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    VAPA VAMP associated protein A [ Homo sapiens (human) ]

    Gene ID: 9218, updated on 1-Oct-2024

    Summary

    Official Symbol
    VAPAprovided by HGNC
    Official Full Name
    VAMP associated protein Aprovided by HGNC
    Primary source
    HGNC:HGNC:12648
    See related
    Ensembl:ENSG00000101558 MIM:605703; AllianceGenome:HGNC:12648
    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
    VAP-A; VAP33; VAMP-A; VAP-33; hVAP-33
    Summary
    The protein encoded by this gene is a type IV membrane protein. It is present in the plasma membrane and intracellular vesicles. It may also be associated with the cytoskeleton. This protein may function in vesicle trafficking, membrane fusion, protein complex assembly and cell motility. Alternative splicing occurs at this locus and two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in adrenal (RPKM 26.8), brain (RPKM 22.1) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See VAPA in Genome Data Viewer
    Location:
    18p11.22
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (9914016..9960021)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (10077467..10123397)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (9914013..9960018)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371982 Neighboring gene Sharpr-MPRA regulatory region 4522 Neighboring gene uncharacterized LOC124904245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9290 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:9914515-9915132 Neighboring gene Sharpr-MPRA regulatory region 12110 Neighboring gene RNA, 5S ribosomal pseudogene 450 Neighboring gene NANOG hESC enhancer GRCh37_chr18:9960172-9960690 Neighboring gene uncharacterized LOC124904246 Neighboring gene uncharacterized LOC105371983

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with VAMP (vesicle-associated membrane protein)-associated protein A (VAPA) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC3745

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables FFAT motif binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables FFAT motif binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables cadherin binding HDA PubMed 
    enables microtubule binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein-membrane adaptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in COPII-coated vesicle budding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ceramide transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cholesterol transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT involved_in endoplasmic reticulum organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endoplasmic reticulum-plasma membrane tethering IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in membrane fusion TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation by host of viral genome replication IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in neuron projection development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in neuron projection development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phospholipid transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation by host of viral genome replication IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of canonical NF-kappaB signal transduction HMP PubMed 
    NOT involved_in protein folding in endoplasmic reticulum IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization to endoplasmic reticulum IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sphingomyelin biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sterol transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in viral release from host cell IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in azurophil granule membrane TAS
    Traceable Author Statement
    more info
     
    colocalizes_with bicellular tight junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endoplasmic reticulum HDA PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT located_in endoplasmic reticulum exit site IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in microtubule cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nuclear membrane IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    vesicle-associated membrane protein-associated protein A
    Names
    33 kDa VAMP-associated protein
    VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa
    epididymis secretory sperm binding protein

    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_003574.6NP_003565.4  vesicle-associated membrane protein-associated protein A isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC006238, AF154847, BG488667, BP209270
      Consensus CDS
      CCDS11847.2
      UniProtKB/Swiss-Prot
      Q9P0L0
      Related
      ENSP00000345656.4, ENST00000340541.4
      Conserved Domains (1) summary
      pfam00635
      Location:14118
      Motile_Sperm; MSP (Major sperm protein) domain
    2. NM_194434.3NP_919415.2  vesicle-associated membrane protein-associated protein A isoform 2

      See identical proteins and their annotated locations for NP_919415.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC006238, BC002992, BP209270
      Consensus CDS
      CCDS11848.2
      UniProtKB/Swiss-Prot
      A6NDZ0, D3DUI3, O75453, Q5U0E7, Q9P0L0, Q9UBZ2
      Related
      ENSP00000382880.3, ENST00000400000.7
      Conserved Domains (1) summary
      pfam00635
      Location:14118
      Motile_Sperm; MSP (Major sperm protein) domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      9914016..9960021
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047437929.1XP_047293885.1  vesicle-associated membrane protein-associated protein A isoform X1

    2. XM_047437932.1XP_047293888.1  vesicle-associated membrane protein-associated protein A isoform X2

    3. XM_047437930.1XP_047293886.1  vesicle-associated membrane protein-associated protein A isoform X1

    4. XM_017026079.2XP_016881568.1  vesicle-associated membrane protein-associated protein A isoform X2

    5. XM_047437928.1XP_047293884.1  vesicle-associated membrane protein-associated protein A isoform X1

    6. XM_047437931.1XP_047293887.1  vesicle-associated membrane protein-associated protein A isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      10077467..10123397
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319357.1XP_054175332.1  vesicle-associated membrane protein-associated protein A isoform X2

    2. XM_054319359.1XP_054175334.1  vesicle-associated membrane protein-associated protein A isoform X2

    3. XM_054319355.1XP_054175330.1  vesicle-associated membrane protein-associated protein A isoform X2

    4. XM_054319356.1XP_054175331.1  vesicle-associated membrane protein-associated protein A isoform X2

    5. XM_054319353.1XP_054175328.1  vesicle-associated membrane protein-associated protein A isoform X1

    6. XM_054319354.1XP_054175329.1  vesicle-associated membrane protein-associated protein A isoform X1

    7. XM_054319358.1XP_054175333.1  vesicle-associated membrane protein-associated protein A isoform X2