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VSIG2 V-set and immunoglobulin domain containing 2 [ Homo sapiens (human) ]

Gene ID: 23584, updated on 10-Oct-2023

Summary

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Official Symbol
VSIG2provided by HGNC
Official Full Name
V-set and immunoglobulin domain containing 2provided by HGNC
Primary source
HGNC:HGNC:17149
See related
Ensembl:ENSG00000019102 MIM:606011; AllianceGenome:HGNC:17149
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CTH; CTXL; 2210413P10Rik
Summary
Predicted to be located in membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in stomach (RPKM 210.7), colon (RPKM 56.0) and 6 other tissues See more
Orthologs
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Genomic context

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See VSIG2 in Genome Data Viewer
Location:
11q24.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (124747474..124752255, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (124776137..124780919, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (124617370..124622151, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4025 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:124615273-124615806 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:124616341-124616874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4027 Neighboring gene neurogranin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:124621349-124621910 Neighboring gene Sharpr-MPRA regulatory region 10895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:124631741-124632244 Neighboring gene endothelial cell adhesion molecule Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4029 Neighboring gene ESAM antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 2909 Neighboring gene Myb/SANT DNA binding domain containing 2 Neighboring gene NANOG hESC enhancer GRCh37_chr11:124663166-124663667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4031 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:124669881-124670488

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. CTX, a Xenopus thymocyte receptor, defines a molecular family conserved throughout vertebrates. Chrétien I, et al. Eur J Immunol, 1998 Dec. PMID 9862345
  2. Trait-stratified genome-wide association study identifies novel and diverse genetic associations with serologic and cytokine phenotypes in systemic lupus erythematosus. Kariuki SN, et al. Arthritis Res Ther, 2010. PMID 20659327, Free PMC Article
  3. Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins. Macaulay IC, et al. Blood, 2007 Apr 15. PMID 17192395, Free PMC Article
  4. Signal peptide prediction based on analysis of experimentally verified cleavage sites. Zhang Z, et al. Protein Sci, 2004 Oct. PMID 15340161, Free PMC Article
  5. Biological insights from 108 schizophrenia-associated genetic loci. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Nature, 2014 Jul 24. PMID 25056061, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. VSIG2 promotes malignant progression of pancreatic ductal adenocarcinoma by enhancing LAMTOR2-mediated mTOR activation.
    Title: VSIG2 promotes malignant progression of pancreatic ductal adenocarcinoma by enhancing LAMTOR2-mediated mTOR activation.
  2. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Trait-stratified genome-wide association study identifies novel and diverse genetic associations with serologic and cytokine phenotypes in systemic lupus erythematosus.
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

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog

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

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in lipid metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
V-set and immunoglobulin domain-containing protein 2
Names
CT-like protein
cortical thymocyte receptor (X. laevis CTX) like
cortical thymocyte-like protein

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.

mRNA and Protein(s)

  1. NM_001329920.2 → NP_001316849.1  V-set and immunoglobulin domain-containing protein 2 isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the C-terminus compared to isoform 1.
    Source sequence(s)
    AK000460, BC012567
    Consensus CDS
    CCDS86258.1
    UniProtKB/Swiss-Prot
    Q96IQ7
    Related
    ENSP00000385013.1, ENST00000403470.1

  2. NM_014312.5 → NP_055127.2  V-set and immunoglobulin domain-containing protein 2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_055127.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    BC007313, BC012567
    Consensus CDS
    CCDS8452.1
    UniProtKB/Swiss-Prot
    O95791, Q96IQ7, Q9NX42
    Related
    ENSP00000318684.5, ENST00000326621.10
    Conserved Domains (2) summary
    pfam07686
    Location:31 → 142
    V-set; Immunoglobulin V-set domain
    cd00096
    Location:164 → 231
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    124747474..124752255 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426685.1 → XP_047282641.1  V-set and immunoglobulin domain-containing protein 2 isoform X2

  2. XM_047426684.1 → XP_047282640.1  V-set and immunoglobulin domain-containing protein 2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    124776137..124780919 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054368251.1 → XP_054224226.1  V-set and immunoglobulin domain-containing protein 2 isoform X2

  2. XM_054368250.1 → XP_054224225.1  V-set and immunoglobulin domain-containing protein 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96IQ7.1 GenPept UniProtKB/Swiss-Prot:Q96IQ7

Gene LinkOut

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