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VSTM2A Gene

protein-coding   GIFtS: 42
GCID: GC07P054578

V-Set And Transmembrane Domain Containing 2A

(Previous name: V-set and transmembrane domain containing 2)
(Previous symbol: VSTM2)
  Search for VSTM2A
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 2A1 2
VSTM21 2 3
V-Set And Transmembrane Domain Containing 21 2
Hypothetical Protein MGC335302
V-Set And Transmembrane Domain-Containing Protein 2A2

External Ids:    HGNC: 284991   Entrez Gene: 2220082   Ensembl: ENSG000001704197   UniProtKB: Q8TAG53   

Export aliases for VSTM2A gene to outside databases

Previous GC identifer: GC07P054447


(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 VSTM2A Gene:
VSTM2A (V-set and transmembrane domain containing 2A) is a protein-coding gene. An important paralog of this gene is VSTM2B.


(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 at NCBI GenBank:
NC_000007.13  NT_007819.18  NC_018918.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the VSTM2A gene promoter:
         HOXA9   HOXA9B   RORalpha1   SRY   FOXD3   Meis-1a   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 5): VSTM2A promoter sequence
   Search Chromatin IP Primers for VSTM2A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VSTM2A


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

Entrez Gene cytogenetic band: 7p11.2   Ensembl cytogenetic band:  7p11.2   HGNC cytogenetic band: 7p11.2

VSTM2A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VSTM2A gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P054578:  view genomic region     (about GC identifiers)

Start:
54,610,018 bp from pter      End:
54,638,773 bp from pter
Size:
28,756 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 54,615,835-54,642,765     

(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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: VTM2A_HUMAN, Q8TAG5 (See protein sequence)
Recommended Name: V-set and transmembrane domain-containing protein 2A precursor  
Size: 236 amino acids; 25833 Da
Sequence caution: Sequence=AAH28404.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=EAL23809.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: A4D2E9 B5MC94
Alternative splicing: 2 isoforms:  Q8TAG5-1   Q8TAG5-2   

Explore the universe of human proteins at neXtProt for VSTM2A: NX_Q8TAG5

Explore proteomics data for VSTM2A at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn35, Asn175

  • See VSTM2A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_872352.2  
    ENSEMBL proteins: 
     ENSP00000303108   ENSP00000384967   ENSP00000384701   ENSP00000384103   ENSP00000385933  

    VSTM2A Human Recombinant Protein Products:

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    Novus Biologicals VSTM2A Lysate
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for VSTM2A 

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    LSBio Antibodies in human, mouse, rat for VSTM2A

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    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for VSTM2A 


    (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 Q8TAG5

    ProtoNet protein and cluster: Q8TAG5

    2 Blocks protein domains:
    IPB003599 Immunoglobulin subtype
    IPB013106 Immunoglobulin V-set


    UniProtKB/Swiss-Prot: VTM2A_HUMAN, Q8TAG5
    Similarity: Contains 1 Ig-like V-type (immunoglobulin-like) domain


    Find genes that share domains with VSTM2A           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, 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 ----
         
    Find genes that share ontologies with VSTM2A           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for VSTM2A
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for VSTM2A
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for VSTM2A

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    6 qRT-PCR Assays for microRNAs that regulate VSTM2A:
    hsa-miR-3689e hsa-miR-3689b hsa-miR-3658 hsa-miR-3689a-5p hsa-miR-3653 hsa-miR-3148
    SwitchGear 3'UTR luciferase reporter plasmidVSTM2A 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for VSTM2A
    Predesigned siRNA for gene silencing in human, mouse, rat VSTM2A

    Gene Editing
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    GenScript: all cDNA clones in your preferred vector: VSTM2A (NM_182546)
    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VSTM2A

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VSTM2A


    (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
    VTM2A_HUMAN, Q8TAG5: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    plasma membrane2
    cytosol1
    endoplasmic reticulum1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    Find genes that share ontologies with VSTM2A           About GenesLikeMe


    (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 VSTM2A
    Interactions:

        Search GeneGlobe Interaction Network for VSTM2A

    (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 VSTM2A (VTM2A)



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for VSTM2A gene: 
    NM_182546.2  

    Unigene Cluster for VSTM2A:

    V-set and transmembrane domain containing 2A
    Hs.335933  [show with all ESTs]
    Unigene Representative Sequence: BC045679
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000302287(uc022adk.1) ENST00000407838(uc010kzf.3) ENST00000495904
    ENST00000404951 ENST00000402613 ENST00000498834 ENST00000466888 ENST00000469952
    ENST00000402026
    miRNA
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    6 qRT-PCR Assays for microRNAs that regulate VSTM2A:
    hsa-miR-3689e hsa-miR-3689b hsa-miR-3658 hsa-miR-3689a-5p hsa-miR-3653 hsa-miR-3148
    SwitchGear 3'UTR luciferase reporter plasmidVSTM2A 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for VSTM2A
    Predesigned siRNA for gene silencing in human, mouse, rat VSTM2A
    Clone
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    OriGene clones in human, mouse for VSTM2A (see all 6)
    OriGene ORF clones in mouse, rat for VSTM2A
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: VSTM2A (NM_182546)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for VSTM2A
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VSTM2A
    Primer
    Products:
        
