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    VNN3P vanin 3, pseudogene [ Homo sapiens (human) ]

    Gene ID: 55350, updated on 28-Oct-2024

    Summary

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    Official Symbol
    VNN3Pprovided by HGNC
    Official Full Name
    vanin 3, pseudogeneprovided by HGNC
    Primary source
    HGNC:HGNC:16431
    See related
    Ensembl:ENSG00000293493 MIM:606592; AllianceGenome:HGNC:16431
    Gene type
    pseudo
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    VNN3; HSA238982
    Summary
    This gene is the central gene in a cluster of three vanin genes on chromosome 6q23-q24. Extensive alternative splicing has been described; the two most common variants are represented as RefSeqs. [provided by RefSeq, Apr 2014]
    Expression
    Biased expression in bone marrow (RPKM 15.1), liver (RPKM 10.5) and 5 other tissues See more
    Orthologs
    all
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    Genomic context

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    See VNN3P in Genome Data Viewer
    Location:
    6q23.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (132722787..132734765, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (133917754..133929732, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (133043926..133055904, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:133004442-133005641 Neighboring gene HLF pseudogene 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_89871 Neighboring gene vanin 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_89876 Neighboring gene cyclin G1 pseudogene 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:133069914-133071113 Neighboring gene vanin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25074 Neighboring gene RNA binding motif protein 11 pseudogene 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. Pharmacologic concentrations of ascorbic acid cause diverse influence on differential expressions of angiogenic chemokine genes in different hepatocellular carcinoma cell lines. Lin ZY, et al. Biomed Pharmacother, 2010 May. PMID 19932582
    2. Expression of the vanin gene family in normal and inflamed human skin: induction by proinflammatory cytokines. Jansen PA, et al. J Invest Dermatol, 2009 Sep. PMID 19322213
    3. Alternative spliced variants in the pantetheinase family of genes expressed in human neutrophils. Nitto T, et al. Gene, 2008 Dec 15. PMID 18805469
    4. Screening genes associated with elevated neutrophil‑to‑lymphocyte ratio in chronic heart failure. Wan G, et al. Mol Med Rep, 2018 Aug. PMID 29901123, Free PMC Article
    5. An ESTs description of the new Vanin gene family conserved from fly to human. Granjeaud S, et al. Immunogenetics, 1999 Oct. PMID 10501839

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The expression of SLC22A4, IL1R2 and VNN3, were independently associated with elevated neutrophil-to-lymphocyte ratio in chronic heart failure patients.
      Title: Screening genes associated with elevated neutrophil‑to‑lymphocyte ratio in chronic heart failure.
    2. vanin-1 and vanin-3 are induced at the mRNA and protein level by psoriasis-associated proinflammatory cytokines (Th17/Th1) but not by Th2 cytokines.
      Title: Expression of the vanin gene family in normal and inflamed human skin: induction by proinflammatory cytokines.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    Other Names

    • pantetheinase pseudogene
    • pantetheinase-associated gene expressed in leukocytes (PAGEL)-alpha
    • vanin 1 pseudogene
    • vascular non-inflammatory molecule 3

    Clone Names

    • MGC171203

    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.

    RNA

    1. NR_173391.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL032821
      Related
      ENST00000425515.7

    2. NR_173392.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL032821
      Related
      ENST00000423615.7

    3. NR_173393.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL032821
      Related
      ENST00000414302.7

    4. NR_173394.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL032821
      Related
      ENST00000819055.1

    5. NR_173395.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL032821
      Related
      ENST00000519686.6

    6. NR_173396.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL032821
      Related
      ENST00000427187.7

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      132722787..132734765 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      133917754..133929732 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001291702.2: Suppressed sequence

      Description
      NM_001291702.2: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    2. NM_001291703.2: Suppressed sequence

      Description
      NM_001291703.2: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    3. NM_001368149.1: Suppressed sequence

      Description
      NM_001368149.1: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    4. NM_001368150.1: Suppressed sequence

      Description
      NM_001368150.1: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    5. NM_001368151.1: Suppressed sequence

      Description
      NM_001368151.1: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    6. NM_001368152.1: Suppressed sequence

      Description
      NM_001368152.1: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    7. NM_001368154.1: Suppressed sequence

      Description
      NM_001368154.1: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    8. NM_001368155.1: Suppressed sequence

      Description
      NM_001368155.1: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    9. NM_001368156.1: Suppressed sequence

      Description
      NM_001368156.1: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    10. NM_018399.3: Suppressed sequence

      Description
      NM_018399.3: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.

    11. NM_078625.2: Suppressed sequence

      Description
      NM_078625.2: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.
    Nucleotide Protein
    Heading Accession and Version

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