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

Tp5g13610

Organism

Thellungiella parvula

Taxonomic ID

98039

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 1382aa MW: 155011 Da PI: 8.1707

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp5g13610	genome	thellungiella	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11.2	0.0012	1265	1290	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sFs+ +L H r+ + Tp5g13610 1265 YQCDmeGCTMSFSSEKQLSLHKRNiC 1290 99********************9877 PP
2	zf-C2H2	14.5	0.00011	1290	1312	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk+F ++ +L++H r+H Tp5g13610 1290 CPvkGCGKTFFSHKYLVQHRRVH 1312 9999*****************99 PP
3	zf-C2H2	11	0.0013	1348	1374	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H Tp5g13610 1348 YVCAepSCGQTFRFVSDFSRHKRKtgH 1374 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	2.5E-16	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	13.952	20	61	IPR003349	JmjN domain
Pfam	PF02375	7.9E-14	21	54	IPR003349	JmjN domain
SMART	SM00558	2.1E-47	199	375	IPR003347	JmjC domain
PROSITE profile	PS51184	33.633	202	375	IPR003347	JmjC domain
SuperFamily	SSF51197	2.53E-24	217	393	No hit	No description
Pfam	PF02373	4.6E-34	232	342	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	6.6E-4	1260	1287	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	9.4	1265	1287	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	13.131	1288	1317	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0024	1288	1312	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.0E-6	1289	1311	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1290	1312	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	6.0E-10	1304	1346	No hit	No description
Gene3D	G3DSA:3.30.160.60	4.7E-10	1312	1339	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0015	1318	1342	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.928	1318	1347	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1320	1342	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	8.24E-8	1336	1370	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.3E-8	1340	1371	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.281	1348	1379	IPR007087	Zinc finger, C2H2
SMART	SM00355	5.5	1348	1374	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1350	1374	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: 1382 aa Download sequence Send to blast
MAISEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPVPPSS 60 KKTAINNLNR SLAARAAARV RDSGRACDYD GGPTFATRQQ QIGFCPRKQR PVQRPVWQSG 120 EHYTFGEFEF KAKSFEKNYL KKCGKKSQLS ALEIETLYWR ATVDKPFSVE YANDMPGSAF 180 IPLSLAAARR RESGGDGGTV GETAWNMRAM ARAEGSLLKF MKEEIPGVTS PMVYIAMMFS 240 WFAWHVEDHD LHSLNYLHMG AGKTWYGVPK DAAVAFEEVV RVHGYGGELN PLVTFSTLGE 300 KTTVMSPEVF VKAGIPCCRL VQNPGDFVVT FPGAYHSGFS HGEKRLFFRF NFGEASNIAT 360 PQWLRMAKDA AIRRAAINYP PMVSHLQLLY DFALALGSRV PASIHTKPRS SRLKDKKRSE 420 GEKLTKELFA QNIIHNNELL RSLGKGSPVG LLPQSSSDIS VCSDLRVGSH LSANQEKPIQ 480 LKSEDLSSDS VMVGLNNSVK DSVSVKEKFT SLCERNRNHL ASKENETHGT PTDVERRRND 540 GAVGLSDQRL FSCVTCGILS FDCVAIVQPK EAAARYLMSA DCSFFNDWTV ASGSANLGQA 600 AELLHPQSTG DHSVNYSYNV PVQTTDHSMK TGDQRTSSSS LTKAHKDNGA LGLLATAYGD 660 SSDSEEEDYK GLDIPVPEEG ACVLEASSFD TDGNEEARHG LSSAFNNERL SCAKGKEVDV 720 SHATSSCSTL SCNSEQNRLS KGGNTSLLDM TLPFIPRSDD DSSRLHVLCL EHAAEVEQQL 780 RPIGGINIML LCHPEYRRIE AEGKIVAEEL GVDHEWSDTE FRNVTREDEE TIQAALANVE 840 AKAGNSDWAV KLGINLSYSA ILSRSPLYSK QMPYNSVIYN AFGRRSPAMS SPTKPQVSGK 900 RSSRQRKYVV GKWCGKVWMS HQVHPFLLQQ DLEGEESERS CHLRVALDED VTGKRSFPYD 960 VSRDSTTMFG RKYCRKRKMR AKAVPRKKLT SFKREDGVSD DTSEDHSYKQ QWRAFGNEED 1020 MSEDSSNQMS DQQQLKEIVI HQGYKEFESD DEVSDRSLGQ EYAVRECAAS ESSMENGFQL 1080 YREKQAMSDH YDDDIDRHPR GIPRSKRTKV FRKPVSYESE ENGLYQQRGR VFTSIAQTSR 1140 MGGGYDSAEN SLEEQDFFST GKRRTRSTAK RKVKTEIVQS RRDTKGRALQ QSGSRKKNQE 1200 VGSSMEGPST RLRVRNLKPS RGSSETNPKK TDKKGRNTSF SAVASEEEVE EDEEEENEEE 1260 ECSPYQCDME GCTMSFSSEK QLSLHKRNIC PVKGCGKTFF SHKYLVQHRR VHSDDRPLKC 1320 PWKGCKMTFK WAWSRTEHIR VHTGARPYVC AEPSCGQTFR FVSDFSRHKR KTGHSVKKTK 1380 KR

