PlantTFDB
Plant Transcription Factor Database
v5.0
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_004490010.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; Cicer
Family Whirly
Protein Properties Length: 242aa    MW: 27137.1 Da    PI: 8.9031
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_004490010.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly193.53.1e-60702071138
          Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalk 95 
                     svyk+ka l+v +++p+f++++sg++k++r+G +ll++a+a+++ +ydW++kq+f+ls+ e+++l++l++k+sce fhdp+ ++++eGkvrk+lk
  XP_004490010.1  70 SVYKGKAVLTVSPRAPEFTSMESGSFKISREGCMLLQFAPAVGVHQYDWNRKQVFSLSVNEMGSLISLGAKDSCEIFHDPFIGKGDEGKVRKVLK 164
                     79********************************************************************************************* PP

          Whirly  96 vePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsll 138
                     vePl dGsG+++nlsv+n++ + nes+ +Pv+kae av++sl+
  XP_004490010.1 165 VEPLQDGSGHMFNLSVQNKIENINESIFIPVTKAELAVFNSLF 207
                     ***************************************9987 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF544472.67E-6467241IPR009044ssDNA-binding transcriptional regulator
Gene3DG3DSA:2.30.31.106.9E-6770227IPR009044ssDNA-binding transcriptional regulator
PfamPF085362.1E-5871205IPR013742Plant transcription factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 242 aa     Download sequence    Send to blast
MLQTQSYTIT TKPFSVSNHS FTTPIKSIPL RHAGPTFSIS LPQFSVTCHH PQLFQQKPFP  60
PPPQRPQPPS VYKGKAVLTV SPRAPEFTSM ESGSFKISRE GCMLLQFAPA VGVHQYDWNR  120
KQVFSLSVNE MGSLISLGAK DSCEIFHDPF IGKGDEGKVR KVLKVEPLQD GSGHMFNLSV  180
QNKIENINES IFIPVTKAEL AVFNSLFHFI MPCLLGWNAF GSSIKPEVYT ANPKHEDYEW  240
NR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A3e-807024143219p24: plant transcriptional regulator PBF-2
1l3a_B3e-807024143219p24: plant transcriptional regulator PBF-2
1l3a_C3e-807024143219p24: plant transcriptional regulator PBF-2
1l3a_D3e-807024143219p24: plant transcriptional regulator PBF-2
4koq_A9e-817022514169Single-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 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_004490010.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004490010.10.0single-stranded DNA-binding protein WHY1, chloroplastic-like isoform X2
SwissprotQ9M9S36e-87WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A1S2XKF31e-179A0A1S2XKF3_CICAR; single-stranded DNA-binding protein WHY1, chloroplastic-like isoform X2
STRINGXP_004490009.11e-161(Cicer arietinum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02740.23e-88ssDNA-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]