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

Gene ID: 58496, updated on 27-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
  • 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)

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

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