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

Bostr.18473s0107.1.p

Organism

Boechera stricta

Taxonomic ID

72658

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Boechereae; Boechera

Family

C2H2

Protein Properties

Length: 151aa MW: 17306.1 Da PI: 9.8283

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Bostr.18473s0107.1.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	11.3	0.001	65	88	2	23
EET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23 kCp C+++F+ + + Hir+H Bostr.18473s0107.1.p 65 KCPwkGCKMTFKWAWSRTEHIRVH 88 799*******************99 PP
2	zf-C2H2	13.1	0.00029	96	120	3	23
ET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirt..H 23 C Cg++F+ s++ rH r+ H Bostr.18473s0107.1.p 96 CAepGCGQTFRFVSDFSRHKRKtgH 120 66669****************9777 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	9.8E-16	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	13.799	20	61	IPR003349	JmjN domain
Pfam	PF02375	4.2E-15	21	54	IPR003349	JmjN domain
SuperFamily	SSF57667	1.73E-11	55	99	No hit	No description
Gene3D	G3DSA:3.30.160.60	7.4E-10	62	87	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.928	64	93	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0015	64	88	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	66	88	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	3.4E-10	88	117	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.907	94	125	IPR007087	Zinc finger, C2H2
SMART	SM00355	3.8	94	120	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	96	120	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 151 aa Download sequence Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPRVHSD 60 DRPLKCPWKG CKMTFKWAWS RTEHIRVHTG ARPYLCAEPG CGQTFRFVSD FSRHKRKTGH 120 SVKKTKKKAL CSQSLNIWNS HCCGQILNLL *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	1e-46	56	128	68	140	Lysine-specific demethylase REF6
6a58_A	1e-46	56	128	68	140	Lysine-specific demethylase REF6
6a59_A	1e-46	56	128	68	140	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Bostr.18473s0107.1.p

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	AL049659	6e-92	AL049659.2 Arabidopsis thaliana DNA chromosome 3, BAC clone T29H11.
GenBank	AY664499	6e-92	AY664499.1 Arabidopsis thaliana relative of early flowering 6 (REF6) mRNA, complete cds.
GenBank	CP002686	6e-92	CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010503472.1	9e-45	PREDICTED: lysine-specific demethylase REF6-like
Swissprot	Q9STM3	3e-44	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A087GW86	3e-43	A0A087GW86_ARAAL; Uncharacterized protein
TrEMBL	A0A087GW87	3e-43	A0A087GW87_ARAAL; Uncharacterized protein
TrEMBL	D7LRW5	2e-43	D7LRW5_ARALL; Uncharacterized protein
TrEMBL	R0FN14	3e-43	R0FN14_9BRAS; Uncharacterized protein
STRING	Bostr.18473s0107.1.p	1e-109	(Boechera stricta)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G48430.1	2e-38	relative of early flowering 6

Link Out ? help Back to Top
Phytozome	Bostr.18473s0107.1.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]