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HCG4 HLA complex group 4 [ Homo sapiens (human) ]

Gene ID: 54435, updated on 10-Oct-2023

Summary

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Official Symbol
HCG4provided by HGNC
Official Full Name
HLA complex group 4provided by HGNC
Primary source
HGNC:HGNC:21241
See related
AllianceGenome:HGNC:21241
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
HCG4P10; HCGIV.9; HCGIV-10
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Genomic context

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Location:
6p22.1
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (29791031..29793073, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (29663053..29665072, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (29758808..29760850, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:29719894-29720566 Neighboring gene interferon induced transmembrane protein 4 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr6:29724174-29724335 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:29726920-29727612 Neighboring gene HLA complex group 26 (non-protein coding) pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:29747845-29748345 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:29757998-29759197 Neighboring gene major histocompatibility complex, class I, V (pseudogene) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:29768209-29768708 Neighboring gene HLA complex group 4 pseudogene 9 Neighboring gene major histocompatibility complex, class I, P (pseudogene) Neighboring gene ribosomal protein L7a pseudogene 7

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. Down-regulation of HLA Class I and NKG2D ligands through a concerted action of MAPK and DNA methyltransferases in colorectal cancer cells. Sers C, et al. Int J Cancer, 2009 Oct 1. PMID 19569244
  2. SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians. Burfoot RK, et al. Tissue Antigens, 2008 Jan. PMID 17971048
  3. A 356-Kb sequence of the subtelomeric part of the MHC Class I region. Hampe A, et al. DNA Seq, 1999. PMID 10727083
  4. Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region. Shiina T, et al. Proc Natl Acad Sci U S A, 1999 Nov 9. PMID 10557312, Free PMC Article
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

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

  • HCGIV-10 pseudogene
  • HLA complex group 4 (non-protein coding)
  • HLA complex group 4 pseudogene 10

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_002139.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AF036977, BC011879, BC021249

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
    29791031..29793073 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
    1056864..1058883 complement
    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
    1274814..1276833 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
    1054016..1056058 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
    1053607..1055649 complement
    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
    1053682..1055724 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
    1054016..1056035 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
    1097182..1099224 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    29663053..29665072 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NG_002741.3: Suppressed sequence

    Description
    NG_002741.3: This RefSeq was permanently suppressed because it is now thought that this gene is transcribed.

  2. NM_018985.1: Suppressed sequence

    Description
    NM_018985.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version

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