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

Pbr036965.1

Organism

Pyrus bretschneideri

Taxonomic ID

225117

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Maleae; Pyrus

Family

C2H2

Protein Properties

Length: 1464aa MW: 163496 Da PI: 8.7802

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pbr036965.1	genome	CPETR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	10.7	0.0017	1347	1372	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 ++C C++sF +k++L H r+ + Pbr036965.1 1347 FECDfeGCTMSFASKHDLSLHKRNiC 1372 789999****************9877 PP
2	zf-C2H2	12.8	0.00034	1372	1394	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Pbr036965.1 1372 CPvkGCGKKFFSHKYLVQHRRVH 1394 9999*****************99 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	2.9E-15	24	65	IPR003349	JmjN domain
PROSITE profile	PS51183	13.605	25	66	IPR003349	JmjN domain
Pfam	PF02375	3.7E-15	26	59	IPR003349	JmjN domain
SMART	SM00558	1.9E-49	200	369	IPR003347	JmjC domain
PROSITE profile	PS51184	32.697	203	369	IPR003347	JmjC domain
SuperFamily	SSF51197	2.09E-25	214	384	No hit	No description
Pfam	PF02373	2.0E-36	233	352	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	7.0E-4	1347	1369	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	16	1347	1369	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1370	1394	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	13.152	1370	1399	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1372	1394	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	4.8E-7	1372	1398	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.27E-9	1386	1428	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.3E-7	1399	1424	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.637	1400	1429	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0017	1400	1424	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1402	1424	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.7E-7	1418	1452	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.8E-8	1425	1453	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.221	1430	1461	IPR007087	Zinc finger, C2H2
SMART	SM00355	4.7	1430	1456	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1432	1456	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:0040010	Biological Process	positive regulation of growth rate
GO:0045815	Biological Process	positive regulation of gene expression, epigenetic
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
GO:0071558	Molecular Function	histone demethylase activity (H3-K27 specific)

Sequence ? help Back to Top
Protein Sequence Length: 1464 aa Download sequence Send to blast
MAASSGLIAE ANPEVFPWLK TLPVAPEYHP TWAEFQDPIA YIFKIEKEAS QYGICKIVPP 60 VPPSTKKTTI GNLNRSLAAR AGVSGSSCPK SEPTFTTRQQ QIGFCPRRPR PVHRPVWQSG 120 EQYTFQEFEV KAKSFEKSYL RKCSKKGGLS PLEIETLYWK ATVDKPFSVE YANDMPGSAF 180 MPVGARKSSS TSRDAGDNVT LGETAWNMRG VSRSKGSLLR FMKEEIPGVT SPMVYIAMLF 240 SWFAWHVEDH DLHSLNYLHM GAGKTWYGVP KDAAVAFEEV VRVQGYAGEI NPLVTFSTLG 300 EKTTVMSPEV FVSSGIPCCR LVQNAGEFVV TFPRAYHTGF SHGFNCAEAA NIATPEWLRV 360 AKDAAIRRAS INYPPMVSHF QLLYDLALAL CSRMPSRISS EPRSSRLKDK RKCEGDIVVK 420 ELFVQDVIQN NDLLNVLGKG SPIVLLPQSS SDLSVCSKLR AGSQSRVNPG FSQGSHSLRE 480 EMKSSGSVSD GLMIDRQQVK GFYSVRGKLA SPSESNTLPS LSGSNNVRGL NSKRSNLNCE 540 RESNVKGEGL SDQRLFSCVT CGILSFACVA IIQPTEEAAR YLMSADCSFF NDWVVGSGLA 600 SEVFPVATGD PITSKNAPCT GLEEYNAPAG LYDVLVQSGD CQIQVVDQGN EMVSNTEMPR 660 ETSALGLVAL NYGNSSDSEE DQVEPDVPVC SDEPNMTNCS LESRYRDQSA SPPWRNPYAG 720 TSGVHSPSSQ GSGCENELRL QTFDHYATDG RKIANFKDSS LQNFDCSADF KTNNSASTAT 780 GFGKAIVPIQ KKSMSFHPGC DEDSSRMHVF CLEHAVEVEQ QLRSIGGVHI LLLCHPDYPR 840 IEDEAKSMAE ELGISYLWND MAFMNSAKED ETRIQLALDS EEAIAGNGDW AVKLGINLFY 900 SASLSRSHLY SKQMPYNSVI YKAFGRSSPA SSPTRIDAYG RRGGKPKKVV AGKWCGKVWM 960 SNQVHSFLVK RDPEEEVEVA EDEEERTFRA WAMPDEDHEV KSEITRKTEK TVKKYARKRK 1020 MTADTRTTKK ARCFDKEDAV SDYSVDDNST QQQRRSKQAK HTESGRTKKP KHVVTEDAVS 1080 DDSMQDDDSL QQSGRFLHSE QVKYIERSDV SDDSMGVESH QQHKRTAKSK QFKPVETDVV 1140 SDDSFEGSSH QPQRVLRSKT TKCTGRENLI SEDVHGFGSH QQRRSISRSK QARARFIERE 1200 DTALDETRED NFQQHKRILR NKQTKPETRG KMRQETPRQV KQGTAPLVKQ GTRTPRNQQT 1260 PQQTKKQTPR LRNNQSEQNS FDLYAEEETE GGPSTRLRKR APKPSKVPGT KPKEQQQTAR 1320 KKAKNASAGK AQGGRNETKL KEEDAEFECD FEGCTMSFAS KHDLSLHKRN ICPVKGCGKK 1380 FFSHKYLVQH RRVHTDDRPL RCPWKGCKMT FKWAWARTEH IRVHTGARPY VCAEPGCAQT 1440 FRFVSDFSRH KRKTGHSVKK SKK*

