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    VDD VERDANDI [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 831667, updated on 15-Oct-2023

    Summary

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    Gene symbol
    VDD
    Gene description
    VERDANDI
    Primary source
    Araport:AT5G18000
    Locus tag
    AT5G18000
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    MCM23.7; MCM23_7; VERDANDI
    Summary
    Encodes VERDANDI (VDD), a putative transcription factor belonging to the reproductive meristem (REM) family. VDD is a direct target of the MADS domain ovule identity complex. Mutation in VDD affects embryo sac differentiation.
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    Genomic context

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    See VDD in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    4
    Sequence:
    Chromosome: 5; NC_003076.8 (5959900..5961642, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene C2 calcium/lipid-binding plant phosphoribosyltransferase family protein Neighboring gene tryptophan biosynthesis 1 Neighboring gene tRNA-Trp Neighboring gene SAUR-like auxin-responsive protein family

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Live and let die: a REM complex promotes fertilization through synergid cell death in Arabidopsis. Mendes MA, et al. Development, 2016 Aug 1. PMID 27338615
    2. VERDANDI is a direct target of the MADS domain ovule identity complex and affects embryo sac differentiation in Arabidopsis. Matias-Hernandez L, et al. Plant Cell, 2010 Jun. PMID 20581305, Free PMC Article
    3. MADS domain transcription factors mediate short-range DNA looping that is essential for target gene expression in Arabidopsis. Mendes MA, et al. Plant Cell, 2013 Jul. PMID 23847151, Free PMC Article
    4. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Wanamaker SA, et al. Nat Methods, 2017 Aug. PMID 28650476, Free PMC Article
    5. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Tabata S, et al. Nature, 2000 Dec 14. PMID 11130714

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data indicate that SEEDSTICK (STK) and SEPALLATA3 (SEP3) dimers can induce loop formation in the VERDANDI (VDD) promoter by binding to two nearby CC(A/T)6GG (CArG) boxes essential for promoter activity.
      Title: MADS domain transcription factors mediate short-range DNA looping that is essential for target gene expression in Arabidopsis.
    2. STK, SHP1, and SHP2 redundantly regulate VERDANDI. The vdd mutant shows defects during the fertilization process resulting in semisterility.
      Title: VERDANDI is a direct target of the MADS domain ovule identity complex and affects embryo sac differentiation in Arabidopsis.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001343531.1
    NM_121805.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within double fertilization forming a zygote and endosperm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryo sac development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within synergid death IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

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    Preferred Names
    VERDANDI
    NP_197301.1
    • VERDANDI (VDD); FUNCTIONS IN: DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: regulation of transcription, DNA-dependent, embryo sac development, double fertilization forming a zygote and endosperm; LOCATED IN: cellular_component unknown; EXPRESSED IN: 13 plant structures; EXPRESSED DURING: 7 growth stages; CONTAINS InterPro DOMAIN/s: Transcriptional factor B3 (InterPro:IPR003340); BEST Arabidopsis thaliana protein match is: AP2/B3-like transcriptional factor family protein (TAIR:AT5G18090.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003076.8 Reference assembly

      Range
      5959900..5961642 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_121805.3 → NP_197301.1  VERDANDI [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_197301.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9FJG2
      UniProtKB/TrEMBL
      A0A5S9Y7E7
      Conserved Domains (1) summary
      smart01019
      Location:20 → 114
      B3; B3 DNA binding domain

    2. NM_001343531.1 → NP_001330241.1  VERDANDI [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178UCQ6, A0A1P8BA45
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9FJG2.1

    Gene LinkOut

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