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

    Gene ID: 104799, updated on 9-Dec-2024

    Summary

    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, Dec 2024]
    Expression
    Ubiquitous expression in CNS E14 (RPKM 16.2), CNS E18 (RPKM 15.9) and 28 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    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

    Expression

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

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     
    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

    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)

    NEW Try the new Transcript table

    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_001142580.1NP_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:26469
      Golgin_A5; Golgin subfamily A member 5
    2. NM_001142581.1NP_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:26450
      Golgin_A5; Golgin subfamily A member 5
    3. NM_134044.3NP_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:26450
      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_036157150.1XP_036013043.1  spermatogenesis-defective protein 39 homolog isoform X2

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

      Conserved Domains (1) summary
      pfam09787
      Location:3359
      Golgin_A5; Golgin subfamily A member 5
    3. XM_006515339.5XP_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:26469
      Golgin_A5; Golgin subfamily A member 5
    4. XM_011243976.4XP_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:26469
      Golgin_A5; Golgin subfamily A member 5