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VAMP4 Gene

protein-coding   GIFtS: 62

GC01M169935
vesicle-associated membrane protein 4
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
VAMP-4 3
VAMP24 2
Descriptions
vesicle-associated membrane protein 4 2
External Ids
HGNC: 126451
Entrez Gene: 86742
UniProtKB: O753793
Ensembl: ENSG000001175337
Search outside databases for aliases for VAMP4 gene

Previous GC identifers: GC01M169237 GC01M167298 GC01M168250 GC01M168908 GC01M168400

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for VAMP4:
Synaptobrevins/VAMPs, syntaxins, and the 25-kD synaptosomal-associated protein SNAP25 are the main
components of a protein complex involved in the docking and/or fusion of synaptic vesicles with
the presynaptic membrane. The protein encoded by this gene is a member of the vesicle-associated
membrane protein (VAMP)/synaptobrevin family. This protein may play a role in trans-Golgi
network-to-endosome transport. [provided by RefSeq]

UniProtKB/Swiss-Prot: VAMP4_HUMAN, O75379
Function: Involved in the pathway that functions to remove an inhibitor (probably synaptotagmin-4)
of calcium-triggered exocytosis during the maturation of secretory granules. May be a marker for
this sorting pathway that is critical for remodeling the secretory response of granule

Gene Wiki entry for VAMP4

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the VAMP4 gene  

Entrez Gene cytogenetic band: 1q24-q25   Ensembl cytogenetic band:  1q24.3   HGNC cytogenetic band: 1q24-q25

VAMP4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M169935:     (about GC identifiers)

Start:
169,935,923 bp from pter
End:
169,977,837 bp from pter
Size:
41,915 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000001.9  NT_004487.18  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: VAMP4_HUMAN, O75379 (See protein sequence)
Recommended Name: Vesicle-associated membrane protein 4  
Size: 141 amino acids; 16397 Da
Subunit: Identified in a complex containing STX6, STX13, VAMP4 and VTI1A (By similarity)
Subcellular location: Golgi apparatus, trans-Golgi network membrane; Single-pass type IV membrane
protein (Probable). Note=Associated with trans Golgi network (TGN) and newly formed immature
secretory granules (ISG). Not found on the mature secretory organelles
Secondary accessions: Q96IY9 Q96J20 Q9UEL7
Alternative splicing: 2 isoforms:  O75379-1   O75379-2   

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_003753.2  

    ENSEMBL proteins: 
    ENSP00000386083 ENSP00000236192 ENSP00000356714 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
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    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (VAMP4)
    Human Recombinant Proteins from Abnova (VAMP4)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    5/6 Gene Ontology (GO) cellular component terms (links to tree view) (see all 6 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139 Golgi membrane TAS9553086
    GO:0005764 lysosome TAS9553086
    GO:0005768 endosome TAS9553086
    GO:0005794 Golgi apparatus IEA--
    GO:0016020 membrane IEA--
    About this table

    Antibodies for VAMP4: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for VAMP4
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (VAMP4), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (VAMP4)
    Novus Biologicals Antibodies for VAMP4

    Assays for VAMP4: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    2 InterPro domains/families:
     IPR016444 Synaptobrevin_met/fun
     IPR001388 Synaptobrevin


       GeneDecks  VAMP4 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry O75379

    ProtoNet protein and cluster: O75379

    1 Blocks protein family: IPB001388 Synaptobrevin

    UniProtKB/Swiss-Prot: VAMP4_HUMAN, O75379
    Similarity: Belongs to the synaptobrevin family
    Similarity: Contains 1 v-SNARE coiled-coil homology domain

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (VAMP4)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_003762

                  Applied Biosystems Silencer® siRNAs for VAMP4

                  Sigma-Aldrich siRNA for VAMP4  
                         Sigma-Aldrich shRNA for VAMP4  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for VAMP4
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_003762
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_003762
                                     untagged cDNA clone in CMV expression vector: NM_003762 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_003762

