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    HCG17 HLA complex group 17 [ Homo sapiens (human) ]

    Gene ID: 414778, updated on 17-Aug-2024

    Summary

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    Official Symbol
    HCG17provided by HGNC
    Official Full Name
    HLA complex group 17provided by HGNC
    Primary source
    HGNC:HGNC:31339
    See related
    Ensembl:ENSG00000270604 AllianceGenome:HGNC:31339
    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
    HCG18; LINC00046; NCRNA00046
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See HCG17 in Genome Data Viewer
    Location:
    6p22.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30234039..30326134, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (30098267..30190339, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30201816..30293911, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene tripartite motif containing 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:30139523-30140072 Neighboring gene tripartite motif containing 15 Neighboring gene MPRA-validated peak5749 silencer Neighboring gene PAIP1 pseudogene 1 Neighboring gene tripartite motif containing 26 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:30168993-30169678 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:30169679-30170363 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30175183-30176130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30181514-30182402 Neighboring gene tripartite motif containing 26B, pseudogene Neighboring gene MPRA-validated peak5750 silencer Neighboring gene major histocompatibility complex, class I, L (pseudogene) Neighboring gene HLA complex group 18 Neighboring gene MPRA-validated peak5752 silencer Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:30292740-30293383 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:30296621-30297820 Neighboring gene TRIM39-RPP21 readthrough Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:30308084-30309283 Neighboring gene tripartite motif containing 39 Neighboring gene ribonuclease P/MRP subunit p21

    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. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. Deng X, et al. PLoS One, 2013. PMID 24324551, Free PMC Article
    2. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

    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
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    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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    Other Names

    • HLA complex group 17 (non-protein coding)
    • long intergenic non-protein coding RNA 46

    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_052012.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BM683300, BQ186667
      Related
      ENST00000453558.1

    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
      30234039..30326134 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
      1490872..1500689 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_001756185.2 RNA Sequence

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      1713805..1805811 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
      1489909..1581974 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
      1544684..1636359 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
      1489135..1581209 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
      1532923..1624588 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      30098267..30190339 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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    Research Materials