PlantTFDB
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 Carubv10005824m
Common NameCARUB_v10005824mg
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family LSD
Protein Properties Length: 186aa    MW: 19696.7 Da    PI: 8.4998
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10005824mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD152.76.6e-17731125
          zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                     C+gCr+lL+YPrGA++VRCalC+t+
  Carubv10005824m  7 CHGCRNLLMYPRGASNVRCALCNTI 31
                     ***********************97 PP

2zf-LSD145.99.4e-155174124
          zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdt 24
                     CggCrt+L+Y+rGA+sVRC++C+t
  Carubv10005824m 51 CGGCRTMLMYTRGASSVRCSCCQT 74
                     ***********************9 PP

3zf-LSD1499.7e-1698122125
          zf-LSD1   1 CggCrtlLsYPrGApsVRCalCdtV 25 
                      Cg+Crt+L+YP+GA+sV+Ca+C++V
  Carubv10005824m  98 CGHCRTTLMYPYGASSVKCAVCQFV 122
                      ***********************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
TIGRFAMsTIGR010531.5E-19434IPR005735Zinc finger, LSD1-type
PfamPF069434.2E-14731IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010531.6E-184878IPR005735Zinc finger, LSD1-type
PfamPF069435.7E-125174IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010538.4E-1495125IPR005735Zinc finger, LSD1-type
PfamPF069435.8E-1498122IPR005735Zinc 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: 186 aa     Download sequence    Send to blast
MQDQLVCHGC RNLLMYPRGA SNVRCALCNT INMVPPPPHA HAGMDMAHIV CGGCRTMLMY  60
TRGASSVRCS CCQTTNLVPG LSNQVPHAPS NQVAQINCGH CRTTLMYPYG ASSVKCAVCQ  120
FVTNVNMSNG RVPIPTNRPN GTMPSTSTST PPSQTQTVVV ENPMSVDESG KLVSNVVVGV  180
TTDKK*
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
PlantRegMapCarubv10005824m
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
GenBankATU878331e-174U87833.1 Arabidopsis thaliana zinc-finger protein Lsd1 (LSD1) mRNA, complete cds.
GenBankAY0808241e-174AY080824.1 Arabidopsis thaliana putative zinc-finger protein Lsd1 (At4g20380) mRNA, complete cds.
GenBankAY0877941e-174AY087794.1 Arabidopsis thaliana clone 38456 mRNA, complete sequence.
GenBankAY1173161e-174AY117316.1 Arabidopsis thaliana putative zinc-finger protein Lsd1 (At4g20380) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006284594.11e-132protein LSD1 isoform X3
RefseqXP_006284595.11e-132protein LSD1 isoform X3
SwissprotP940771e-105LSD1_ARATH; Protein LSD1
TrEMBLR0F6R01e-131R0F6R0_9BRAS; Uncharacterized protein
STRINGXP_006284594.11e-132(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM53452650
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G20380.71e-103LSD 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]