PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Previous version: v3.0 v4.0

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Glyma.05G171000.1.p

Common Name

GLYMA_05G171000, LOC100776394

Organism

Glycine max

Taxonomic ID

3847

Taxonomic Lineage

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

Family

LSD

Protein Properties

Length: 178aa MW: 18724.6 Da PI: 8.551

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.05G171000.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	43	7.6e-14	7	31	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr lL YPrGA++V+CalC+t+ Glyma.05G171000.1.p 7 CNGCRSLLLYPRGATNVCCALCNTI 31 ***********************97 PP
2	zf-LSD1	49.6	6.2e-16	46	70	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggCrtlL+Y+rGA+sVRC++C+tV Glyma.05G171000.1.p 46 CGGCRTLLMYTRGATSVRCSCCHTV 70 ************************9 PP
3	zf-LSD1	51.6	1.5e-16	85	109	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Crt+L+YP+GApsV+CalC+++ Glyma.05G171000.1.p 85 CGNCRTTLMYPYGAPSVKCALCHFI 109 ***********************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.90.10.10	4.3E-4	4	114	No hit	No description
TIGRFAMs	TIGR01053	4.7E-13	4	34	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	8.6E-12	7	31	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	1.2E-17	43	73	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.7E-13	46	70	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	1.2E-12	82	111	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	6.8E-15	85	109	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 178 aa Download sequence Send to blast
MQSQVVCNGC RSLLLYPRGA TNVCCALCNT ITSVPPPGME MSQLYCGGCR TLLMYTRGAT 60 SVRCSCCHTV NLVPPASNQV AHVHCGNCRT TLMYPYGAPS VKCALCHFIT NVSTNNGRLP 120 IPVHRPNGTT NAGTLPTTST SMPQSQSQTV VVENPMSVDS SGKLVSNVVV GVTTDKK*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Gma.31998	0.0	leaf\| root

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	Glyma.05G171000.1.p

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	BT096707	0.0	BT096707.1 Soybean clone JCVI-FLGm-21G1 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001241344.1	1e-125	uncharacterized protein LOC100776394
Refseq	XP_028233008.1	1e-125	protein LSD1-like isoform X3
Swissprot	P94077	4e-74	LSD1_ARATH; Protein LSD1
TrEMBL	A0A445KPP0	1e-123	A0A445KPP0_GLYSO; Protein LSD1 isoform B
TrEMBL	A0A445KPZ8	1e-124	A0A445KPZ8_GLYSO; Protein LSD1 isoform A
STRING	GLYMA05G30490.1	1e-124	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4027	33	61
Representative plant	OGRP1146	17	53

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	5e-73	LSD family protein

Link Out ? help Back to Top
Phytozome	Glyma.05G171000.1.p
Entrez Gene	100776394

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]