PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_013595615.1
Organism
Brassica oleracea
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family Whirly
Protein Properties Length: 260aa    MW: 28635.5 Da    PI: 10.1003
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013595615.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly215.16.6e-67822211139
          Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpa.akgsneGkvrkal 94 
                     s+yk+kaal++++++p+f+al+sg++kl+++G+lll++a+a+++r+ydW++kq+f+ls+te++++v+l+++esceffhdp   kgs+eGkvrk+l
  XP_013595615.1  82 SIYKGKAALTIEPRAPEFVALESGAFKLSKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNVVSLGPRESCEFFHDPNkGKGSDEGKVRKVL 176
                     7********************************************************************************45679********* PP

          Whirly  95 kvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                     kvePlpdGsG f+nlsv+n+l++++es+++P++kaefavl+s+++
  XP_013595615.1 177 KVEPLPDGSGRFFNLSVQNKLLNVDESVYIPITKAEFAVLISAFN 221
                     ******************************************996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.102.0E-7770243IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544477.06E-8074260IPR009044ssDNA-binding transcriptional regulator
PfamPF085363.2E-5883218IPR013742Plant 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: 260 aa     Download sequence    Send to blast
MSQLLSSPPM AANSKTFLTH RFPEARVLNA AGGFVGKRHG FAVRPTERVK LTVKSRYSDS  60
SSPAYSPQNG EGSSPRFYVG HSIYKGKAAL TIEPRAPEFV ALESGAFKLS KEGFLLLQFA  120
PAAGVRQYDW SRKQVFSLSV TEIGNVVSLG PRESCEFFHD PNKGKGSDEG KVRKVLKVEP  180
LPDGSGRFFN LSVQNKLLNV DESVYIPITK AEFAVLISAF NFILPHLIGW QAFASSIKPE  240
DSNRLNNASP KYGGDYEWSR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koq_A1e-112702382169Single-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
PlantRegMapXP_013595615.1
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_013595615.10.0PREDICTED: single-stranded DNA-binding protein WHY3, chloroplastic isoform X1
RefseqXP_013703747.10.0single-stranded DNA-binding protein WHY3, chloroplastic-like isoform X1
RefseqXP_013703758.10.0single-stranded DNA-binding protein WHY3, chloroplastic-like isoform X1
SwissprotQ66GR61e-156WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBLA0A0D3DAE80.0A0A0D3DAE8_BRAOL; Uncharacterized protein
STRINGBo7g080560.10.0(Brassica oleracea)
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
AT2G02740.11e-155ssDNA-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]