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 Medtr5g038560.1
Common NameMTR_5g038560
Organism
Medicago truncatula
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago
Family Whirly
Protein Properties Length: 262aa    MW: 29618 Da    PI: 10.1244
Description Whirly family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Medtr5g038560.1genomeMtView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Whirly188.21.3e-58872251139
           Whirly   1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkal 94 
                      svyk+ka l v +v+p+f++ dsg++k++++G +ll+++++++ r+ydW++kq+f+ls+ e+++l++l+++esce fhdp+++ s+eGkvrk+l
  Medtr5g038560.1  87 SVYKGKAVLVVSPVLPKFTSSDSGTFKISKEGLMLLQFVPSAGFRQYDWNRKQVFSLSVDEMGNLINLGARESCEIFHDPFMGRSDEGKVRKVL 180
                      79******************************************************************************************** PP

           Whirly  95 kvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139
                      kvePl dGsG++++lsv+n+l + +e++ +Pv+kaefav++sl++
  Medtr5g038560.1 181 KVEPLHDGSGHMFKLSVQNQLKNIDENIFIPVTKAEFAVFNSLFS 225
                      ****************************************99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.30.31.103.0E-6976244IPR009044ssDNA-binding transcriptional regulator
SuperFamilySSF544471.1E-6581259IPR009044ssDNA-binding transcriptional regulator
PfamPF085361.6E-5688222IPR013742Plant 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: 262 aa     Download sequence    Send to blast
MKMLQLQPPQ SYTTTNPFSV PTHSFIINTP KKSIFLRRVG PTFSLTCHHP ELFHPKPFPP  60
PQRPQSSSSS FSSSVGELPA RVHVSRSVYK GKAVLVVSPV LPKFTSSDSG TFKISKEGLM  120
LLQFVPSAGF RQYDWNRKQV FSLSVDEMGN LINLGARESC EIFHDPFMGR SDEGKVRKVL  180
KVEPLHDGSG HMFKLSVQNQ LKNIDENIFI PVTKAEFAVF NSLFSFIMPY LLGWNAFADS  240
IKPEVNIANP RRREEDFEWN R*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4koo_A4e-83782425169Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B4e-83782425169Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C4e-83782425169Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D4e-83782425169Single-stranded DNA-binding protein WHY1, chloroplastic
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Mtr.168310.0root
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
PlantRegMapMedtr5g038560.1
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1362861e-121AC136286.30 Medicago truncatula clone mth2-6c9, complete sequence.
GenBankAC1468541e-121AC146854.19 Medicago truncatula clone mth2-10i14, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_003613602.10.0single-stranded DNA-binding protein WHY1, chloroplastic
SwissprotQ9M9S36e-91WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBLG7KB190.0G7KB19_MEDTR; Putative transcription factor ssDNA-binding-TF family
STRINGAES965600.0(Medicago truncatula)
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
AT1G14410.18e-90ssDNA-binding transcriptional regulator
Publications ? help Back to Top
  1. Young ND, et al.
    The Medicago genome provides insight into the evolution of rhizobial symbioses.
    Nature, 2011. 480(7378): p. 520-4
    [PMID:22089132]
  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]