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    ATP6V1G2-DDX39B ATP6V1G2-DDX39B readthrough (NMD candidate) [ Homo sapiens (human) ]

    Gene ID: 100532737, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ATP6V1G2-DDX39Bprovided by HGNC
    Official Full Name
    ATP6V1G2-DDX39B readthrough (NMD candidate)provided by HGNC
    Primary source
    HGNC:HGNC:41999
    See related
    Ensembl:ENSG00000254870 AllianceGenome:HGNC:41999
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This locus represents naturally occurring read-through transcription between the neighboring ATP6V1G2 (ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2) and DDX39B (DEAD box polypeptide 39B) genes located in the major histocompatibility complex class III region of chromosome 6. The read-through transcript and is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]
    Expression
    Ubiquitous expression in ovary (RPKM 72.1), endometrium (RPKM 72.1) and 25 other tissues See more
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    Genomic context

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    See ATP6V1G2-DDX39B in Genome Data Viewer
    Location:
    6p21.33
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31530219..31546848, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31383315..31399936, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31497996..31514625, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene peptidylprolyl isomerase A pseudogene 9 Neighboring gene ribosomal protein L15 pseudogene 4 Neighboring gene mitochondrial coiled-coil domain 1 Neighboring gene DExD-box helicase 39B Neighboring gene small nucleolar RNA, C/D box 117 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:31509210-31510409 Neighboring gene DDX39B antisense RNA 1 Neighboring gene small nucleolar RNA, C/D box 84 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:31513919-31514418 Neighboring gene ATPase H+ transporting V1 subunit G2 Neighboring gene NFKB inhibitor like 1 Neighboring gene uncharacterized LOC100287329 Neighboring gene lymphotoxin alpha

    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. The haplotype block, NFKBIL1-ATP6V1G2-BAT1-MICB-MICA, within the class III-class I boundary region of the human major histocompatibility complex may control susceptibility to hepatitis C virus-associated dilated cardiomyopathy. Shichi D, et al. Tissue Antigens, 2005 Sep. PMID 16101831
    2. Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatitis. Paternoster L, et al. Nat Genet, 2011 Dec 25. PMID 22197932, Free PMC Article
    3. A whole-genome association study of major determinants for allopurinol-related Stevens-Johnson syndrome and toxic epidermal necrolysis in Japanese patients. Tohkin M, et al. Pharmacogenomics J, 2013 Feb. PMID 21912425
    4. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. Prakash T, et al. PLoS One, 2010 Oct 12. PMID 20967262, Free PMC Article
    5. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. Choudhury NR, et al. BMC Biol, 2017 Nov 8. PMID 29117863, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A whole-genome association study of major determinants for allopurinol-related Stevens-Johnson syndrome and toxic epidermal necrolysis in Japanese patients.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatitis.
    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

    Other Names

    • ATP6V1G2-DDX39B readthrough (non-protein coding)

    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_037853.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL662801, BC004350
      Related
      ENST00000376185.5

    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
      31530219..31546848 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      2862768..2871733 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      3007552..3024174 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      2777992..2794614 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      2835292..2851897 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      2872162..2888783 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      2786081..2802700 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      2829503..2846132 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      31383315..31399936 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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