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 MLOC_11586.1
Organism
Hordeum vulgare
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Triticodae; Triticeae; Hordeinae; Hordeum
Family Whirly
Protein Properties Length: 193aa    MW: 21659.7 Da    PI: 9.2618
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
MLOC_11586.1genomeIBSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly193.53.1e-60181561139
        Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalkve 97 
                   s+yk+kaal  +++ p+f+ l+sg+ k+ ++G++ll++a+a+++r+ydW +kq+f+ls+ e+++l+ l+  +sceffhdp+++ s+eGkvrk+lkve
  MLOC_11586.1  18 SIYKGKAALAFDPRPPQFVPLESGAYKVAKEGFVLLQFAPAVGPRQYDWARKQVFSLSVWEMGTLLTLGLTDSCEFFHDPFKGRSDEGKVRKVLKVE 114
                   7************************************************************************************************ PP

        Whirly  98 PlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                   P pdG G f+nlsv+n l++++e++++P++k+e+av+ s ++
  MLOC_11586.1 115 PTPDGNGRFFNLSVQNRLLNVDENIYIPITKGEYAVIVSTFN 156
                   *************************************99875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.101.1E-788178IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544471.02E-7411193IPR009044ssDNA-binding transcriptional regulator
PfamPF085368.2E-5919153IPR013742Plant 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: 193 aa     Download sequence    Send to blast
GGPPVPGGQA GRVFASYSIY KGKAALAFDP RPPQFVPLES GAYKVAKEGF VLLQFAPAVG  60
PRQYDWARKQ VFSLSVWEMG TLLTLGLTDS CEFFHDPFKG RSDEGKVRKV LKVEPTPDGN  120
GRFFNLSVQN RLLNVDENIY IPITKGEYAV IVSTFNYIIP HIMGWSTFTN SIKPEESQPY  180
NRPQSSPELE WRR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A2e-91719132218p24: plant transcriptional regulator PBF-2
1l3a_B2e-91719132218p24: plant transcriptional regulator PBF-2
1l3a_C2e-91719132218p24: plant transcriptional regulator PBF-2
1l3a_D2e-91719132218p24: 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
PlantRegMapMLOC_11586.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3537950.0AK353795.1 Hordeum vulgare subsp. vulgare mRNA for predicted protein, complete cds, clone: NIASHv1002M22.
GenBankAK3654520.0AK365452.1 Hordeum vulgare subsp. vulgare mRNA for predicted protein, complete cds, clone: NIASHv2034E15.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020186783.11e-139single-stranded DNA-binding protein WHY1, chloroplastic-like
SwissprotB2LXS71e-120WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLF2CQ931e-138F2CQ93_HORVV; Predicted protein
STRINGMLOC_11586.11e-141(Hordeum vulgare)
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
AT2G02740.22e-94ssDNA-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]