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    VAPB VAMP associated protein B and C [ Homo sapiens (human) ]

    Gene ID: 9217, updated on 5-Aug-2018

    Summary

    Official Symbol
    VAPBprovided by HGNC
    Official Full Name
    VAMP associated protein B and Cprovided by HGNC
    Primary source
    HGNC:HGNC:12649
    See related
    Ensembl:ENSG00000124164 MIM:605704; Vega:OTTHUMG00000032840
    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
    ALS8; VAP-B; VAMP-B
    Summary
    The protein encoded by this gene is a type IV membrane protein found in plasma and intracellular vesicle membranes. The encoded protein is found as a homodimer and as a heterodimer with VAPA. This protein also can interact with VAMP1 and VAMP2 and may be involved in vesicle trafficking. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 14.9), brain (RPKM 14.3) and 25 other tissues See more
    Orthologs

    Genomic context

    See VAPB in Genome Data Viewer
    Location:
    20q13.32
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 20 NC_000020.11 (58389119..58451101)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (56964175..57026157)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 4 regulatory subunit 1 like (pseudogene) Neighboring gene RAB22A, member RAS oncogene family Neighboring gene APC down-regulated 1 like Neighboring gene APCDD1L divergent transcript

    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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Metabolism, organism-specific biosystem (from REACTOME)
      Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
    • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
      Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
    • Sphingolipid de novo biosynthesis, organism-specific biosystem (from REACTOME)
      Sphingolipid de novo biosynthesis, organism-specific biosystemThe main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
    • Sphingolipid metabolism, organism-specific biosystem (from REACTOME)
      Sphingolipid metabolism, organism-specific biosystemSphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    FFAT motif binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    FFAT motif binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    beta-tubulin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cadherin binding HDA PubMed 
    enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    microtubule binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT endoplasmic reticulum exit site IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    vesicle-associated membrane protein-associated protein B/C
    Names
    VAMP (vesicle-associated membrane protein)-associated protein B and C
    VAMP-associated 33 kDa protein

    NCBI Reference Sequences (RefSeq)

    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_008073.2 RefSeqGene

      Range
      4931..66913
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_656

    mRNA and Protein(s)

    1. NM_001195677.1NP_001182606.1  vesicle-associated membrane protein-associated protein B/C isoform 2

      See identical proteins and their annotated locations for NP_001182606.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as VAPC and VAMPC) lacks three exons in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (2, also known as VAPC and VAMPC) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AF086629, AK124571, AL035455, BM968517, DA450527
      Consensus CDS
      CCDS56198.1
      UniProtKB/Swiss-Prot
      O95292
      Related
      ENSP00000379147.3, OTTHUMP00000174286, ENST00000395802.7, OTTHUMT00000267817
      Conserved Domains (1) summary
      pfam00635
      Location:890
      Motile_Sperm; MSP (Major sperm protein) domain
    2. NM_004738.4NP_004729.1  vesicle-associated membrane protein-associated protein B/C isoform 1

      See identical proteins and their annotated locations for NP_004729.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK023241, AK124571, AL035455, BM968517, DA450527
      Consensus CDS
      CCDS33498.1
      UniProtKB/Swiss-Prot
      O95292
      UniProtKB/TrEMBL
      Q53XM7
      Related
      ENSP00000417175.1, OTTHUMP00000031393, ENST00000475243.5, OTTHUMT00000079875
      Conserved Domains (1) summary
      pfam00635
      Location:8111
      Motile_Sperm; MSP (Major sperm protein) domain

    RNA

    1. NR_036633.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as VAPB-3,4) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK023241, AK124571, AK298036, AL035455, BM968517, DA450527

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p12 Primary Assembly

      Range
      58389119..58451101
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_001754433.2 RNA Sequence

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