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 Pahal.J00203.1
Organism
Panicum hallii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family Whirly
Protein Properties Length: 301aa    MW: 33400.2 Da    PI: 10.2891
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pahal.J00203.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly198.31e-611252631139
          Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalk 95 
                     s+yk+kaal+ +++ p+f+ ldsg+ k+ ++G++ll++a+a+a+r+ydW +kq+f+ls+ e+++l+ l++ +sceffhdp+++ s+eGkvrk+lk
  Pahal.J00203.1 125 SIYKGKAALSFDPRPPQFVPLDSGAYKVAKEGFVLLQFAPAVATRQYDWTRKQVFSLSVWEIGTLLTLGPTDSCEFFHDPFKGRSEEGKVRKVLK 219
                     7********************************************************************************************** PP

          Whirly  96 vePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                     veP pdG G f+nlsv+n l++++es+++P++k+efav+ s ++
  Pahal.J00203.1 220 VEPTPDGNGRFFNLSVQNRLLNVDESIYIPITKGEFAVIVSTFN 263
                     ***************************************99875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.101.3E-79113285IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544472.12E-75118300IPR009044ssDNA-binding transcriptional regulator
PfamPF085361.1E-58126260IPR013742Plant transcription factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006281Biological ProcessDNA repair
GO:0032211Biological Processnegative regulation of telomere maintenance via telomerase
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0045910Biological Processnegative regulation of DNA recombination
GO:0009508Cellular Componentplastid chromosome
GO:0009570Cellular Componentchloroplast stroma
GO:0003697Molecular Functionsingle-stranded DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0003723Molecular FunctionRNA binding
GO:0042162Molecular Functiontelomeric DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 301 aa     Download sequence    Send to blast
SQAHRSTDRH RINPFAVGTP TRPRRLLVRS PFGDMPPPAP LFLSLPSPPP PLLPVHHPRA  60
LQTVALSLAP PLASSRKPAL PACPVASPRH SDYFDPRAPP PPRGDGGYGR PPNGAHEGRV  120
FTSYSIYKGK AALSFDPRPP QFVPLDSGAY KVAKEGFVLL QFAPAVATRQ YDWTRKQVFS  180
LSVWEIGTLL TLGPTDSCEF FHDPFKGRSE EGKVRKVLKV EPTPDGNGRF FNLSVQNRLL  240
NVDESIYIPI TKGEFAVIVS TFNYIIPHLM GWSTFTSSIK PEESRPYSRP QSAPEYEWRR  300
*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A9e-898929912219p24: plant transcriptional regulator PBF-2
1l3a_B9e-898929912219p24: plant transcriptional regulator PBF-2
1l3a_C9e-898929912219p24: plant transcriptional regulator PBF-2
1l3a_D9e-898929912219p24: plant transcriptional regulator PBF-2
4koq_A2e-891192808169Single-stranded DNA-binding protein WHY3, chloroplastic
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}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0433600.0BT043360.1 Zea mays full-length cDNA clone ZM_BFc0169P08 mRNA, complete cds.
GenBankEU5956640.0EU595664.1 Zea mays Whirly family nucleic acid binding protein (WHY1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025810386.10.0single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotB2LXS71e-169WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A2T8JEU80.0A0A2T8JEU8_9POAL; Uncharacterized protein
STRINGSi006951m1e-174(Setaria italica)
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
AT2G02740.21e-95ssDNA-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]