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VSTM4 Gene

protein-coding   GIFtS: 41
GCID: GC10M050223

V-Set And Transmembrane Domain Containing 4

(Previous name: chromosome 10 open reading frame 72)
(Previous symbol: C10orf72)
Alzheimer's & Parkinson's Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
V-Set And Transmembrane Domain Containing 41 2
C10orf721 2 3
Chromosome 10 Open Reading Frame 721
V-Set And Transmembrane Domain-Containing Protein 42

External Ids:    HGNC: 264701   Entrez Gene: 1967402   Ensembl: ENSG000001656337   UniProtKB: Q8IW003   

Export aliases for VSTM4 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for VSTM4 Gene:
VSTM4 (V-set and transmembrane domain containing 4) is a protein-coding gene. Diseases associated with VSTM4 include breast and colorectal cancer, and alzheimer's disease.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000010.11  NT_030059.14  NC_018921.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for VSTM4
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for VSTM4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VSTM4


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

Entrez Gene cytogenetic band: 10q11.23   Ensembl cytogenetic band:  10q11.23   HGNC cytogenetic band: 10q11.23

VSTM4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VSTM4 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M050223:  view genomic region     (about GC identifiers)

Start:
50,222,290 bp from pter      End:
50,323,559 bp from pter
Size:
101,270 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: VSTM4_HUMAN, Q8IW00 (See protein sequence)
Recommended Name: V-set and transmembrane domain-containing protein 4 precursor  
Size: 320 amino acids; 36146 Da
Secondary accessions: B4DNI6 Q96MX7
Alternative splicing: 2 isoforms:  Q8IW00-1   Q8IW00-2   

Explore the universe of human proteins at neXtProt for VSTM4: NX_Q8IW00

Explore proteomics data for VSTM4 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn25, Asn41, Asn89, Asn144
  • Modification sites at PhosphoSitePlus

  • See VSTM4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001026916.2  NP_659421.1  

    ENSEMBL proteins: 
     ENSP00000331062   ENSP00000298454  

    VSTM4 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    VSET: Immunoglobulin superfamily / V-set domain containing

    4 InterPro protein domains:
     IPR013783 Ig-like_fold
     IPR013106 Ig_V-set
     IPR007110 Ig-like_dom
     IPR003599 Ig_sub

    Graphical View of Domain Structure for InterPro Entry Q8IW00

    ProtoNet protein and cluster: Q8IW00

    UniProtKB/Swiss-Prot: VSTM4_HUMAN, Q8IW00
    Similarity: Contains 1 Ig-like (immunoglobulin-like) domain


    VSTM4 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    VSTM4 for ontologies           About GeneDecksing


    Animal Models:
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    Selected qRT-PCR Assays for microRNAs that regulate VSTM4 (see all 39):
    hsa-miR-323-3p hsa-miR-4291 hsa-miR-3607-3p hsa-miR-30d hsa-miR-30a hsa-miR-629* hsa-miR-761 hsa-miR-3688-3p
    SwitchGear 3'UTR luciferase reporter plasmidVSTM4 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    VSTM4_HUMAN, Q8IW00: Cell membrane; Single-pass type I membrane protein (Potential)

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016021integral component of membrane IEA--

    VSTM4 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for VSTM4
    Interactions:

        Search GeneGlobe Interaction Network for VSTM4

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for VSTM4 (ENSP000003310624) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    BCANENSP000003312104STRING: ENSP00000331210
    OPTCENSP000003561914STRING: ENSP00000356191
    PPP1CCENSP000003350844STRING: ENSP00000335084
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for VSTM4



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for VSTM4 gene (2 alternative transcripts): 
    NM_001031746.4  NM_144984.3  

    Unigene Cluster for VSTM4:

    V-set and transmembrane domain containing 4
    Hs.522928  [show with all ESTs]
    Unigene Representative Sequence: NM_001031746
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000332853(uc001jhf.2) ENST00000476018 ENST00000298454(uc001jhh.2)


    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate VSTM4 (see all 39):
    hsa-miR-323-3p hsa-miR-4291 hsa-miR-3607-3p hsa-miR-30d hsa-miR-30a hsa-miR-629* hsa-miR-761 hsa-miR-3688-3p
    SwitchGear 3'UTR luciferase reporter plasmidVSTM4 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat VSTM4
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    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat VSTM4
      QuantiTect SYBR Green Assays in human, mouse, rat VSTM4
      QuantiFast Probe-based Assays in human, mouse, rat VSTM4

    Additional mRNA sequence: 

    AK001062.1 AK021993.1 AK056299.1 AK297931.1 AL080114.1 AL833529.1 BC017010.1 BC041414.1 

    6 DOTS entries:

    DT.409201  DT.40107634  DT.95135114  DT.451893  DT.92418143  DT.40245291 

    Selected AceView cDNA sequences (see all 110):