    OriGene qPCR primer pairs and template standards for VSTM2A
    OriGene qSTAR qPCR primer pairs in human, mouse for VSTM2A
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat VSTM2A
      QuantiTect SYBR Green Assays in human, mouse, rat VSTM2A
      QuantiFast Probe-based Assays in human, mouse, rat VSTM2A

    Additional mRNA sequence: 

    AB074160.1 BC037834.2 BC045679.1 NR_038994.1 

    2 DOTS entries:

    DT.211156  DT.95320961 

    Selected AceView cDNA sequences (see all 70):

    BI752069 CR613464 H18140 BX418762 CR617415 BX101004 BQ184626 BQ639021 
    BF477987 BQ186600 AI420977 AI340204 AL529738 NM_182546 BQ222545 BI553644 
    BQ219240 BI819596 AI658939 BC045679 BI755592 BC028404 BF341844 H18099 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for VSTM2A    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c
    SP1:                          -     -           -                     
    SP2:                          -     -           -                     
    SP3:                          -     -                                 
    SP4:                                -           -                     
    SP5:                                            -                     


    ECgene alternative splicing isoforms for VSTM2A

    (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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    VSTM2A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    VSTM2A Expression
    About this image


    VSTM2A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Brain (Nervous System)    fully expand to see all 7 entries
             Medulla Oblongata
             brain/midbrain/lateral wall   
     
     Neural Tube (Nervous System)    fully expand to see all 4 entries
             Metencephalon
             brain/midbrain/lateral wall   
     
     Neurons
             nGnG Amacrine Cells Inner Nuclear Layer
     
     Eye (Sensory Organs)
             nGnG Amacrine Cells Inner Nuclear Layer
    VSTM2A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VSTM2A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.335933
        Custom PCR Arrays for VSTM2A
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VSTM2A

    (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 VSTM2A gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vstm2a1 , 5 V-set and transmembrane domain containing 2A1, 5 89.83(n)1
    91.95(a)1
      11 (8.89 cM)5
    2117391  NM_145967.21  NP_666079.21 
     162577245 
    chicken
    (Gallus gallus)
    Aves VSTM2A1 V-set and transmembrane domain containing 2A 80.97(n)
    85.85(a)
      420951  XM_004935153.1  XP_004935210.1 
    lizard
    (Anolis carolinensis)
    Reptilia VSTM2A6
    V-set and transmembrane domain containing 2A
    74(a)
    1 ↔ 1
    GL343345.1(246043-351830)
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1108521 zgc:110852 62.85(n)
    55.95(a)
      503750  NM_001013328.1  NP_001013346.1 


    ENSEMBL Gene Tree for VSTM2A (if available)
    TreeFam Gene Tree for VSTM2A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for VSTM2A gene
    VSTM2B2  VSTM2L2  
    2 SIMAP similar genes for VSTM2A using alignment to 3 protein entries:     VTM2A_HUMAN (see all proteins):
    VSTM2L    VSTM2B

    Find genes that share paralogs with VSTM2A           About GenesLikeMe



    (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 VSTM2A (see all 342)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1463774661,2
    --54608028(+) ATCAGG/TCACTT 1 -- us2k10--------
    rs1847890761,2
    --54608050(+) AACAAA/GAGACT 1 -- us2k10--------
    rs1461250021,2
    C--54608076(+) TCTCC-/TTTTTT 1 -- us2k10--------
    rs1147468271,2
    F--54608155(+) ATTCAA/GTGGCT 1 -- us2k11Minor allele frequency- G:0.03WA 118
    rs1996880311,2
    C--54608205(+) CACTC-/TTAAGCT 1 -- us2k10--------
    rs1394101731,2
    C--54608264(+) AATAGC/TTGAAA 1 -- us2k10--------
    rs117678641,2
    C,F,H--54608326(+) ATATTG/AAGAAC 1 -- us2k11Minor allele frequency- A:0.01NA 120
    rs1155844411,2
    C,F--54608599(+) CTTAGA/GACGAT 1 -- us2k11Minor allele frequency- G:0.07WA 118
    rs284095321,2
    --54608601(+) TAGAAC/TGATAA 1 -- us2k10--------
    rs1879774971,2
    --54608602(+) AGAACA/GATAAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for VSTM2A (54610018 - 54638773 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for VSTM2A:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2734425CNV Deletion23290073
    esv2272226CNV Deletion18987734
    esv2734431CNV Deletion23290073
    nsv888052CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
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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.)
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    Find genes that share disorders with VSTM2A           About GenesLikeMe

    Genetic Association Database (GAD): VSTM2A

    Export disorders for VSTM2A 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 VSTM2A gene integrated from 10 sources:
    (articles sorted by number of sources associating them with VSTM2A)
        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. Human chromosome 7: DNA sequence and biology. (PubMed id 12690205)1, 2 Scherer S.W.... Tsui L.-C. (Science 2003)
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    4. A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study. (PubMed id 17903292)4 Hwang S.J....Fox C.S. (BMC Med. Genet. 2007)
    5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
    6. The DNA sequence of human chromosome 7. (PubMed id 12853948)2 Hillier L.W.... Wilson R.K. (Nature 2003)

    (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: 222008 HGNC: 28499 AceView: MGC33530 Ensembl:ENSG00000170419 euGenes: HUgn222008
    ECgene: VSTM2A H-InvDB: VSTM2A

    (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)
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    NameDescription
    PharmGKB entry for VSTM2A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    (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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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