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

MDP0000298212

Organism

Malus domestica

Taxonomic ID

3750

Taxonomic Lineage

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

Family

C3H

Protein Properties

Length: 1840aa MW: 205909 Da PI: 6.6063

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MDP0000298212	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	10.7	0.0016	1469	1494	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 ++C C++sF ++++L H r+ + MDP0000298212 1469 FVCDleGCTMSFASRHELSLHKRNiC 1494 899999****************9877 PP
2	zf-C2H2	12.5	0.00044	1494	1516	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H MDP0000298212 1494 CPvkGCGKKFFSHKYLVQHRRVH 1516 9999*****************99 PP
3	zf-CCCH	37.7	3.5e-12	1791	1813	4	26
---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 4 elCrffartGtCkyGdrCkFaHg 26 e C+++++tG Ck+G++CkF+H+ MDP0000298212 1791 EDCSYYLKTGSCKFGSNCKFNHP 1813 89********************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	4.3E-16	142	183	IPR003349	JmjN domain
PROSITE profile	PS51183	13.619	143	184	IPR003349	JmjN domain
Pfam	PF02375	4.7E-15	144	177	IPR003349	JmjN domain
SuperFamily	SSF51197	9.61E-26	233	296	No hit	No description
SMART	SM00558	7.9E-49	318	487	IPR003347	JmjC domain
PROSITE profile	PS51184	32.776	321	487	IPR003347	JmjC domain
SuperFamily	SSF51197	9.61E-26	336	503	No hit	No description
Pfam	PF02373	9.5E-36	351	470	IPR003347	JmjC domain
SMART	SM00355	18	1469	1491	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	13.152	1492	1521	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0045	1492	1516	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1494	1516	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	7.6E-7	1494	1515	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	8.67E-10	1508	1550	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.4E-8	1516	1542	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.824	1522	1551	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0017	1522	1546	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1524	1546	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.32E-7	1540	1574	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.0E-8	1543	1575	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.512	1552	1583	IPR007087	Zinc finger, C2H2
SMART	SM00355	4.7	1552	1578	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1554	1578	IPR007087	Zinc finger, C2H2
SuperFamily	SSF90229	7.06E-6	1786	1815	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.094	1787	1815	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.0E-6	1787	1814	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	9.7E-10	1791	1813	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	6.0E-5	1793	1813	IPR000571	Zinc finger, CCCH-type

