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

Gene ID: 100532737, updated on 8-Nov-2023

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_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31530219..31546848, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31383315..31399936, complement)
105.20220307 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)

Genotypes

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_2023_10

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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