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 Sobic.010G035200.1.p
Common NameSb10g003170, SORBIDRAFT_10g003170
Organism
Sorghum bicolor
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
Family Whirly
Protein Properties Length: 267aa    MW: 29552.7 Da    PI: 9.8846
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.010G035200.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly198.78e-62912291139
                Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGk 89 
                           s+yk+kaal+ +++ p+f+ ldsg+ k+ ++G++ll++a+a+a+r+ydW +kq+f+ls+ e+++l+ l++ +sceffhdp+++ s+eGk
  Sobic.010G035200.1.p  91 SIYKGKAALSFDPRPPQFVPLDSGAYKVAKEGFVLLQFAPAVATRQYDWTRKQVFSLSVWEIGTLLTLGPTDSCEFFHDPFKGRSEEGK 179
                           7**************************************************************************************** PP

                Whirly  90 vrkalkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                           vrk+lkveP pdG G f+nlsv+n l++++es+++P++k+efav+ s ++
  Sobic.010G035200.1.p 180 VRKVLKVEPTPDGNGRFFNLSVQNRLINVDESIYIPITKGEFAVIVSTFN 229
                           *********************************************99875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.101.5E-7979250IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544472.35E-7484266IPR009044ssDNA-binding transcriptional regulator
PfamPF085369.7E-5992226IPR013742Plant 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: 267 aa     Download sequence    Send to blast
MPPPPAPRFL SLASPPALLP VHHHHNHPRS LLPPLVASTR KAAALPACPV ASPRHSDYFD  60
PRAPPPPRGD GGGYGRAPNG AQDGRVFTSY SIYKGKAALS FDPRPPQFVP LDSGAYKVAK  120
EGFVLLQFAP AVATRQYDWT RKQVFSLSVW EIGTLLTLGP TDSCEFFHDP FKGRSEEGKV  180
RKVLKVEPTP DGNGRFFNLS VQNRLINVDE SIYIPITKGE FAVIVSTFNY IIPHLMGWST  240
FASSIKPEES RLYSRPQSTS EYEWRR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A3e-898026532219p24: plant transcriptional regulator PBF-2
1l3a_B3e-898026532219p24: plant transcriptional regulator PBF-2
1l3a_C3e-898026532219p24: plant transcriptional regulator PBF-2
1l3a_D3e-898026532219p24: plant transcriptional regulator PBF-2
4koq_A8e-90852468169Single-stranded DNA-binding protein WHY3, chloroplastic
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.57400.0embryo| leaf| pollen
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
PlantRegMapSobic.010G035200.1.p
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.
GenBankEU9558610.0EU955861.1 Zea mays clone 1549286 DNA-binding protein p24 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002436467.10.0single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotB2LXS71e-164WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLC5Z3X10.0C5Z3X1_SORBI; Uncharacterized protein
STRINGSb10g003170.10.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP30123885
Representative plantOGRP23161635
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02740.23e-96ssDNA-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]