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

Gene ID: 9217, updated on 29-Mar-2023

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; AllianceGenome:HGNC:12649
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
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Genomic context

See VAPB in Genome Data Viewer
Location:
20q13.32
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (58389229..58451101)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (60170197..60232150)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (56964285..57026157)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RAB22A, member RAS oncogene family Neighboring gene NANOG hESC enhancer GRCh37_chr20:56947914-56948415 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56988153-56988944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56988945-56989734 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:57002581-57003275 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:57021533-57022034 Neighboring gene APC down-regulated 1 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57089058-57090056 Neighboring gene APCDD1L divergent transcript Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:57116639-57117838

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables FFAT motif binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables FFAT motif binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables FFAT motif binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables beta-tubulin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables cadherin binding HDA PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables microtubule binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein 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 IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
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
PubMed 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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)

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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_001195677.2NP_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, ENST00000395802.7
    Conserved Domains (1) summary
    pfam00635
    Location:890
    Motile_Sperm; MSP (Major sperm protein) domain
  2. NM_004738.5NP_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
    Consensus CDS
    CCDS33498.1
    UniProtKB/Swiss-Prot
    O95292, Q9P0H0
    UniProtKB/TrEMBL
    Q53XM7
    Related
    ENSP00000417175.1, ENST00000475243.6
    Conserved Domains (1) summary
    pfam00635
    Location:8111
    Motile_Sperm; MSP (Major sperm protein) domain

RNA

  1. NR_036633.2 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: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    58389229..58451101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001754433.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    60170197..60232150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_008485316.1 RNA Sequence