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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

VMP1 Gene

protein-coding   GIFtS: 46
GCID: GC17P057785

vacuole membrane protein 1

(Previous name: transmembrane protein 49 )
(Previous symbol: TMEM49)
 Explore 9 diseases affiliated with
VMP1 via our new
 Human Malady Compendium 
Biological research products
for VMP1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Vacuole Membrane Protein 11 2     TANGO51 2
TMEM491 2 3 5     Ectopic P-Granules Autophagy Protein 3 Homolog2
Transmembrane Protein 491 2 3     Transport And Golgi Organization 5 Homolog2
EPG31 2     TDC13

External Ids:    HGNC: 295591   Entrez Gene: 816712   Ensembl: ENSG000000627167   OMIM: 6117535   UniProtKB: Q96GC93   

Export aliases for VMP1 gene to outside databases

Previous GC identifers: GC17P057536 GC17P060234 GC17P058126 GC17P058259 GC17P055139


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

UniProtKB/Swiss-Prot: VMP1_HUMAN, Q96GC9
Function: Stress-induced protein that, when overexpressed, promotes formation of intracellular vacuoles followed by
cell death. May be involved in the cytoplasmic vacuolization of acinar cells during the early stage of acute
pancreatitis. Plays a role in the initial stages of the autophagic process through its interaction with BECN1 (By
similarity). Involved in cell-cell adhesion. Plays an essential role in formation of cell junctions

Gene Wiki entry for VMP1 (TMEM49)


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NC_018928.1  NT_010783.15  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for VMP1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVMP1 promoter sequence
   Search SABiosciences Chromatin IP Primers for VMP1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VMP1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17q23.1   Ensembl cytogenetic band:  17q23.1   HGNC cytogenetic band: 17q23.2

VMP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VMP1 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P057785:  view genomic region     (about GC identifiers)

Start:
57,784,553 bp from pter      End:
57,919,616 bp from pter
Size:
135,064 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: VMP1_HUMAN, Q96GC9 (See protein sequence)
Recommended Name: Vacuole membrane protein 1  
Size: 406 amino acids; 46238 Da
Subunit: Interacts with BECN1. Interacts with TJP1. Interacts with TP53INP2
Subcellular location: Endoplasmic reticulum-Golgi intermediate compartment membrane; Multi-pass membrane protein (By
similarity). Cell membrane; Multi-pass membrane protein. Vacuole membrane; Multi-pass membrane protein (By
similarity). Endoplasmic reticulum
Secondary accessions: Q9H0P4 Q9P089

Explore the universe of human proteins at neXtProt for VMP1: NX_Q96GC9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96GC9

  • VMP1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_112200.2  
    ENSEMBL proteins: 
     ENSP00000262291   ENSP00000465972   ENSP00000466579   ENSP00000465947   ENSP00000466413  
     ENSP00000466198   ENSP00000467093   ENSP00000466511   ENSP00000465397   ENSP00000465911  
     ENSP00000467350   ENSP00000446230   ENSP00000445130   ENSP00000444969   ENSP00000439959  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for VMP1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000407pre-autophagosomal structure IEA--
    GO:0000421autophagic vacuole membrane ISS--
    GO:0005783endoplasmic reticulum IDA--
    GO:0005886plasma membrane IEA--
    GO:0016021integral to membrane IEA--


    VMP1 for ontologies           About GeneDecksing



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

    ProtoNet protein and cluster: Q96GC9

    UniProtKB/Swiss-Prot: VMP1_HUMAN, Q96GC9
    Similarity: Belongs to the VMP1 family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: VMP1_HUMAN, Q96GC9
    Function: Stress-induced protein that, when overexpressed, promotes formation of intracellular vacuoles followed by
    cell death. May be involved in the cytoplasmic vacuolization of acinar cells during the early stage of acute
    pancreatitis. Plays a role in the initial stages of the autophagic process through its interaction with BECN1 (By
    similarity). Involved in cell-cell adhesion. Plays an essential role in formation of cell junctions

    miRNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI19056683


    VMP1 for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for VMP1:
     Downregulation of NF-kappaB pa  Downregulation of NF-kappaB pa  Synthetic lethal with Ras 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for VMP1

