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

Thhalv10010068m

Common Name

EUTSA_v10010068mg

Organism

Eutrema salsugineum

Taxonomic ID

72664

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 1365aa MW: 154111 Da PI: 8.0399

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thhalv10010068m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15.1	6.7e-05	1272	1294	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H+r+H Thhalv10010068m 1272 CPvkGCGKNFFSHKYLVQHQRVH 1294 9999*****************99 PP
2	zf-C2H2	10.8	0.0016	1330	1356	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C C+++F+ s++ rH r+ H Thhalv10010068m 1330 YVCAepGCDQTFRFVSDFSRHKRKtgH 1356 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	3.4E-16	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	14.077	20	61	IPR003349	JmjN domain
Pfam	PF02375	1.0E-14	21	54	IPR003349	JmjN domain
SMART	SM00558	1.1E-50	199	368	IPR003347	JmjC domain
PROSITE profile	PS51184	33.062	202	368	IPR003347	JmjC domain
SuperFamily	SSF51197	2.5E-26	214	386	No hit	No description
Pfam	PF02373	1.9E-37	232	351	IPR003347	JmjC domain
SMART	SM00355	11	1247	1269	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	13.173	1270	1299	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.01	1270	1294	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.2E-6	1271	1293	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1272	1294	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	4.03E-10	1286	1328	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.0E-9	1294	1320	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.928	1300	1329	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0015	1300	1324	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1302	1324	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	5.87E-8	1318	1352	No hit	No description
Gene3D	G3DSA:3.30.160.60	4.7E-9	1321	1353	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.242	1330	1361	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.9	1330	1356	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1332	1356	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: 1365 aa Download sequence Send to blast
MVVSEQSPDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KIVPPVPPPS 60 KKTTISNLNR SLASLATARV RDGGDAFDYD GAPTFATRQQ QIGFCPRKQR PVQRPVWQSG 120 EHYSFGEFEF KAKNFEKNYL RKCGKKSQLS ALEIETLYWR ATVDKPFSVE YANDMPGSAF 180 IPLSLAAARR RESGGDGGTV GETAWNMRAM ARAEGSLLKF MKEEIPGVTS PMVYIAMMFS 240 WFAWHVEDHD LHSLNYLHMG ASKTWYGVPK DAAVAFEEVV RVHGYGGELN PLVTFSTLGD 300 KTTVMSPEVF VKAGIPCCRL VQNPGEFVVT FPRAYHSGFS HGFNCGEASN IATPEWLRIA 360 KDAAIRRAAI NYPPMVSHLQ LLYDFALALC SRVPTSIHTK PRSSRLKDKK RSEGEKLTKE 420 LFVQNIIHNN ELLRSLGKRS PVALLPQSSS DVSVCSDLRV GSHLRTNQER PIQLKSEDFS 480 SDSIMAGLSN GFKDVVSVKE KFTSLCERNR NYLASRENET QGTLTDAERK NDRAVGLSDQ 540 RLFSCVTCGI LCFDCVAIVQ PKEAAARYLM SADCSFFNDW TATSGSANLG QDSRFSAVKP 600 HSESTGKHDV DDFYNVPVQT TDERTSTTSL TKAQKEDGAL GLLASAYGDS SDSEEEDHKG 660 LDTIISEERK YDHNGIEEAT DGQAFDNSSQ RLSCGKGKGV VEGSNAAEHD RLSNGGSTSN 720 LEIAFPFVPR SDDDSSRLHV FCLEHAAEVE QQLRPLGGIR IMLLCHPEYP RIEAEAKIVA 780 DELGVNHEWN DTEFRNVTRE DEEMIQAALD NVEAKAGNSD WSVKLGINLS YSAILSRSPL 840 YSKQMPYNSV IYNAFGRGSP ATSSPTKPQV SGKRSSRQRK YVVGKWCGKV WMSHQVHPFL 900 LQQDLEGDES ERSCHLRGAL DDDVTGKRLS PCDVSRDATT MFGRKYCRKR KMRAKAVPRK 960 KLTSFKREDG VSDDTSEDHS YKQQWRASRN EEESYFETGN TVSGDSSNEM SDSQLKRIRR 1020 DKGVKEFESD DEVSDRSLGE EYAVRECAVS ESSMENNFQP YKQSVDRKPL EDTVYGHNDD 1080 IIYRYPRGIP RSKRKKVFRN PVSYDSEEND IYQQRRNIQA TGEYVSAEDS LEEQDFYTTG 1140 KRQTRSTAKR KVKTEIVQSR RDTRCRTLQQ SGSGKMNQEL NSYMEGPSTR LRVRNQNPSR 1200 GFSETKPKKT SKKRRSNASF SRIVSEEELE EEDKEEVENE EEECAAYRCD MEGCRMSFNS 1260 EKQLSLHKRN ICPVKGCGKN FFSHKYLVQH QRVHSDDRPL KCPWKGCKMT FKWAWSRTEH 1320 IRVHTGARPY VCAEPGCDQT FRFVSDFSRH KRKTGHSVKK AKRR*

