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    HLA-J major histocompatibility complex, class I, J (pseudogene) [ Homo sapiens (human) ]

    Gene ID: 3137, updated on 17-Sep-2024

    Summary

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    Official Symbol
    HLA-Jprovided by HGNC
    Official Full Name
    major histocompatibility complex, class I, J (pseudogene)provided by HGNC
    Primary source
    HGNC:HGNC:4967
    See related
    Ensembl:ENSG00000290574 AllianceGenome:HGNC:4967
    Gene type
    pseudo
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CDA12; D6S203; HLA-59; HLA-CDA12
    Summary
    This major histocompatibility complex gene represents a transcribed pseudogene, possibly derived from HLA-A. [provided by RefSeq, May 2010]
    Expression
    Broad expression in spleen (RPKM 1.8), duodenum (RPKM 1.6) and 24 other tissues See more
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    Genomic context

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    See HLA-J in Genome Data Viewer
    Location:
    6p22.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30005971..30009956)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (29869861..29873846)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (29973748..29977733)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene HLA complex group 26 (non-protein coding) pseudogene Neighboring gene POLR1H antisense, pseudogene Neighboring gene HLA complex group 4 pseudogene 3 Neighboring gene eukaryotic translation termination factor 1 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30028069-30028935 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30028936-30029801 Neighboring gene RNA polymerase I subunit H Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 11

    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. Validation of new HLA-J alleles assigned by next generation sequencing. Paganini J, et al. HLA, 2021 Aug. PMID 33914413
    2. A physical map including a new class I gene (cda12) of the human major histocompatibility complex (A2/B13 haplotype) derived from a monosomy 6 mutant cell line. Ragoussis J, et al. Genomics, 1989 Apr. PMID 2497062
    3. HLA-J, a second inactivated class I HLA gene related to HLA-G and HLA-A. Implications for the evolution of the HLA-A-related genes. Messer G, et al. J Immunol, 1992 Jun 15. PMID 1602142
    4. Paradoxical downregulation of HLA-A expression by IFNγ associated with schizophrenia and noncoding genes. Gu S, et al. Immunobiology, 2013 May. PMID 23083632
    5. Identification of independent risk loci for Graves' disease within the MHC in the Japanese population. Nakabayashi K, et al. J Hum Genet, 2011 Nov. PMID 21900946

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The downregulated expression of HLA-A9 and HLA-A10 by IFN-gamma in schizophrenic patients homozygous for HLA-J M80469.
      Title: Paradoxical downregulation of HLA-A expression by IFNγ associated with schizophrenia and noncoding genes.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Identification of independent risk loci for Graves' disease within the MHC in the Japanese population.
    EBI GWAS Catalog

    Variation

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    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    General gene information

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    Markers

    Clone Names

    • MGC71446, MGC105145

    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_024240.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL671277, BC020891, BC089454, DA965044
      Related
      ENST00000462773.6

    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
      30005971..30009956
      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
      1263680..1267665
      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
      1485356..1489341
      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
      1261506..1265491
      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
      1266702..1270687
      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
      1350027..1354012
      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
      1261068..1265040
      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
      1303778..1307763
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      29869861..29873846
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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