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 RrC1543_p4
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family Whirly
Protein Properties Length: 216aa    MW: 23944.4 Da    PI: 10.1527
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1543_p4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly88.48.5e-2886148163
      Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsateva 63 
                 s+yk+kaal++++++p+f++l+sg++kl+++G+lll++a+a+++r+ydW++kq+f+ls+te++
  RrC1543_p4  86 SIYKGKAALTIEPRAPEFVSLQSGAFKLSKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIG 148
                 7************************************************************98 PP
2Whirly22.81.5e-07149177111139
      Whirly 111 vtnslvkgnesfsvPvskaefavlrsllv 139
                 v+n+l++++es+++P++kaefavl+s+++
  RrC1543_p4 149 VQNKLLNVDESVYIPITKAEFAVLISAFN 177
                 99************************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-3175148IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544474.47E-5579216IPR009044ssDNA-binding transcriptional regulator
PfamPF085369.6E-2587148IPR013742Plant transcription factor
Gene3DG3DSA:2.30.31.102.9E-16149200IPR009044ssDNA-binding transcriptional regulator
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006281Biological ProcessDNA repair
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009508Cellular Componentplastid chromosome
GO:0009570Cellular Componentchloroplast stroma
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 216 aa     Download sequence    Send to blast
MSQLLSSPPM AVNSRTFLTH RFPEARFLTA GGFVGKGHCF AVKVKPMEER VKLTLKSRYS  60
DSSSPPYSPP KNGEGGSSTR FYVGHSIYKG KAALTIEPRA PEFVSLQSGA FKLSKEGFLL  120
LQFAPAAGVR QYDWSRKQVF SLSVTEIGVQ NKLLNVDESV YIPITKAEFA VLISAFNFIL  180
PHLIGWQAFA NSIKPEDSNR LNNASPKYGG DYEWSR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koq_A2e-67771945169Single-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}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By salicylic acid (SA). {ECO:0000269|PubMed:19669906}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2302051e-81AK230205.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL22-96-O15.
GenBankBT0153361e-81BT015336.1 Arabidopsis thaliana At2g02740 gene, complete cds.
GenBankBT0156411e-81BT015641.1 Arabidopsis thaliana At2g02740 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018483253.11e-137PREDICTED: single-stranded DNA-binding protein WHY3, chloroplastic isoform X1
RefseqXP_018483254.11e-137PREDICTED: single-stranded DNA-binding protein WHY3, chloroplastic isoform X2
SwissprotQ66GR61e-105WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBLA0A3P6EY561e-123A0A3P6EY56_BRAOL; Uncharacterized protein
STRINGBo7g080560.11e-123(Brassica oleracea)
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
AT2G02740.21e-105ssDNA-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]