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

XP_009149820.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 1382aa MW: 154348 Da PI: 7.2454

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009149820.1	genome	NCBI	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+ + XP_009149820.1 1265 YQCDmeGCTMSFSSEKQLSLHKRNiC 1290 99********************9877 PP
2	zf-C2H2	15.1	6.8e-05	1290	1312	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H+r+H XP_009149820.1 1290 CPvkGCGKNFFSHKYLVQHQRVH 1312 9999*****************99 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	4.1E-17	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	14.284	20	61	IPR003349	JmjN domain
Pfam	PF02375	1.7E-15	21	54	IPR003349	JmjN domain
SMART	SM00558	1.7E-54	198	367	IPR003347	JmjC domain
PROSITE profile	PS51184	34.513	201	367	IPR003347	JmjC domain
SuperFamily	SSF51197	1.24E-27	213	384	No hit	No description
Pfam	PF02373	2.4E-37	231	350	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	0.001	1264	1287	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	9.4	1265	1287	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.01	1288	1312	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	13.609	1288	1317	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.1E-7	1289	1316	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1290	1312	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	6.91E-11	1304	1346	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.4E-10	1317	1341	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.801	1318	1347	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0015	1318	1342	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1320	1342	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.95E-8	1336	1370	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.9E-10	1342	1371	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	1.7	1348	1374	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.492	1348	1379	IPR007087	Zinc finger, C2H2
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
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPMAYICKI EEEASRYGIC KIVPPVPPSS 60 KKTAINNLNR SLAARARARA RDGGKPDYDG GPTFTTRQQQ IGFCPRRQRP VQRPVWQSGE 120 RYTFDEFEFK AKNFEKSYLK KCGKKGSVSP LEVETLYWRA SVDKPFSVEY ANDMPGSAFV 180 PLSLAAARRR ESGGDCGTVG ETAWNMRAMA RAEGSLLKFM KEEIPGVTSP MVYIAMMFSW 240 FAWHVEDHDL HSLNYLHMGA GKTWYGVPKD AAMAFEEVVR VHGYGEELNP LVTFSTLGEK 300 TTVMSPEVFV RAGIPCCRLV QNPGDFVITF PGAYHSGFSH GFNFGEASNI ATPQWLRMAK 360 DAAIRRASIN YPPMVSHLQL LYDYALALGS RVPDSIHNKP RSSRLKDKKK SEGEKLTNEL 420 FVQNIIHNNE LLHSLGKGSP IALLPQSSSD VSVCSDVRIG SHLGANQGQT TLLIKSEDLS 480 SDSVMVSLSN GVKEKFTSLC ERNRDHLASK EDETQGTSTD VERRKNNGAV GLSDQRLFSC 540 VTCGVLSFDC VAIIQPKEAA ARYLMSADCS FLNDWTVASG SGNLGQDVVM PPSGKQDVGD 600 LYNAPVQTPY HSTTKTVDQR TSSSSLTKES GALGLLASAY GDSSDSEEED HKGLDNPVSD 660 EVACVLEASS FVTDGNDEAG NGLSSALNSQ GLTCEKGKEV DVSHANLSKG GNASSVEITL 720 PFIPRSDDDF SRLHVFCLEH AAEVEQRLHP IGGINIMLLC HPDYPRIEAE GKVVAKELGV 780 NHEWNYTEFK NVTREDEETI QAALANVEAK AGNSDWAVKL GINLSHSAIL SRSPLYSKQM 840 PYNSVIYNVF GRTSPATPQV SGIRSSRQRK YVAGKWCGKV WMSHQVHPFL LEEDFEGEET 900 ERSHLRAALD EDVTVHGNDS RDATTMFGRK YSRKRKARGK AAPRKKLTSF KREAGVSDDT 960 SEDHSYKQQW RAYGDEEESY FETGNEVSGD SSNQMSDQQQ LKGVESDDDE VSERSLGQEY 1020 TVRREYASSE SSKENGFQVY REDQPMYGDN DMYRHPRGIP RSKRTKVFRD LVSYDSEDQQ 1080 RERVFTSDAQ TSRMDDEYDS EENSLEEQDF CSSGKRQTRS IAKRKVKTKI VQSLGDTGGR 1140 TLLQSGSRKK MKELDSYMEG PSTRLRVRTP KPSRGSSATK PKKTGKKGRN VSFSEVASEE 1200 EVEENEEESE EASTRIRVRT LKPPRRSLET KPKKTGKKGS NVSSLSGVAS EEEVEEDEQE 1260 ECLPYQCDME GCTMSFSSEK QLSLHKRNIC PVKGCGKNFF SHKYLVQHQR VHSDERPLKC 1320 PWKGCKMTFK WAWSRTEHIR VHTGERPYVC AEPGCSQTFR FVSDFSRHKR KTGHSAKKIK 1380 KK

