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VDD VERDANDI [ Arabidopsis thaliana (thale cress) ]

Gene ID: 831667, updated on 18-Sep-2024

Summary

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Official Symbol
VDD
Official Full Name
VERDANDI
Primary source
TAIR:AT5G18000
Locus tag
AT5G18000
See related
Araport: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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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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