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

RrC5438_p5

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

LSD

Protein Properties

Length: 170aa MW: 18302.4 Da PI: 8.8146

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC5438_p5	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	43.6	4.7e-14	7	31	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C gCrt+L+YPrGA++V+CalC t+ RrC5438_p5 7 CRGCRTTLMYPRGATNVCCALCRTI 31 9**********************97 PP
2	zf-LSD1	30.1	8.1e-10	44	67	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 C gC+++L+Y+r A+sVRC++C+t RrC5438_p5 44 CCGCGIMLMYTRSATSVRCSCCHT 67 99*********************8 PP
3	zf-LSD1	45	1.8e-14	83	107	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Cr++L+YP+GA+sV+Ca+C+ V RrC5438_p5 83 CGHCRIILMYPYGASSVKCAVCQYV 107 ***********************87 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	6.8E-12	4	31	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.8E-12	7	31	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	4.5E-10	42	71	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	3.4E-7	44	67	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	3.7E-12	81	110	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.4E-13	83	107	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 170 aa Download sequence Send to blast
MQEQLVCRGC RTTLMYPRGA TNVCCALCRT ISPPQGMDMA RIVCCGCGIM LMYTRSATSV 60 RCSCCHTLNL VPAPSNQTAR INCGHCRIIL MYPYGASSVK CAVCQYVTNV NMSNGRAPLS 120 MNRPNLTASP STRVPSTSTT QTVVVENPMS LDESGKLVSN VVVGVTTHKK

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}.

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018480681.1	1e-117	PREDICTED: protein LSD1-like
Swissprot	P94077	1e-73	LSD1_ARATH; Protein LSD1
TrEMBL	A0A3P6E0U8	1e-104	A0A3P6E0U8_BRAOL; Uncharacterized protein
STRING	Bo7g067690.1	1e-103	(Brassica oleracea)

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	3e-71	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]