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 OB06G12750.1
Organism
Oryza brachyantha
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: 269aa    MW: 30292.8 Da    PI: 8.4066
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
OB06G12750.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly66.35.9e-2168125158
        Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfals 58 
                   s+yk+kaal++++  p+f  ldsg+ k+ ++G++ll++a+a+a+r+ydW +kq fa +
  OB06G12750.1  68 SIYKGKAALSLDPSPPQFAPLDSGAYKVVKEGFVLLQFAPAVATRQYDWTRKQLFAGA 125
                   7******************************************************865 PP
2Whirly111.65.9e-3514623253139
        Whirly  53 qsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                   q+f+ls+ e+++l+ l++ +sceffhdp+++ s+eGkvrk+lkveP pdG   f+nlsv+n l++ +e++++P+sk+efav+ s ++
  OB06G12750.1 146 QVFSLSVWEMGSLLTLGPTDSCEFFHDPFKGRSDEGKVRKVLKVEPTPDGNSRFFNLSVQNRLLNIDENIYIPISKGEFAVIVSTFN 232
                   89********************************************************************************99875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.102.2E-2657123IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544475.49E-2260123IPR009044ssDNA-binding transcriptional regulator
PfamPF085367.9E-2169145IPR013742Plant transcription factor
SuperFamilySSF544471.1E-48146269IPR009044ssDNA-binding transcriptional regulator
Gene3DG3DSA:2.30.31.102.0E-45146254IPR009044ssDNA-binding transcriptional regulator
PfamPF085362.6E-32146229IPR013742Plant 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
Sequence ? help Back to Top
Protein Sequence    Length: 269 aa     Download sequence    Send to blast
MALALAWTLP GRRVSSVCPV ASQRHSDYFD PRAPPPXXXX XXGYGSPPYS SPPAAPGTQN  60
GRVFSTYSIY KGKAALSLDP SPPQFAPLDS GAYKVVKEGF VLLQFAPAVA TRQYDWTRKQ  120
LFAGAKYESF NFSREIDICE TLDFYQVFSL SVWEMGSLLT LGPTDSCEFF HDPFKGRSDE  180
GKVRKVLKVE PTPDGNSRFF NLSVQNRLLN IDENIYIPIS KGEFAVIVST FNYIIPHLMG  240
WSTFTNSIKP EDSRTYTRPQ SGPEYEWRR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A2e-845726732218p24: plant transcriptional regulator PBF-2
1l3a_B2e-845726732218p24: plant transcriptional regulator PBF-2
1l3a_C2e-845726732218p24: plant transcriptional regulator PBF-2
1l3a_D2e-845726732218p24: 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapOB06G12750.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankCT8361941e-176CT836194.1 Oryza sativa (indica cultivar-group) cDNA clone:OSIGCEA048P18, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015641336.11e-138single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotB2LXS71e-124WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLJ3MB810.0J3MB81_ORYBR; Uncharacterized protein
STRINGOB06G12750.10.0(Oryza brachyantha)
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
AT2G02740.26e-89ssDNA-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]