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

KN541440.1_FGP002

Organism

Oryza longistaminata

Taxonomic ID

4528

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza

Family

C2H2

Protein Properties

Length: 1072aa MW: 119404 Da PI: 7.9315

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KN541440.1_FGP002	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	13.2	0.00027	953	976	1	22
EEET..TTTEEESSHHHHHHHHHH CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt 22 ++C C++sFs++ +L H r KN541440.1_FGP002 953 FPCDieGCDMSFSTQQDLLLHKRD 976 789999***************985 PP
2	zf-C2H2	12.2	0.00054	1036	1062	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C+ Cg++F+ s++ rH r+ H KN541440.1_FGP002 1036 YECQepGCGQTFRFVSDFSRHKRKtgH 1062 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00558	3.7E-29	1	149	IPR003347	JmjC domain
PROSITE profile	PS51184	29.653	1	149	IPR003347	JmjC domain
SuperFamily	SSF51197	6.87E-22	7	146	No hit	No description
Pfam	PF02373	1.8E-34	12	132	IPR003347	JmjC domain
SMART	SM00355	9.7	953	975	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	15	976	1000	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.907	976	1005	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	978	1000	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.16E-14	987	1042	No hit	No description
Gene3D	G3DSA:3.30.160.60	4.0E-11	1003	1030	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	8.6E-4	1006	1030	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.655	1006	1035	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1008	1030	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	9.1E-10	1031	1059	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.18	1036	1062	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.926	1036	1067	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1038	1062	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: 1072 aa Download sequence Send to blast
MARDVAGVTT PMLYVAMLYS WFAWHVEDHE LHSLNFLHFG KAKTWYGVPR DAMLAFEETV 60 RVHGYADDLN AIRVAFQTLN EKTTVLSPEV LLSAGVPCCR LVQKAGEFVI TFPGAYHSGF 120 SHGFNCGEAS NIATPHWLQV AKEAAIRRAS TNCGPMVSHY QLLYELALSL RPREPKNFYS 180 VPRSSRLRDK NKNEGDIMVK ENFVGSVTEN NNLLSALLDK NSCIIVPNAD FFVPSFPVAL 240 ESEVTVKQRF TAGPCSISQQ GAENMAADHV AVDKVTEIQD MSGSLYPCET SLVGCSNRKL 300 YETKYGQRDA AALCLSTSEI QSRGIDTARS HPAGGILDQG RLPCVQCGIL SFACVAIIQP 360 REAAVQFIMS KECISSSAKQ GGIGASDDTS NWIDQSHEIS PPPGPASGTD DNVKHAVSLA 420 HVSDRCRELY ASNTDGCTSA LGLLASAYDS SDSDDETTED VSKHSKKNDS VNQSTDPQIL 480 ETSASCSSTV QCQKTNSHLH EEECEARATS LMKPLQQIGG ADIMLLCHPE YPRAESAAKV 540 IAEELGIKHD WKDITFKEAT EEDVKKIQLA LQDEDAEPTG SDWAVKMGIN IYYSAKQSKS 600 PLYSKQIPYN SIIYKAFGQE NPDSLTDYGC QKSGSTKKKV AGWWCGKVWM SNQVHPLLAR 660 EREEQNSSVV YGKAMFTTIS HGKVQDEAST RCNTSNRTPS RRTSRRKKGV SAEKSKPKNK 720 RSTASDEASM HCSGLGMNSG VIHDQTENSD DYDKHGNGDE IEEGINPQKY QQRKLQNVTR 780 KSSSKKRKDE KRTDSFHELY DEDNGVDYWL NMGSGDDATL GNSRQQSPDP VKVKSGGKLQ 840 GKRKSSKYKS NDDLLNEENK LQKMNKKSSS KKQKNDKINR QLQEDQTEDD HMDHLVDVAV 900 ADEVTLDNED KITEDKIDDV KVKSRGKSQN GKRKGSKHQA TDGLRAGNKV AKFPCDIEGC 960 DMSFSTQQDL LLHKRDICPV KGCKKKFFCH KYLLQHRKVH IDERPLKCTW KGCKKAFKWP 1020 WARTEHMRVH TGVRPYECQE PGCGQTFRFV SDFSRHKRKT GHSSDKRRKN ST

