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    VSIG1 V-set and immunoglobulin domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 340547, updated on 27-Nov-2024

    Summary

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    Official Symbol
    VSIG1provided by HGNC
    Official Full Name
    V-set and immunoglobulin domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:28675
    See related
    Ensembl:ENSG00000101842 MIM:300620; AllianceGenome:HGNC:28675
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GPA34; dJ889N15.1; 1700062D20Rik
    Summary
    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]
    Expression
    Biased expression in stomach (RPKM 88.2), testis (RPKM 34.6) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See VSIG1 in Genome Data Viewer
    Location:
    Xq22.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (108018879..108079184)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (106456465..106516780)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (107288295..107322414)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107192029-107192530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107192531-107193030 Neighboring gene TMEM230 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:107203211-107203710 Neighboring gene NACHT, LRR and PYD domains-containing protein 10-like Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:107234349-107235548 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:107239283-107239988 Neighboring gene NLR family pyrin domain containing 3 pseudogene 1 Neighboring gene testis expressed 13B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29839 Neighboring gene proteasome 26S subunit, non-ATPase 10 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:107370111-107370674 Neighboring gene autophagy related 4A cysteine peptidase Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107399852-107400352 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:107419738-107420424 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107420425-107421109 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107421110-107421795 Neighboring gene collagen type IV alpha 6 chain Neighboring gene uncharacterized LOC124905205

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. V-set and immunoglobulin domain containing 1 (VSIG1) as an emerging target for epithelial-mesenchymal transition of gastric cancer. Satala CB, et al. Sci Rep, 2022 Sep 28. PMID 36171238, Free PMC Article
    2. Characterization of V-set and immunoglobulin domain containing 1 exerting a tumor suppressor function in gastric, lung, and esophageal cancer cells. Inoue Y, et al. Cancer Sci, 2017 Aug. PMID 28603843, Free PMC Article
    3. Decreased expression of V-set and immunoglobulin domain containing 1 (VSIG1) is associated with poor prognosis in primary gastric cancer. Chen Y, et al. J Surg Oncol, 2012 Sep 1. PMID 22095633
    4. Glycoprotein A34, a novel target for antibody-based cancer immunotherapy. Scanlan MJ, et al. Cancer Immun, 2006 Jan 12. PMID 16405301
    5. Interaction between cadherins, vimentin, and V-set and immunoglobulin domain containing 1 in gastric-type hepatocellular carcinoma. Gurzu S, et al. Histochem Cell Biol, 2021 Oct. PMID 34170400

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. V-set and immunoglobulin domain containing 1 (VSIG1) as an emerging target for epithelial-mesenchymal transition of gastric cancer.
      Title: V-set and immunoglobulin domain containing 1 (VSIG1) as an emerging target for epithelial-mesenchymal transition of gastric cancer.
    2. Interaction between cadherins, vimentin, and V-set and immunoglobulin domain containing 1 in gastric-type hepatocellular carcinoma.
      Title: Interaction between cadherins, vimentin, and V-set and immunoglobulin domain containing 1 in gastric-type hepatocellular carcinoma.
    3. Study showed that VSIG1 is expressed tissue specifically in both non-cancerous and cancerous tissues, and that VSIG1 has suppressive functions in proliferation, migration, and invasion in cancer cells.
      Title: Characterization of V-set and immunoglobulin domain containing 1 exerting a tumor suppressor function in gastric, lung, and esophageal cancer cells.
    4. VSIG1 expression was significantly reduced at both the mRNA and protein levels in gastric cancer tissues. loss of VSIG1 expression was significantly correlated with poor overall survival and disease-free survival in gastric cancer patients.
      Title: Decreased expression of V-set and immunoglobulin domain containing 1 (VSIG1) is associated with poor prognosis in primary gastric cancer.
    5. expressed, both at the mRNA and protein level, in gastric, esophageal, and ovarian cancers, while expression in normal tissues was restricted to testis and stomach
      Title: Glycoprotein A34, a novel target for antibody-based cancer immunotherapy.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC44287

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in epithelial cell morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in maintenance of gastrointestinal epithelium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in basolateral plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    V-set and immunoglobulin domain-containing protein 1
    Names
    cell surface A33 antigen
    glycoprotein A34

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_016264.2 RefSeqGene

      Range
      31188..65307
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001170553.2 → NP_001164024.1  V-set and immunoglobulin domain-containing protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001164024.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK301311, AL031177, BX648658
      Consensus CDS
      CCDS55474.1
      UniProtKB/TrEMBL
      A8K8V7
      Related
      ENSP00000402219.3, ENST00000415430.7
      Conserved Domains (3) summary
      cd00096
      Location:193 → 260
      Ig; Immunoglobulin domain
      smart00410
      Location:190 → 263
      IG_like; Immunoglobulin like
      cl11960
      Location:28 → 163
      Ig; Immunoglobulin domain

    2. NM_182607.5 → NP_872413.1  V-set and immunoglobulin domain-containing protein 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_872413.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame coding exon, as compared to variant 1. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      AL031177, BX648658
      Consensus CDS
      CCDS14535.1
      UniProtKB/Swiss-Prot
      C9J4P2, Q6MZS4, Q86XK7
      UniProtKB/TrEMBL
      A8K8V7
      Related
      ENSP00000217957.3, ENST00000217957.10
      Conserved Domains (3) summary
      pfam13927
      Location:142 → 215
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 127
      Ig; Immunoglobulin domain
      cl25865
      Location:275 → 342
      Trypan_PARP; Procyclic acidic repetitive protein (PARP)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      108018879..108079184
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011530936.3 → XP_011529238.1  V-set and immunoglobulin domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A8K8V7
      Conserved Domains (3) summary
      cd00096
      Location:212 → 279
      Ig; Immunoglobulin domain
      smart00410
      Location:209 → 282
      IG_like; Immunoglobulin like
      cl11960
      Location:90 → 182
      Ig; Immunoglobulin domain

    2. XM_047442073.1 → XP_047298029.1  V-set and immunoglobulin domain-containing protein 1 isoform X4

    3. XM_005262127.5 → XP_005262184.1  V-set and immunoglobulin domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A8K8V7
      Conserved Domains (3) summary
      cd00096
      Location:219 → 286
      Ig; Immunoglobulin domain
      smart00410
      Location:216 → 289
      IG_like; Immunoglobulin like
      cl11960
      Location:97 → 189
      Ig; Immunoglobulin domain

    4. XM_047442072.1 → XP_047298028.1  V-set and immunoglobulin domain-containing protein 1 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      106456465..106516780
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326974.1 → XP_054182949.1  V-set and immunoglobulin domain-containing protein 1 isoform X4

    2. XM_054326972.1 → XP_054182947.1  V-set and immunoglobulin domain-containing protein 1 isoform X1

    3. XM_054326973.1 → XP_054182948.1  V-set and immunoglobulin domain-containing protein 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86XK7.1 GenPept UniProtKB/Swiss-Prot:Q86XK7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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