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

    Gene ID: 54621, updated on 28-Oct-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, Oct 2024]
    Expression
    Broad expression in small intestine (RPKM 12.6), colon (RPKM 8.8) and 24 other tissues See more
    Orthologs
    mouse all
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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 (10) 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)

    Genotypes

    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
    		  
    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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