Format

Send to:

Choose Destination
    • Showing Current items.

    VIPAS39 VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog [ Homo sapiens (human) ]

    Gene ID: 63894, updated on 4-Jul-2021

    Summary

    Official Symbol
    VIPAS39provided by HGNC
    Official Full Name
    VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homologprovided by HGNC
    Primary source
    HGNC:HGNC:20347
    See related
    Ensembl:ENSG00000151445 MIM:613401
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SPE39; VIPAR; SPE-39; VPS16B; hSPE-39; C14orf133
    Summary
    This gene encodes a protein involved in the sorting of lysosomal proteins. Mutations in this gene are associated with ARCS2 (arthrogryposis, renal dysfunction, and cholestasis-2). Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jul 2010]
    Expression
    Ubiquitous expression in testis (RPKM 8.8), ovary (RPKM 6.7) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VIPAS39 in Genome Data Viewer
    Location:
    14q24.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (77426675..77457727, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (77893018..77923944, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene sterile alpha motif domain containing 15 Neighboring gene HNF1 motif-containing MPRA enhancer 277 Neighboring gene NADP dependent oxidoreductase domain containing 1 Neighboring gene activator of HSP90 ATPase activity 1 Neighboring gene isthmin 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ12707

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    NOT involved_in autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in collagen fibril organization IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within collagen metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT involved_in endosome to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endosome to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in intracellular protein transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within peptidyl-lysine hydroxylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in post-translational protein modification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in vacuolar transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT part_of HOPS complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in recycling endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    spermatogenesis-defective protein 39 homolog
    Names
    VPS33B-interacting protein involved in polarity and apical protein restriction

    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.

    Genomic

    1. NG_023421.2 RefSeqGene

      Range
      5040..35966
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1019

    mRNA and Protein(s)

    1. NM_001193314.2NP_001180243.1  spermatogenesis-defective protein 39 homolog isoform 1

      See identical proteins and their annotated locations for NP_001180243.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).
      Source sequence(s)
      AF111168
      Consensus CDS
      CCDS9862.1
      UniProtKB/Swiss-Prot
      Q9H9C1
      UniProtKB/TrEMBL
      Q6IA61
      Related
      ENSP00000452181.1, ENST00000553888.5
      Conserved Domains (1) summary
      pfam09787
      Location:26471
      Golgin_A5; Golgin subfamily A member 5
    2. NM_001193315.2NP_001180244.1  spermatogenesis-defective protein 39 homolog isoform 1

      See identical proteins and their annotated locations for NP_001180244.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).
      Source sequence(s)
      AF111168, AK022769, AW629161
      Consensus CDS
      CCDS9862.1
      UniProtKB/Swiss-Prot
      Q9H9C1
      UniProtKB/TrEMBL
      Q6IA61
      Related
      ENSP00000452191.1, ENST00000557658.6
      Conserved Domains (1) summary
      pfam09787
      Location:26471
      Golgin_A5; Golgin subfamily A member 5
    3. NM_001193316.2NP_001180245.1  spermatogenesis-defective protein 39 homolog isoform 2

      See identical proteins and their annotated locations for NP_001180245.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      AF111168
      Consensus CDS
      CCDS53905.1
      UniProtKB/Swiss-Prot
      Q9H9C1
      Related
      ENSP00000404815.2, ENST00000448935.6
      Conserved Domains (1) summary
      pfam09787
      Location:26422
      Golgin_A5; Golgin subfamily A member 5
    4. NM_001193317.2NP_001180246.1  spermatogenesis-defective protein 39 homolog isoform 1

      See identical proteins and their annotated locations for NP_001180246.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).
      Source sequence(s)
      AF111168
      Consensus CDS
      CCDS9862.1
      UniProtKB/Swiss-Prot
      Q9H9C1
      UniProtKB/TrEMBL
      B4DMB7, Q6IA61
      Related
      ENSP00000451857.1, ENST00000556412.4
      Conserved Domains (1) summary
      pfam09787
      Location:26471
      Golgin_A5; Golgin subfamily A member 5
    5. NM_022067.4NP_071350.2  spermatogenesis-defective protein 39 homolog isoform 1

      See identical proteins and their annotated locations for NP_071350.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).
      Source sequence(s)
      AF111168
      Consensus CDS
      CCDS9862.1
      UniProtKB/Swiss-Prot
      Q9H9C1
      UniProtKB/TrEMBL
      Q6IA61
      Related
      ENSP00000339122.2, ENST00000343765.6
      Conserved Domains (1) summary
      pfam09787
      Location:26471
      Golgin_A5; Golgin subfamily A member 5

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

      Range
      77426675..77457727 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024449688.1XP_024305456.1  spermatogenesis-defective protein 39 homolog isoform X1

    2. XM_011537066.2XP_011535368.1  spermatogenesis-defective protein 39 homolog isoform X1

      Conserved Domains (1) summary
      pfam09787
      Location:26440
      Golgin_A5; Golgin subfamily A member 5
    3. XM_017021581.2XP_016877070.1  spermatogenesis-defective protein 39 homolog isoform X2

    4. XM_017021580.2XP_016877069.1  spermatogenesis-defective protein 39 homolog isoform X2

    RNA

    1. XR_001750501.2 RNA Sequence

    Support Center