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

Manes.14G055900.1.p

Organism

Manihot esculenta

Taxonomic ID

3983

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Crotonoideae; Manihoteae; Manihot

Family

C2H2

Protein Properties

Length: 1783aa MW: 201965 Da PI: 8.7732

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Manes.14G055900.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	13.6	0.0002	1666	1691	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L++H r+ + Manes.14G055900.1.p 1666 YQCDieGCSMSFGTKQELTVHKRNiC 1691 99********************9877 PP
2	zf-C2H2	12.6	0.00041	1691	1713	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Manes.14G055900.1.p 1691 CPvkGCGKKFFSHKYLVQHRRVH 1713 9999*****************99 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	2.4E-14	26	67	IPR003349	JmjN domain
PROSITE profile	PS51183	14.492	27	68	IPR003349	JmjN domain
Pfam	PF02375	9.2E-15	28	61	IPR003349	JmjN domain
SMART	SM00558	5.2E-49	194	363	IPR003347	JmjC domain
PROSITE profile	PS51184	33.593	194	363	IPR003347	JmjC domain
SuperFamily	SSF51197	1.29E-26	212	381	No hit	No description
Pfam	PF02373	2.3E-36	227	346	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	4.9E-5	1662	1688	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	6.8	1666	1688	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1689	1713	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.799	1689	1718	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	4.2E-6	1690	1717	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1691	1713	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.13E-9	1705	1747	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.7E-8	1718	1743	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1719	1743	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1719	1748	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1721	1743	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	8.3E-8	1737	1771	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.6E-9	1744	1772	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	1.1	1749	1775	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.928	1749	1780	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1751	1775	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: 1783 aa Download sequence Send to blast
MAASGGLVSE PSSQQEVFQW LKNLPLAPEY HPTLAEFQDP IAYIFKIEKE AAKYGICKIV 60 PPVLAAPRKA AIANLNRSLA ARAGSSSSKS PPTFTTRQQQ IGFCPRKPRP VQKPVWQSGE 120 NYTFQEFETK AKSFERSYLK KCSKKGAPSP LEIETLYWKA TVDKPFSVEY ANDMPGSAFS 180 PKKTGGKEVA EGVTVGETDW NMRGVSRAKG SLLRFMKEEI PGVTSPMVYV AMMFSWFAWH 240 VEDHDLHSLN YLHMGAGKTW YGVPREAAVA FEEVVRVHGY GGEMNPLVTF AILGEKTTVM 300 SPEVFVGAGV PCCRLVQNAG EFVVTFPRAY HSGFSHGFNC GEAANIATPE WLRVAKHAAI 360 RRASINYPPM VSHFQLLYDL ALELCTRMPL SISAKPRSSR LKDKQKGEGE TLVKELFIKN 420 VIHNNGLLHI LGKGSSIVLL PRSSSDISVC SNLRVGSQLR ASPALGSWSN KGIMKSSKDS 480 VPDEIMLERN NRINHAKGLF SVKEKFASLC GRNRFSSLDG NDNMNSTETG NENRESIHGD 540 KLSDQRLFSC VTCGILSFDC IAVIQPREAA ARYLMSADCS FFNDWMVGSG VTKDGFTIAH 600 GDTNTSEQNS STKWVEKNNV DGLYDVPVQS ANYQIQMMDQ NIVASNVETQ RATSALGLLA 660 LNYGNSSDSE DDQVEPDVSH QATEIDMTNC SSESKHQYQI SALPSFKQEF HHDTTGSHIV 720 SLSRHDNGHE VTLQTLDGHA EHGHGHMPAN FKDGSDQTLD SSVEFETDNL ASLESNGLEH 780 TFKDSMLTSL KTSSCSPVVH DTEKVVVPRE NTDESFAQRS DEDSSRMHVF CLEHAVEVEQ 840 QCRPIGGVHI LLLCHPEYPR IEAEAKLVTE ELGIDYFWND ITFRDATKED KDNIQSALDS 900 EEAIPGNGDW AVKLGINLFY SANLGRSSLY SKQMPYNSVI YKAFGRVSPA SLPTKFNVYR 960 RKPSKQKKVV AGRWCGKVWM SNQVHPFLTK QDSDDQDQEQ EQDRSFRGWT RPDEKLERKS 1020 ENIYKTETTL AARKSGRKRR MTVPSGPGKK VKCLDAEDAA SDESEEDVSH KQHTRVYSRK 1080 RTKRIEREVS LDSLEDDFHL HYEKRTHRNK QAKSVDREDA ISDDSLRCNT NQHRRTLRSK 1140 QVKYIESEND ISYAFADNKI NKQYSRIQRT RTNQAKYAQT VREISDDSLE GDIHEWHGRV 1200 PKSTLAKFTR EDAVSDDSPE ESSRRSVKRQ NRTSGGSQAK FIERDGEVSD DVLEENAYQQ 1260 HTGSRRSRES KFIDRESAVS DDQLEGNTYQ QRMRIFRTKQ AKISKTENAI SDDSSEENVQ 1320 QQRRGIPRRK RAKFVESEDA VSDDLLEDDT ALEHKRRTPR SRKAKVVGRE DAVSDDLLED 1380 NTHLEHRRMP RSRKAKVVGT EGVSDDLQDN RQWQPRKTPR GKQAQFIDSE DVSDDQLEED 1440 AHWQPRKLSR CKQAVSIERE DVSIDLEEGN THWQPKMTPS RKQAKFSESE DVSDDLQEDD 1500 NHWQPRKTPR GKQPKLIERE DAVLDDLVEE YSNKQQQRIL RSKQKKPVAL SKMKRGAIEL 1560 VKQGSSRPKK KENFRSIKQE KQMPETPRLR NGKAKHNARR VESRDEELEG GPSTRLRKRP 1620 SKASKESETK LKEKLQNSRK KVKNASSVKP LSGQKNVKNK VEEAEYQCDI EGCSMSFGTK 1680 QELTVHKRNI CPVKGCGKKF FSHKYLVQHR RVHLDERPLK CPWKGCKMTF KWAWARTEHI 1740 RVHTGARPYI CAEEGCGQTF RFVSDFSRHK RKTGHSVKKS RG*

