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

    Gene ID: 364033, updated on 9-Dec-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, Dec 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
    • 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
      A0A096MJ99, A6ID94

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

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      A0A096MJ99, A6ID95

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

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      A0A096MJ99, 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

    Gene LinkOut

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