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

Tp57577_TGAC_v2_mRNA6487

Organism

Trifolium pratense

Taxonomic ID

57577

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium

Family

LSD

Protein Properties

Length: 177aa MW: 18586.5 Da PI: 8.5461

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp57577_TGAC_v2_mRNA6487	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	41.8	1.8e-13	7	31	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr +L YPrGA++V+CalC+t+ Tp57577_TGAC_v2_mRNA6487 7 CNGCRSMLLYPRGATNVCCALCNTI 31 ***********************97 PP
2	zf-LSD1	49.7	6.1e-16	46	70	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggCrtlL+Y+rGA+sVRC++C+tV Tp57577_TGAC_v2_mRNA6487 46 CGGCRTLLMYTRGATSVRCSCCHTV 70 ************************9 PP
3	zf-LSD1	47.5	2.9e-15	84	107	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 Cg+Crt+L+YP+GApsV+Ca+C+ Tp57577_TGAC_v2_mRNA6487 84 CGNCRTTLMYPYGAPSVKCAVCHY 107 **********************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	2.6E-13	4	33	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.8E-11	7	31	IPR005735	Zinc finger, LSD1-type
Gene3D	G3DSA:3.90.10.10	7.9E-4	7	111	No hit	No description
TIGRFAMs	TIGR01053	6.2E-17	43	72	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.6E-13	46	70	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	5.1E-12	81	110	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.3E-14	84	108	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: 177 aa Download sequence Send to blast
MQSQIVCNGC RSMLLYPRGA TNVCCALCNT ITPVPPPGMD MAQLYCGGCR TLLMYTRGAT 60 SVRCSCCHTV NLAPASNQVA HVPCGNCRTT LMYPYGAPSV KCAVCHYITN INMSNGRLPI 120 PGQRPNGTTN SGTMPSTSTS MPQSQSQTVV VENPMSVDSS GKLVSNVVVG VTTDKK*

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	Tp57577_TGAC_v2_mRNA6487

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	BT141068	0.0	BT141068.1 Medicago truncatula clone JCVI-FLMt-7B6 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024629307.1	1e-117	protein LSD1
Swissprot	P94077	1e-75	LSD1_ARATH; Protein LSD1
TrEMBL	A0A2K3MUM5	1e-123	A0A2K3MUM5_TRIPR; Protein LSD1-like (Fragment)
STRING	AET04489	1e-117	(Medicago truncatula)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4027	33	61

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	2e-73	LSD family protein

Link Out ? help Back to Top
Phytozome	Tp57577_TGAC_v2_mRNA6487

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]