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

Summary

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: mouse all
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Genomic context

Location:: 11q24.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (124747474..124752255, complement)
110	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_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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 EBI GWAS CatalogPubMed

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

STS-R69114 (e-PCR)
- UniSTS:19984

WI-16853 (e-PCR)
- UniSTS:45413

RH18180 (e-PCR)
- UniSTS:25983

Homology

Homologs of the VSIG2 gene: The VSIG2 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, and frog.
Orthologs from Annotation Pipeline: 216 organisms have orthologs with human gene VSIG2
Orthologs

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)

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
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

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: Homo sapiens Annotation Release 110 details...

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

124747474..124752255 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047426685.1 → XP_047282641.1 V-set and immunoglobulin domain-containing protein 2 isoform X2
XM_047426684.1 → XP_047282640.1 V-set and immunoglobulin domain-containing protein 2 isoform X1