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

Gene ID: 340547, updated on 2-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
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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 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)

Genotypes

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

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