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    LY6G5B lymphocyte antigen 6 family member G5B [ Homo sapiens (human) ]

    Gene ID: 58496, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LY6G5Bprovided by HGNC
    Official Full Name
    lymphocyte antigen 6 family member G5Bprovided by HGNC
    Primary source
    HGNC:HGNC:13931
    See related
    Ensembl:ENSG00000240053 MIM:610433; AllianceGenome:HGNC:13931
    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
    G5b; C6orf19
    Summary
    LY6G5B 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
    Ubiquitous expression in bone marrow (RPKM 22.7), skin (RPKM 15.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LY6G5B 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 (31669976..31673546)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31523010..31526580)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31637753..31641323)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31627653-31628190 Neighboring gene chromosome 6 open reading frame 47 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31628191-31628727 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 G5C Neighboring gene ReSE screen-validated silencer GRCh37_chr6:31647890-31648097 Neighboring gene uncharacterized LOC105375019

    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. Localization of eight additional genes in the human major histocompatibility complex, including the gene encoding the casein kinase II beta subunit (CSNK2B). Albertella MR, et al. Genomics, 1996 Sep 1. PMID 8812450
    2. Intron retention and transcript chimerism conserved across mammals: Ly6g5b and Csnk2b-Ly6g5b as examples. Hernández-Torres F, et al. BMC Genomics, 2013 Mar 22. PMID 23521802, Free PMC Article
    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. Several loci in the HLA class III region are associated with T1D risk after adjusting for DRB1-DQB1. Valdes AM, et al. Diabetes Obes Metab, 2009 Feb. PMID 19143814, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: CSNK2B

    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 G5b
    Names
    lymphocyte antigen 6 complex, locus G5B

    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_021221.3 → NP_067044.2  lymphocyte antigen 6 complex locus protein G5b precursor

      See identical proteins and their annotated locations for NP_067044.2

      Status: VALIDATED

      Source sequence(s)
      AL662899
      Consensus CDS
      CCDS34400.1
      UniProtKB/Swiss-Prot
      B0UXB2, B0UZ65, B0UZP8, B7ZCA3, Q5SQ62, Q5SST3, Q8NDX9, Q9UKT0, Q9UMQ0
      UniProtKB/TrEMBL
      A0A1U9X7Y3, A0A1U9X7Y5, A0A1U9X7Y7, A0A1U9X7Y8, N0E641
      Related
      ENSP00000365024.4, ENST00000375864.5

    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
      31669976..31673546
      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
      3147267..3150837
      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
      2917748..2921318
      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
      2975023..2978593
      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
      3011848..3015418
      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
      2925800..2929370
      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
      2969260..2972830
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      31523010..31526580
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NDX9.1 GenPept UniProtKB/Swiss-Prot:Q8NDX9

    Gene LinkOut

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

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