PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Potri.001G442400.3
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family LSD
Protein Properties Length: 187aa    MW: 19847 Da    PI: 7.8598
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.001G442400.3genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD130.17.8e-102549125
             zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                        C gC  +L YP GA++V+CalC tV
  Potri.001G442400.3 25 CRGCASVLLYPSGASNVCCALCSTV 49
                        9**********************99 PP
2zf-LSD138.61.8e-126488125
             zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                        C gCr lL+YP GA+ VRC++C+ V
  Potri.001G442400.3 64 CRGCRSLLMYPHGATTVRCSCCHVV 88
                        9**********************98 PP
3zf-LSD1391.3e-12102126125
             zf-LSD1   1 CggCrtlLsYPrGApsVRCalCdtV 25 
                         Cg+Crt L+YP G+psV+C++C+ V
  Potri.001G442400.3 102 CGNCRTALMYPNGSPSVKCPVCHYV 126
                         **********************987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
TIGRFAMsTIGR010534.0E-92252IPR005735Zinc finger, LSD1-type
PfamPF069431.0E-72549IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010534.1E-136190IPR005735Zinc finger, LSD1-type
PfamPF069431.9E-106488IPR005735Zinc finger, LSD1-type
Gene3DG3DSA:3.30.40.102.2E-479129IPR013083Zinc finger, RING/FYVE/PHD-type
TIGRFAMsTIGR010532.0E-1199129IPR005735Zinc finger, LSD1-type
PfamPF069431.0E-11102126IPR005735Zinc finger, LSD1-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000303Biological Processresponse to superoxide
GO:0001666Biological Processresponse to hypoxia
GO:0002240Biological Processresponse to molecule of oomycetes origin
GO:0009626Biological Processplant-type hypersensitive response
GO:0009862Biological Processsystemic acquired resistance, salicylic acid mediated signaling pathway
GO:0010104Biological Processregulation of ethylene-activated signaling pathway
GO:0010310Biological Processregulation of hydrogen peroxide metabolic process
GO:0010602Biological Processregulation of 1-aminocyclopropane-1-carboxylate metabolic process
GO:0010618Biological Processaerenchyma formation
GO:0043069Biological Processnegative regulation of programmed cell death
Sequence ? help Back to Top
Protein Sequence    Length: 187 aa     Download sequence    Send to blast
MGFLMFCCRE EEEDRQREMQ SQVVCRGCAS VLLYPSGASN VCCALCSTVT SIPSPGMDMA  60
QLICRGCRSL LMYPHGATTV RCSCCHVVNI APGYNQAAHV NCGNCRTALM YPNGSPSVKC  120
PVCHYVTNVS MANMRIPLPA NRPNGIGGTA PSTSMTQTVV VENPMSVDES GKLVSNVVVG  180
VTTEKK*
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in cotyledons, roots, rosette leaves, stems, inflorescences and flowers. {ECO:0000269|PubMed:20456049}.
Functional Description ? help Back to Top
Source Description
UniProtNegative 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
SourceLink
PlantRegMapPotri.001G442400.3
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By methyl viologen. {ECO:0000269|PubMed:20456049}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1826841e-87AC182684.2 Populus trichocarpa clone Pop1-37C15, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024462592.11e-134protein LOL2 isoform X3
SwissprotP940772e-63LSD1_ARATH; Protein LSD1
TrEMBLA0A2K2CD301e-133A0A2K2CD30_POPTR; Uncharacterized protein
STRINGPOPTR_0001s43300.11e-114(Populus trichocarpa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G20380.72e-65LSD family protein
Publications ? help Back to Top
  1. Spedaletti V, et al.
    Characterization of a lysine-specific histone demethylase from Arabidopsis thaliana.
    Biochemistry, 2008. 47(17): p. 4936-47
    [PMID:18393445]
  2. 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]
  3. 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]
  4. 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]