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

Gene ID: 11326, updated on 15-Apr-2019

Summary

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
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

Genomic context

See VSIG4 in Genome Data Viewer
Location:
Xq12
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (66021738..66040125, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (65241580..65259967, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein X-linked pseudogene Neighboring gene microRNA 223 Neighboring gene ataxin 7 like 3 pseudogene Neighboring gene eukaryotic translation initiation factor 4B pseudogene 9

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 BioSystems

  • Complement and coagulation cascades, organism-specific biosystem (from KEGG)
    Complement and coagulation cascades, organism-specific biosystemThe complement system is a proteolytic cascade in blood plasma and a mediator of innate immunity, a nonspecific defense mechanism against pathogens. There are three pathways of complement activation:...
  • Complement and coagulation cascades, conserved biosystem (from KEGG)
    Complement and coagulation cascades, conserved biosystemThe complement system is a proteolytic cascade in blood plasma and a mediator of innate immunity, a nonspecific defense mechanism against pathogens. There are three pathways of complement activation:...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

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)

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
    5001..23388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001100431.1NP_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:26116
    IG_like; Immunoglobulin like
    cl11960
    Location:35136
    Ig; Immunoglobulin domain
  2. NM_001184830.1NP_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/Swiss-Prot
    Q9Y279
    Related
    ENSP00000411581.2, ENST00000455586.6
    Conserved Domains (3) summary
    cd00096
    Location:161223
    Ig; Immunoglobulin domain
    smart00410
    Location:154223
    IG_like; Immunoglobulin like
    cl11960
    Location:35136
    Ig; Immunoglobulin domain
  3. NM_001184831.1NP_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:26116
    IG_like; Immunoglobulin like
    cl11960
    Location:35136
    Ig; Immunoglobulin domain
  4. NM_001257403.1NP_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, BX482258
    UniProtKB/Swiss-Prot
    Q9Y279
    Conserved Domains (3) summary
    cd00096
    Location:161223
    Ig; Immunoglobulin domain
    smart00410
    Location:154223
    IG_like; Immunoglobulin like
    cl11960
    Location:35136
    Ig; Immunoglobulin domain
  5. NM_007268.3NP_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
    Q9Y279
    Related
    ENSP00000363869.4, ENST00000374737.9
    Conserved Domains (2) summary
    cd16082
    Location:146231
    IgC_CRIg; Immunoglobulin (Ig) constant domain in complement receptor of the immunoglobulin superfamily (CRIg)
    cd16089
    Location:26137
    IgV_CRIg; Immunoglobulin variable (IgV)-like domain in complement receptor of the immunoglobulin superfamily (CRIg)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p12 Primary Assembly

    Range
    66021738..66040125 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029251.2XP_016884740.1  V-set and immunoglobulin domain-containing protein 4 isoform X1

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