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 Cagra.0534s0030.1.p
Organism
Capsella grandiflora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family Whirly
Protein Properties Length: 270aa    MW: 29893 Da    PI: 9.8146
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.0534s0030.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly216.13.3e-67912301139
               Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpa.akgsneGk 89 
                          s+yk+kaal+v++++p+f+al+sg++kl+++G+lll++a+a+++r+ydW++kq+f+ls+te+++l++l+++esceffhdp+  kgs+eGk
  Cagra.0534s0030.1.p  91 SIYKGKAALTVEPRAPEFVALESGAFKLTKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLISLGPRESCEFFHDPFkGKGSDEGK 180
                          7********************************************************************************44679**** PP

               Whirly  90 vrkalkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                          vrk+lkvePlpdGsG f+nlsv+n l++++e++++P++kaefavl+s+++
  Cagra.0534s0030.1.p 181 VRKVLKVEPLPDGSGRFFNLSVQNRLLNVDENVYIPITKAEFAVLISAFN 230
                          ***********************************************996 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-7879252IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544474.47E-8083269IPR009044ssDNA-binding transcriptional regulator
PfamPF085361.3E-5892227IPR013742Plant 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:0045910Biological Processnegative regulation of DNA recombination
GO:0009508Cellular Componentplastid chromosome
GO:0009570Cellular Componentchloroplast stroma
GO:0003677Molecular FunctionDNA binding
GO:0003723Molecular FunctionRNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 270 aa     Download sequence    Send to blast
MSQLLSSPPM AVFSETFVNH QFTDARFLSS HSILTSGGFA GKIVPLKPTA RLKLTVKSRQ  60
GDYFEKQRFG DSSSPPQNTE GSSPRFYVGH SIYKGKAALT VEPRAPEFVA LESGAFKLTK  120
EGFLLLQFAP AAGVRQYDWS RKQVFSLSVT EIGNLISLGP RESCEFFHDP FKGKGSDEGK  180
VRKVLKVEPL PDGSGRFFNL SVQNRLLNVD ENVYIPITKA EFAVLISAFN FILPHLIGWN  240
TFATSIKPED SNRLNNASPK YGGDYEWSR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koq_A1e-113792472169Single-stranded DNA-binding protein WHY3, chloroplastic
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtSingle-stranded DNA-binding protein that functions in both chloroplasts and nucleus. In chloroplasts, maintains plastid genome stability by preventing break-induced and short homology-dependent illegitimate recombinations. In the nucleus, is recruited to a distal element upstream of the kinesin KP1 to mediate the transcriptional repression of KP1. Can bind double-stranded DNA in vivo. {ECO:0000269|PubMed:19666500, ECO:0000269|PubMed:19669906, ECO:0000269|PubMed:20551348, ECO:0000269|PubMed:21911368}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.0534s0030.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By salicylic acid (SA). {ECO:0000269|PubMed:19669906}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0153360.0BT015336.1 Arabidopsis thaliana At2g02740 gene, complete cds.
GenBankBT0156410.0BT015641.1 Arabidopsis thaliana At2g02740 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006291681.10.0single-stranded DNA-binding protein WHY3, chloroplastic
SwissprotQ66GR60.0WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBLR0H5N70.0R0H5N7_9BRAS; Uncharacterized protein
STRINGCagra.0534s0030.1.p0.0(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM50232752
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02740.10.0ssDNA-binding transcriptional regulator
Publications ? help Back to Top
  1. Lepage É,Zampini É,Brisson N
    Plastid genome instability leads to reactive oxygen species production and plastid-to-nucleus retrograde signaling in Arabidopsis.
    Plant Physiol., 2013. 163(2): p. 867-81
    [PMID:23969600]
  2. Zampini É,Lepage É,Tremblay-Belzile S,Truche S,Brisson N
    Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans.
    Genome Res., 2015. 25(5): p. 645-54
    [PMID:25800675]
  3. Karpinska B,Alomrani SO,Foyer CH
    Inhibitor-induced oxidation of the nucleus and cytosol in Arabidopsis thaliana: implications for organelle to nucleus retrograde signalling.
    Philos. Trans. R. Soc. Lond., B, Biol. Sci., 2018.
    [PMID:28808105]