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

Gene ID: 55350, updated on 2-Nov-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)

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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