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    5 Interacting proteins for VMP1 (Q96GC93 ENSP000002622914) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TJP1Q071573, ENSP000002815374I2D: score=1 STRING: ENSP00000281537
    HGSO149643, ENSP000003312014I2D: score=1 STRING: ENSP00000331201
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    BECN1Q144573I2D: score=1 
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006914autophagy IEA--
    GO:0007566embryo implantation IEA--
    GO:0010506regulation of autophagy ISS--
    GO:0016337cell-cell adhesion IMP17724469
    GO:0034329cell junction assembly IMP17724469


    VMP1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for VMP1
    Search CenterWatch for drugs/clinical trials and news about VMP1 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for VMP1 gene: 
    NM_030938.3  

    Unigene Cluster for VMP1:

    Vacuole membrane protein 1
    Hs.444569  [show with all ESTs]
    Unigene Representative Sequence: AY699265
    18/21 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 21):
    ENST00000588915 ENST00000262291(uc002ixu.4 uc010wog.2 uc010woh.2 uc010woi.2 uc010woj.2)
    ENST00000593168 ENST00000586245 ENST00000585847 ENST00000587945 ENST00000588131
    ENST00000589823 ENST00000592106 ENST00000591315 ENST00000587259 ENST00000592619
    ENST00000591877 ENST00000591782 ENST00000588617 ENST00000592790 ENST00000587470
    ENST00000545362

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    Additional cDNA sequence: 

    AB047551.1 AF161410.1 AK024969.1 AK025987.1 AK293578.1 AK293664.1 AK294854.1 AK301254.1 
    AL136711.1 AY699265.1 BC009758.2 BC053563.1 CR533521.1 

    24/48 DOTS entries (see all 48):

    DT.101970657  DT.120930755  DT.40108044  DT.120930349  DT.217547  DT.100890885  DT.100890846  DT.120930612 
    DT.100643276  DT.416288  DT.120930768  DT.99938105  DT.120930472  DT.40108214  DT.120930578  DT.97851773 
    DT.120930568  DT.92469321  DT.100024551  DT.120930585  DT.95374904  DT.120930532  DT.120930764  DT.97859832 

    24/653 AceView cDNA sequences (see all 653):

    BM023256 AU279823 CA414094 AI056918 CA413734 AI356566 CR533521 AI828293 
    BM788778 AI249704 AI123394 BM955992 AA235803 BM713015 AI680714 BM806964 
    AI273257 BM802162 BM803108 BQ775808 CB216599 AW029493 Z45792 AA485530 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for VMP1 (see all 7)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b · 14c
    SP1:              -                 -                                               -     -                                 
    SP2:                                                                                                                        
    SP3:                                -                                                                                       
    SP4:                                                                                                                        
    SP5:                                                                                            -                           


    ECgene alternative splicing isoforms for VMP1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    VMP1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATCTCAAAGA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See VMP1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for VMP1

    SOURCE GeneReport for Unigene cluster: Hs.444569
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VMP1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for VMP1 gene from 9/31 species (see all 31)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vmp11 , 5 vacuole membrane protein 11, 5 91.05(n)1
    94.09(a)1
      11 (51.82 cM)5
    759091  NM_029478.31  NP_083754.21 
     865838655 
    chicken
    (Gallus gallus)
    Aves VMP11 vacuole membrane protein 1 80.54(n)
    85.47(a)
      417635  XM_415880.3  XP_415880.1 
    lizard
    (Anolis carolinensis)
    Reptilia VMP16
    --
    85(a)
    1 ↔ 1
    GL343470.1(231974-295025)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.136972 Xenopus laevis transcribed sequence with weak similarity more 80(n)    BJ627024.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.9822 Danio rerio, Similar to vacuole Membrane Protein 1, more 76.97(n)    BC046904.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Tango51 Transport and Golgi organization 5 55.8(n)
    55.71(a)
      326232  NM_001169245.1  NP_001162716.1 
    worm
    (Caenorhabditis elegans)
    Secernentea Y37D8A.223
    epg-31
    Protein EPG-31 51(a)3
    54.74(n)1
    49.45(a)1
      III(13005825-13007934)3
    1767121  NM_067287.41  NP_499688.21 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT4G149501 SNARE associated Golgi protein 49.27(n)
    38.74(a)
      827153  NM_117581.4  NP_567450.1 
    rice
    (Oryza sativa)
    Liliopsida Os.143512 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 72.69(n)    AK064933.1 


