VIP3 Transducin/WD40 repeat-like superfamily protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: VIP3
Official Full Name: Transducin/WD40 repeat-like superfamily protein
Primary source: TAIR:AT4G29830
Locus tag: AT4G29830
See related: Araport:AT4G29830
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: A. thaliana homolog of yeast SKI8; F27B13.70; F27B13_70; SKI8; vernalization independence 3
Summary: The protein is composed of repeats of WD motif which is involved in protein complex formation. The gene is involved in flower timing and flower development. This gene is predicted to encode a protein with a DWD motif. It can bind to DDB1a in Y2H assays, and DDB1b in co-IP assays, and may be involved in the formation of a CUL4-based E3 ubiquitin ligase. Loss of gene function leads to a redistribution of H3K4me3 and K3K36me2 modifications within genes but not a change in the overall abundance of these modifications within chromatin.
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Genomic context

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See VIP3 in Genome Data Viewer

Location:: chromosome: 4

Exon count:: 2

Sequence:: Chromosome: 4; NC_003075.7 (14597559..14599300)

Chromosome 4 - NC_003075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phyllotaxis regularity depends on the function of VIP proteins, components of the RNA polymerase II-associated factor 1 complex (Paf1c). Divergence angles between successive organs along the stem exhibited increased variance in vip3-1 and vip3-2 compared with the wild type, in two different growth conditions.
Title: Phyllotactic regularity requires the Paf1 complex in Arabidopsis.
boq-1 missense mutation enhances meristem formation.
Title: Enhancement of meristem formation by bouquet-1, a mis-sense allele of the vernalization independence 3 gene encoding a WD40 repeat protein in Arabidopsis thaliana.
phenotypic aspects of VIP3 function in Paf1c and the SKI complex can be separated; we provide evidence that the dual role of SKI8 homologs(VIP3) in Paf1c and the SKI complex appears to depend on the species-specific cellular context.
Title: Context-dependent dual role of SKI8 homologs in mRNA synthesis and turnover.
We showed that the Arabidopsis Ski8 was required for normal plant development and growth, suggesting a conserved somatic function, but that it was not required for meiotic recombination or progression [SKI8]
Title: Non conservation of the meiotic function of the Ski8/Rec103 homolog in Arabidopsis.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

NM_119129.3

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within negative regulation of flower development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of flower development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of wax biosynthetic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within post-transcriptional gene silencing	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Cdc73/Paf1 complex	IDA Inferred from Direct Assay more info	PubMed
part_of Cul4-RING E3 ubiquitin ligase complex	IPI Inferred from Physical Interaction more info	PubMed
located_in cytoplasm	ISM Inferred from Sequence Model more info
located_in cytosol	HDA more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	HDA more info	PubMed

General protein information

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Preferred Names: Transducin/WD40 repeat-like superfamily protein

NP_194712.1

vernalization independence 3 (VIP3); FUNCTIONS IN: protein binding, nucleotide binding; INVOLVED IN: histone H3-K4 methylation, histone H3-K36 methylation, negative regulation of flower development; LOCATED IN: CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: WD40 repeat 2 (InterPro:IPR019782), WD40 repeat, conserved site (InterPro:IPR019775), WD40 repeat (InterPro:IPR001680), G-protein beta WD-40 repeat, region (InterPro:IPR020472), WD40 repeat-like-containing domain (InterPro:IPR011046), WD40-repeat-containing domain (InterPro:IPR017986), WD40/YVTN repeat-like-containing domain (InterPro:IPR015943), WD40 repeat, subgroup (InterPro:IPR019781); BEST Arabidopsis thaliana protein match is: WD-40 repeat family protein / small nuclear ribonucleoprotein Prp4p-related (TAIR:AT2G41500.1); Has 81424 Blast hits to 33679 proteins in 849 species: Archae - 94; Bacteria - 9736; Metazoa - 32144; Fungi - 18699; Plants - 10476; Viruses - 0; Other Eukaryotes - 10275 (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

NC_003075.7 Reference assembly

Range

14597559..14599300

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_119129.3 → NP_194712.1 Transducin/WD40 repeat-like superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_194712.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9SZQ5

UniProtKB/TrEMBL

A0A178UYC1, A0A5S9XXU4

Conserved Domains (2) summary

cd00200
Location:13 → 319

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

sd00039
Location:17 → 58

7WD40; WD40 repeat [structural motif]