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

Gene ID: 414778, updated on 8-Nov-2023

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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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

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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