    ENSEMBL Gene Tree for VMP1 (if available)
    TreeFam Gene Tree for VMP1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for VMP1 gene
    1 SIMAP similar gene for VMP1 using alignment to 15 protein entries:     VMP1_HUMAN (see all proteins):
    TMEM49

    VMP1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for VMP1
    PGOHUM00000259608


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1770 NCBI SNPs in VMP1 are shown (see all 1770    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs589013521,2
    C,--57786944(+) AGATAC/TGTCAG 1 -- int11Minor allele frequency- T:0.50WA 2
    rs766517011,2
    F,--57786994(+) TATCAC/TATACT 1 -- int11Minor allele frequency- T:0.14WA 118
    rs733330371,2
    C,--57787043(+) AAAGAA/GTAGTT 1 -- int12Minor allele frequency- G:0.04WA 120
    rs1485761511,2
    --57787367(+) TCCTGC/GCTAAT 1 -- int10--------
    rs1117230171,2
    --57787431(+) CAGGCC/GCCTGT 1 -- int11Minor allele frequency- G:0.00CSA 1
    rs1477188071,2
    --57787455(+) CCGGAC/GGCTGA 1 -- int10--------
    rs1815172441,2
    --57787489(+) GGAGGC/TGGAGC 1 -- int10--------
    rs1864084421,2
    --57787490(+) GAGGCA/GGAGCT 1 -- int10--------
    rs1915628321,2
    --57787529(+) CTCCAG/TCCTGG 1 -- int10--------
    rs1828997981,2
    --57787603(+) TTAGAA/GTTAGA 1 -- int10--------

    HapMap Linkage Disequilibrium report for VMP1 (57784553 - 57919616 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for VMP1: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing VMP1
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    VMP1 for disorders           About GeneDecksing

    OMIM gene information: 611753    OMIM disorders: --

    9 diseases for VMP1:    About MalaCards
    fanconi's anemia    acute pancreatitis    anemia    pancreatitis
    pancreatic cancer    breast cancer    hypoxia    malaria
    carcinoma


    Export disorders for VMP1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for VMP1 gene, integrated from 9 sources (see all 25):
    (articles sorted by number of sources associating them with VMP1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2, 3 Wiemann S.... Poustka A. (2001)
    2. The TP53INP2 protein is required for autophagy in mammalian cells. (PubMed id 19056683)1, 2 Nowak J....Iovanna J.L. (2009)
    3. Reduced expression of vacuole membrane protein 1 affects the invasion capacity of tumor cells. (PubMed id 17724469)1, 2 Sauermann M....Arlt D. (2008)
    4. Cloning and expression of the rat vacuole membrane pr otein 1 (VMP1), a new gene activated in pancreas with acute pancreatitis, which promotes vacuole formation. (PubMed id 11785947)1, 3 Dusetti N.J....Iovanna J.L. (2002)
    5. Novel AKT1-GLI3-VMP1 pathway mediates KRAS oncogene-in duced autophagy in cancer cells. (PubMed id 22535956)1 Lo Re A.E....Fernandez-Zapico M.E. (2012)
    6. Zymophagy, a novel selective autophagy pathway mediat ed by VMP1-USP9x-p62, prevents pancreatic cell death. (PubMed id 21173155)1 Grasso D....Vaccaro M.I. (2011)
    7. Hypoxia-inducible microRNA-210 augments the metastati c potential of tumor cells by targeting vacuole membrane protein 1 in hepatocel lular carcinoma. (PubMed id 22144109)1 Ying Q....He X. (2011)
    8. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    9. Transcriptional consequences of genomic structural ab errations in breast cancer. (PubMed id 21467264)1 Inaki K....Liu E.T. (2011)
    10. [Expression and prognostic value of vacuole membrane p rotein 1 in non-small-cell lung cancer]. (PubMed id 22333543)1 Zhou S.Q....Liu X.G. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 81671 HGNC: 29559 AceView: VMP1 Ensembl:ENSG00000062716 euGenes: HUgn81671
    ECgene: VMP1 H-InvDB: VMP1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for VMP1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for VMP1 gene:
    Search GeneIP for patents involving VMP1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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