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 AHYPO_000360-RA
Organism
Amaranthus hypochondriacus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Amaranthaceae; Amaranthus
Family Whirly
Protein Properties Length: 205aa    MW: 22526.3 Da    PI: 9.4059
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AHYPO_000360-RAgenomeBYUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly85.66.2e-27101167167
           Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvd 67 
                      s+yk+kaal+v++++p+f  l+sg++kl+r+G ++l++a+a ++r+ydW++kq+f+ls+ e+++l  
  AHYPO_000360-RA 101 SIYKGKAALTVEPRAPDFLPLESGAFKLSREGCIMLQFAPASGVRQYDWSRKQVFSLSVSEIGSLFI 167
                      7***************************************************************975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.102.7E-3292165IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544471.26E-3393193IPR009044ssDNA-binding transcriptional regulator
PfamPF085362.2E-26102183IPR013742Plant 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: 205 aa     Download sequence    Send to blast
MAHQLLLSPP NFSIGTQLQT HGLNSNHFPS FSSHNSIITS ISHLKQTNNW VSNVSLSKPL  60
LSGVKCRQSS DYFEQSPSKL SSSYSPNSSP GVSPRVFVGH SIYKGKAALT VEPRAPDFLP  120
LESGAFKLSR EGCIMLQFAP ASGVRQYDWS RKQVFSLSVS EIGSLFILPY LIGWHAFVDS  180
IKPDDSNTTI SSNSRNLDSE WSRY*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1l3a_A8e-40601684110p24: plant transcriptional regulator PBF-2
1l3a_B8e-40601684110p24: plant transcriptional regulator PBF-2
1l3a_C8e-40601684110p24: plant transcriptional regulator PBF-2
1l3a_D8e-40601684110p24: 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 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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010683246.12e-73PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotQ66GR61e-41WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBLA0A3N6U4Y73e-47A0A3N6U4Y7_BRACR; Uncharacterized protein
STRINGXP_010683246.16e-73(Beta vulgaris)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02740.11e-38ssDNA-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]