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 Sevir.4G032700.1.p
Organism
Setaria viridis
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; Cenchrinae; Setaria
Family Whirly
Protein Properties Length: 269aa    MW: 29699.9 Da    PI: 9.7493
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sevir.4G032700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly198.77.8e-62932311139
              Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvr 91 
                         s+yk+kaal+ +++ p+f+ ldsg+ k+ ++G++ll++a+a+a+r+ydW +kq+f+ls+ e+++l+ l++ +sceffhdp+++ s+eGkvr
  Sevir.4G032700.1.p  93 SIYKGKAALSFDPRPPQFVPLDSGAYKVAKEGFVLLQFAPAVATRQYDWTRKQVFSLSVWEIGTLLTLGPTDSCEFFHDPFKGRSEEGKVR 183
                         7****************************************************************************************** PP

              Whirly  92 kalkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                         k+lkveP pdG G f+nlsv+n l++++es+++P++k+efav+ s ++
  Sevir.4G032700.1.p 184 KVLKVEPTPDGNGRFFNLSVQNRLLNVDESIYIPITKGEFAVIVSTFN 231
                         *******************************************99875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.108.4E-8081253IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544474.24E-7686268IPR009044ssDNA-binding transcriptional regulator
PfamPF085368.6E-5994228IPR013742Plant 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
MPPPAPLFLS LPSPPPPLLP VHHHPKAPQA LSLAPPLASS RKAALPACPV ASSRHSDYFD  60
PRAPPPPPPP RGDGGYGRPP NGAHEGRVFT SYSIYKGKAA LSFDPRPPQF VPLDSGAYKV  120
AKEGFVLLQF APAVATRQYD WTRKQVFSLS VWEIGTLLTL GPTDSCEFFH DPFKGRSEEG  180
KVRKVLKVEP TPDGNGRFFN LSVQNRLLNV DESIYIPITK GEFAVIVSTF NYIIPHLMGW  240
STFTSSIKPE DSRSYNRPQS TPEYEWRR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A7e-918226732219p24: plant transcriptional regulator PBF-2
1l3a_B7e-918226732219p24: plant transcriptional regulator PBF-2
1l3a_C7e-918226732219p24: plant transcriptional regulator PBF-2
1l3a_D7e-918226732219p24: 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
PlantRegMapSevir.4G032700.1.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_004964537.10.0single-stranded DNA-binding protein WHY1, chloroplastic isoform X1
SwissprotB2LXS71e-166WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A368QQA50.0A0A368QQA5_SETIT; Uncharacterized protein
STRINGSi006951m0.0(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
AT2G02740.25e-97ssDNA-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]