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

Gene ID: 80741, updated on 3-Apr-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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Location:
6p21.33
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31676684..31681067, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31529718..31534101, complement)
105.20220307 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: 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. 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)

Genotypes

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_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
    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

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

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

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