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    VSTM2B V-set and transmembrane domain containing 2B [ Homo sapiens (human) ]

    Gene ID: 342865, updated on 27-Nov-2024

    Summary

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    Official Symbol
    VSTM2Bprovided by HGNC
    Official Full Name
    V-set and transmembrane domain containing 2Bprovided by HGNC
    Primary source
    HGNC:HGNC:33595
    See related
    Ensembl:ENSG00000187135 AllianceGenome:HGNC:33595
    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 be active in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward brain (RPKM 9.7) See more
    Orthologs
    mouse all
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    Genomic context

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    See VSTM2B in Genome Data Viewer
    Location:
    19q12
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (29525418..29564551)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (32051016..32090146)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (30016325..30055458)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14405 Neighboring gene UQCRFS1 divergent transcript Neighboring gene RNA, 7SL, cytoplasmic 340, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr19:29763000-29763195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14406 Neighboring gene VSTM2B divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29799690-29800520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29802083-29802584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29802585-29803084 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29814030-29814530 Neighboring gene MPRA-validated peak3428 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29862474-29863068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29863069-29863661 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50790 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50793 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29895755-29896381 Neighboring gene Sharpr-MPRA regulatory region 9443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29908074-29908807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:29910274-29911005 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50884 Neighboring gene uncharacterized LOC124904683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30025281-30025781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30030190-30030690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30030691-30031191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30053547-30054047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30055952-30056800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:30059413-30059913 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:30087367-30087867 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:30086866-30087366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:30100801-30101312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14409 Neighboring gene Sharpr-MPRA regulatory region 12961 Neighboring gene uncharacterized LOC105372353 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:30156127-30156680 Neighboring gene POP4 homolog, ribonuclease P/MRP subunit

    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. Genome-wide meta-analysis for severe diabetic retinopathy. Grassi MA, et al. Hum Mol Genet, 2011 Jun 15. PMID 21441570, Free PMC Article
    2. Genetic variants associated with disordered eating. Wade TD, et al. Int J Eat Disord, 2013 Sep. PMID 23568457, Free PMC Article
    3. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Trynka G, et al. Gut, 2009 Aug. PMID 19240061
    4. The DNA sequence and biology of human chromosome 19. Grimwood J, et al. Nature, 2004 Apr 1. PMID 15057824
    5. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Fasci D, et al. Mol Cell Proteomics, 2018 Oct. PMID 30021884, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    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
    Genetic variants associated with disordered eating.
    EBI GWAS Catalog
    Genome-wide meta-analysis for severe diabetic retinopathy.
    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

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    V-set and transmembrane domain-containing protein 2B

    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_001146339.2 → NP_001139811.1  V-set and transmembrane domain-containing protein 2B isoform 1 precursor

      See identical proteins and their annotated locations for NP_001139811.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC011474
      Consensus CDS
      CCDS46034.1
      UniProtKB/Swiss-Prot
      A6NLU5
      Related
      ENSP00000335038.6, ENST00000335523.8
      Conserved Domains (2) summary
      smart00410
      Location:34 → 139
      IG_like; Immunoglobulin like
      cl11960
      Location:32 → 138
      Ig; Immunoglobulin domain

    2. NM_001384640.1 → NP_001371569.1  V-set and transmembrane domain-containing protein 2B isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AC011474
      Conserved Domains (2) summary
      smart00410
      Location:34 → 129
      IG_like; Immunoglobulin like
      cd00096
      Location:29 → 33
      Ig; Ig strand A [structural motif]

    3. NM_001384641.1 → NP_001371570.1  V-set and transmembrane domain-containing protein 2B isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC011474
      Conserved Domains (2) summary
      cd00096
      Location:29 → 34
      Ig; Ig strand C' [structural motif]
      cl11960
      Location:20 → 92
      Ig; Immunoglobulin domain

    4. NM_001384642.1 → NP_001371571.1  V-set and transmembrane domain-containing protein 2B isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC011474
      Conserved Domains (2) summary
      cd00096
      Location:16 → 23
      Ig; Ig strand C [structural motif]
      cl11960
      Location:16 → 78
      Ig; Immunoglobulin domain

    5. NM_001384643.1 → NP_001371572.1  V-set and transmembrane domain-containing protein 2B isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC011474
      Conserved Domains (1) summary
      smart00409
      Location:8 → 51
      IG; Immunoglobulin

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      29525418..29564551
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011526902.3 → XP_011525204.1  V-set and transmembrane domain-containing protein 2B isoform X1

      See identical proteins and their annotated locations for XP_011525204.1

      UniProtKB/Swiss-Prot
      A6NLU5
      Conserved Domains (2) summary
      smart00410
      Location:34 → 139
      IG_like; Immunoglobulin like
      cl11960
      Location:32 → 138
      Ig; Immunoglobulin domain

    2. XM_011526903.3 → XP_011525205.1  V-set and transmembrane domain-containing protein 2B isoform X2

      Conserved Domains (2) summary
      smart00410
      Location:34 → 129
      IG_like; Immunoglobulin like
      cd00096
      Location:29 → 33
      Ig; Ig strand A [structural motif]

    3. XM_011526905.3 → XP_011525207.1  V-set and transmembrane domain-containing protein 2B isoform X3

      Conserved Domains (1) summary
      smart00410
      Location:37 → 75
      IG_like; Immunoglobulin like

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      32051016..32090146
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320837.1 → XP_054176812.1  V-set and transmembrane domain-containing protein 2B isoform X1

      UniProtKB/Swiss-Prot
      A6NLU5

    2. XM_054320838.1 → XP_054176813.1  V-set and transmembrane domain-containing protein 2B isoform X2

    3. XM_054320839.1 → XP_054176814.1  V-set and transmembrane domain-containing protein 2B isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6NLU5.2 GenPept UniProtKB/Swiss-Prot:A6NLU5

    Gene LinkOut

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

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