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    LY6G5C lymphocyte antigen 6 family member G5C [ Homo sapiens (human) ]

    Gene ID: 80741, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LY6G5Cprovided by HGNC
    Official Full Name
    lymphocyte antigen 6 family member G5Cprovided by HGNC
    Primary source
    HGNC:HGNC:13932
    See related
    Ensembl:ENSG00000204428 MIM:610434; AllianceGenome:HGNC:13932
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    G5C; NG33; C6orf20; LY6G5CA; LY6G5CB
    Summary
    LY6G5C 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
    Broad expression in testis (RPKM 3.1), spleen (RPKM 1.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LY6G5C in Genome Data Viewer
    Location:
    6p21.33
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31676684..31681067, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31529718..31534101, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31644461..31648844, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene G-patch domain and ankyrin repeats 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31633065-31633659 Neighboring gene casein kinase 2 beta Neighboring gene lymphocyte antigen 6 family member G5B Neighboring gene ReSE screen-validated silencer GRCh37_chr6:31647890-31648097 Neighboring gene uncharacterized LOC105375019 Neighboring gene uncharacterized LOC105375018 Neighboring gene abhydrolase domain containing 16A, phospholipase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. 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
    2. Fine mapping of the MHC Class III region demonstrates association of AIF1 and rheumatoid arthritis. Harney SM, et al. Rheumatology (Oxford), 2008 Dec. PMID 18835879
    3. 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
    4. Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins. Macaulay IC, et al. Blood, 2007 Apr 15. PMID 17192395, Free PMC Article
    5. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. Barcellos LF, et al. PLoS Genet, 2009 Oct. PMID 19851445, Free PMC Article

    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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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    colocalizes_with external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with external side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lymphocyte antigen 6 complex locus protein G5c
    Names
    lymphocyte antigen 6 complex, locus G5C
    lymphocyte antigen-6 G5C

    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.

    mRNA and Protein(s)

    1. NM_025262.4 → NP_079538.3  lymphocyte antigen 6 complex locus protein G5c precursor

      See identical proteins and their annotated locations for NP_079538.3

      Status: VALIDATED

      Source sequence(s)
      AL662899
      Consensus CDS
      CCDS34401.2
      UniProtKB/Swiss-Prot
      A6NCW4, B0UXB3, B0UXB4, B0UZ69, B0UZQ0, B1B0L9, O95871, Q5SQ59, Q5SRR4, Q8NDY0, Q8NDY1
      UniProtKB/TrEMBL
      A0A1U9X7Y6, A0A1U9X7Z9
      Related
      ENSP00000372724.4, ENST00000383237.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      31676684..31681067 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
      3153975..3158358 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
      2924456..2928840 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
      2981731..2986115 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
      3018556..3022939 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
      2932508..2938411 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331185.1 → XP_054187160.1  lymphocyte antigen 6 complex locus protein G5c isoform X1

      UniProtKB/Swiss-Prot
      A6NCW4, B0UXB3, B0UXB4, B0UZ69, B0UZQ0, B1B0L9, O95871, Q5SQ59, Q5SRR4, Q8NDY0, Q8NDY1
      UniProtKB/TrEMBL
      A0A1U9X7Y6, A0A1U9X7Z9

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      2975968..2981871 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331427.1 → XP_054187402.1  lymphocyte antigen 6 complex locus protein G5c isoform X1

      UniProtKB/Swiss-Prot
      A6NCW4, B0UXB3, B0UXB4, B0UZ69, B0UZQ0, B1B0L9, O95871, Q5SQ59, Q5SRR4, Q8NDY0, Q8NDY1
      UniProtKB/TrEMBL
      A0A1U9X7Y6, A0A1U9X7Z9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      31529718..31534101 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001002848.1: Suppressed sequence

      Description
      NM_001002848.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    2. NM_001002849.1: Suppressed sequence

      Description
      NM_001002849.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5SRR4.1 GenPept UniProtKB/Swiss-Prot:Q5SRR4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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