Sequence ? help Back to Top

Protein Sequence Length: 1382 aa Download sequence Send to blast

MAISEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPVPPSS  60
KKTAINNLNR SLAARAAARV RDSGRACDYD GGPTFATRQQ QIGFCPRKQR PVQRPVWQSG  120
EHYTFGEFEF KAKSFEKNYL KKCGKKSQLS ALEIETLYWR ATVDKPFSVE YANDMPGSAF  180
IPLSLAAARR RESGGDGGTV GETAWNMRAM ARAEGSLLKF MKEEIPGVTS PMVYIAMMFS  240
WFAWHVEDHD LHSLNYLHMG AGKTWYGVPK DAAVAFEEVV RVHGYGGELN PLVTFSTLGE  300
KTTVMSPEVF VKAGIPCCRL VQNPGDFVVT FPGAYHSGFS HGEKRLFFRF NFGEASNIAT  360
PQWLRMAKDA AIRRAAINYP PMVSHLQLLY DFALALGSRV PASIHTKPRS SRLKDKKRSE  420
GEKLTKELFA QNIIHNNELL RSLGKGSPVG LLPQSSSDIS VCSDLRVGSH LSANQEKPIQ  480
LKSEDLSSDS VMVGLNNSVK DSVSVKEKFT SLCERNRNHL ASKENETHGT PTDVERRRND  540
GAVGLSDQRL FSCVTCGILS FDCVAIVQPK EAAARYLMSA DCSFFNDWTV ASGSANLGQA  600
AELLHPQSTG DHSVNYSYNV PVQTTDHSMK TGDQRTSSSS LTKAHKDNGA LGLLATAYGD  660
SSDSEEEDYK GLDIPVPEEG ACVLEASSFD TDGNEEARHG LSSAFNNERL SCAKGKEVDV  720
SHATSSCSTL SCNSEQNRLS KGGNTSLLDM TLPFIPRSDD DSSRLHVLCL EHAAEVEQQL  780
RPIGGINIML LCHPEYRRIE AEGKIVAEEL GVDHEWSDTE FRNVTREDEE TIQAALANVE  840
AKAGNSDWAV KLGINLSYSA ILSRSPLYSK QMPYNSVIYN AFGRRSPAMS SPTKPQVSGK  900
RSSRQRKYVV GKWCGKVWMS HQVHPFLLQQ DLEGEESERS CHLRVALDED VTGKRSFPYD  960
VSRDSTTMFG RKYCRKRKMR AKAVPRKKLT SFKREDGVSD DTSEDHSYKQ QWRAFGNEED  1020
MSEDSSNQMS DQQQLKEIVI HQGYKEFESD DEVSDRSLGQ EYAVRECAAS ESSMENGFQL  1080
YREKQAMSDH YDDDIDRHPR GIPRSKRTKV FRKPVSYESE ENGLYQQRGR VFTSIAQTSR  1140
MGGGYDSAEN SLEEQDFFST GKRRTRSTAK RKVKTEIVQS RRDTKGRALQ QSGSRKKNQE  1200
VGSSMEGPST RLRVRNLKPS RGSSETNPKK TDKKGRNTSF SAVASEEEVE EDEEEENEEE  1260
ECSPYQCDME GCTMSFSSEK QLSLHKRNIC PVKGCGKTFF SHKYLVQHRR VHSDDRPLKC  1320
PWKGCKMTFK WAWSRTEHIR VHTGARPYVC AEPSCGQTFR FVSDFSRHKR KTGHSVKKTK  1380
KR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	2e-76	1262	1382	20	140	Lysine-specific demethylase REF6
6a58_A	2e-76	1262	1382	20	140	Lysine-specific demethylase REF6
6a59_A	2e-76	1262	1382	20	140	Lysine-specific demethylase REF6
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	975	987	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	Tp5g13610

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_006404261.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A1J3JIY4	0.0	A0A1J3JIY4_NOCCA; Lysine-specific demethylase REF6
STRING	XP_006404261.1	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

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]