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: 1840 aa Download sequence Send to blast
MVEDIKHQGE LNGKKILNNC LALPVCDVDY MYSVGNPEME VLVGLTLSMS ELNEEPWKGN 60 AFQTLIKGLR ELNGSSYNLQ NVVTRLRSRR SKLVRVVPSE LLCIDHSKLN HSRIDWYGCX 120 RALKEHXEAN PEVFQWLKTL PVAPEYHPTW AEFQDPIAYI FKIEKEASQY GICKIVPPVP 180 PSSKKTTIGN LNRSLAARAG VLGSSGQKSQ PTFTTRQQQI GFCPRRPRPV HRPVWQSGEH 240 YTFQEFEAKA KSFEKSYLRK CSKKGGLSPL EIETLYWKAT VDKPFSVEYA NDMPGSAFVP 300 VSARKSSSTS KDAGDNVTLG DTAWNMRGVS RSKGSLLRFM KEEIPGVTSP MVYIAMLFSW 360 FAWHVEDHDL HSLNYLHMGA GKTWYGVPRD AAVAFEEVVR VQGYAGEINP LVTFSTLGEK 420 TTVMSPEVFV SSGIPCCRLV QNAGEFVVTF PRAYHTGFSH GFNFAEAANI ATPEWLRVAK 480 DAAIRRASIN YPPMVSHFQL LYDLALALCS RMPARISSEP RSSRLKDKRK GEGDIVVKEL 540 FVQDVIQNND LLHVLGKGSP IVLLPQSSSD LSVCSKLRVG SQSRVNPGFS QGSYNLKEEM 600 KSSGSVSDGL MIDGQQVKGF YSXRGKLASL SESNSLPSLS GCNNVCGLNL KRSNLSCERE 660 SHVEGEGLSD QRLFSCVTCG ILSFACVAII QPTEEAARYL MSADCSFFND WVVGSGLGSK 720 AFSVVTGDPV TSNDAPCTGL EENNAPNGLY DVPVHSGNYQ IQVVDQRNEV VSNTEMPRET 780 SALGLLALNY GNSSDLEEDQ VETDAPVCSD EPKVTNCSLE SRYRDQSASL PSGGTSGVHS 840 PSSPGSDCEN ELRLQNFDHY ATDGRKIANF KDTGHQDIDS SADFRTNNYA STATGFGKAI 900 VPIQKTNTSC HPGCDEDSSR MHVFCLEHAV EVQQQLRSIG GVHILLLCHP DYPRIEDEAK 960 SMAEELGISY LWNDMAFMNA TKEDETRIKL ALDSEDAIAG NGDWAVKLGI NLFYSASLSR 1020 SHLYSKQMPY NSVIYKAFGR SSPASSPTRI DVYGRRGGKP KKVVAGKWCG KVWMSNQVHS 1080 FLVKRDPEEE VEVAEDEEER PFRAWAMPEE DDEVKSEITR RTEKTVKKYA RKRKMTADTR 1140 TAKKAKCFEK EDAVSDYSLD DNSHQQQRRL PKSKQAKHIE RGRTKKAKGI ETHDAFSDDX 1200 MQEDDSHQQN GRILHSEQVE YIERSDVSDD SVGIDSHQQH RRTAKSKQFK PVETDVVSDD 1260 SFEGSSHQPR RVLRSKTTKC TGRENLISED VRGFSSHQQR RSISRSKQAR ARFMEREDTS 1320 LDETPEDTSH QHKRNLRNKQ TKPETRGKMR QETSRQVKQG TAPLVKQGTR TLRNQQTPQX 1380 XKKQTPRLRN NQSEQNNQSE QNSFDLYAED ETEGGPSTRL RKRAPKPSKV PGTKSKEQQQ 1440 TARKKAKNAS AGKTQAGRNE TKREEDGEFV CDLEGCTMSF ASRHELSLHK RNICPVKGCG 1500 KKFFSHKYLV QHRRVHTDDR PLRCPWKGCK MTFKWAWSRT EHIRVHTGAR PYVCAEPGCA 1560 QTFRFVSDFS RHKRKTGHSA KKRRMALSEA TSVVPPNPET PSTNHAHSDQ GSLPSSPDPD 1620 PTPSDLDHAV LDELHKLDLK EPVXEGDGEP DELQELDSTE KVEEDGVGEL QNVDLKEEED 1680 GVGELQKVDL KEEEDGAGEL QKLDLXEEEE GGEGEEEEEK SSGEREVEIL NGEENERQSE 1740 QSYQSDGGGG GEGWGGNQGW EEDGGEVEEK KAEETQESNR RYQYPVRPEA EDCSYYLKTG 1800 SCKFGSNCKF NHPVSRKTNQ VPRERVKDES AENPSQTECK

