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

XP_013598154.1

Organism

Brassica oleracea

Taxonomic ID

3712

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: 190aa MW: 20153.2 Da PI: 8.6183

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013598154.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	49.4	7.4e-16	7	31	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr++L YPrGA++VRCalC+t+ XP_013598154.1 7 CHGCRNTLLYPRGATNVRCALCNTI 31 ***********************97 PP
2	zf-LSD1	47.9	2.1e-15	54	78	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggCrt+L+Y+rGA+sVRC++C+tV XP_013598154.1 54 CGGCRTMLMYTRGASSVRCSCCQTV 78 ************************9 PP
3	zf-LSD1	52.1	1e-16	95	119	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Crt+L+YP+GApsVRCa+C++V XP_013598154.1 95 CGNCRTTLMYPYGAPSVRCAVCQFV 119 ***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	2.9E-17	4	34	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	7.6E-13	7	31	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	7.4E-19	51	81	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	9.1E-13	54	78	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	2.2E-13	92	122	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.2E-14	95	119	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 190 aa Download sequence Send to blast
MQDQLVCHGC RNTLLYPRGA TNVRCALCNT INMVPLHPPP PPPHHGMDMA HIVCGGCRTM 60 LMYTRGASSV RCSCCQTVNL VPATPPANQP AHVNCGNCRT TLMYPYGAPS VRCAVCQFVT 120 NVNMGNGRVP FPTNQPNGTA SSPGSMPSTS TQSTPPSQTQ TVVVENPMSV NESGKLVSNV 180 VVGVTTDKKK

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	XP_013598154.1

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	AF453323	0.0	AF453323.1 Brassica oleracea zinc finger protein LSD2 (LSD2) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013598154.1	1e-135	PREDICTED: protein LSD1-like isoform X5
Swissprot	P94077	8e-88	LSD1_ARATH; Protein LSD1
TrEMBL	A0A0D3DF64	1e-122	A0A0D3DF64_BRAOL; Uncharacterized protein
STRING	Bo7g107120.1	1e-123	(Brassica oleracea)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	1e-86	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] 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]