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VSIG4 V-set and immunoglobulin domain containing 4 [ Homo sapiens (human) ]

Gene ID: 11326, updated on 27-Nov-2024

Summary

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Official Symbol
VSIG4provided by HGNC
Official Full Name
V-set and immunoglobulin domain containing 4provided by HGNC
Primary source
HGNC:HGNC:17032
See related
Ensembl:ENSG00000155659 MIM:300353; AllianceGenome:HGNC:17032
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
CRIg; Z39IG
Summary
This gene encodes a v-set and immunoglobulin-domain containing protein that is structurally related to the B7 family of immune regulatory proteins. The encoded protein may be a negative regulator of T-cell responses. This protein is also a receptor for the complement component 3 fragments C3b and iC3b. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
Expression
Broad expression in placenta (RPKM 50.4), lung (RPKM 39.9) and 19 other tissues See more
Orthologs
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Genomic context

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See VSIG4 in Genome Data Viewer
Location:
Xq12
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (66021738..66040080, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (64448234..64467291, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (65241580..65259922, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene RBMX pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:65190667-65191168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:65191169-65191668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29719 Neighboring gene Sharpr-MPRA regulatory region 12317 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29720 Neighboring gene MIR223 host gene Neighboring gene microRNA 223 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:65252367-65253566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29721 Neighboring gene ATXN7L3 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 4431 Neighboring gene eukaryotic translation initiation factor 4B pseudogene 9

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. VSIG4 ameliorates intestinal inflammation through inhibiting macrophages NLRP3 inflammasome and pyroptosis. Liao Y, et al. Tissue Cell, 2024 Feb. PMID 38113649
  2. Cloning of Z39Ig, a novel gene with immunoglobulin-like domains located on human chromosome X. Langnaese K, et al. Biochim Biophys Acta, 2000 Jul 24. PMID 11004523
  3. Z39Ig is co-expressed with activated macrophage genes. Walker MG. Biochim Biophys Acta, 2002 Apr 12. PMID 11997108
  4. Characterization of monoclonal antibody specific to the Z39Ig protein, a member of immunoglobulin superfamily. Kim JK, et al. Immunol Lett, 2005 Jul 15. PMID 16009265
  5. Z39Ig is expressed on macrophages and may mediate inflammatory reactions in arthritis and atherosclerosis. Lee MY, et al. J Leukoc Biol, 2006 Oct. PMID 16882875

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The immunomodulatory role of paracrine signalling factor VSIG4 in peritoneal metastases.
    Title: The immunomodulatory role of paracrine signalling factor VSIG4 in peritoneal metastases.
  2. VSIG4 ameliorates intestinal inflammation through inhibiting macrophages NLRP3 inflammasome and pyroptosis.
    Title: VSIG4 ameliorates intestinal inflammation through inhibiting macrophages NLRP3 inflammasome and pyroptosis.
  3. V-Set Immunoglobulin Domain-Containing Protein 4 as a Novel Serum Biomarker of Lupus Nephritis and Renal Pathology Activity.
    Title: V-Set Immunoglobulin Domain-Containing Protein 4 as a Novel Serum Biomarker of Lupus Nephritis and Renal Pathology Activity.
  4. CRIg on liver macrophages clears pathobionts and protects against alcoholic liver disease.
    Title: CRIg on liver macrophages clears pathobionts and protects against alcoholic liver disease.
  5. Rab18 interacted with V-set and immunoglobulin domain-containing 4 (VSIG4) to involve in the apoptosis of glioma and the sensitivity to temozolomide.
    Title: Rab18 interacted with V-set and immunoglobulin domain-containing 4 (VSIG4) to involve in the apoptosis of glioma and the sensitivity to temozolomide.
  6. Impact of VSIG4 gene polymorphisms on susceptibility and functional status of rheumatoid arthritis.
    Title: Impact of VSIG4 gene polymorphisms on susceptibility and functional status of rheumatoid arthritis.
  7. The results indicated that Vsig4 expression was markedly down-regulated in fatty livers of nonalcoholic fatty liver disease patients and obese mice.
    Title: Expression of Vsig4 attenuates macrophage-mediated hepatic inflammation and fibrosis in high fat diet (HFD)-induced mice.
  8. this study shows that CRIg/FH ameliorates renal ischemia reperfusion injury via activation of PI3K/AKT signaling
    Title: Complement Inhibitor CRIg/FH Ameliorates Renal Ischemia Reperfusion Injury via Activation of PI3K/AKT Signaling.
  9. CRIg is a novel interacting partner of TRIM72 in the lung.
    Title: Inhibition of Macrophage Complement Receptor CRIg by TRIM72 Polarizes Innate Immunity of the Lung.
  10. Soluble VSIG4 levels are associated with the progression and recurrence of ovarian cancer, indicating that soluble VSIG4 may be used as a potential biomarker for predicting tumor prognosis.
    Title: The Significance of VSIG4 Expression in Ovarian Cancer.
Submit: New GeneRIF Correction See all GeneRIFs (25)