    UniProtKB/Swiss-Prot: VAMP4_HUMAN, O75379
    Function: Involved in the pathway that functions to remove an inhibitor (probably synaptotagmin-4)
    of calcium-triggered exocytosis during the maturation of secretory granules. May be a marker for
    this sorting pathway that is critical for remodeling the secretory response of granule

    1 MGI phenotypic allele for Vamp4 (no phenotypes)


    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


    1 Kegg Pathway  (Kegg details for VAMP4):
     hsa04130 SNARE interactions in vesicular transport

       GeneDecks  VAMP4 for the pathways selected above  
    About GeneDecksing
     Gene Network CentralTM Interacting Genes and Proteins Network for  VAMP4 


    5/18 Interacting proteins for VAMP4 (ENSP000003567143 O753792) via UniProtKB, MINT, and/or STRING (see all 18 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    STX6O437522STRING (score=.999) MINT-4052274 MINT-4052302 MINT-4052327 MINT-4052351
    VTI1AQ96AJ92STRING (score=.998) MINT-4052274 MINT-4052302 MINT-4052327 MINT-4052351
    STX4Q128462STRING (score=.94) MINT-66593
    STX12Q86Y822MINT-4052274 MINT-4052302 MINT-4052327 MINT-4052351
    VTI1BENSP000002164563STRING (score=.969)
    About this table

    1 Gene Ontology (GO) biological process term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016192 vesicle-mediated transport IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for VAMP4

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (VAMP4)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_003762

                  Sigma-Aldrich siRNA for VAMP4  
                         Sigma-Aldrich shRNA for VAMP4  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_003762  

    REFSEQ mRNAs for VAMP4 gene: 

    NM_003762.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_003762  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_003762
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_003762
                                     untagged cDNA clone in CMV expression vector: NM_003762 

    Additional cDNA sequence: 

    AF044310.1 AF052100.1 AK056124.1 AK123624.1 AK290441.1 AL035296.1 BC005974.1 BC007019.1 
    CR457011.1 

    12 DOTS entries:

    DT.92420174  DT.315028  DT.97799210  DT.92420173  DT.95268191  DT.100655461  DT.121348983  DT.95081374 
    DT.100716530  DT.121348988  DT.121348991  DT.92054278 

    24/137 AceView cDNA sequences (see all 137 ):

    AW295713 AI801689 NM_003762 AI758204 BM927117 T16554 AA771953 AK056124 
    AW473740 AA299279 AL597489 BU156636 BG428093 AV649282 T16866 AA991347 
    AI472802 CB123535 BM763166 Z44493 AL035296 BU178915 AA954039 F05174 

    highest scoring ESTs for VAMP4:

    AL035296 AA400295 AF052100 AA374514 AA490730 AA774871 AF044310 AL597489 AL602755 AL701821 

    Unigene Cluster for VAMP4:

    Vesicle-associated membrane protein 4
    Hs.6651  [show with all ESTs]
    Unigene Representative Sequence: AK123624


    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for VAMP4 (see all 7 )

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c · 9d ^ 10a · 10b
    SP1:                                      -     -     -                             -                       -     -     -               
    SP2:                                      -     -     -                             -                                                   
    SP3:                                      -     -     -                             -                                                   
    SP4:                                      -                                                                                             
    SP5:                                                                          -     -                                                   

    About this scheme

    ECgene alternative splicing isoforms for VAMP4

    3 Ensembl transcripts including schematic representations:
    ENST00000401589  ENST00000236192  ENST00000367740  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    VAMP4 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for VAMP4

    1 / 2 / 3

    10 probe-sets matching VAMP4 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    37119_at2, 3 U95-A 1 1.00 1.00 0.23 0.80 AL035296 1.00 0.90 0.95 1
    84216_at2, 3 U95-D 1 1.00 1.00 0.82 1.05 AA400295 0.80 1.00 0.91 1
    85151_at2, 3 U95-D 1 1.00 1.00 0.91 1.04 AA993736 0.60 1.00 0.82 1

