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

GSBRNA2T00138078001

Common Name

GSBRNA2T00138078001

Organism

Brassica napus

Taxonomic ID

3708

Taxonomic Lineage

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

Family

LSD

Protein Properties

Length: 195aa MW: 20487.7 Da PI: 8.6217

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00138078001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	51	2.4e-16	7	31	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr++L+YPrGA++VRCalC+ V GSBRNA2T00138078001 7 CHGCRNTLMYPRGATNVRCALCHIV 31 ***********************98 PP
2	zf-LSD1	47.9	2.2e-15	60	84	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggCrt+L+Y+rGA+sVRC++C+tV GSBRNA2T00138078001 60 CGGCRTMLMYTRGASSVRCSCCQTV 84 ************************9 PP
3	zf-LSD1	49.2	8.6e-16	101	125	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Crt+L+YP+GA+sV+Ca+C++V GSBRNA2T00138078001 101 CGNCRTTLMYPYGASSVKCAVCQFV 125 ***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	3.4E-17	4	34	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	4.4E-13	7	31	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	7.7E-19	57	87	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	9.3E-13	60	84	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	6.3E-14	98	128	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	3.9E-14	101	125	IPR005735	Zinc finger, LSD1-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000303	Biological Process	response to superoxide
GO:0001666	Biological Process	response to hypoxia
GO:0002240	Biological Process	response to molecule of oomycetes origin
GO:0009626	Biological Process	plant-type hypersensitive response
GO:0009862	Biological Process	systemic acquired resistance, salicylic acid mediated signaling pathway
GO:0010104	Biological Process	regulation of ethylene-activated signaling pathway
GO:0010310	Biological Process	regulation of hydrogen peroxide metabolic process
GO:0010602	Biological Process	regulation of 1-aminocyclopropane-1-carboxylate metabolic process
GO:0010618	Biological Process	aerenchyma formation
GO:0043069	Biological Process	negative regulation of programmed cell death

Sequence ? help Back to Top
Protein Sequence Length: 195 aa Download sequence Send to blast
MQDQLVCHGC RNTLMYPRGA TNVRCALCHI VNMVPLHPHP PPPPPPHHAH AGMDMAHIVC 60 GGCRTMLMYT RGASSVRCSC CQTVNLVPGP PPSNQVAHIN CGNCRTTLMY PYGASSVKCA 120 VCQFVTNVNM SNGRVPLASN RPNGTAAPGT MPSTSTQSTP PSQTQTVVVE NPMSVNESGK 180 LVSNVVVGVT TGQK*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bna.8729	0.0	microspore-derived embryo\| seed

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in cotyledons, roots, rosette leaves, stems, inflorescences and flowers. {ECO:0000269\|PubMed:20456049}.

Functional Description ? help Back to Top
Source	Description
UniProt	Negative regulator of reactive oxygen-induced cell death, cold stress-induced cell death, pathogen-induced hypersensitive response (HR), basal disease resistance. May be involved in the induction of the copper/zinc superoxide dismutase CSD1 and CSD2 that detoxify accumulating superoxide before the reactive oxygen species (ROS) can trigger a cell death cascade. LSD1 and LOL1 have antagonistic effects on CSD1 and CSD2 accumulation to regulate oxidative stress-induced cell death. Antagonizes the function of BZIP10, a positive regulator of cell death, by interacting in the cytoplasm and preventing its nuclear localization. Controls lysigenous aerenchyma in hypocotyls under root hypoxia. Required for leaf acclimation in response to excess excitation energy. {ECO:0000269\|PubMed:10550898, ECO:0000269\|PubMed:11595797, ECO:0000269\|PubMed:11844114, ECO:0000269\|PubMed:12732715, ECO:0000269\|PubMed:15347794, ECO:0000269\|PubMed:16957775, ECO:0000269\|PubMed:18055613, ECO:0000269\|PubMed:18790826, ECO:0000269\|PubMed:20456049, ECO:0000269\|PubMed:21097903}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00138078001

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By methyl viologen. {ECO:0000269\|PubMed:20456049}.

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	AF453322	0.0	AF453322.1 Brassica oleracea zinc finger protein LSD1 (LSD1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013635811.1	1e-137	PREDICTED: protein LSD1 isoform X3
Swissprot	P94077	1e-85	LSD1_ARATH; Protein LSD1
TrEMBL	A0A3P6FIX0	1e-136	A0A3P6FIX0_BRAOL; Uncharacterized protein
STRING	Bra013460.1-P	1e-120	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5345	26	50

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	2e-84	LSD family protein

Publications ? help Back to Top
Spedaletti V, et al. Characterization of a lysine-specific histone demethylase from Arabidopsis thaliana. Biochemistry, 2008. 47(17): p. 4936-47 [PMID:18393445] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] Szechyńska-Hebda M,Czarnocka W,Hebda M,Bernacki MJ,Karpiński S PAD4, LSD1 and EDS1 regulate drought tolerance, plant biomass production, and cell wall properties. Plant Cell Rep., 2016. 35(3): p. 527-39 [PMID:26754794] Czarnocka W, et al. The dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator. Plant Cell Environ., 2017. 40(11): p. 2644-2662 [PMID:28555890] Bernacki MJ, et al. LSD1-, EDS1- and PAD4-dependent conditional correlation among salicylic acid, hydrogen peroxide, water use efficiency and seed yield in Arabidopsis thaliana. Physiol Plant, 2019. 165(2): p. 369-382 [PMID:30461017]