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 XP_009101242.1
Organism
Brassica rapa
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: 261aa    MW: 28804.8 Da    PI: 10.0853
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009101242.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly217.41.4e-67822211139
          Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpa.akgsneGkvrkal 94 
                     s+yk+kaal++++++p+f+al+sg++kl+++G+lll++a+a+++r+ydW++kq+f+ls+te+++lv+l++kesceffhdp   kgs+eGkvrk+l
  XP_009101242.1  82 SIYKGKAALTIEPRAPEFVALESGAFKLSKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPKESCEFFHDPNkGKGSDEGKVRKVL 176
                     7********************************************************************************45679********* PP

          Whirly  95 kvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                     kvePlpdGsG f+nlsv+n+l++++es+++P++kaefavl+s+++
  XP_009101242.1 177 KVEPLPDGSGRFFNLSVQNKLLNVDESVYIPITKAEFAVLISAFN 221
                     ******************************************996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.105.1E-7870243IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544472.2E-7874261IPR009044ssDNA-binding transcriptional regulator
PfamPF085361.5E-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: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: 261 aa     Download sequence    Send to blast
MSQLLSSTPP LAVNSRIFLT HRFPEARFLT AGVFVGKGRG FSVKPTERVK LTVKSRYSDS  60
SSPAYSQQNG EGSSPRFYVG HSIYKGKAAL TIEPRAPEFV ALESGAFKLS KEGFLLLQFA  120
PAAGVRQYDW SRKQVFSLSV TEIGNLVSLG PKESCEFFHD PNKGKGSDEG KVRKVLKVEP  180
LPDGSGRFFN LSVQNKLLNV DESVYIPITK AEFAVLISAF NFILPHLIGW QAFASSIKPE  240
DSNRLNNASS PKYGGDYEWS R
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_009101242.1
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_009101242.10.0PREDICTED: single-stranded DNA-binding protein WHY3, chloroplastic isoform X1
SwissprotQ66GR61e-152WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBLM4E7Q30.0M4E7Q3_BRARP; Uncharacterized protein
STRINGBra024809.1-P0.0(Brassica rapa)
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-150ssDNA-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]