Sequence ? help Back to Top

Protein Sequence Length: 1365 aa Download sequence Send to blast

MVVSEQSPDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KIVPPVPPPS  60
KKTTISNLNR SLASLATARV RDGGDAFDYD GAPTFATRQQ QIGFCPRKQR PVQRPVWQSG  120
EHYSFGEFEF KAKNFEKNYL RKCGKKSQLS ALEIETLYWR ATVDKPFSVE YANDMPGSAF  180
IPLSLAAARR RESGGDGGTV GETAWNMRAM ARAEGSLLKF MKEEIPGVTS PMVYIAMMFS  240
WFAWHVEDHD LHSLNYLHMG ASKTWYGVPK DAAVAFEEVV RVHGYGGELN PLVTFSTLGD  300
KTTVMSPEVF VKAGIPCCRL VQNPGEFVVT FPRAYHSGFS HGFNCGEASN IATPEWLRIA  360
KDAAIRRAAI NYPPMVSHLQ LLYDFALALC SRVPTSIHTK PRSSRLKDKK RSEGEKLTKE  420
LFVQNIIHNN ELLRSLGKRS PVALLPQSSS DVSVCSDLRV GSHLRTNQER PIQLKSEDFS  480
SDSIMAGLSN GFKDVVSVKE KFTSLCERNR NYLASRENET QGTLTDAERK NDRAVGLSDQ  540
RLFSCVTCGI LCFDCVAIVQ PKEAAARYLM SADCSFFNDW TATSGSANLG QDSRFSAVKP  600
HSESTGKHDV DDFYNVPVQT TDERTSTTSL TKAQKEDGAL GLLASAYGDS SDSEEEDHKG  660
LDTIISEERK YDHNGIEEAT DGQAFDNSSQ RLSCGKGKGV VEGSNAAEHD RLSNGGSTSN  720
LEIAFPFVPR SDDDSSRLHV FCLEHAAEVE QQLRPLGGIR IMLLCHPEYP RIEAEAKIVA  780
DELGVNHEWN DTEFRNVTRE DEEMIQAALD NVEAKAGNSD WSVKLGINLS YSAILSRSPL  840
YSKQMPYNSV IYNAFGRGSP ATSSPTKPQV SGKRSSRQRK YVVGKWCGKV WMSHQVHPFL  900
LQQDLEGDES ERSCHLRGAL DDDVTGKRLS PCDVSRDATT MFGRKYCRKR KMRAKAVPRK  960
KLTSFKREDG VSDDTSEDHS YKQQWRASRN EEESYFETGN TVSGDSSNEM SDSQLKRIRR  1020
DKGVKEFESD DEVSDRSLGE EYAVRECAVS ESSMENNFQP YKQSVDRKPL EDTVYGHNDD  1080
IIYRYPRGIP RSKRKKVFRN PVSYDSEEND IYQQRRNIQA TGEYVSAEDS LEEQDFYTTG  1140
KRQTRSTAKR KVKTEIVQSR RDTRCRTLQQ SGSGKMNQEL NSYMEGPSTR LRVRNQNPSR  1200
GFSETKPKKT SKKRRSNASF SRIVSEEELE EEDKEEVENE EEECAAYRCD MEGCRMSFNS  1260
EKQLSLHKRN ICPVKGCGKN FFSHKYLVQH QRVHSDDRPL KCPWKGCKMT FKWAWSRTEH  1320
IRVHTGARPY VCAEPGCDQT FRFVSDFSRH KRKTGHSVKK AKRR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	5e-75	1244	1364	20	140	Lysine-specific demethylase REF6
6a58_A	5e-75	1244	1364	20	140	Lysine-specific demethylase REF6
6a59_A	5e-75	1244	1364	20	140	Lysine-specific demethylase REF6
6ip0_A	5e-73	9	456	4	413	Transcription factor jumonji (Jmj) family protein
6ip4_A	5e-73	9	456	4	413	Arabidopsis JMJ13
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	948	960	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Thhalv10010068m

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_006404260.1	0.0	lysine-specific demethylase REF6
Refseq	XP_024013589.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	V4M0K3	0.0	V4M0K3_EUTSA; Uncharacterized protein
STRING	XP_006404260.1	0.0	(Eutrema salsugineum)

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	Thhalv10010068m
Entrez Gene	18020750

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]