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

Gene ID: 9217, updated on 3-Jun-2018
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
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

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • 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...
Products Interactant Other Gene Complex Source Pubs Description

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
 
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

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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