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

VSIG1 Gene

protein-coding   GIFtS: 48
GCID: GC0XP107288

V-set and immunoglobulin domain containing 1
 Explore 5 diseases affiliated with
VSIG1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for VSIG1    

Aliases
for VSIG1 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 Immunoglobulin Domain Containing 11 2     MGC442871
Cell Surface A33 Antigen2 3     1700062D20Rik2
Glycoprotein A342 3     DJ889N15.11
GPA342 3     V-Set And Immunoglobulin Domain-Containing Protein 12

External Ids:    HGNC: 286751   Entrez Gene: 3405472   Ensembl: ENSG000001018427   OMIM: 3006205   UniProtKB: Q86XK73   

Export aliases for VSIG1 gene to outside databases

Previous GC identifers: GC0XP107094 GC0XP107174 GC0XP096911


Summaries
for VSIG1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for VSIG1:
This gene encodes a member of the junctional adhesion molecule (JAM) family. The encoded protein contains multiple
glycosylation sites at the N-terminal region, and multiple phosphorylation sites and glutamic acid/proline (EP)
repeats at the C-terminal region. The gene is expressed in normal stomach and testis, as well as in gastric,
esophageal and ovarian cancers. Alternatively spliced transcript variants encoding different isoforms have been found
for this gene. (provided by RefSeq, Dec 2009)




Genomic Views
for VSIG1 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_000023.10  NC_018934.1  NT_011651.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VSIG1 gene promoter:
         FOXF2   MyoD   FOXO3   NF-kappaB   FOXO3b   SRY   FOXO3a   LyF-1   NF-kappaB1   En-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: VSIG1 promoter sequence
   Search SABiosciences Chromatin IP Primers for VSIG1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VSIG1


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

Entrez Gene cytogenetic band: Xq22.3   Ensembl cytogenetic band:  Xq22.3   HGNC cytogenetic band: Xq22.3

VSIG1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VSIG1 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP107288:  view genomic region     (about GC identifiers)

Start:
 107,288,200 bp from pter      End:
 107,322,414 bp from pter
Size:
 34,215 bases      Orientation:
 plus strand

Proteins
for VSIG1 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: VSIG1_HUMAN, Q86XK7 (See protein sequence)
Recommended Name: V-set and immunoglobulin domain-containing protein 1 precursor  
Size: 387 amino acids; 41811 Da
Subcellular location: Membrane; Single-pass type I membrane protein (Potential)
Sequence caution: Sequence=CAE45954.1; Type=Erroneous initiation;
Secondary accessions: C9J4P2 Q6MZS4
Alternative splicing: 2 isoforms:  Q86XK7-1   Q86XK7-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for VSIG1: NX_Q86XK7

Post-translational modifications:

  • Highly N-glycosylated. Appears not to contain significant amounts of O-linked carbohydrates or sialic acid in its sugar
    • moieties1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q86XK7

    • VSIG1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001164024.1  NP_872413.1  

    ENSEMBL proteins: 
     ENSP00000217957   ENSP00000407102   ENSP00000402219  

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    Uscn Proteins for VSIG1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--


    VSIG1 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for VSIG1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    VSIG1 for domains           About GeneDecksing

    5/6 InterPro domains/families (see all 6):
     IPR003598 Ig_sub2
     IPR007110 Ig-like_dom
     IPR003599 Ig_sub
     IPR013783 Ig-like_fold
     IPR013106 Ig_V-set

    Graphical View of Domain Structure for InterPro Entry Q86XK7

    ProtoNet protein and cluster: Q86XK7

    1 Blocks protein family: IPB003598 Immunoglobulin C-2 type

    UniProtKB/Swiss-Prot: VSIG1_HUMAN, Q86XK7
    Similarity: Contains 1 Ig-like C2-type (immunoglobulin-like) domain
    Similarity: Contains 1 Ig-like V-type (immunoglobulin-like) domain


    Function
    for VSIG1 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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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat VSIG1
    8/10 QIAGEN miScript miRNA Assays for microRNAs that regulate VSIG1 (see all 10):
    hsa-miR-144* hsa-miR-499-3p hsa-miR-496 hsa-miR-3914 hsa-miR-873 hsa-miR-23b* hsa-miR-4279 hsa-miR-493*
    SwitchGear 3'UTR luciferase reporter plasmid: VSIG1 3' UTR sequence
    Inhib. RNA
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    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VSIG1

    1 GenomeRNAi human phenotype for VSIG1:
     Increased S DNA content 


    Pathways & Interactions
    for VSIG1 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 VSIG1

    Drugs & Compounds
    for VSIG1 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
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    Browse Tocris compounds for VSIG1
    Search CenterWatch for drugs/clinical trials and news about VSIG1 

    Transcripts
    for VSIG1 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,
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    About This Section
    REFSEQ mRNAs for VSIG1 gene (2 alternative transcripts): 
    NM_001170553.1  NM_182607.4  

    Unigene Cluster for VSIG1:

    V-set and immunoglobulin domain containing 1
    Hs.177164  [show with all ESTs]
    Unigene Representative Sequence: NM_001170553
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000217957 ENST00000458383 ENST00000485533 ENST00000479635 ENST00000415430(uc011msk.2 uc004eno.3)