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)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 downregulates the expression of V-set and immunoglobulin domain containing 4 (VSIG4) in peptide-treated PBMCs PubMed
Nef nef The yeast two-hybrid screen identifies the HIV-1 Nef interacting human protein V-set and immunoglobulin domain containing 4 (VSIG4) in cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables complement component C3b binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables complement component C3b binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in complement activation, alternative pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of T cell proliferation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of complement activation, alternative pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of complement activation, alternative pathway IPI
Inferred from Physical Interaction
more info
 PubMed 
involved_in negative regulation of interleukin-2 production IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of macrophage activation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
part_of protein-containing complex IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
V-set and immunoglobulin domain-containing protein 4
Names
Ig superfamily protein
complement receptor of the immunoglobulin superfamily
protein Z39Ig

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_021306.1 RefSeqGene

    Range
    5046..23388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001100431.2 → NP_001093901.1  V-set and immunoglobulin domain-containing protein 4 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001093901.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as CRIg(S), lacks an alternate in-frame segment compared to variant 1, resulting in a shorter isoform (2), compared to isoform 1.
    Source sequence(s)
    AL552873, BX482258, CA310184, CA405669
    Consensus CDS
    CCDS48132.1
    UniProtKB/Swiss-Prot
    Q9Y279
    Related
    ENSP00000394143.2, ENST00000412866.2
    Conserved Domains (2) summary
    smart00410
    Location:26 → 116
    IG_like; Immunoglobulin like
    cl11960
    Location:35 → 136
    Ig; Immunoglobulin domain

  2. NM_001184830.2 → NP_001171759.1  V-set and immunoglobulin domain-containing protein 4 isoform 4 precursor

    See identical proteins and their annotated locations for NP_001171759.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' UTR and 3' coding region, compared to variant 1. The encoded isoform (4) has a shorter C-terminus, compared to isoform 4.
    Source sequence(s)
    AJ132502, AY358341, BX482258
    Consensus CDS
    CCDS55435.1
    UniProtKB/TrEMBL
    A0A494C0F5
    Related
    ENSP00000411581.2, ENST00000455586.6
    Conserved Domains (3) summary
    cd00096
    Location:161 → 223
    Ig; Immunoglobulin domain
    smart00410
    Location:154 → 223
    IG_like; Immunoglobulin like
    cl11960
    Location:35 → 136
    Ig; Immunoglobulin domain

  3. NM_001184831.2 → NP_001171760.1  V-set and immunoglobulin domain-containing protein 4 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AJ132502, AK298389, AY358341, BX482258
    UniProtKB/Swiss-Prot
    Q9Y279
    Conserved Domains (2) summary
    smart00410
    Location:26 → 116
    IG_like; Immunoglobulin like
    cl11960
    Location:35 → 136
    Ig; Immunoglobulin domain

  4. NM_001257403.2 → NP_001244332.1  V-set and immunoglobulin domain-containing protein 4 isoform 5 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice junction at the 5' end of a coding exon compared to variant 1. The resulting isoform (5) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AJ132502, AL542949, AL553835
    UniProtKB/TrEMBL
    A0A494C0F5
    Conserved Domains (3) summary
    cd00096
    Location:161 → 223
    Ig; Immunoglobulin domain
    smart00410
    Location:154 → 223
    IG_like; Immunoglobulin like
    cl11960
    Location:35 → 136
    Ig; Immunoglobulin domain

  5. NM_007268.3 → NP_009199.1  V-set and immunoglobulin domain-containing protein 4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_009199.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is also called CRIg(L). It encodes the longest isoform (1).
    Source sequence(s)
    AJ132502, BP292528, BX482258
    Consensus CDS
    CCDS14383.1
    UniProtKB/Swiss-Prot
    Q6UXI4, Q9Y279
    Related
    ENSP00000363869.4, ENST00000374737.9
    Conserved Domains (2) summary
    cd16082
    Location:146 → 231
    IgC_CRIg; Immunoglobulin (Ig) constant domain in complement receptor of the immunoglobulin superfamily (CRIg)
    cd16089
    Location:26 → 137
    IgV_CRIg; Immunoglobulin variable (IgV)-like domain in complement receptor of the immunoglobulin superfamily (CRIg)

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
    66021738..66040080 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    64448234..64467291 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y279.1 GenPept UniProtKB/Swiss-Prot:Q9Y279

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