PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os08g06280.9
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: 132aa    MW: 13723.4 Da    PI: 7.9939
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os08g06280.9genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD144.32.8e-142751125
           zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                      C+gCr+lL+YP+GA+sV+Ca+C tV
  LOC_Os08g06280.9 27 CSGCRNLLMYPAGATSVCCAVCSTV 51
                      ***********************99 PP
2zf-LSD1474.1e-156690125
           zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                      CggC+tlL+Y rGA+sV+C++C+tV
  LOC_Os08g06280.9 66 CGGCHTLLMYIRGATSVQCSCCHTV 90
                      ************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
TIGRFAMsTIGR010538.6E-142454IPR005735Zinc finger, LSD1-type
PfamPF069431.5E-112751IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010537.3E-156392IPR005735Zinc finger, LSD1-type
PfamPF069431.1E-126690IPR005735Zinc 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: 132 aa     Download sequence    Send to blast
MPVPLAPYPT PPVPFTPPNG AQSQLVCSGC RNLLMYPAGA TSVCCAVCST VTAVPAPGTE  60
MAQLVCGGCH TLLMYIRGAT SVQCSCCHTV NLAMEGTTKI YHPPPLLQLV YSVALIPVCK  120
ILLLNRIFSC G*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.576821e-122callus| flower| leaf| panicle| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329691711e-122
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_Os08g06280.9
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
GenBankAJ6206761e-159AJ620676.1 Oryza sativa Japonica Group mRNA for zinc finger protein, clone Z52.
GenBankAK1117591e-159AK111759.1 Oryza sativa Japonica Group cDNA clone:J023055E16, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025875668.11e-61protein LSD1 isoform X2
SwissprotQ0J7V92e-51LSD1_ORYSJ; Protein LSD1
TrEMBLA0A0D3GWK02e-60A0A0D3GWK0_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0AR363e-60A0A0E0AR36_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0QEL72e-60A0A0E0QEL7_ORYRU; Uncharacterized protein
STRINGOMERI08G03620.12e-61(Oryza meridionalis)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G32540.33e-31lsd 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]