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_Os06g05350.1
Common NameLOC4340109, Os06g0145800, OsJ_20114, OSJNBa0007O20.30, OSNPB_060145800, P0036F10.13
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 Whirly
Protein Properties Length: 273aa    MW: 30161.4 Da    PI: 9.73
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os06g05350.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly192.94.7e-60972351139
            Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrka 93 
                       s+yk+kaa++++++ p+f+ ldsg+ k+ ++G++ll++a+a+a+r+ydW +kq+f+ls+ e+++l+ l++ +sceffhdp+++ s+eGkvrk+
  LOC_Os06g05350.1  97 SIYKGKAAMSLDPRPPQFVPLDSGAYKVVKEGFVLLQFAPAVATRQYDWTRKQVFSLSVWEMGSLLTLGPTDSCEFFHDPFKGRSDEGKVRKV 189
                       7******************************************************************************************** PP

            Whirly  94 lkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                       lkveP pdG   f+nlsv+n l++ +e++++P++k+efav+ s ++
  LOC_Os06g05350.1 190 LKVEPTPDGNSRFFNLSVQNRLLNIDENIYIPITKGEFAVIVSTFN 235
                       *****************************************99875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.103.1E-7984257IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544476.91E-7889272IPR009044ssDNA-binding transcriptional regulator
PfamPF085369.1E-5998232IPR013742Plant transcription factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006281Biological ProcessDNA repair
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0045910Biological Processnegative regulation of DNA recombination
GO:0009508Cellular Componentplastid chromosome
GO:0009570Cellular Componentchloroplast stroma
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0003723Molecular FunctionRNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009009anatomyplant embryo
PO:0001081developmental stagemature plant embryo stage
PO:0007042developmental stagewhole plant fruit formation stage
Sequence ? help Back to Top
Protein Sequence    Length: 273 aa     Download sequence    Send to blast
MPPPSPPLFL SLPSPPPPPL PHLLPSHRPA AALTLAPALS SRRVSSVCPV ASQRHSDYFD  60
PRAPPPPPPR DGYGGPAYSP PAAQGGQQNG RVFSTYSIYK GKAAMSLDPR PPQFVPLDSG  120
AYKVVKEGFV LLQFAPAVAT RQYDWTRKQV FSLSVWEMGS LLTLGPTDSC EFFHDPFKGR  180
SDEGKVRKVL KVEPTPDGNS RFFNLSVQNR LLNIDENIYI PITKGEFAVI VSTFNYIIPH  240
LMGWSTFTNS IKPEDSRAYT RPQSGPEYEW RR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A6e-919127037218p24: plant transcriptional regulator PBF-2
1l3a_B6e-919127037218p24: plant transcriptional regulator PBF-2
1l3a_C6e-919127037218p24: plant transcriptional regulator PBF-2
1l3a_D6e-919127037218p24: plant transcriptional regulator PBF-2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.82720.0callus| panicle| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2976051650.0
Expression AtlasQ5VP52-
Functional Description ? help Back to Top
Source Description
UniProtSingle-stranded DNA and RNA binding protein that maintains plastid genome stability by preventing break-induced and short homology-dependent illegitimate recombinations. Functions in RNA metabolism and is involved in the maturation of the atpF and 23S ribosomal RNAs. {ECO:0000269|PubMed:18676978, ECO:0000269|PubMed:19666500}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os06g05350.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs06g05350
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankCT8361940.0CT836194.1 Oryza sativa (indica cultivar-group) cDNA clone:OSIGCEA048P18, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015641336.10.0single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotB2LXS71e-141WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A0E0HL110.0A0A0E0HL11_ORYNI; Uncharacterized protein
TrEMBLA0A0E0PTG90.0A0A0E0PTG9_ORYRU; Uncharacterized protein
TrEMBLQ5VP520.0Q5VP52_ORYSJ; Os06g0145800 protein
STRINGORUFI06G03010.10.0(Oryza rufipogon)
STRINGOS06T0145800-000.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP30123885
Representative plantOGRP23161635
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02740.22e-96ssDNA-binding transcriptional regulator
Publications ? help Back to Top
  1. Soderlund C, et al.
    Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.
    PLoS Genet., 2009. 5(11): p. e1000740
    [PMID:19936069]