Sequence ? help Back to Top

Protein Sequence Length: 1840 aa Download sequence Send to blast

MVEDIKHQGE LNGKKILNNC LALPVCDVDY MYSVGNPEME VLVGLTLSMS ELNEEPWKGN  60
AFQTLIKGLR ELNGSSYNLQ NVVTRLRSRR SKLVRVVPSE LLCIDHSKLN HSRIDWYGCX  120
RALKEHXEAN PEVFQWLKTL PVAPEYHPTW AEFQDPIAYI FKIEKEASQY GICKIVPPVP  180
PSSKKTTIGN LNRSLAARAG VLGSSGQKSQ PTFTTRQQQI GFCPRRPRPV HRPVWQSGEH  240
YTFQEFEAKA KSFEKSYLRK CSKKGGLSPL EIETLYWKAT VDKPFSVEYA NDMPGSAFVP  300
VSARKSSSTS KDAGDNVTLG DTAWNMRGVS RSKGSLLRFM KEEIPGVTSP MVYIAMLFSW  360
FAWHVEDHDL HSLNYLHMGA GKTWYGVPRD AAVAFEEVVR VQGYAGEINP LVTFSTLGEK  420
TTVMSPEVFV SSGIPCCRLV QNAGEFVVTF PRAYHTGFSH GFNFAEAANI ATPEWLRVAK  480
DAAIRRASIN YPPMVSHFQL LYDLALALCS RMPARISSEP RSSRLKDKRK GEGDIVVKEL  540
FVQDVIQNND LLHVLGKGSP IVLLPQSSSD LSVCSKLRVG SQSRVNPGFS QGSYNLKEEM  600
KSSGSVSDGL MIDGQQVKGF YSXRGKLASL SESNSLPSLS GCNNVCGLNL KRSNLSCERE  660
SHVEGEGLSD QRLFSCVTCG ILSFACVAII QPTEEAARYL MSADCSFFND WVVGSGLGSK  720
AFSVVTGDPV TSNDAPCTGL EENNAPNGLY DVPVHSGNYQ IQVVDQRNEV VSNTEMPRET  780
SALGLLALNY GNSSDLEEDQ VETDAPVCSD EPKVTNCSLE SRYRDQSASL PSGGTSGVHS  840
PSSPGSDCEN ELRLQNFDHY ATDGRKIANF KDTGHQDIDS SADFRTNNYA STATGFGKAI  900
VPIQKTNTSC HPGCDEDSSR MHVFCLEHAV EVQQQLRSIG GVHILLLCHP DYPRIEDEAK  960
SMAEELGISY LWNDMAFMNA TKEDETRIKL ALDSEDAIAG NGDWAVKLGI NLFYSASLSR  1020
SHLYSKQMPY NSVIYKAFGR SSPASSPTRI DVYGRRGGKP KKVVAGKWCG KVWMSNQVHS  1080
FLVKRDPEEE VEVAEDEEER PFRAWAMPEE DDEVKSEITR RTEKTVKKYA RKRKMTADTR  1140
TAKKAKCFEK EDAVSDYSLD DNSHQQQRRL PKSKQAKHIE RGRTKKAKGI ETHDAFSDDX  1200
MQEDDSHQQN GRILHSEQVE YIERSDVSDD SVGIDSHQQH RRTAKSKQFK PVETDVVSDD  1260
SFEGSSHQPR RVLRSKTTKC TGRENLISED VRGFSSHQQR RSISRSKQAR ARFMEREDTS  1320
LDETPEDTSH QHKRNLRNKQ TKPETRGKMR QETSRQVKQG TAPLVKQGTR TLRNQQTPQX  1380
XKKQTPRLRN NQSEQNNQSE QNSFDLYAED ETEGGPSTRL RKRAPKPSKV PGTKSKEQQQ  1440
TARKKAKNAS AGKTQAGRNE TKREEDGEFV CDLEGCTMSF ASRHELSLHK RNICPVKGCG  1500
KKFFSHKYLV QHRRVHTDDR PLRCPWKGCK MTFKWAWSRT EHIRVHTGAR PYVCAEPGCA  1560
QTFRFVSDFS RHKRKTGHSA KKRRMALSEA TSVVPPNPET PSTNHAHSDQ GSLPSSPDPD  1620
PTPSDLDHAV LDELHKLDLK EPVXEGDGEP DELQELDSTE KVEEDGVGEL QNVDLKEEED  1680
GVGELQKVDL KEEEDGAGEL QKLDLXEEEE GGEGEEEEEK SSGEREVEIL NGEENERQSE  1740
QSYQSDGGGG GEGWGGNQGW EEDGGEVEEK KAEETQESNR RYQYPVRPEA EDCSYYLKTG  1800
SCKFGSNCKF NHPVSRKTNQ VPRERVKDES AENPSQTECK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	2e-73	134	508	6	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	2e-73	134	508	6	353	Arabidopsis JMJ13
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Mdo.11372	0.0	bud\| leaf\| stem

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}.

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_008374335.2	0.0	LOW QUALITY PROTEIN: lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A498JKN1	0.0	A0A498JKN1_MALDO; Uncharacterized protein
STRING	XP_008374335.1	0.0	(Malus domestica)

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

Link Out ? help Back to Top
Phytozome	MDP0000298212

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]