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 Pavir.4KG032400.1.p
Organism
Panicum virgatum
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: 271aa    MW: 29853.1 Da    PI: 9.771
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.4KG032400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly198.77.9e-62952331139
               Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkv 90 
                          s+yk+kaal+ +++ p+f+ ldsg+ k+ ++G++ll++a+a+a+r+ydW +kq+f+ls+ e+++l+ l++ +sceffhdp+++ s+eGkv
  Pavir.4KG032400.1.p  95 SIYKGKAALSFDPRPPQFVPLDSGAYKVAKEGFVLLQFAPAVATRQYDWTRKQVFSLSVWEIGTLLTLGPTDSCEFFHDPFKGRSEEGKV 184
                          7***************************************************************************************** PP

               Whirly  91 rkalkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                          rk+lkveP pdG G f+nlsv+n l++++es+++P++k+efav+ s ++
  Pavir.4KG032400.1.p 185 RKVLKVEPTPDGNGRFFNLSVQNRLLNVDESIYIPITKGEFAVIVSTFN 233
                          ********************************************99875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.103.2E-7983255IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544475.1E-7588270IPR009044ssDNA-binding transcriptional regulator
PfamPF085368.7E-5996230IPR013742Plant 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:0009508Cellular Componentplastid chromosome
GO:0009570Cellular Componentchloroplast stroma
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 271 aa     Download sequence    Send to blast
MPPPAPLFLS LPSPPPPPLL PAHHPRAPQS VSLSLSPPLA ASRRPAALPA CPVASPRHSD  60
YFDPRAPPPP PPRGDGGYGR PPNGAHEGRV FTSYSIYKGK AALSFDPRPP QFVPLDSGAY  120
KVAKEGFVLL QFAPAVATRQ YDWTRKQVFS LSVWEIGTLL TLGPTDSCEF FHDPFKGRSE  180
EGKVRKVLKV EPTPDGNGRF FNLSVQNRLL NVDESIYIPI TKGEFAVIVS TFNYIIPHLM  240
GWSTFSSSIK PEESRPYSRP QSAPEYEWRR *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koq_A3e-90892508169Single-stranded DNA-binding protein WHY3, chloroplastic
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.398040.0leaf
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
PlantRegMapPavir.4KG032400.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
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_025810386.11e-172single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotB2LXS71e-170WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A2T7E3101e-170A0A2T7E310_9POAL; Uncharacterized protein
STRINGPavir.Da02402.1.p0.0(Panicum virgatum)
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]