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Vipas39 VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog [ Mus musculus (house mouse) ]

Gene ID: 104799, updated on 14-Nov-2024

Summary

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Official Symbol
Vipas39provided by MGI
Official Full Name
VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homologprovided by MGI
Primary source
MGI:MGI:2144805
See related
Ensembl:ENSMUSG00000021038 AllianceGenome:MGI:2144805
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Spe39; Vipar; SPE-39; hSPE-39; 6720456H09Rik; 9330175H22Rik
Summary
Acts upstream of or within several processes, including collagen fibril organization; collagen metabolic process; and peptidyl-lysine hydroxylation. Predicted to be located in Golgi apparatus and endosome. Predicted to be part of vesicle tethering complex. Predicted to be active in cytoplasm. Is expressed in several structures, including central nervous system; retina layer; and skeletal muscle. Used to study ARC syndrome. Human ortholog(s) of this gene implicated in arthrogryposis, renal dysfunction, and cholestasis 2. Orthologous to human VIPAS39 (VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in CNS E14 (RPKM 16.2), CNS E18 (RPKM 15.9) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Vipas39 in Genome Data Viewer
Location:
12 D2; 12 41.44 cM
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (87285647..87313426, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (87238875..87266378, complement)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene transmembrane p24 trafficking protein 8 Neighboring gene STARR-positive B cell enhancer ABC_E9041 Neighboring gene sterile alpha motif domain containing 15 Neighboring gene NADP+ dependent oxidoreductase domain containing 1 Neighboring gene AHA1, activator of heat shock protein ATPase 1 Neighboring gene predicted gene, 53736 Neighboring gene STARR-seq mESC enhancer starr_32874 Neighboring gene isthmin 2 Neighboring gene predicted gene, 51956

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. VPS33B and VIPAR are essential for epidermal lamellar body biogenesis and function. Rogerson C, et al. Biochim Biophys Acta Mol Basis Dis, 2018 May. PMID 29409756, Free PMC Article
  2. Mutations in VIPAR cause an arthrogryposis, renal dysfunction and cholestasis syndrome phenotype with defects in epithelial polarization. Cullinane AR, et al. Nat Genet, 2010 Apr. PMID 20190753, Free PMC Article
  3. Regulation of post-Golgi LH3 trafficking is essential for collagen homeostasis. Banushi B, et al. Nat Commun, 2016 Jul 20. PMID 27435297, Free PMC Article
  4. Epilepsy- and intellectual disability-associated CYFIP2 interacts with both actin regulators and RNA-binding proteins in the neonatal mouse forebrain. Lee Y, et al. Biochem Biophys Res Commun, 2020 Aug 13. PMID 32560809
  5. Phosphoproteomic analysis of the developing mouse brain. Ballif BA, et al. Mol Cell Proteomics, 2004 Nov. PMID 15345747

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. VPS33B and VIPAR are essential for epidermal lamellar body biogenesis and function
    Title: VPS33B and VIPAR are essential for epidermal lamellar body biogenesis and function.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
  
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within collagen fibril organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within collagen metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within collagen metabolic process ISO
Inferred from Sequence Orthology
more info
 PubMed 
involved_in endosome to lysosome transport IEA
Inferred from Electronic Annotation
more info
  
involved_in endosome to lysosome transport ISO
Inferred from Sequence Orthology
more info
  
involved_in intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within intracellular protein transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intracellular protein transport ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within peptidyl-lysine hydroxylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within peptidyl-lysine hydroxylation ISO
Inferred from Sequence Orthology
more info
 PubMed 
acts_upstream_of_or_within post-translational protein modification IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in vacuolar transport IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in early endosome IEA
Inferred from Electronic Annotation
more info
  
