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    LY6G6E lymphocyte antigen 6 family member G6E (pseudogene) [ Homo sapiens (human) ]

    Gene ID: 79136, updated on 10-Oct-2023

    Summary

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    Official Symbol
    LY6G6Eprovided by HGNC
    Official Full Name
    lymphocyte antigen 6 family member G6E (pseudogene)provided by HGNC
    Primary source
    HGNC:HGNC:13934
    See related
    MIM:610437; AllianceGenome:HGNC:13934
    Gene type
    pseudo
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    G6e; C6orf22
    Summary
    LY6G6E belongs to a cluster of leukocyte antigen-6 (LY6) genes located in the major histocompatibility complex (MHC) class III region on chromosome 6. Members of the LY6 superfamily typically contain 70 to 80 amino acids, including 8 to 10 cysteines. Most LY6 proteins are attached to the cell surface by a glycosylphosphatidylinositol (GPI) anchor that is directly involved in signal transduction (Mallya et al., 2002 [PubMed 12079290]).[supplied by OMIM, Mar 2008]
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See LY6G6E in Genome Data Viewer
    Location:
    6p21.33
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31711976..31714065, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31565011..31567100, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31679753..31681842, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene abhydrolase domain containing 16A, phospholipase Neighboring gene microRNA 4646 Neighboring gene LY6G6F-LY6G6D readthrough Neighboring gene lymphocyte antigen 6 family member G6F Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31681075-31681858 Neighboring gene lymphocyte antigen 6 family member G6D Neighboring gene lymphocyte antigen 6 family member G6C Neighboring gene megakaryocyte and platelet inhibitory receptor G6b

    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. Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium. . Nature, 1999 Oct 28. PMID 10553908
    2. Genes encoding three new members of the leukocyte antigen 6 superfamily and a novel member of Ig superfamily, together with genes encoding the regulatory nuclear chloride ion channel protein (hRNCC) and an N omega-N omega-dimethylarginine dimethylaminohydrolase homologue, are found in a 30-kb segment of the MHC class III region. Ribas G, et al. J Immunol, 1999 Jul 1. PMID 10384126
    3. Transcriptional analysis of a novel cluster of LY-6 family members in the human and mouse major histocompatibility complex: five genes with many splice forms. Mallya M, et al. Genomics, 2002 Jul. PMID 12079290
    4. Characterization of the five novel Ly-6 superfamily members encoded in the MHC, and detection of cells expressing their potential ligands. Mallya M, et al. Protein Sci, 2006 Oct. PMID 17008713, Free PMC Article
    5. Genetic association of the major histocompatibility complex with rheumatoid arthritis implicates two non-DRB1 loci. Vignal C, et al. Arthritis Rheum, 2009 Jan. PMID 19116923

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.
    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 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

    • lymphocyte antigen 6 complex, locus G6E (pseudogene)

    Clone Names

    • FLJ50806

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_003673.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate 3' exon and is shorter than variant 1.
      Source sequence(s)
      AJ315538, DA786728

    2. NR_024541.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) is the longer transcript.
      Source sequence(s)
      DA786728

    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
      31711976..31714065 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
      3189260..3191349 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
      2959738..2961827 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
      3017026..3019115 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
      3053853..3055942 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
      2967796..2969885 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
      3011272..3013361 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      31565011..31567100 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001003721.1: Suppressed sequence

      Description
      NM_001003721.1: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.

    2. NM_024123.1: Suppressed sequence

      Description
      NM_024123.1: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.
    Nucleotide Protein
    Heading Accession and Version

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