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

DCAR_023885

Organism

Daucus carota

Taxonomic ID

4039

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Apiales; Apiineae; Apiaceae; Apioideae; Scandiceae; Daucinae; Daucus

Family

C2H2

Protein Properties

Length: 105aa MW: 12149.9 Da PI: 10.4381

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
DCAR_023885	genome	ARS-USDA	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.2	1.4e-05	18	40	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 C+ Cgk F ++ +L +H+++H DCAR_023885 18 CSvkGCGKKFASHKYLIHHQKVH 40 77779****************99 PP
2	zf-C2H2	12.6	0.00041	47	70	2	23
EET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23 +C+ C+k+F+ + Hir+H DCAR_023885 47 QCTweGCTKTFKWAWARTEHIRVH 70 79999*****************99 PP
3	zf-C2H2	16.2	3.1e-05	76	102	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C C+k+F+ s++ rH r+ H DCAR_023885 76 YTCAetGCSKTFRFVSDFSRHRRKtgH 102 99*********************9777 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00355	0.011	16	40	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.487	16	45	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	18	40	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.3E-6	18	44	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	7.31E-15	30	82	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.1E-11	45	70	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0026	46	70	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.03	46	75	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	48	70	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	7.8E-11	71	99	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.8	76	102	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.552	76	104	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	78	102	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: 105 aa Download sequence Send to blast
MMNFGSKKEL GLHEKNICSV KGCGKKFASH KYLIHHQKVH REDRPLQCTW EGCTKTFKWA 60 WARTEHIRVH TGDRPYTCAE TGCSKTFRFV SDFSRHRRKT GHSG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	2e-53	2	103	32	133	Lysine-specific demethylase REF6
6a58_A	2e-53	2	103	32	133	Lysine-specific demethylase REF6
6a59_A	2e-53	2	103	32	133	Lysine-specific demethylase REF6
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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_017217471.1	1e-73	PREDICTED: lysine-specific demethylase REF6-like
Refseq	XP_017217475.1	5e-73	PREDICTED: lysine-specific demethylase REF6-like
Refseq	XP_017217476.1	1e-73	PREDICTED: lysine-specific demethylase REF6-like
Swissprot	Q9STM3	3e-50	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A175Y9Q8	3e-72	A0A175Y9Q8_DAUCS; Uncharacterized protein
STRING	VIT_17s0000g09980.t01	6e-52	(Vitis vinifera)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA4988	23	31

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G48430.1	1e-52	relative of early flowering 6

Link Out ? help Back to Top
Phytozome	DCAR_023885

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]