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 orange1.1g027008m
Common NameCISIN_1g024467mg
Organism
Citrus sinensis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family Whirly
Protein Properties Length: 230aa    MW: 25192.8 Da    PI: 9.4681
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g027008mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly217.61.1e-67902281139
             Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrk 92 
                        s+yk+kaal+v+++ p+f++ldsg++kl+r+G+++l++a+a+++r+ydW++kq+f+ls+te+++lv l+++esceffhdp++++s+eGkvrk
  orange1.1g027008m  90 SIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRK 181
                        7******************************************************************************************* PP

             Whirly  93 alkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                        +lkvePlpdGsG+f+nlsv+n+l++ +es+++Pv++ae++vl s+++
  orange1.1g027008m 182 VLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
                        ******************************************99986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.108.6E-6780228IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544471.02E-6184228IPR009044ssDNA-binding transcriptional regulator
PfamPF085363.5E-6191225IPR013742Plant 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: 230 aa     Download sequence    Send to blast
MMLQLQCLSS QTLNPKLCPF HSLSNSKGNG FGSISVTEST SIKKKKLYVK CRQSEYYEQK  60
SFSASPSNSS YAPTDVAVGT LPTRVYVGHS IYKGKAALTV EPRGPEFVSL DSGAVKLSRE  120
GFVMLQFAPA AGVRQYDWSR KQVFSLSVTE IGSLVALGAR ESCEFFHDPF KGKSEEGKVR  180
KVLKVEPLPD GSGHFFNLSV QNKLINLDES IYIPVTRAEY TVLVSAFNV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koo_A2e-94812285152Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B2e-94812285152Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C2e-94812285152Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D2e-94812285152Single-stranded DNA-binding protein WHY1, chloroplastic
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Csi.61351e-69callus| fruit| root
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006483225.11e-167single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotQ9M9S32e-98WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A067GSY11e-168A0A067GSY1_CITSI; Uncharacterized protein
STRINGXP_006483225.11e-167(Citrus sinensis)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G14410.11e-97ssDNA-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]