Sequence ? help Back to Top

Protein Sequence Length: 1464 aa Download sequence Send to blast

MAASSGLIAE ANPEVFPWLK TLPVAPEYHP TWAEFQDPIA YIFKIEKEAS QYGICKIVPP  60
VPPSTKKTTI GNLNRSLAAR AGVSGSSCPK SEPTFTTRQQ QIGFCPRRPR PVHRPVWQSG  120
EQYTFQEFEV KAKSFEKSYL RKCSKKGGLS PLEIETLYWK ATVDKPFSVE YANDMPGSAF  180
MPVGARKSSS TSRDAGDNVT LGETAWNMRG VSRSKGSLLR FMKEEIPGVT SPMVYIAMLF  240
SWFAWHVEDH DLHSLNYLHM GAGKTWYGVP KDAAVAFEEV VRVQGYAGEI NPLVTFSTLG  300
EKTTVMSPEV FVSSGIPCCR LVQNAGEFVV TFPRAYHTGF SHGFNCAEAA NIATPEWLRV  360
AKDAAIRRAS INYPPMVSHF QLLYDLALAL CSRMPSRISS EPRSSRLKDK RKCEGDIVVK  420
ELFVQDVIQN NDLLNVLGKG SPIVLLPQSS SDLSVCSKLR AGSQSRVNPG FSQGSHSLRE  480
EMKSSGSVSD GLMIDRQQVK GFYSVRGKLA SPSESNTLPS LSGSNNVRGL NSKRSNLNCE  540
RESNVKGEGL SDQRLFSCVT CGILSFACVA IIQPTEEAAR YLMSADCSFF NDWVVGSGLA  600
SEVFPVATGD PITSKNAPCT GLEEYNAPAG LYDVLVQSGD CQIQVVDQGN EMVSNTEMPR  660
ETSALGLVAL NYGNSSDSEE DQVEPDVPVC SDEPNMTNCS LESRYRDQSA SPPWRNPYAG  720
TSGVHSPSSQ GSGCENELRL QTFDHYATDG RKIANFKDSS LQNFDCSADF KTNNSASTAT  780
GFGKAIVPIQ KKSMSFHPGC DEDSSRMHVF CLEHAVEVEQ QLRSIGGVHI LLLCHPDYPR  840
IEDEAKSMAE ELGISYLWND MAFMNSAKED ETRIQLALDS EEAIAGNGDW AVKLGINLFY  900
SASLSRSHLY SKQMPYNSVI YKAFGRSSPA SSPTRIDAYG RRGGKPKKVV AGKWCGKVWM  960
SNQVHSFLVK RDPEEEVEVA EDEEERTFRA WAMPDEDHEV KSEITRKTEK TVKKYARKRK  1020
MTADTRTTKK ARCFDKEDAV SDYSVDDNST QQQRRSKQAK HTESGRTKKP KHVVTEDAVS  1080
DDSMQDDDSL QQSGRFLHSE QVKYIERSDV SDDSMGVESH QQHKRTAKSK QFKPVETDVV  1140
SDDSFEGSSH QPQRVLRSKT TKCTGRENLI SEDVHGFGSH QQRRSISRSK QARARFIERE  1200
DTALDETRED NFQQHKRILR NKQTKPETRG KMRQETPRQV KQGTAPLVKQ GTRTPRNQQT  1260
PQQTKKQTPR LRNNQSEQNS FDLYAEEETE GGPSTRLRKR APKPSKVPGT KPKEQQQTAR  1320
KKAKNASAGK AQGGRNETKL KEEDAEFECD FEGCTMSFAS KHDLSLHKRN ICPVKGCGKK  1380
FFSHKYLVQH RRVHTDDRPL RCPWKGCKMT FKWAWARTEH IRVHTGARPY VCAEPGCAQT  1440
FRFVSDFSRH KRKTGHSVKK SKK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	6e-74	18	390	8	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	6e-74	18	390	8	353	Arabidopsis JMJ13
Search in ModeBase

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	Pbr036965.1

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_009359508.1	0.0	PREDICTED: lysine-specific demethylase REF6-like
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A498I3J3	0.0	A0A498I3J3_MALDO; Uncharacterized protein
STRING	XP_009359508.1	0.0	(Pyrus x bretschneideri)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF5648	32	50

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]