Sequence ? help Back to Top

Protein Sequence Length: 1382 aa Download sequence Send to blast

MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPMAYICKI EEEASRYGIC KIVPPVPPSS  60
KKTAINNLNR SLAARARARA RDGGKPDYDG GPTFTTRQQQ IGFCPRRQRP VQRPVWQSGE  120
RYTFDEFEFK AKNFEKSYLK KCGKKGSVSP LEVETLYWRA SVDKPFSVEY ANDMPGSAFV  180
PLSLAAARRR ESGGDCGTVG ETAWNMRAMA RAEGSLLKFM KEEIPGVTSP MVYIAMMFSW  240
FAWHVEDHDL HSLNYLHMGA GKTWYGVPKD AAMAFEEVVR VHGYGEELNP LVTFSTLGEK  300
TTVMSPEVFV RAGIPCCRLV QNPGDFVITF PGAYHSGFSH GFNFGEASNI ATPQWLRMAK  360
DAAIRRASIN YPPMVSHLQL LYDYALALGS RVPDSIHNKP RSSRLKDKKK SEGEKLTNEL  420
FVQNIIHNNE LLHSLGKGSP IALLPQSSSD VSVCSDVRIG SHLGANQGQT TLLIKSEDLS  480
SDSVMVSLSN GVKEKFTSLC ERNRDHLASK EDETQGTSTD VERRKNNGAV GLSDQRLFSC  540
VTCGVLSFDC VAIIQPKEAA ARYLMSADCS FLNDWTVASG SGNLGQDVVM PPSGKQDVGD  600
LYNAPVQTPY HSTTKTVDQR TSSSSLTKES GALGLLASAY GDSSDSEEED HKGLDNPVSD  660
EVACVLEASS FVTDGNDEAG NGLSSALNSQ GLTCEKGKEV DVSHANLSKG GNASSVEITL  720
PFIPRSDDDF SRLHVFCLEH AAEVEQRLHP IGGINIMLLC HPDYPRIEAE GKVVAKELGV  780
NHEWNYTEFK NVTREDEETI QAALANVEAK AGNSDWAVKL GINLSHSAIL SRSPLYSKQM  840
PYNSVIYNVF GRTSPATPQV SGIRSSRQRK YVAGKWCGKV WMSHQVHPFL LEEDFEGEET  900
ERSHLRAALD EDVTVHGNDS RDATTMFGRK YSRKRKARGK AAPRKKLTSF KREAGVSDDT  960
SEDHSYKQQW RAYGDEEESY FETGNEVSGD SSNQMSDQQQ LKGVESDDDE VSERSLGQEY  1020
TVRREYASSE SSKENGFQVY REDQPMYGDN DMYRHPRGIP RSKRTKVFRD LVSYDSEDQQ  1080
RERVFTSDAQ TSRMDDEYDS EENSLEEQDF CSSGKRQTRS IAKRKVKTKI VQSLGDTGGR  1140
TLLQSGSRKK MKELDSYMEG PSTRLRVRTP KPSRGSSATK PKKTGKKGRN VSFSEVASEE  1200
EVEENEEESE EASTRIRVRT LKPPRRSLET KPKKTGKKGS NVSSLSGVAS EEEVEEDEQE  1260
ECLPYQCDME GCTMSFSSEK QLSLHKRNIC PVKGCGKNFF SHKYLVQHQR VHSDERPLKC  1320
PWKGCKMTFK WAWSRTEHIR VHTGERPYVC AEPGCSQTFR FVSDFSRHKR KTGHSAKKIK  1380
KK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	8e-74	1262	1382	20	140	Lysine-specific demethylase REF6
6a58_A	8e-74	1262	1382	20	140	Lysine-specific demethylase REF6
6a59_A	8e-74	1262	1382	20	140	Lysine-specific demethylase REF6
6ip0_A	3e-70	9	390	4	355	Transcription factor jumonji (Jmj) family protein
6ip4_A	3e-70	9	390	4	355	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	933	945	KRKARGKAAPRKK

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269\|PubMed:15377760, ECO:0000269\|PubMed:18713399}.

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	XP_009149820.1

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009149820.1	0.0	PREDICTED: lysine-specific demethylase REF6 isoform X2
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A397YY33	0.0	A0A397YY33_BRACM; Uncharacterized protein
TrEMBL	M4DNH3	0.0	M4DNH3_BRARP; Uncharacterized protein
STRING	Bra018060.1-P	0.0	(Brassica rapa)

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]