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

Csa12g038910.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

LSD

Protein Properties

Length: 183aa MW: 19163 Da PI: 8.5642

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa12g038910.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	32.8	1.1e-10	1	17	9	25
zf-LSD1 9 sYPrGApsVRCalCdtV 25 +YPrGA++VRCalC+t+ Csa12g038910.1 1 MYPRGASNVRCALCNTI 17 9**************97 PP
2	zf-LSD1	45.9	9.2e-15	43	66	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 CggCrt+L+Y+rGA+sVRC++C+t Csa12g038910.1 43 CGGCRTMLMYTRGASSVRCSCCQT 66 ***********************9 PP
3	zf-LSD1	49.1	9.5e-16	90	114	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Crt+L+YP+GA+sV+Ca+C++V Csa12g038910.1 90 CGHCRTTLMYPYGASSVKCAVCQFV 114 ***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	5.0E-11	1	20	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.7E-8	1	17	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	1.5E-18	40	70	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.6E-12	43	66	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	8.2E-14	87	117	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.6E-14	90	114	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 183 aa Download sequence Send to blast
MYPRGASNVR CALCNTINMV PPPHPHPPPP HAHAGMDMAH IVCGGCRTML MYTRGASSVR 60 CSCCQTTNLV PGLSNQVPHA PSNQVAQINC GHCRTTLMYP YGASSVKCAV CQFVTNVNMS 120 NGRVPLPTNR PNGTACPGTM PSSSTSTPPS QTQTVVVENP MSVDESGKLV SNVVVGVTTD 180 KK*

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	Csa12g038910.1

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	ATU87833	1e-152	U87833.1 Arabidopsis thaliana zinc-finger protein Lsd1 (LSD1) mRNA, complete cds.
GenBank	AY080824	1e-152	AY080824.1 Arabidopsis thaliana putative zinc-finger protein Lsd1 (At4g20380) mRNA, complete cds.
GenBank	AY087794	1e-152	AY087794.1 Arabidopsis thaliana clone 38456 mRNA, complete sequence.
GenBank	AY117316	1e-152	AY117316.1 Arabidopsis thaliana putative zinc-finger protein Lsd1 (At4g20380) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010434286.1	1e-109	PREDICTED: protein LSD1 isoform X2
Refseq	XP_019086113.1	1e-109	PREDICTED: protein LSD1 isoform X2
Swissprot	P94077	4e-93	LSD1_ARATH; Protein LSD1
TrEMBL	R0F6R0	1e-102	R0F6R0_9BRAS; Uncharacterized protein
STRING	XP_006284594.1	1e-103	(Capsella rubella)

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	7e-92	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]