    AI127523 AL553283 CR617276 NM_144984 AK056299 BG166446 AL080114 AV703112 
    AW023532 BF197544 BF939323 AI769171 AI127432 AU137553 AW513534 AV710402 
    AU119015 AL833529 AI161256 BQ184996 BX393423 AW451033 AW444679 BE645778 

    GeneLoc Exon Structure


    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    VSTM4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGGTTTTCT
    VSTM4 Expression
    About this image

    VSTM4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VSTM4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.522928
        Custom PCR Arrays for VSTM4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VSTM4

    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for VSTM4 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vstm41 , 5 RIKEN cDNA E130203B14 gene5
    V-set and transmembrane domain containing 41
    86.82(n)1
    88.7(a)1
      14 (19.40 cM)5
    3207361  NM_178791.41  NP_848906.11 
     328567565 
    chicken
    (Gallus gallus)
    Aves VSTM41 V-set and transmembrane domain containing 4 68.67(n)
    68(a)
      423782  XM_421654.4  XP_421654.3 
    lizard
    (Anolis carolinensis)
    Reptilia VSTM46
    V-set and transmembrane domain containing 4
    62(a)
    1 ↔ 1
    GL343297.1(711188-762041)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia vstm41 V-set and transmembrane domain containing 4 54.05(n)
    48.57(a)
      101732447  XM_004915914.1  XP_004915971.1 
    zebrafish
    (Danio rerio)
    Actinopterygii vstm4b1 V-set and transmembrane domain containing 4b 57.22(n)
    49.49(a)
      100142652  XM_002664016.3  XP_002664062.2 


    ENSEMBL Gene Tree for VSTM4 (if available)
    TreeFam Gene Tree for VSTM4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for VSTM4 (see all 2213)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0355394
    A colorectal cancer sample4--see VAR_0355392 R H mis40--------
    rs1476505851,2
    C--50221883(+) GAGGTC/TGCCAG 1 -- ds50010--------
    rs1156000361,2
    C,F--50221884(+) AGGTCG/ACCAGG 1 -- ds50011Minor allele frequency- A:0.04WA 118
    rs78971391,2
    H--50221915(+) TCCTTA/TGTTTG 1 -- ds50014Minor allele frequency- T:0.00NS EA 420
    rs1405879491,2
    --50221968(+) ACACTA/GGCTTA 1 -- ds50010--------
    rs1444799551,2
    --50222079(+) AAAAAC/TTCCTG 1 -- ds50010--------
    rs111009731,2
    H--50222106(+) CTGAGA/GTCCAT 1 -- ds50014Minor allele frequency- G:0.00NS EA 420
    rs1478264551,2
    C--50222143(+) AAGTGC/TACACA 1 -- ds50010--------
    rs1488640261,2
    --50222287(+) TGATGC/GAGGAC 1 -- ds50010--------
    rs1179140541,2
    F--50222412(+) CTAAAT/ATGGAG 1 -- ut311Minor allele frequency- A:0.01NA 120

    HapMap Linkage Disequilibrium report for VSTM4 (50222290 - 50323559 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for VSTM4 (see all 12):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2845CNV Deletion18987735
    esv2736485CNV Deletion23290073
    esv6657CNV Loss19470904
    esv21974CNV Loss19812545
    nsv522731CNV Loss19592680
    nsv895365CNV Loss21882294
    nsv6620CNV Loss18451855
    nsv895375CNV Gain21882294
    nsv895371CNV Gain21882294
    nsv895369CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing VSTM4
    DNA2.0 Custom Variant and Variant Library Synthesis for VSTM4

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    3 diseases for VSTM4:    
    About MalaCards
    breast and colorectal cancer    alzheimer's disease    colorectal cancer


    VSTM4 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    Export disorders for VSTM4 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)
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    PubMed articles for VSTM4 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with VSTM4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Genome-wide meta-analysis identifies new susceptibility loci for migraine. (PubMed id 23793025)1 Anttila V.... . (Nat. Genet. 2013)
    4. A genome-wide association study of serum uric acid in African Americans. (PubMed id 21294900)1 Charles B.A....Rotimi C.N. (BMC Med Genomics 2011)
    5. Identification of the human testis protein phosphatase 1 interactome. (PubMed id 21382349)1 Fardilha M....da Cruz e Silva E.F. (Biochem. Pharmacol. 2011)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    7. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (Science 2006)
    8. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PubMed id 16385451)1 Grupe A....Goate A. (Am. J. Hum. Genet. 2006)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    10. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)2 Deloukas P.... Rogers J. (Nature 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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, Kegg, and/or H-InvDB)
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    Entrez Gene: 196740 HGNC: 26470 AceView: C10orf72 Ensembl:ENSG00000165633 euGenes: HUgn196740
    ECgene: VSTM4 H-InvDB: VSTM4

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for VSTM4 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for VSTM4 gene:
    Search GeneIP for patents involving VSTM4

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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