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 Lus10037206
Organism
Linum usitatissimum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum
Family Whirly
Protein Properties Length: 375aa    MW: 41799.3 Da    PI: 8.9944
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lus10037206genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly63.73.6e-20109164156
       Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfa 56 
                  s+yk+kaal+v+++ p+f+ l+sg++kl r+G+++l++a+a + r+ydW++kq+  
  Lus10037206 109 SIYKGKAALTVEPKSPEFTPLESGAFKLVREGFVFLQFAPASGLRQYDWSRKQVIY 164
                  7****************************************************865 PP
2Whirly129.61.6e-4024233546139
       Whirly  46 kydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                  + d+   q f+ls+te+++lv+l++kesceffhdp +++s+eGk+rk+lkvePlpdGsG+f+nlsv+n+ ++ +es+++Pv++aef+vl s+++
  Lus10037206 242 TVDFTYLQMFSLSVTEIGTLVSLGTKESCEFFHDPNKGKSDEGKIRKVLKVEPLPDGSGHFFNLSVQNKPLNLDESIYIPVTRAEFTVLVSAFN 335
                  6788889**********************************************************************************99986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.104.5E-2497163IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544474.08E-22103164IPR009044ssDNA-binding transcriptional regulator
PfamPF085361.9E-18110164IPR013742Plant transcription factor
SuperFamilySSF544474.16E-47230374IPR009044ssDNA-binding transcriptional regulator
Gene3DG3DSA:2.30.31.104.2E-45241356IPR009044ssDNA-binding transcriptional regulator
PfamPF085361.7E-34243332IPR013742Plant 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: 375 aa     Download sequence    Send to blast
MLQLNSLSSS SSSSSLLRTQ NPKVCSQHSL ASVEFNHGAF RVPTKRRCDV SFSRTAGTRS  60
RNLAVKCRQS SYFEQQNFSN SSGNSSSSSR GQGASNGGEL PARVYVGHSI YKGKAALTVE  120
PKSPEFTPLE SGAFKLVREG FVFLQFAPAS GLRQYDWSRK QVIYGSWCPK LLSLARRSDL  180
YTTLMLLGID FDSDMCKLFL RDFKHFDAKP WSNFEVLTLV GEKLCSYCCF MSMYGSYINI  240
TTVDFTYLQM FSLSVTEIGT LVSLGTKESC EFFHDPNKGK SDEGKIRKVL KVEPLPDGSG  300
HFFNLSVQNK PLNLDESIYI PVTRAEFTVL VSAFNYLLPY LIGWHAYANS ITPGESTKPN  360
NASARYGSDY EWSR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A5e-6610337337219p24: plant transcriptional regulator PBF-2
1l3a_B5e-6610337337219p24: plant transcriptional regulator PBF-2
1l3a_C5e-6610337337219p24: plant transcriptional regulator PBF-2
1l3a_D5e-6610337337219p24: 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLus10037206
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_009110543.16e-73PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic
RefseqXP_018447906.16e-73PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotQ9M9S31e-71WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
STRINGLus100372060.0(Linum usitatissimum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF64163251
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G14410.11e-73ssDNA-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]