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_009110543.1
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: 269aa    MW: 29404.1 Da    PI: 9.7406
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009110543.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly221.19.9e-69922301139
          Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalk 95 
                     s+yk+kaal+v++++p+f++ldsg++kl+++G+lll++a+a+++r+ydW+kkq+f+ls+ e+++lv+l+++esceffhdp +++s+eGkvrk+lk
  XP_009110543.1  92 SIYKGKAALTVEPRAPEFVSLDSGAFKLSKDGFLLLQFAPAAGVRQYDWSKKQVFSLSVSEIGTLVSLGPRESCEFFHDPNKGKSDEGKVRKVLK 186
                     7********************************************************************************************** PP

          Whirly  96 vePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                     vePlpdGsG+f+nlsv+n+l++++es+++P+++aef+vl s+++
  XP_009110543.1 187 VEPLPDGSGHFFNLSVQNKLLNVDESIYIPITRAEFTVLVSAFN 230
                     ***************************************99986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.103.3E-7982253IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544476.04E-8086269IPR009044ssDNA-binding transcriptional regulator
PfamPF085366.5E-6193227IPR013742Plant transcription factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006281Biological ProcessDNA repair
GO:0032211Biological Processnegative regulation of telomere maintenance via telomerase
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0009507Cellular Componentchloroplast
GO:0009508Cellular Componentplastid chromosome
GO:0003697Molecular Functionsingle-stranded DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0042162Molecular Functiontelomeric DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 269 aa     Download sequence    Send to blast
MSQLLSSPLM AASYSPFTSP RFLSSSSSSV LVAGGGLAVK RHGLASKPVR TVNLSVKSRQ  60
SDYFEKQRFG DSSSSSSQNG EGGPARFYVG HSIYKGKAAL TVEPRAPEFV SLDSGAFKLS  120
KDGFLLLQFA PAAGVRQYDW SKKQVFSLSV SEIGTLVSLG PRESCEFFHD PNKGKSDEGK  180
VRKVLKVEPL PDGSGHFFNL SVQNKLLNVD ESIYIPITRA EFTVLVSAFN FVLPYLIGWH  240
AFANSIKPEE SNRTNNASPN YGGDYEWNR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koo_A1e-115802472169Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B1e-115802472169Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C1e-115802472169Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D1e-115802472169Single-stranded DNA-binding protein WHY1, chloroplastic
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.79520.0flower| root| silique
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 nucleus, modulates telomere length homeostasis by inhibiting the action of the telomerase at the extreme termini of chromosomes. Is recruited to a distal element upstream of the kinesin KP1 to mediate the transcriptional repression of KP1. Is required for full salicylic acid-dependent plant disease resistance responses. Can bind double-stranded DNA in vivo. {ECO:0000269|PubMed:14960277, ECO:0000269|PubMed:17217467, ECO:0000269|PubMed:19666500, ECO:0000269|PubMed:19669906, ECO:0000269|PubMed:20551348, ECO:0000269|PubMed:21911368}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009110543.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By salicylic acid (SA) and infection by H.parasitica. {ECO:0000269|PubMed:14960277, 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
GenBankAF3324520.0AF332452.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
GenBankAF3701560.0AF370156.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
GenBankAY0590970.0AY059097.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009110543.10.0PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotQ9M9S31e-162WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLM4DJM40.0M4DJM4_BRARP; Uncharacterized protein
STRINGBra016702.1-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
AT1G14410.11e-152ssDNA-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. Carella P,Wilson DC,Cameron RK
    Some things get better with age: differences in salicylic acid accumulation and defense signaling in young and mature Arabidopsis.
    Front Plant Sci, 2014. 5: p. 775
    [PMID:25620972]
  3. 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]
  4. Ren Y,Li Y,Jiang Y,Wu B,Miao Y
    Phosphorylation of WHIRLY1 by CIPK14 Shifts Its Localization and Dual Functions in Arabidopsis.
    Mol Plant, 2017. 10(5): p. 749-763
    [PMID:28412544]
  5. 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]
  6. Huang D,Lin W,Deng B,Ren Y,Miao Y
    Dual-Located WHIRLY1 Interacting with LHCA1 Alters Photochemical Activities of Photosystem I and Is Involved in Light Adaptation in Arabidopsis.
    Int J Mol Sci, 2018.
    [PMID:29112140]
  7. Guan Z,Wang W,Yu X,Lin W,Miao Y
    Comparative Proteomic Analysis of Coregulation of CIPK14 and WHIRLY1/3 Mediated Pale Yellowing of Leaves in Arabidopsis.
    Int J Mol Sci, 2018.
    [PMID:30065159]