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

Gene ID: 3137, updated on 10-Oct-2023

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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Location:
6p22.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30005971..30009956)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (29869861..29873846)
105.20220307 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
  • 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)

Genotypes

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_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
    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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