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VSIG10 V-set and immunoglobulin domain containing 10 [ Homo sapiens (human) ]

Gene ID: 54621, updated on 14-Nov-2024

Summary

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Official Symbol
VSIG10provided by HGNC
Official Full Name
V-set and immunoglobulin domain containing 10provided by HGNC
Primary source
HGNC:HGNC:26078
See related
Ensembl:ENSG00000176834 AllianceGenome:HGNC:26078
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
Summary
Predicted to enable cell adhesion molecule binding activity. Predicted to be involved in cell-cell adhesion. Predicted to be located in membrane. Predicted to be active in cell-cell junction and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in small intestine (RPKM 12.6), colon (RPKM 8.8) and 24 other tissues See more
Orthologs
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Genomic context

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See VSIG10 in Genome Data Viewer
Location:
12q24.23
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (118063593..118104011, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (118050893..118091265, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (118501398..118541816, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene kinase suppressor of ras 2 Neighboring gene uncharacterized LOC105370011 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:118274024-118274569 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr12:118284773-118285290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:118312867-118313667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4919 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:118442171-118442363 Neighboring gene MPRA-validated peak1990 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24987 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7106 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:118489679-118490878 Neighboring gene uncharacterized LOC124903030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4921 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:118523172-118523714 Neighboring gene replication factor C subunit 5 Neighboring gene uncharacterized LOC124903029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4922 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:118543551-118544266 Neighboring gene WD repeat and SOCS box containing 2 Neighboring gene Sharpr-MPRA regulatory region 1292 Neighboring gene uncharacterized LOC101928274 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancers GRCh37_chr12:118557876-118558588 and GRCh37_chr12:118558589-118559300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:118560014-118560725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:118560726-118561438 Neighboring gene Sharpr-MPRA regulatory region 10186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:118564319-118564855 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:118573724-118574224 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4923 Neighboring gene phosphatidylethanolamine binding protein 1

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. Loss of ancestral N-glycosylation sites in conserved proteins during human evolution. Kim DS, et al. Int J Mol Med, 2015 Dec. PMID 26458842
  2. Genome-wide admixture and association analysis identifies African ancestry-specific risk loci of eosinophilic esophagitis in African Americans. Gautam Y, et al. J Allergy Clin Immunol, 2023 May. PMID 36400179, Free PMC Article
  3. TAOK3, a novel genome-wide association study locus associated with morphine requirement and postoperative pain in a retrospective pediatric day surgery population. Cook-Sather SD, et al. Pain, 2014 Sep. PMID 24909733, Free PMC Article
  4. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article
  5. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. Aregger M, et al. Nat Metab, 2020 Jun. PMID 32694731, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genome-wide admixture and association analysis identifies African ancestry-specific risk loci of eosinophilic esophagitis in African Americans.
    Title: Genome-wide admixture and association analysis identifies African ancestry-specific risk loci of eosinophilic esophagitis in African Americans.
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
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog
TAOK3, a novel genome-wide association study locus associated with morphine requirement and postoperative pain in a retrospective pediatric day surgery population.
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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC1013, FLJ20674

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cell adhesion molecule binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cell-cell junction IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in 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 10

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_019086.6 → NP_061959.2  V-set and immunoglobulin domain-containing protein 10 precursor

    See identical proteins and their annotated locations for NP_061959.2

    Status: VALIDATED

    Source sequence(s)
    AC026366, AC131238, BC034471, DA995625
    Consensus CDS
    CCDS44992.1
    UniProtKB/Swiss-Prot
    Q8N0Z9, Q9NWQ7
    Related
    ENSP00000352172.5, ENST00000359236.10
    Conserved Domains (4) summary
    cd00096
    Location:327 → 402
    Ig; Immunoglobulin domain
    smart00410
    Location:31 → 119
    IG_like; Immunoglobulin like
    pfam00047
    Location:136 → 208
    ig; Immunoglobulin domain
    pfam07686
    Location:29 → 119
    V-set; Immunoglobulin V-set domain

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    118063593..118104011 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006719467.3 → XP_006719530.1  V-set and immunoglobulin domain-containing protein 10 isoform X3

    Conserved Domains (3) summary
    cd00096
    Location:226 → 301
    Ig; Immunoglobulin domain
    smart00410
    Location:31 → 119
    IG_like; Immunoglobulin like
    pfam07686
    Location:29 → 119
    V-set; Immunoglobulin V-set domain

  2. XM_011538502.2 → XP_011536804.1  V-set and immunoglobulin domain-containing protein 10 isoform X1

    Conserved Domains (4) summary
    cd00096
    Location:327 → 402
    Ig; Immunoglobulin domain
    smart00410
    Location:31 → 119
    IG_like; Immunoglobulin like
    pfam00047
    Location:136 → 208
    ig; Immunoglobulin domain
    pfam07686
    Location:29 → 119
    V-set; Immunoglobulin V-set domain

  3. XM_005253908.5 → XP_005253965.1  V-set and immunoglobulin domain-containing protein 10 isoform X4

    Conserved Domains (2) summary
    cd00096
    Location:155 → 230
    Ig; Immunoglobulin domain
    smart00410
    Location:152 → 233
    IG_like; Immunoglobulin like

  4. XM_006719468.2 → XP_006719531.1  V-set and immunoglobulin domain-containing protein 10 isoform X5

    Conserved Domains (2) summary
    cd00096
    Location:94 → 169
    Ig; Immunoglobulin domain
    smart00410
    Location:91 → 172
    IG_like; Immunoglobulin like

  5. XM_047429032.1 → XP_047284988.1  V-set and immunoglobulin domain-containing protein 10 isoform X2

RNA

  1. XR_002957343.2 RNA Sequence

  2. XR_002957342.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    118050893..118091265 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372347.1 → XP_054228322.1  V-set and immunoglobulin domain-containing protein 10 isoform X3

  2. XM_054372345.1 → XP_054228320.1  V-set and immunoglobulin domain-containing protein 10 isoform X1

  3. XM_054372348.1 → XP_054228323.1  V-set and immunoglobulin domain-containing protein 10 isoform X4

  4. XM_054372349.1 → XP_054228324.1  V-set and immunoglobulin domain-containing protein 10 isoform X5

  5. XM_054372346.1 → XP_054228321.1  V-set and immunoglobulin domain-containing protein 10 isoform X2

RNA

  1. XR_008488623.1 RNA Sequence

  2. XR_008488625.1 RNA Sequence

  3. XR_008488624.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N0Z9.1 GenPept UniProtKB/Swiss-Prot:Q8N0Z9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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