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 Gorai.013G077400.12
Common NameB456_013G077400
Organism
Gossypium raimondii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family Whirly
Protein Properties Length: 161aa    MW: 17992.6 Da    PI: 10.3937
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.013G077400.12genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly72.57e-2392144153
               Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkq 53 
                          s+yk+kaal+v++++p+f+ ldsg++k++r+G++ll++a+a+++r+ydW++kq
  Gorai.013G077400.12  92 SIYKGKAALTVEPRAPEFVPLDSGAFKISREGFVLLQFAPAAGVRQYDWSRKQ 144
                          7***************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.102.2E-2584145IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544474.47E-2386144IPR009044ssDNA-binding transcriptional regulator
PfamPF085365.1E-2093145IPR013742Plant 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:0045910Biological Processnegative regulation of DNA recombination
GO:0009508Cellular Componentplastid chromosome
GO:0009570Cellular Componentchloroplast stroma
GO:0003697Molecular Functionsingle-stranded DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0003723Molecular FunctionRNA binding
GO:0042162Molecular Functiontelomeric DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 161 aa     Download sequence    Send to blast
MLQLQLLSSP PLTPQTLNLN SISNPKLFPS FSSLNSSQTR SFKFNPLSKP SKFSLKCRQS  60
EYFDQKQRFN DSSSSTSPSS LGLPARFYVG HSIYKGKAAL TVEPRAPEFV PLDSGAFKIS  120
REGFVLLQFA PAAGVRQYDW SRKQIKCKIF VVKDEYVLET *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koo_A9e-3682145467Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B9e-3682145467Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C9e-3682145467Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D9e-3682145467Single-stranded DNA-binding protein WHY1, chloroplastic
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Gra.5560.0seedling
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO487461810.0
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}.
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
GenBankJX6176091e-90JX617609.1 Gossypium hirsutum clone NBRI_GE62797 microsatellite sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012463276.13e-98PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic-like isoform X2
SwissprotQ9M9S35e-48WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A0D2VAT41e-111A0A0D2VAT4_GOSRA; Uncharacterized protein
STRINGGorai.013G077400.12e-90(Gossypium raimondii)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G14410.11e-44ssDNA-binding transcriptional regulator
Publications ? help Back to Top
  1. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]