA EVEQKLLPIG 780 GIHLMLLSHP EYPRIEAEAK IVSEELVINH DWNDTEFRNV TREDEETIQA ALDNVEAKAG 840 NSDWTVKLGI NLSYSAILSR SPLYSKQMPY NSVIYNAFGR SSPAKSSPLK PEIFGRRSSR 900 QRKYVVGKWC GKVWMSHQVH PFLLEQDLEG EESERSCHLR AAMDEDAAGK RFFPNNVSRD 960 ATTMFGRKYC RKRKVRAKTV PRKKLTSFKR EDGVSDDTSE DHSYKQQWRA SGNEEESYFE 1020 TGNTVSGDSS NQMSDQQLKG IRRHRGVKEF ESNDEVSDRS LGEEYAVRER AISESSTENS 1080 FQLYGHSIDD NALEGSLYGH DDNKLYKHPK GLPRSKQTNV FRNPVSYDSE ENDVYQQRGN 1140 IQASRIGGEY ESEEDSLEEE DFCSTRKRQT RSTAKRKVKT EIVQSPRETN KEFDSYMEGP 1200 STRLRVKIPK PSRVSSETKA KKIGKKGSRN ASFSRVATEE DVEEEEEEEE KENEEEECAA 1260 YQCDMEGCTM SFSSEKQLTL HKRNICPVKG CGKNFFSHKY LVQHQRVHSD DRPLKCPWKG 1320 CNMTFKWAWS RTEHIRVHTG ARPYVCAEPG CGQTFRFVSD FSRHKRKTGH SVKKTKKR*

Sequence ? help Back to Top

Protein Sequence Length: 1379 aa Download sequence Send to blast

MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPLPPPS  60
KKTSISNLNR SLAARAAARV RDGGESSFDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS  120
GEHYSFGEFE AKAKTFEKNY LKKCGKKSQL SALEIETLYW RATVDKPFSV EYANDMPGSA  180
FIPLSLAAAR RREYGGDGGT VGETAWNMRA MSRAEGSLLK FMKEEIPGVT SPMVYIAMMF  240
SWFAWHVEDH DLHSLNYLHM GAGKTWYGVP KDAAVAFEEV VRVHGYGGEL NPLVTISTLG  300
EKTTVMSPEV FVKAGIPCCR LVQNPGEFVV TFPRAYHSGF SHGFNCGEAS NIATPEWLRV  360
AKDAAIRRAA INYPPMVSHL QLLYDYALAL GSRVPTSINT KPRSSRLKDK KRSEGERLTK  420
KLFVQNIIHN NELLSSLGKG SPVALLPQSS SDISVCSDLR IGSNLITNQE NPIQLKSEDL  480
SSHSVMVGLN NGLKNTVSVK EKFTSLCERN RNHLASSEKE TQETLSDAER RKNDRAVALS  540
DQRLFSCVTC GVLSFDCVAI VQPKEAAARY LMSADCSFFN DWTVVSGSAN LGQAARSLHL  600
QSTEKHDMDF FYNVPSQTTD HSMNTGDQKT STVSLTTAHK KDGALSLLAS AYGDSSDSEE  660
EGHKVLDAFV SEDRKYDQSG SCAYEASSFD TDGKEEARDG QSSDSNRQRL VCRKETGVVQ  720
GSNATSTCST LSCTTEHSRL RKGSNTSLPF VPRSDNDSSR LHVFCLEHAA EVEQKLLPIG  780
GIHLMLLSHP EYPRIEAEAK IVSEELVINH DWNDTEFRNV TREDEETIQA ALDNVEAKAG  840
NSDWTVKLGI NLSYSAILSR SPLYSKQMPY NSVIYNAFGR SSPAKSSPLK PEIFGRRSSR  900
QRKYVVGKWC GKVWMSHQVH PFLLEQDLEG EESERSCHLR AAMDEDAAGK RFFPNNVSRD  960
ATTMFGRKYC RKRKVRAKTV PRKKLTSFKR EDGVSDDTSE DHSYKQQWRA SGNEEESYFE  1020
TGNTVSGDSS NQMSDQQLKG IRRHRGVKEF ESNDEVSDRS LGEEYAVRER AISESSTENS  1080
FQLYGHSIDD NALEGSLYGH DDNKLYKHPK GLPRSKQTNV FRNPVSYDSE ENDVYQQRGN  1140
IQASRIGGEY ESEEDSLEEE DFCSTRKRQT RSTAKRKVKT EIVQSPRETN KEFDSYMEGP  1200
STRLRVKIPK PSRVSSETKA KKIGKKGSRN ASFSRVATEE DVEEEEEEEE KENEEEECAA  1260
YQCDMEGCTM SFSSEKQLTL HKRNICPVKG CGKNFFSHKY LVQHQRVHSD DRPLKCPWKG  1320
CNMTFKWAWS RTEHIRVHTG ARPYVCAEPG CGQTFRFVSD FSRHKRKTGH SVKKTKKR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	1e-78	1258	1378	20	140	Lysine-specific demethylase REF6
6a58_A	1e-78	1258	1378	20	140	Lysine-specific demethylase REF6
6a59_A	1e-78	1258	1378	20	140	Lysine-specific demethylase REF6
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	971	983	KRKVRAKTVPRKK

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	906087

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	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_020880349.1	0.0	lysine-specific demethylase REF6 isoform X1
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	D7LRW6	0.0	D7LRW6_ARALL; Uncharacterized protein
STRING	scaffold_501791.1	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	906087
Entrez Gene	9311971

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]