Sequence ? help Back to Top

Protein Sequence Length: 1783 aa Download sequence Send to blast

MAASGGLVSE PSSQQEVFQW LKNLPLAPEY HPTLAEFQDP IAYIFKIEKE AAKYGICKIV  60
PPVLAAPRKA AIANLNRSLA ARAGSSSSKS PPTFTTRQQQ IGFCPRKPRP VQKPVWQSGE  120
NYTFQEFETK AKSFERSYLK KCSKKGAPSP LEIETLYWKA TVDKPFSVEY ANDMPGSAFS  180
PKKTGGKEVA EGVTVGETDW NMRGVSRAKG SLLRFMKEEI PGVTSPMVYV AMMFSWFAWH  240
VEDHDLHSLN YLHMGAGKTW YGVPREAAVA FEEVVRVHGY GGEMNPLVTF AILGEKTTVM  300
SPEVFVGAGV PCCRLVQNAG EFVVTFPRAY HSGFSHGFNC GEAANIATPE WLRVAKHAAI  360
RRASINYPPM VSHFQLLYDL ALELCTRMPL SISAKPRSSR LKDKQKGEGE TLVKELFIKN  420
VIHNNGLLHI LGKGSSIVLL PRSSSDISVC SNLRVGSQLR ASPALGSWSN KGIMKSSKDS  480
VPDEIMLERN NRINHAKGLF SVKEKFASLC GRNRFSSLDG NDNMNSTETG NENRESIHGD  540
KLSDQRLFSC VTCGILSFDC IAVIQPREAA ARYLMSADCS FFNDWMVGSG VTKDGFTIAH  600
GDTNTSEQNS STKWVEKNNV DGLYDVPVQS ANYQIQMMDQ NIVASNVETQ RATSALGLLA  660
LNYGNSSDSE DDQVEPDVSH QATEIDMTNC SSESKHQYQI SALPSFKQEF HHDTTGSHIV  720
SLSRHDNGHE VTLQTLDGHA EHGHGHMPAN FKDGSDQTLD SSVEFETDNL ASLESNGLEH  780
TFKDSMLTSL KTSSCSPVVH DTEKVVVPRE NTDESFAQRS DEDSSRMHVF CLEHAVEVEQ  840
QCRPIGGVHI LLLCHPEYPR IEAEAKLVTE ELGIDYFWND ITFRDATKED KDNIQSALDS  900
EEAIPGNGDW AVKLGINLFY SANLGRSSLY SKQMPYNSVI YKAFGRVSPA SLPTKFNVYR  960
RKPSKQKKVV AGRWCGKVWM SNQVHPFLTK QDSDDQDQEQ EQDRSFRGWT RPDEKLERKS  1020
ENIYKTETTL AARKSGRKRR MTVPSGPGKK VKCLDAEDAA SDESEEDVSH KQHTRVYSRK  1080
RTKRIEREVS LDSLEDDFHL HYEKRTHRNK QAKSVDREDA ISDDSLRCNT NQHRRTLRSK  1140
QVKYIESEND ISYAFADNKI NKQYSRIQRT RTNQAKYAQT VREISDDSLE GDIHEWHGRV  1200
PKSTLAKFTR EDAVSDDSPE ESSRRSVKRQ NRTSGGSQAK FIERDGEVSD DVLEENAYQQ  1260
HTGSRRSRES KFIDRESAVS DDQLEGNTYQ QRMRIFRTKQ AKISKTENAI SDDSSEENVQ  1320
QQRRGIPRRK RAKFVESEDA VSDDLLEDDT ALEHKRRTPR SRKAKVVGRE DAVSDDLLED  1380
NTHLEHRRMP RSRKAKVVGT EGVSDDLQDN RQWQPRKTPR GKQAQFIDSE DVSDDQLEED  1440
AHWQPRKLSR CKQAVSIERE DVSIDLEEGN THWQPKMTPS RKQAKFSESE DVSDDLQEDD  1500
NHWQPRKTPR GKQPKLIERE DAVLDDLVEE YSNKQQQRIL RSKQKKPVAL SKMKRGAIEL  1560
VKQGSSRPKK KENFRSIKQE KQMPETPRLR NGKAKHNARR VESRDEELEG GPSTRLRKRP  1620
SKASKESETK LKEKLQNSRK KVKNASSVKP LSGQKNVKNK VEEAEYQCDI EGCSMSFGTK  1680
QELTVHKRNI CPVKGCGKKF FSHKYLVQHR RVHLDERPLK CPWKGCKMTF KWAWARTEHI  1740
RVHTGARPYI CAEEGCGQTF RFVSDFSRHK RKTGHSVKKS RG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	1e-78	13	384	1	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	1e-78	13	384	1	353	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1629	1640	KLKEKLQNSRKK

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	Manes.14G055900.1.p

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_021634678.1	0.0	lysine-specific demethylase REF6-like isoform X1
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A2C9UK42	0.0	A0A2C9UK42_MANES; Uncharacterized protein
STRING	cassava4.1_000096m	0.0	(Manihot esculenta)

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	Manes.14G055900.1.p

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]