    36818_at2, 3 U95-A 1 1.00 1.00 0.73 1.12 AF052100 0.80 1.00 0.91 1

    207350_s_at2, 3 U133-A 1 1.00 1.00 -- -- NM_003762 0.60 1.00 0.82 1

    213480_at2, 3 U133-A 1 1.00 1.00 -- -- AF052100 0.80 1.00 0.91 1

    211760_s_at2, 3 U133-A 1 1.00 1.00 -- -- BC005974 0.80 0.88 0.84 1

    207350_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    213480_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    211760_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  VAMP4 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: TGCCCTGTTC

    SOURCE GeneReport for Unigene cluster: Hs.6651

    Expression variation in blood from EXPOLDB for VAMP4

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for VAMP4 gene from 5/10 species (see all 10 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    VAMP41   -- vesicle-associated membrane protein 4 96.9(n)
    97.14(a)
    480074  XM_537195.2  XP_537195.1 
    chimpanzee
    (Pan troglodytes)
    VAMP41   -- vesicle-associated membrane protein 4 100(n)
    100(a)
    457513  XM_513997.2  XP_513997.2 
    cow
    (Bos taurus)
    VAMP41   -- vesicle-associated membrane protein 4 96.93(n)
    98.58(a)
    616923  NM_001076438.1  NP_001069906.1 
    rat
    (Rattus norvegicus)
    Vamp41   -- vesicle-associated membrane protein 4 93.85(n)
    97.87(a)
    364033  XM_344168.3  XP_344169.2 
    mouse
    (Mus musculus)
    Vamp41, 5 1 (85.00 cM)5
    vesicle-associated membrane protein 41, 5 92.94(n)1
    95.62(a)1
    533301  NM_016796.31  NP_058076.21 
     AA2096555  AF0615165  (see all 16)
    About this table        Species with no ortholog for VAMP4

    ENSEMBL Gene Tree for VAMP4
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for VAMP4 gene
    VAMP82  VAMP52  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/199 NCBI SNPs in VAMP4 are shown (see all 199 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 81)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 1 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs75475741,2
    A,C,F,H169979355(+) TCATAC/GCGCAC 1 -- ng314Minor allele frequency- G:0.13EU EA WA 388
    rs75566441,2
    A,C,F,H169979491(+) ATGGGA/CTATTT 1 -- ng3113Minor allele frequency- C:0.11NA EU EA WA 1158
    rs109135761,2
    C,F,H169978773(+) CATAAA/GAATAA 1 -- ng314Minor allele frequency- G:0.11EU EA WA 418
    rs156551,2
    C,F,H169939895(+) TGACCC/ACCAGC 1 -- ut316Minor allele frequency- A:0.31MN EU EA WA 790
    rs10526701,2
    C,H169946539(-) CATGCA/CAGAAA 1 Q/P mis15Minor allele frequency- C:0.00MN EU EA WA 602
    --
    rs2368951,2
    A169939182(+) TGTGTG/TTGTGT 1 -- ut310--------
    rs10526761,2
    F169939677(-) AGAGAA/GTGTGT 1 -- ut311Minor allele frequency- G:0.14MN 184
    rs125620981,2
    C169977925(+) TTCACC/TTAAAA 1 -- ng310--------
    rs125685631,2
    H169979053(+) atgttC/Atgaga 1 -- ng314Minor allele frequency- A:0.00EU EA WA 418
    rs109031,2
    F169939859(+) TTTCAG/ACATAT 1 -- ut312Minor allele frequency- A:0.17MN 372
    About this table

    HapMap Linkage Disequilibrium images for VAMP4 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 606909

    Genetic Association Database: VAMP4
    Human Genome Epidemiology Navigator: VAMP4 (1 document)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/22 PubMed articles for VAMP4 gene (see all 22 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 8674 HGNC: 12645 AceView: VAMP4 Ensembl:ENSG00000117533 euGenes: HUgn8674
    ECgene: VAMP4 H-InvDB: VAMP4
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for VAMP4:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for VAMP4 Antibodies for VAMP4
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
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