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    HCG9 HLA complex group 9 [ Homo sapiens (human) ]

    Gene ID: 10255, updated on 8-Nov-2023

    Summary

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    Official Symbol
    HCG9provided by HGNC
    Official Full Name
    HLA complex group 9provided by HGNC
    Primary source
    HGNC:HGNC:21243
    See related
    Ensembl:ENSG00000204625 MIM:615797; AllianceGenome:HGNC:21243
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HCGIX; HCGIX4
    Summary
    This gene lies within the MHC class I region on chromosome 6p21.3. This gene is believed to be non-coding, but its function has not been determined. [provided by RefSeq, Jul 2009]
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    Location:
    6p22.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (29975115..29978403)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (29838996..29842285)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (29942892..29946180)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene HLA complex group 4 pseudogene 4 Neighboring gene major histocompatibility complex, class I, W (pseudogene) Neighboring gene nonconserved acetylation island sequence 101 enhancer Neighboring gene MHC class I polypeptide-related sequence D (pseudogene) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:29942669-29943319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:29943320-29943969 Neighboring gene DEAD-box helicase 39B pseudogene 2 Neighboring gene mitochondrial coiled-coil domain 1 pseudogene 2

    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. High Precision DNA Modification Analysis of HCG9 in Major Psychosis. Pal M, et al. Schizophr Bull, 2016 Jan. PMID 26078387, Free PMC Article
    2. A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder. Kaminsky Z, et al. Mol Psychiatry, 2012 Jul. PMID 21647149
    3. A new non-HLA multigene family associated with the PERB11 family within the MHC class I region. Pichon L, et al. Immunogenetics, 1996. PMID 8753856
    4. Physical map of the HLA-A/HLA-F subregion and identification of two new coding sequences. Pichon L, et al. Immunogenetics, 1996. PMID 8575815
    5. Long Noncoding RNA HCG9 Promotes Osteosarcoma Progression through RAD51 by Acting as a ceRNA of miR-34b-3p. Wang L, et al. Mediators Inflamm, 2021. PMID 34456631, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Long Noncoding RNA HCG9 Promotes Osteosarcoma Progression through RAD51 by Acting as a ceRNA of miR-34b-3p.
      Title: Long Noncoding RNA HCG9 Promotes Osteosarcoma Progression through RAD51 by Acting as a ceRNA of miR-34b-3p.
    2. Significant differences were detected in both CpG and CpH modifications in the brains of individuals affected with schizophrenia or bipolar disorder and unaffected controls
      Title: High Precision DNA Modification Analysis of HCG9 in Major Psychosis.
    3. The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD.
      Title: A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder.
    4. 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
    A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy.
    EBI GWAS Catalog
    Genome-wide association analysis demonstrates the highly polygenic character of age-related hearing impairment.
    EBI GWAS Catalog
    Genome-wide association study of proneness to anger.
    EBI GWAS Catalog
    Genome-wide association study of ulcerative colitis in Koreans suggests extensive overlapping of genetic susceptibility with Caucasians.
    EBI GWAS Catalog
    Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo.
    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

    General gene information

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    Markers

    Other Names

    • HLA complex group 9 (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_028032.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      DA293452, X95289
      Related
      ENST00000376800.7

    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
      29975115..29978403
      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
      1454489..1457778
      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
      1230641..1233930
      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
      1235853..1239139
      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
      1319168..1322457
      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
      1230088..1233379
      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
      1272918..1276204
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      29838996..29842285
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_005844.2: Suppressed sequence

      Description
      NM_005844.2: This RefSeq was permanently suppressed because the transcript is a nonsense-mediated mRNA decay (NMD) candidate, and it is now thought that this gene does not encode a protein.
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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