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 ONIVA06G03980.1
Organism
Oryza nivara
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
Family Whirly
Protein Properties Length: 505aa    MW: 55940.7 Da    PI: 10.5035
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA06G03980.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly191.11.8e-59972341138
           Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkal 94 
                      s+yk+kaa++++++ p+f+ ldsg+ k+ ++G++ll++a+a+a+r+ydW +kq+f+ls+ e+++l+ l++ +sceffhdp+++ s+eGkvrk+l
  ONIVA06G03980.1  97 SIYKGKAAMSLDPRPPQFVPLDSGAYKVVKEGFVLLQFAPAVATRQYDWTRKQVFSLSVWEMGSLLTLGPTDSCEFFHDPFKGRSDEGKVRKVL 190
                      79******************************************************************************************** PP

           Whirly  95 kvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsll 138
                      kveP pdG   f+nlsv+n l++ +e++++P++k+efav+ s +
  ONIVA06G03980.1 191 KVEPTPDGNSRFFNLSVQNRLLNIDENIYIPITKGEFAVIVSTF 234
                      ****************************************9987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.101.4E-7884257IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544474.08E-7789272IPR009044ssDNA-binding transcriptional regulator
PfamPF085363.5E-5898232IPR013742Plant transcription factor
PfamPF145477.2E-6468504IPR027923Hydrophobic seed protein
SuperFamilySSF476992.04E-5468504IPR016140Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain
Gene3DG3DSA:1.10.110.108.0E-7471504No hitNo description
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
Sequence ? help Back to Top
Protein Sequence    Length: 505 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 RSLSQCSTWT GAMGATEDFV RRVVWNRDQT  300
WSLVPKQSNA QPCSVESTRR QKNARSERCG RRCLAARDLA HAALVEIPDS PMEKSLPTPA  360
IHPPTTESFL PRRHQPRRHE DQIHGGLGID WNGAGAATNK ITKENQVTQN HTRKIKNTER  420
RGEAAASTTP PVLEPPPRTL RRSAPSSRPP PWSGRRRALP PRTPRSAAAV CKRGNILGIN  480
LNLPVDLSLI LNYCGKRVPT GFKCF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A8e-889127037218p24: plant transcriptional regulator PBF-2
1l3a_B8e-889127037218p24: plant transcriptional regulator PBF-2
1l3a_C8e-889127037218p24: plant transcriptional regulator PBF-2
1l3a_D8e-889127037218p24: plant transcriptional regulator PBF-2
Search in ModeBase
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
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-138WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A0E0HL100.0A0A0E0HL10_ORYNI; Uncharacterized protein
STRINGONIVA06G03980.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP30123885
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02740.23e-93ssDNA-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]