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Vamp4 vesicle-associated membrane protein 4 [ Rattus norvegicus (Norway rat) ]

Gene ID: 364033, updated on 28-Oct-2024

Summary

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Official Symbol
Vamp4provided by RGD
Official Full Name
vesicle-associated membrane protein 4provided by RGD
Primary source
RGD:1309753
See related
EnsemblRapid:ENSRNOG00000003071 AllianceGenome:RGD:1309753
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Involved in endosomal transport; regulation of synaptic vesicle endocytosis; and vesicle-mediated transport in synapse. Is active in glutamatergic synapse. Orthologous to human VAMP4 (vesicle associated membrane protein 4). [provided by Alliance of Genome Resources, Oct 2024]
Expression
Biased expression in Brain (RPKM 131.3), Thymus (RPKM 89.7) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Vamp4 in Genome Data Viewer
Location:
13q22
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (77453135..77475909)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (74919872..74942791)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (80460699..80483597)

Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene methyltransferase 13, eEF1A N-terminus and K55 Neighboring gene uncharacterized LOC120096299 Neighboring gene myocilin Neighboring gene proline-rich coiled-coil 2C Neighboring gene uncharacterized LOC134481577

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. VAMP4 Maintains a Ca(2+)-Sensitive Pool of Spontaneously Recycling Synaptic Vesicles. Lin PY, et al. J Neurosci, 2020 Jul 8. PMID 32532887, Free PMC Article
  2. VAMP4 Is an Essential Cargo Molecule for Activity-Dependent Bulk Endocytosis. Nicholson-Fish JC, et al. Neuron, 2015 Dec 2. PMID 26607000, Free PMC Article
  3. The regulated exocytosis of enlargeosomes is mediated by a SNARE machinery that includes VAMP4. Cocucci E, et al. J Cell Sci, 2008 Sep 15. PMID 18713833
  4. The vSNAREs VAMP2 and VAMP4 control recycling and intracellular sorting of post-synaptic receptors in neuronal dendrites. Bakr M, et al. Cell Rep, 2021 Sep 7. PMID 34496238
  5. VAMP4 directs synaptic vesicles to a pool that selectively maintains asynchronous neurotransmission. Raingo J, et al. Nat Neurosci, 2012 Mar 11. PMID 22406549, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The vSNAREs VAMP2 and VAMP4 control recycling and intracellular sorting of post-synaptic receptors in neuronal dendrites.
    Title: The vSNAREs VAMP2 and VAMP4 control recycling and intracellular sorting of post-synaptic receptors in neuronal dendrites.
  2. VAMP4 Maintains a Ca(2+)-Sensitive Pool of Spontaneously Recycling Synaptic Vesicles.
    Title: VAMP4 Maintains a Ca(2+)-Sensitive Pool of Spontaneously Recycling Synaptic Vesicles.
  3. The results of this study suggested that the VAMP4 is the first identified Activity-dependent bulk endocytosis cargo and is essential for this endocytosis mode to proceed.
    Title: VAMP4 Is an Essential Cargo Molecule for Activity-Dependent Bulk Endocytosis.
  4. Data show that VAMP4, an R-SNARE that has never been shown to participate in regulated exocytoses, appears to be harboured in the membrane of enlargeosomes and to be a member of the machinery mediating their regulated exocytosis.
    Title: The regulated exocytosis of enlargeosomes is mediated by a SNARE machinery that includes VAMP4.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Process Evidence Code Pubs
involved_in Golgi ribbon formation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within Golgi to plasma membrane protein transport ISO
Inferred from Sequence Orthology
more info
  
involved_in SNARE complex assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in SNARE complex assembly ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within cellular response to type II interferon ISO
Inferred from Sequence Orthology
more info
  
involved_in endocytic recycling ISO
Inferred from Sequence Orthology
more info
  
involved_in neurotransmitter receptor transport, endosome to postsynaptic membrane IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in neurotransmitter receptor transport, endosome to postsynaptic membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of Golgi to plasma membrane protein transport ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of synaptic vesicle endocytosis EXP
Inferred from Experiment
more info
 PubMed 
involved_in regulation of synaptic vesicle endocytosis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of synaptic vesicle endocytosis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in synaptic vesicle to endosome fusion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in synaptic vesicle to endosome fusion IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in synaptic vesicle to endosome fusion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in vesicle-mediated transport in synapse IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in vesicle-mediated transport in synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
  
part_of SNARE complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of SNARE complex ISO
Inferred from Sequence Orthology
more info
  
located_in cell surface ISO
Inferred from Sequence Orthology
more info
  
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in phagocytic vesicle ISO
Inferred from Sequence Orthology
more info
  
is_active_in presynaptic endosome membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in trans-Golgi network ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
vesicle-associated membrane protein 4

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.

mRNA and Protein(s)

  1. NM_001108856.2 → NP_001102326.1  vesicle-associated membrane protein 4 isoform 1

    See identical proteins and their annotated locations for NP_001102326.1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013
    UniProtKB/TrEMBL
    A0A096MJ99, A6ID94
    Conserved Domains (1) summary
    cd15869
    Location:50 → 116
    R-SNARE_VAMP4; SNARE motif of VAMP4

  2. NM_001429888.1 → NP_001416817.1  vesicle-associated membrane protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013
    UniProtKB/TrEMBL
    A6ID94

  3. NM_001429889.1 → NP_001416818.1  vesicle-associated membrane protein 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013
    UniProtKB/TrEMBL
    A6ID95

  4. NM_001429890.1 → NP_001416819.1  vesicle-associated membrane protein 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013
    UniProtKB/TrEMBL
    A6ID95

RNA

  1. NR_190825.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013

  2. NR_190826.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013

  3. NR_190827.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000013

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086031.1 Reference GRCr8

    Range
    77453135..77475909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006250184.5 → XP_006250246.1  vesicle-associated membrane protein 4 isoform X1

    Related
    ENSRNOP00000100323.1, ENSRNOT00000121837.1
    Conserved Domains (1) summary
    cd15869
    Location:50 → 116
    R-SNARE_VAMP4; SNARE motif of VAMP4

  2. XM_006250186.4 → XP_006250248.1  vesicle-associated membrane protein 4 isoform X2

    Related
    ENSRNOP00000111299.1, ENSRNOT00000169917.1
    Conserved Domains (1) summary
    cd15869
    Location:50 → 116
    R-SNARE_VAMP4; SNARE motif of VAMP4

  3. XM_039090953.2 → XP_038946881.1  vesicle-associated membrane protein 4 isoform X3

    Conserved Domains (1) summary
    cl22856
    Location:50 → 89
    SNARE; SNARE motif

  4. XM_039090952.2 → XP_038946880.1  vesicle-associated membrane protein 4 isoform X1

    Conserved Domains (1) summary
    cd15869
    Location:50 → 116
    R-SNARE_VAMP4; SNARE motif of VAMP4

  5. XM_063272518.1 → XP_063128588.1  vesicle-associated membrane protein 4 isoform X2

RNA

  1. XR_005492263.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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