PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os08g06280.1
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: 202aa    MW: 21129.7 Da    PI: 7.9543
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os08g06280.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD143.45.4e-1485109125
           zf-LSD1   1 CggCrtlLsYPrGApsVRCalCdtV 25 
                       C+gCr+lL+YP+GA+sV+Ca+C tV
  LOC_Os08g06280.1  85 CSGCRNLLMYPAGATSVCCAVCSTV 109
                       ***********************99 PP
2zf-LSD146.17.9e-15124148125
           zf-LSD1   1 CggCrtlLsYPrGApsVRCalCdtV 25 
                       CggC+tlL+Y rGA+sV+C++C+tV
  LOC_Os08g06280.1 124 CGGCHTLLMYIRGATSVQCSCCHTV 148
                       ************************9 PP
3zf-LSD141.22.7e-13162186125
           zf-LSD1   1 CggCrtlLsYPrGApsVRCalCdtV 25 
                       Cg+Cr lL+Y +GA+sV+Ca+C++V
  LOC_Os08g06280.1 162 CGNCRMLLMYQYGARSVKCAVCNFV 186
                       ***********************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
TIGRFAMsTIGR010531.7E-1382112IPR005735Zinc finger, LSD1-type
PfamPF069432.9E-1185109IPR005735Zinc finger, LSD1-type
SuperFamilySSF486951.67E-585183IPR011031Multihaem cytochrome
TIGRFAMsTIGR010531.5E-14121150IPR005735Zinc finger, LSD1-type
PfamPF069432.1E-12124148IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010531.1E-11159187IPR005735Zinc finger, LSD1-type
PfamPF069431.7E-12162186IPR005735Zinc 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: 202 aa     Download sequence    Send to blast
MCIAEPIFCC IKSPETSCCK LKRFLSCRER KGDFSCLTAA RICEASTSDA VVQAAGTAMP  60
VPLAPYPTPP VPFTPPNGAQ SQLVCSGCRN LLMYPAGATS VCCAVCSTVT AVPAPGTEMA  120
QLVCGGCHTL LMYIRGATSV QCSCCHTVNL AMEANQVAHV NCGNCRMLLM YQYGARSVKC  180
AVCNFVTSFQ ASPGTDQKPS S*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.687413e-98flower| leaf| panicle| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2977216643e-98
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_Os08g06280.1
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
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_015648106.11e-142protein LSD1 isoform X3
RefseqXP_015648107.11e-142protein LSD1 isoform X3
SwissprotQ0J7V91e-125LSD1_ORYSJ; Protein LSD1
TrEMBLI1QFV11e-141I1QFV1_ORYGL; Uncharacterized protein
STRINGORGLA08G0030200.11e-142(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP134738124
Representative plantOGRP11461753
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G32540.31e-58lsd 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]