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 Oropetium_20150105_24966A
Organism
Oropetium thomaeum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Chloridoideae; Cynodonteae; Tripogoninae; Oropetium
Family Whirly
Protein Properties Length: 267aa    MW: 29387.7 Da    PI: 9.5279
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Oropetium_20150105_24966AgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly195.76.4e-61912281138
                     Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakg 84 
                                s+yk+kaal+ +++ p+f+ ldsg+ k+ ++G +ll++a+a+a+r+ydW +kq+f+ls+ e+++l+ l++ +sceffhdp+++ 
  Oropetium_20150105_24966A  91 SIYKGKAALSFDPRPPQFVPLDSGAYKVAKEGCVLLQFAPAVATRQYDWTRKQVFSLSVWEIGTLLTLGPTDSCEFFHDPFKGR 174
                                7*********************************************************************************** PP

                     Whirly  85 sneGkvrkalkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsll 138
                                s+eGkvrk+lkveP pdG G f+nlsv+n l++ +es+++P+sk+efav+ s l
  Oropetium_20150105_24966A 175 SEEGKVRKVLKVEPTPDGNGRFFNLSVQNRLLNIDESIYIPISKGEFAVIVSTL 228
                                **************************************************9877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.108.8E-7979249IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544477.85E-7584266IPR009044ssDNA-binding transcriptional regulator
PfamPF085367.7E-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
MPPPPPLFLS LTSPVRPLLP VHPPKGAQTI ALASPVPSFM KPALLPACSV ASPRHSDYFD  60
PRAPPPPPRG DGYGRSPPNG AQDGRVFTSY SIYKGKAALS FDPRPPQFVP LDSGAYKVAK  120
EGCVLLQFAP AVATRQYDWT RKQVFSLSVW EIGTLLTLGP TDSCEFFHDP FKGRSEEGKV  180
RKVLKVEPTP DGNGRFFNLS VQNRLLNIDE SIYIPISKGE FAVIVSTLNY IIPHLMGWST  240
FTSSIKPEDP RPFSRPQSGP EFEWQR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A1e-905426512219p24: plant transcriptional regulator PBF-2
1l3a_B1e-905426512219p24: plant transcriptional regulator PBF-2
1l3a_C1e-905426512219p24: plant transcriptional regulator PBF-2
1l3a_D1e-905426512219p24: 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
PlantRegMapOropetium_20150105_24966A
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025810386.11e-152single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotB2LXS71e-153WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A2T8JEU81e-151A0A2T8JEU8_9POAL; Uncharacterized protein
STRINGGRMZM2G155662_P011e-151(Zea mays)
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
AT2G02740.29e-94ssDNA-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]