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 Thecc1EG011795t1
Common NameTCM_011795
Organism
Theobroma cacao
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma
Family Whirly
Protein Properties Length: 271aa    MW: 30045 Da    PI: 9.8127
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG011795t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly215.84.2e-67932311139
            Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrka 93 
                       svyk+kaal+v++++p+f+ ldsg++k++r+G++ll++a+a+++r+ydW++kq+f+ls+te++ l++l+++esceffhdp++++s+eGkvrk+
  Thecc1EG011795t1  93 SVYKGKAALTVEPRAPEFVPLDSGAFKISREGFVLLQFAPAAGVRQYDWSRKQVFSLSVTEIGALISLGARESCEFFHDPFKGKSEEGKVRKV 185
                       79******************************************************************************************* PP

            Whirly  94 lkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                       lkvePlpdGsG+f+nl v+n l++ +e++++P+++aef+vl+s+++
  Thecc1EG011795t1 186 LKVEPLPDGSGHFFNLGVQNRLLNLDENIYIPITRAEFTVLNSAFS 231
                       ******************************************9985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.106.7E-7884253IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544475.57E-7886270IPR009044ssDNA-binding transcriptional regulator
PfamPF085366.2E-6194228IPR013742Plant 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: 271 aa     Download sequence    Send to blast
MLQLQFLSSP PLSAQSLNPN SNTNLLSSFS SLKSTQTHAF KLNPLSLTPK PSKFSLKCRQ  60
SEYFDQQQRF SNSSSTASPP ASGLPPRFYV GHSVYKGKAA LTVEPRAPEF VPLDSGAFKI  120
SREGFVLLQF APAAGVRQYD WSRKQVFSLS VTEIGALISL GARESCEFFH DPFKGKSEEG  180
KVRKVLKVEP LPDGSGHFFN LGVQNRLLNL DENIYIPITR AEFTVLNSAF SFILPYLLGW  240
HAFANSIKPE EASRVNNANP RYGGDYEWSR *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A1e-1108626936219p24: plant transcriptional regulator PBF-2
1l3a_B1e-1108626936219p24: plant transcriptional regulator PBF-2
1l3a_C1e-1108626936219p24: plant transcriptional regulator PBF-2
1l3a_D1e-1108626936219p24: plant transcriptional regulator PBF-2
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}.
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_007046213.20.0PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotQ9M9S31e-136WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLA0A061EAM10.0A0A061EAM1_THECC; SsDNA-binding transcriptional regulator isoform 1
STRINGEOY020450.0(Theobroma cacao)
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-126ssDNA-binding transcriptional regulator
Publications ? help Back to Top
  1. Motamayor JC, et al.
    The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.
    Genome Biol., 2013. 14(6): p. r53
    [PMID:23731509]
  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]