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

VSTM2A Gene

protein-coding   GIFtS: 40
GCID: GC07P054578

V-set and transmembrane domain containing 2A

(Previous name: V-set and transmembrane domain containing 2 )
(Previous symbol: VSTM2)
  Search for VSTM2A
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Biological research products
for VSTM2A    

Aliases
for VSTM2A gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
V-Set And Transmembrane Domain Containing 2A1 2
VSTM21 2 3
V-Set And Transmembrane Domain Containing 21 2
MGC335301
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


Summaries
for VSTM2A gene

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

Genomic Views
for VSTM2A gene

(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_000007.13  NC_018918.1  NT_033968.6  NT_079592.2  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for VSTM2A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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     

Proteins
for VSTM2A gene

(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: VTM2A_HUMAN, Q8TAG5 (See protein sequence)
Recommended Name: V-set and transmembrane domain-containing protein 2A precursor  
Size: 236 amino acids; 25833 Da
Subcellular location: Secreted (Potential)
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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8TAG5

    • VSTM2A Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

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

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    Uscn Proteins for VSTM2A

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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


    VSTM2A for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for VSTM2A gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    VSTM2A for domains           About GeneDecksing

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

    Graphical View of Domain Structure for InterPro Entry Q8TAG5

    ProtoNet protein and cluster: Q8TAG5

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


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


    Function
    for VSTM2A gene

    (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
    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmid: VSTM2A 3' UTR sequence
    Inhib. RNA
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    Gene Editing
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    Pathways & Interactions
    for VSTM2A gene

    (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 VSTM2A

    Drugs & Compounds
    for VSTM2A gene

    (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 VSTM2A
    Search CenterWatch for drugs/clinical trials and news about VSTM2A / VTM2A 

    Transcripts
    for VSTM2A gene

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    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 VSTM2A gene: 
    NM_182546.2  

    Unigene Clusters for VSTM2A:

    V-set and transmembrane domain containing 2A
    Hs.335933  [show with all ESTs], Hs.731937  [show with all ESTs]
    Unigene Representative Sequences: BC045679, BC028404
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000302287(uc022adk.1) ENST00000407838(uc010kzf.3) ENST00000495904
    ENST00000404951 ENST00000402613 ENST00000498834 ENST00000466888 ENST00000469952
    ENST00000402026

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    hsa-miR-3689e hsa-miR-3689b hsa-miR-3658 hsa-miR-3689a-5p hsa-miR-3653 hsa-miR-3148
    SwitchGear 3'UTR luciferase reporter plasmid: VSTM2A 3' UTR sequence
    Inhib. RNA
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    Browse OriGene 29mer shRNA kits
    OriGene siRNA: VSTM2A
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    Clone
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    Primer
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    Additional cDNA sequence: BC028404.1 

    7 DOTS entries:

    DT.211156  DT.100000161  DT.95320961  DT.95110802  DT.95123597  DT.40109727  DT.40308481 

    24/70 AceView cDNA sequences (see all 70):

    BF477987 BX418762 BX101004 H18140 BQ639021 CR617415 BQ184626 BQ186600 
    BI752069 AI420977 CR613464 BX420936 BI667944 Z42293 H18099 AI340204 
    AL529738 BC028404 NM_182546 BQ219240 BI756787 BF341844 AI310135 BI819596 

    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

    Expression
    for VSTM2A gene

    (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

    VSTM2A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

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

    VSTM2A expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    7 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    EyeInner Nuclear LayernGnG Amacrine CellsAmacrine, Retina
    Spinal CordSpinal Ventral ColumnsVentral Spinal Cord Progenitor CellsMotor Neurons
    BrainHypothalamusBrain
    BrainMedulla OblongataBrain
    Neural TubeMetencephalonNeural Tube
    Neural TubeTelencephalonNeural Tube
    Spinal CordSpinal Ventral ColumnsSpinal Cord
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Sclerotome cells (Primary Cell)Bone, Cartilage, Somite

    See VSTM2A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for VSTM2A

    SOURCE GeneReport for Unigene clusters: Hs.335933 Hs.731937
        SABiosciences Custom PCR Arrays for VSTM2A
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    In Situ
    Assay Products:     
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    Orthologs
    for VSTM2A gene

    (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 chordates.

    Orthologs for VSTM2A gene from 3/10 species (see all 10)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves VSTM2A1 V-set and transmembrane domain containing 2A 83.19(n)
    87.71(a)    		   420951  XM_419036.2  XP_419036.3 
    lizard
    (Anolis carolinensis)    		 Reptilia VSTM2A6
    		 --
    		 81(a)
    		 1 ↔ 1
    		 GL343345.1(328572-351830)
    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
    for VSTM2A gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    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

    VSTM2A for paralogs           About GeneDecksing



    Genomic Variants
    for VSTM2A gene

    (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

    10/469 NCBI SNPs in VSTM2A are shown (see all 469)     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
    		--54608205(+) CACTC-/TTAAGCT 1 -- us2k10--------
    rs1394101731,2
    		--54608264(+) AATAGC/TTGAAA 1 -- us2k10--------
    rs117678641,2
    		C,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 (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for VSTM2A: --

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    Disorders / Diseases
    for VSTM2A gene

    (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
    		   --

    Publications
    for VSTM2A gene

    (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 VSTM2A gene integrated from 9 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. (2004)
    2. Human chromosome 7: DNA sequence and biology. (PubMed id 12690205)1, 2 Scherer S.W.... Tsui L.-C. (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. (2002)
    4. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    5. The DNA sequence of human chromosome 7. (PubMed id 12853948)2 Hillier L.W.... Wilson R.K. (2003)

    External Searches for VSTM2A gene

    (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)

    Genome Databases showing VSTM2A gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 222008 HGNC: 28499 AceView: MGC33530 Ensembl:ENSG00000170419 euGenes: HUgn222008
    ECgene: VSTM2A H-InvDB: VSTM2A

    Other Databases showing VSTM2A gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing VSTM2A gene

    (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 VSTM2A Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for VSTM2A gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for VSTM2A gene:
    Search GeneIP for patents involving VSTM2A

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



    Products
    for VSTM2A gene

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     Browse OriGene Antibodies   Browse OriGene shRNA RFPs  
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     QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat VSTM2A
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     GenScript Custom Purified and Recombinant Proteins Services for VSTM2A GenScript cDNA clones with any tag delivered in your preferred vector for VSTM2A
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     Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies
     Novus Tissue Slides
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     Search for Antibodies for VSTM2A at Abcam
     See all of Abcam's Antibodies, Kits and Proteins for VSTM2A
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     VSTM2A Proteins, Antibodies, CLIAs, and ELISAs
     Search LifeMap BioReagents cell lines for VSTM2A
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     Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VSTM2A
     SwitchGear 3'UTR luciferase reporter plasmids for VSTM2A
     SwitchGear Promoter luciferase reporter plasmids for VSTM2A
     Search ThermoFisher Antibodies for VSTM2A
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VSTM2A
           
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