located_in early endosome ISO
Inferred from Sequence Orthology
more info
  
located_in endosome ISO
Inferred from Sequence Orthology
more info
  
located_in late endosome IEA
Inferred from Electronic Annotation
more info
  
located_in late endosome ISO
Inferred from Sequence Orthology
more info
  
located_in recycling endosome IEA
Inferred from Electronic Annotation
more info
  
located_in recycling endosome ISO
Inferred from Sequence Orthology
more info
  
part_of vesicle tethering complex IEA
Inferred from Electronic Annotation
more info
  
part_of vesicle tethering complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
spermatogenesis-defective protein 39 homolog
Names
VPS33B-interacting protein in apical-basolateral polarity regulator
VPS33B-interacting protein in polarity and apical restriction
protein spe-39 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001142580.1 → NP_001136052.1  spermatogenesis-defective protein 39 homolog isoform a

    See identical proteins and their annotated locations for NP_001136052.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AK079055, AK082261, BB610654
    Consensus CDS
    CCDS49119.1
    UniProtKB/Swiss-Prot
    Q8BGQ1, Q8BL55, Q8CIK4, Q91YI3
    UniProtKB/TrEMBL
    Q3UM95
    Related
    ENSMUSP00000072527.8, ENSMUST00000072744.15
    Conserved Domains (1) summary
    pfam09787
    Location:26 → 469
    Golgin_A5; Golgin subfamily A member 5

  2. NM_001142581.1 → NP_001136053.1  spermatogenesis-defective protein 39 homolog isoform b

    See identical proteins and their annotated locations for NP_001136053.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. It encodes isoform b, which is shorter than isoform a. Variants 2 and 3 both encode isoform b.
    Source sequence(s)
    AC151967
    Consensus CDS
    CCDS26074.1
    UniProtKB/TrEMBL
    Q3UM95
    Related
    ENSMUSP00000137190.2, ENSMUST00000179379.9
    Conserved Domains (1) summary
    pfam09787
    Location:26 → 450
    Golgin_A5; Golgin subfamily A member 5

  3. NM_134044.3 → NP_598805.2  spermatogenesis-defective protein 39 homolog isoform b

    See identical proteins and their annotated locations for NP_598805.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. It encodes isoform b, which is shorter than isoform a. Variants 2 and 3 both encode isoform b.
    Source sequence(s)
    AC151967
    Consensus CDS
    CCDS26074.1
    UniProtKB/TrEMBL
    Q3UM95
    Related
    ENSMUSP00000021426.10, ENSMUST00000021426.10
    Conserved Domains (1) summary
    pfam09787
    Location:26 → 450
    Golgin_A5; Golgin subfamily A member 5

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000078.7 Reference GRCm39 C57BL/6J

    Range
    87285647..87313426 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036157150.1 → XP_036013043.1  spermatogenesis-defective protein 39 homolog isoform X2

  2. XM_011243977.3 → XP_011242279.1  spermatogenesis-defective protein 39 homolog isoform X2

    Conserved Domains (1) summary
    pfam09787
    Location:3 → 359
    Golgin_A5; Golgin subfamily A member 5

  3. XM_006515339.5 → XP_006515402.1  spermatogenesis-defective protein 39 homolog isoform X1

    See identical proteins and their annotated locations for XP_006515402.1

    UniProtKB/Swiss-Prot
    Q8BGQ1, Q8BL55, Q8CIK4, Q91YI3
    UniProtKB/TrEMBL
    Q3UM95
    Conserved Domains (1) summary
    pfam09787
    Location:26 → 469
    Golgin_A5; Golgin subfamily A member 5

  4. XM_011243976.4 → XP_011242278.1  spermatogenesis-defective protein 39 homolog isoform X1

    See identical proteins and their annotated locations for XP_011242278.1

    UniProtKB/Swiss-Prot
    Q8BGQ1, Q8BL55, Q8CIK4, Q91YI3
    UniProtKB/TrEMBL
    Q3UM95
    Conserved Domains (1) summary
    pfam09787
    Location:26 → 469
    Golgin_A5; Golgin subfamily A member 5
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8BGQ1.1 GenPept UniProtKB/Swiss-Prot:Q8BGQ1

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