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 LOC_Os08g06280.3
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family LSD
Protein Properties Length: 160aa    MW: 16800.6 Da    PI: 7.5002
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os08g06280.3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD143.93.8e-142751125
           zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                      C+gCr+lL+YP+GA+sV+Ca+C tV
  LOC_Os08g06280.3 27 CSGCRNLLMYPAGATSVCCAVCSTV 51
                      ***********************99 PP
2zf-LSD146.65.6e-156690125
           zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                      CggC+tlL+Y rGA+sV+C++C+tV
  LOC_Os08g06280.3 66 CGGCHTLLMYIRGATSVQCSCCHTV 90
                      ************************9 PP
3zf-LSD141.72e-13104128125
           zf-LSD1   1 CggCrtlLsYPrGApsVRCalCdtV 25 
                       Cg+Cr lL+Y +GA+sV+Ca+C++V
  LOC_Os08g06280.3 104 CGNCRMLLMYQYGARSVKCAVCNFV 128
                       ***********************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
TIGRFAMsTIGR010531.2E-132454IPR005735Zinc finger, LSD1-type
PfamPF069432.1E-112751IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010531.0E-146392IPR005735Zinc finger, LSD1-type
PfamPF069431.5E-126690IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010534.6E-12101131IPR005735Zinc finger, LSD1-type
PfamPF069431.2E-12104128IPR005735Zinc finger, LSD1-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009814Biological Processdefense response, incompatible interaction
GO:0034051Biological Processnegative regulation of plant-type hypersensitive response
GO:0034052Biological Processpositive regulation of plant-type hypersensitive response
GO:0045595Biological Processregulation of cell differentiation
GO:2000121Biological Processregulation of removal of superoxide radicals
GO:0005634Cellular Componentnucleus
Sequence ? help Back to Top
Protein Sequence    Length: 160 aa     Download sequence    Send to blast
MPVPLAPYPT PPVPFTPPNG AQSQLVCSGC RNLLMYPAGA TSVCCAVCST VTAVPAPGTE  60
MAQLVCGGCH TLLMYIRGAT SVQCSCCHTV NLAMEANQVA HVNCGNCRML LMYQYGARSV  120
KCAVCNFVTS VGVSVHQQDT SISYLVPLSE NIQFYSSII*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.576821e-108callus| flower| leaf| panicle| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329691711e-108
Functional Description ? help Back to Top
Source Description
UniProtNegative regulator of programmed cell death and hypersensitive response (HR). Positive regulator of callus differentiation. {ECO:0000269|PubMed:15915636}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os08g06280.3
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. Down-regulated by dark. {ECO:0000269|PubMed:15915636}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs08g06280
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ6206760.0AJ620676.1 Oryza sativa Japonica Group mRNA for zinc finger protein, clone Z52.
GenBankAK1117590.0AK111759.1 Oryza sativa Japonica Group cDNA clone:J023055E16, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015648106.17e-92protein LSD1 isoform X3
RefseqXP_015648107.17e-92protein LSD1 isoform X3
SwissprotQ0J7V93e-93LSD1_ORYSJ; Protein LSD1
TrEMBLA0A0E0I7G55e-91A0A0E0I7G5_ORYNI; Uncharacterized protein
STRINGOGLUM08G03690.19e-92(Oryza glumipatula)
STRINGONIVA08G03570.18e-92(Oryza nivara)
STRINGOBART08G03580.19e-92(Oryza barthii)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G32540.33e-61lsd one like 1
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]