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

Aco003541.1

Organism

Ananas comosus

Taxonomic ID

4615

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Bromeliaceae; Ananas

Family

C2H2

Protein Properties

Length: 1178aa MW: 132021 Da PI: 9.1159

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Aco003541.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.4	0.00049	1061	1086	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 ++C C++sF++k++L H r+ + Aco003541.1 1061 FPCDmeGCSMSFNTKHDLALHKRNiC 1086 789999****************9876 PP
2	zf-C2H2	13	0.00031	1144	1170	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C+ Cg++F+ s++ rH r+ H Aco003541.1 1144 YVCKeaGCGQTFRFVSDFSRHKRKtgH 1170 99********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	6.3E-16	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	14.118	20	61	IPR003349	JmjN domain
Pfam	PF02375	3.3E-14	21	54	IPR003349	JmjN domain
SMART	SM00558	4.4E-51	198	367	IPR003347	JmjC domain
PROSITE profile	PS51184	34.156	198	367	IPR003347	JmjC domain
SuperFamily	SSF51197	6.04E-26	216	365	No hit	No description
Pfam	PF02373	7.4E-37	231	350	IPR003347	JmjC domain
SMART	SM00355	14	1061	1083	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.026	1084	1108	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.071	1084	1113	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	5.9E-4	1086	1112	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1086	1108	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.71E-9	1101	1142	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.5E-8	1113	1137	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0012	1114	1138	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.616	1114	1143	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1116	1138	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	7.9E-8	1132	1166	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.6E-9	1138	1167	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.427	1144	1175	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.21	1144	1170	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1146	1170	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: 1178 aa Download sequence Send to blast
MAIDPCGAEV PQWLKTLPLA PEYHPTLAEF QDPIAYIFKI EREASQYGIC KIVPPLPAPP 60 KKTTMANLNR SFASRNCSGS GSSGGDRKGP TFTTRQQQVG FCPRRQRPVQ RPVWQSGAHY 120 TFQEFEAKAK QFERAQLKKS SRKPLSPLDV EALFWKACAD KPFSVEYAND MPGSGFAPLE 180 SAGGKKKLLA RREEEAGNVG ESAWNMRGVS RAKGSLLRFM KEEIPGVTSP MVYVAMMFSW 240 FAWHVEDHDL HSLNYLHMGA GKTWYGVPRD ARLAFEEVIR VHGYGEEVNP LVTFTMLGEK 300 TTVMSPEVLI GAGIPCCRLV QNAGEFVVTF PGSYHSGFSH GFNCGEAANI ATPEWLRVAK 360 DAAVRRASTN CPPMVSHYQL LYALALSFCL GVPTSCGSEP RSSRLKGKMR SEGEMLVKEI 420 FVETVRKNNE LLNILLGEES CIVLPQQTAS TRTQLKIKPR SSIGFQRYEQ AMEEKCAERE 480 EFNGFCSARE SSTSVSLEMK PYSVKCSKFG AESQNLVSKN DGALQGDGLL DQGLLSCVTC 540 GILSFACVAV VQPREAAVRY LMSSDCGFLN DQSAGSGGTS EVDNISKWRS LDYHMVSGSG 600 KAPTTADHLV STRCSVKVSD DCKQIYSKTA RKGVSALDLL ASAYGASDSD EESPNEMILS 660 TDENDLKCSS VSNHQFSSAS EDLNIEDSTN GDSENEASAV GAHLKNESPV KESPMLDMLK 720 YDRDSSRMHV FCLEHALEVE KQLQQIGGAN IILLCHPEYP KFEKEAKLLA EEIGVDHQWN 780 KISFRKATEE DEERIKLVLE DEEAIPMNSD WTVKMGINLY YSSNQSKSPI YSKQLPYNAI 840 IYRAFGRDSP NSSPREVVST QDRSGRQKKI VVAGRWCGKV WMSNQVHPYL ARVNEDKEDY 900 EREDRVYQSS FKGKVNMEHS KRVDLSRETV VLNTPPARKS SRKRKKSTEK SRTKKQKRAK 960 LCKSENTEDV AEISPPLSSR VLRSSADKHA STSKRNEKQS LGEMKLKDEP KEELITRSRR 1020 RHTKLEGVKI KSKTQKKTSN KRARKKDQTK DSSSKEEEGE FPCDMEGCSM SFNTKHDLAL 1080 HKRNICPHKG CGKKFFSHKY LLQHRKVHMD DRPLKCPWKG CKMTFKWPWA RTEHIRVHTG 1140 ARPYVCKEAG CGQTFRFVSD FSRHKRKTGH SSKKGRK*

