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 Araha.22300s0005.1.p
Organism
Arabidopsis halleri
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family Whirly
Protein Properties Length: 191aa    MW: 21105 Da    PI: 8.9443
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.22300s0005.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly218.84.9e-68121511139
                Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpa.akgsneG 88 
                           s+yk+kaal++++++p+f+al+sg++kl+++G+lll++a+a+++r+ydW++kq+f+ls+te+++lv+l+++esceffhdp+  kgs+eG
  Araha.22300s0005.1.p  12 SIYKGKAALTIEPRAPEFVALESGAFKLTKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPRESCEFFHDPFkGKGSDEG 100
                           7********************************************************************************44679*** PP

                Whirly  89 kvrkalkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                           kvrk+lkvePlpdGsG f+nlsv+n+l++++es+++P++kaefavl+s+++
  Araha.22300s0005.1.p 101 KVRKVLKVEPLPDGSGRFFNLSVQNKLLNVDESVYIPITKAEFAVLISAFN 151
                           ************************************************996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.101.4E-773173IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544472.82E-804190IPR009044ssDNA-binding transcriptional regulator
PfamPF085361.3E-5813148IPR013742Plant transcription factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0045910Biological Processnegative regulation of DNA recombination
GO:0009570Cellular Componentchloroplast stroma
GO:0003677Molecular FunctionDNA binding
GO:0003723Molecular FunctionRNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 191 aa     Download sequence    Send to blast
EGSSPRFYVG HSIYKGKAAL TIEPRAPEFV ALESGAFKLT KEGFLLLQFA PAAGVRQYDW  60
SRKQVFSLSV TEIGNLVSLG PRESCEFFHD PFKGKGSDEG KVRKVLKVEP LPDGSGRFFN  120
LSVQNKLLNV DESVYIPITK AEFAVLISAF NFILPHLIGW SAFANSIKPE DANRLNNASP  180
KYGGDYEWTR *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koq_A1e-11611683169Single-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 the nucleus, is recruited to a distal element upstream of the kinesin KP1 to mediate the transcriptional repression of KP1. Can bind double-stranded DNA in vivo. {ECO:0000269|PubMed:19666500, ECO:0000269|PubMed:19669906, ECO:0000269|PubMed:20551348, ECO:0000269|PubMed:21911368}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapAraha.22300s0005.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By salicylic acid (SA). {ECO:0000269|PubMed:19669906}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0153360.0BT015336.1 Arabidopsis thaliana At2g02740 gene, complete cds.
GenBankBT0156410.0BT015641.1 Arabidopsis thaliana At2g02740 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020879963.11e-137single-stranded DNA-binding protein WHY3, chloroplastic isoform X1
SwissprotQ66GR61e-136WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBLD7LQ571e-135D7LQ57_ARALL; ATWHY3/PTAC11
STRINGfgenesh2_kg.5__172__AT2G02740.11e-136(Arabidopsis lyrata)
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
AT2G02740.11e-139ssDNA-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. 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]
  3. 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]