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 Potri.003G048700.1
Common NamePOPTR_0003s04700g
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family Whirly
Protein Properties Length: 230aa    MW: 25117.9 Da    PI: 10.2402
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.003G048700.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly199.83.6e-62531891137
              Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvr 91 
                         sv+k+kaal+v++v+ptf++  sgnl+++r+G+++l++ +a++erkyd+ek+q+falsatev++l++ ++k+sceffhdp++ +sn+G+vr
  Potri.003G048700.1  53 SVFKGKAALSVEPVLPTFSKFGSGNLRVDRRGSMMLTFLPAIGERKYDYEKRQKFALSATEVGSLISTGPKDSCEFFHDPSMLSSNAGQVR 143
                         79***************************************************************************************** PP

              Whirly  92 kalkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsl 137
                         k l+++P++dGsG+fv+lsv n+++k+ e+f+vPv+ aef+vl+++
  Potri.003G048700.1 144 KNLSIKPHADGSGYFVSLSVVNNILKTTERFTVPVTTAEFTVLKTA 189
                         *******************************************997 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-7443205IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544473.22E-6546227IPR009044ssDNA-binding transcriptional regulator
PfamPF085364.5E-5954188IPR013742Plant transcription factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006281Biological ProcessDNA repair
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005739Cellular Componentmitochondrion
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 230 aa     Download sequence    Send to blast
MMKLSRFLNF NRNAVGKPTD VRDGSALHAL TFQASISTGG KSSIQDRVFA PYSVFKGKAA  60
LSVEPVLPTF SKFGSGNLRV DRRGSMMLTF LPAIGERKYD YEKRQKFALS ATEVGSLIST  120
GPKDSCEFFH DPSMLSSNAG QVRKNLSIKP HADGSGYFVS LSVVNNILKT TERFTVPVTT  180
AEFTVLKTAC SFALPHIMGW DRLTTPLPGT LASKLSKVDP QMPDLEWDK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4kop_A5e-924720710170Single-stranded DNA-binding protein WHY2, mitochondrial
4kop_B5e-924720710170Single-stranded DNA-binding protein WHY2, mitochondrial
4kop_C5e-924720710170Single-stranded DNA-binding protein WHY2, mitochondrial
4kop_D5e-924720710170Single-stranded DNA-binding protein WHY2, mitochondrial
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pth.31390.0stem
Functional Description ? help Back to Top
Source Description
UniProtSingle-stranded DNA-binding protein that may be involved in the maintenance of mitochondrial genome stability by preventing break-induced DNA rearrangements. {ECO:0000269|PubMed:21911368}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPotri.003G048700.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEF1460250.0EF146025.1 Populus trichocarpa clone WS0115_A07 unknown mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002303313.21e-170single-stranded DNA-binding protein WHY2, mitochondrial
SwissprotD9J0343e-97WHY2_SOLTU; Single-stranded DNA-binding protein WHY2, mitochondrial
TrEMBLA9PCM91e-168A9PCM9_POPTR; Whirly family protein
STRINGcassava4.1_015441m1e-117(Manihot esculenta)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF113833338
Representative plantOGRP23161635
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G71260.12e-98WHIRLY 2
Publications ? help Back to Top
  1. Ralph SG, et al.
    Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding.
    BMC Genomics, 2008. 9: p. 57
    [PMID:18230180]