Sequence ? help Back to Top

Protein Sequence Length: 1178 aa Download sequence Send to blast

MAIDPCGAEV PQWLKTLPLA PEYHPTLAEF QDPIAYIFKI EREASQYGIC KIVPPLPAPP  60
KKTTMANLNR SFASRNCSGS GSSGGDRKGP TFTTRQQQVG FCPRRQRPVQ RPVWQSGAHY  120
TFQEFEAKAK QFERAQLKKS SRKPLSPLDV EALFWKACAD KPFSVEYAND MPGSGFAPLE  180
SAGGKKKLLA RREEEAGNVG ESAWNMRGVS RAKGSLLRFM KEEIPGVTSP MVYVAMMFSW  240
FAWHVEDHDL HSLNYLHMGA GKTWYGVPRD ARLAFEEVIR VHGYGEEVNP LVTFTMLGEK  300
TTVMSPEVLI GAGIPCCRLV QNAGEFVVTF PGSYHSGFSH GFNCGEAANI ATPEWLRVAK  360
DAAVRRASTN CPPMVSHYQL LYALALSFCL GVPTSCGSEP RSSRLKGKMR SEGEMLVKEI  420
FVETVRKNNE LLNILLGEES CIVLPQQTAS TRTQLKIKPR SSIGFQRYEQ AMEEKCAERE  480
EFNGFCSARE SSTSVSLEMK PYSVKCSKFG AESQNLVSKN DGALQGDGLL DQGLLSCVTC  540
GILSFACVAV VQPREAAVRY LMSSDCGFLN DQSAGSGGTS EVDNISKWRS LDYHMVSGSG  600
KAPTTADHLV STRCSVKVSD DCKQIYSKTA RKGVSALDLL ASAYGASDSD EESPNEMILS  660
TDENDLKCSS VSNHQFSSAS EDLNIEDSTN GDSENEASAV GAHLKNESPV KESPMLDMLK  720
YDRDSSRMHV FCLEHALEVE KQLQQIGGAN IILLCHPEYP KFEKEAKLLA EEIGVDHQWN  780
KISFRKATEE DEERIKLVLE DEEAIPMNSD WTVKMGINLY YSSNQSKSPI YSKQLPYNAI  840
IYRAFGRDSP NSSPREVVST QDRSGRQKKI VVAGRWCGKV WMSNQVHPYL ARVNEDKEDY  900
EREDRVYQSS FKGKVNMEHS KRVDLSRETV VLNTPPARKS SRKRKKSTEK SRTKKQKRAK  960
LCKSENTEDV AEISPPLSSR VLRSSADKHA STSKRNEKQS LGEMKLKDEP KEELITRSRR  1020
RHTKLEGVKI KSKTQKKTSN KRARKKDQTK DSSSKEEEGE FPCDMEGCSM SFNTKHDLAL  1080
HKRNICPHKG CGKKFFSHKY LLQHRKVHMD DRPLKCPWKG CKMTFKWPWA RTEHIRVHTG  1140
ARPYVCKEAG CGQTFRFVSD FSRHKRKTGH SSKKGRK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	7e-72	12	381	7	346	Transcription factor jumonji (Jmj) family protein
6ip4_A	7e-72	12	381	7	346	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	941	945	RKRKK

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

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_020106930.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A199W9P8	0.0	A0A199W9P8_ANACO; Lysine-specific demethylase REF6
STRING	VIT_17s0000g09980.t01	0.0	(Vitis vinifera)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP5346	32	46

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	Aco003541.1

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]