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    8/10 QIAGEN miScript miRNA Assays for microRNAs that regulate VSIG1 (see all 10):
    hsa-miR-144* hsa-miR-499-3p hsa-miR-496 hsa-miR-3914 hsa-miR-873 hsa-miR-23b* hsa-miR-4279 hsa-miR-493*
    SwitchGear 3'UTR luciferase reporter plasmid: VSIG1 3' UTR sequence
    Inhib. RNA
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    Clone
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    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat VSIG1

    Additional cDNA sequence: 

    AK292472.1 AK301311.1 AK301783.1 AK315846.1 BC043216.2 BX640913.1 BX648658.1 

    2 DOTS entries:

    DT.95148618  DT.121322785 

    19 AceView cDNA sequences:

    BQ027344 BM782237 AW864876 NM_182607 BG772843 BC043216 BI459739 AI581519 
    BX640913 BX648658 BI464536 AI803868 CD358701 CD698346 AW085312 CD690155 
    BQ435687 BQ376500 BE939144 

    GeneLoc Exon Structure


    Expression
    for VSIG1 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

    VSIG1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATCATATTTC

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

    VSIG1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Pancreatic endoderm/endocrine precursor-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See VSIG1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for VSIG1

    SOURCE GeneReport for Unigene cluster: Hs.177164

    UniProtKB/Swiss-Prot: VSIG1_HUMAN, Q86XK7
    Tissue specificity: Detected only in stomach mucosa and testis, and to a much lesser level in pancreas (at protein
    level). Detected in gastric cancers (31%), esophageal carcinomas (50%) and ovarian cancers (23%)

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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VSIG1

    Orthologs
    for VSIG1 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 VSIG1 gene from 2/8 species (see all 8)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves VSIG11 V-set and immunoglobulin domain containing 1 56.78(n)
    47.67(a)    		   414795  NM_001001745.1  NP_001001745.1 
    lizard
    (Anolis carolinensis)    		 Reptilia VSIG16
    		 --
    		 36(a)
    		 1 ↔ 1
    		 GL343202.1(3956865-3965611)


    ENSEMBL Gene Tree for VSIG1 (if available)
    TreeFam Gene Tree for VSIG1 (if available) 

    Paralogs
    for VSIG1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for VSIG1 gene
    CLMP2  ESAM2  VSIG82  GPA332  JAM22  CXADR2  VSIG22  C1orf2042  
    IGSF112  JAM32  F11R2  
    2 SIMAP similar genes for VSIG1 using alignment to 2 protein entries:     VSIG1_HUMAN (see all proteins):
    VSIG2    GPA33

    VSIG1 for paralogs           About GeneDecksing



    Genomic Variants
    for VSIG1 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

    10/414 NCBI SNPs in VSIG1 are shown (see all 414)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr X posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1876282301,2
    		--107286241(+) TTGGAA/GCATGA 2 -- us2k10--------
    rs1457606851,2
    		--107286303(+) CCAGGA/GGGCCG 2 -- us2k10--------
    rs15476261,2
    		C,F,A,H,--107286348(-) TTGCAT/CGTCTC 2 -- us2k110Minor allele frequency- C:0.28NA EA NS WA CSA 675
    rs1470848081,2
    		--107286527(+) AGACTC/TATATT 2 -- us2k10--------
    rs1911466341,2
    		--107286595(+) TGGGAC/TACGCT 2 -- us2k10--------
    rs1840723821,2
    		--107286617(+) TGGGAA/GCTGCC 2 -- us2k10--------
    rs1871142671,2
    		--107286650(+) CTGGAA/GGGATT 2 -- us2k10--------
    rs59629321,2
    		C,F,H,--107286766(+) GCTAGG/AGTGGT 2 -- us2k113Minor allele frequency- A:0.07NS EA CSA 1979
    rs1916256691,2
    		--107287020(+) TTTCCC/TGTAAA 2 -- us2k10--------
    rs1853381021,2
    		--107287049(+) AACATA/GTCACT 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for VSIG1 (107288200 - 107322414 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for VSIG1: --
    Locus Specific Mutation Databases (LSDB): VSIG1

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    Disorders / Diseases
    for VSIG1 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
    VSIG1 for disorders           About GeneDecksing

    OMIM gene information: 300620    OMIM disorders: --

    5 diseases for VSIG1:    About MalaCards
    ovarian cancer    esophagitis    esophageal carcinoma    gastric cancer
    carcinoma


    Export disorders for VSIG1 gene to outside databases

    Publications
    for VSIG1 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 VSIG1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with VSIG1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Glycoprotein A34, a novel target for antibody-based cancer immunotherapy. (PubMed id 16405301)1, 2, 9 Scanlan M.J.... Jungbluth A.A. (2006)
    2. 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)
    3. Decreased expression of V-set and immunoglobulin domai n containing 1 (VSIG1) is associated with poor prognosis in primary gastric canc er. (PubMed id 22095633)1 Chen Y....Li Q. (2012)
    4. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    5. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (2005)
    6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)

    External Searches for VSIG1 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 VSIG1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 340547 HGNC: 28675 AceView: VSIG1 Ensembl:ENSG00000101842 euGenes: HUgn340547
    ECgene: VSIG1 H-InvDB: VSIG1

    Other Databases showing VSIG1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing VSIG1 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 VSIG1 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for VSIG1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for VSIG1 gene:
    Search GeneIP for patents involving VSIG1

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



    Products
    for VSIG1 gene

    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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    About This Section

     
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