Sequence ? help Back to Top

Protein Sequence Length: 1072 aa Download sequence Send to blast

MARDVAGVTT PMLYVAMLYS WFAWHVEDHE LHSLNFLHFG KAKTWYGVPR DAMLAFEETV  60
RVHGYADDLN AIRVAFQTLN EKTTVLSPEV LLSAGVPCCR LVQKAGEFVI TFPGAYHSGF  120
SHGFNCGEAS NIATPHWLQV AKEAAIRRAS TNCGPMVSHY QLLYELALSL RPREPKNFYS  180
VPRSSRLRDK NKNEGDIMVK ENFVGSVTEN NNLLSALLDK NSCIIVPNAD FFVPSFPVAL  240
ESEVTVKQRF TAGPCSISQQ GAENMAADHV AVDKVTEIQD MSGSLYPCET SLVGCSNRKL  300
YETKYGQRDA AALCLSTSEI QSRGIDTARS HPAGGILDQG RLPCVQCGIL SFACVAIIQP  360
REAAVQFIMS KECISSSAKQ GGIGASDDTS NWIDQSHEIS PPPGPASGTD DNVKHAVSLA  420
HVSDRCRELY ASNTDGCTSA LGLLASAYDS SDSDDETTED VSKHSKKNDS VNQSTDPQIL  480
ETSASCSSTV QCQKTNSHLH EEECEARATS LMKPLQQIGG ADIMLLCHPE YPRAESAAKV  540
IAEELGIKHD WKDITFKEAT EEDVKKIQLA LQDEDAEPTG SDWAVKMGIN IYYSAKQSKS  600
PLYSKQIPYN SIIYKAFGQE NPDSLTDYGC QKSGSTKKKV AGWWCGKVWM SNQVHPLLAR  660
EREEQNSSVV YGKAMFTTIS HGKVQDEAST RCNTSNRTPS RRTSRRKKGV SAEKSKPKNK  720
RSTASDEASM HCSGLGMNSG VIHDQTENSD DYDKHGNGDE IEEGINPQKY QQRKLQNVTR  780
KSSSKKRKDE KRTDSFHELY DEDNGVDYWL NMGSGDDATL GNSRQQSPDP VKVKSGGKLQ  840
GKRKSSKYKS NDDLLNEENK LQKMNKKSSS KKQKNDKINR QLQEDQTEDD HMDHLVDVAV  900
ADEVTLDNED KITEDKIDDV KVKSRGKSQN GKRKGSKHQA TDGLRAGNKV AKFPCDIEGC  960
DMSFSTQQDL LLHKRDICPV KGCKKKFFCH KYLLQHRKVH IDERPLKCTW KGCKKAFKWP  1020
WARTEHMRVH TGVRPYECQE PGCGQTFRFV SDFSRHKRKT GHSSDKRRKN ST

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	8e-57	950	1069	20	139	Lysine-specific demethylase REF6
6a58_A	8e-57	950	1069	20	139	Lysine-specific demethylase REF6
6a59_A	8e-57	950	1069	20	139	Lysine-specific demethylase REF6
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	KN541440.1_FGP002

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK065251	0.0	AK065251.1 Oryza sativa Japonica Group cDNA clone:J013002J08, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015620626.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	1e-166	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A0E0BRB6	0.0	A0A0E0BRB6_9ORYZ; Uncharacterized protein
STRING	OGLUM12G09840.1	0.0	(Oryza glumipatula)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP6718	30	35

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G48430.1	1e-109	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]