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Ly6c1 lymphocyte antigen 6 family member C1 [ Mus musculus (house mouse) ]

Gene ID: 17067, updated on 27-Nov-2024

Summary

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Official Symbol
Ly6c1provided by MGI
Official Full Name
lymphocyte antigen 6 family member C1provided by MGI
Primary source
MGI:MGI:96882
See related
Ensembl:ENSMUSG00000079018 AllianceGenome:MGI:96882
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Ly6c; Ly-6C; Ly-6C1
Summary
Predicted to enable acetylcholine receptor binding activity and acetylcholine receptor inhibitor activity. Predicted to be involved in acetylcholine receptor signaling pathway. Located in external side of plasma membrane. Is expressed in several structures, including hemolymphoid system; liver; metanephros; midgut; and nasal cavity. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in lung adult (RPKM 119.9), mammary gland adult (RPKM 114.7) and 19 other tissues See more
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Genomic context

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See Ly6c1 in Genome Data Viewer
Location:
15 D3; 15 34.29 cM
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (74915867..74920690, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (75044018..75048920, complement)

Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene 28068 Neighboring gene predicted gene, 41348 Neighboring gene STARR-seq mESC enhancer starr_39006 Neighboring gene lymphocyte antigen 6 family member A Neighboring gene STARR-positive B cell enhancer ABC_E8596 Neighboring gene STARR-seq mESC enhancer starr_39007 Neighboring gene predicted gene 5960 Neighboring gene STARR-seq mESC enhancer starr_39009 Neighboring gene STARR-positive B cell enhancer ABC_E11591 Neighboring gene lymphocyte antigen 6 family memberC2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Accelerated dendritic cell differentiation from migrating Ly6C(lo) bone marrow monocytes in early dermal West Nile virus infection. Davison AM, et al. J Immunol, 2011 Feb 15. PMID 21248254
  2. A recombination event in the 5' flanking region of the Ly-6C gene correlates with impaired expression in the NOD, NZB and ST strains of mice. Philbrick WM, et al. EMBO J, 1990 Aug. PMID 2164472, Free PMC Article
  3. Isolation and expression of an IFN-responsive Ly-6C chromosomal gene. Bothwell A, et al. J Immunol, 1988 Apr 15. PMID 3356904
  4. B cells express Ly-6C in a Th1 but not Th2 cytokine environment. Schlueter AJ, et al. J Interferon Cytokine Res, 2002 Jul. PMID 12184918
  5. Ly6C induces clustering of LFA-1 (CD11a/CD18) and is involved in subtype-specific adhesion of CD8 T cells. Jaakkola I, et al. J Immunol, 2003 Feb 1. PMID 12538687

See all (68) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Primate-conserved carbonic anhydrase IV and murine-restricted LY6C1 enable blood-brain barrier crossing by engineered viral vectors.
    Title: Primate-conserved carbonic anhydrase IV and murine-restricted LY6C1 enable blood-brain barrier crossing by engineered viral vectors.
  2. Ly6c as a New Marker of Mouse Blood Vessels: Qualitative and Quantitative Analyses on Intact and Ischemic Retinas.
    Title: Ly6c as a New Marker of Mouse Blood Vessels: Qualitative and Quantitative Analyses on Intact and Ischemic Retinas.
  3. Infection-induced type I interferons critically modulate the homeostasis and function of CD8(+) naive T cells.
    Title: Infection-induced type I interferons critically modulate the homeostasis and function of CD8(+) naïve T cells.
  4. Ly6CLo Monocyte/Macrophages are Essential for Thrombus Resolution in a Murine Model of Venous Thrombosis.
    Title: Ly6CLo Monocyte/Macrophages are Essential for Thrombus Resolution in a Murine Model of Venous Thrombosis.
  5. Ly6c(Lo) non-classical monocytes promote resolution of rhesus rotavirus-mediated perinatal hepatic inflammation.
    Title: Ly6c(Lo) non-classical monocytes promote resolution of rhesus rotavirus-mediated perinatal hepatic inflammation.
  6. Splenic Ly6Chi monocytes are critical players in dystrophic muscle injury and repair.
    Title: Splenic Ly6Chi monocytes are critical players in dystrophic muscle injury and repair.
  7. The Ym1(+)Ly6C(hi) monocytes greatly expanded in bone marrow during the recovery phase of systemic inflammation or tissue injury.
    Title: Emergence of immunoregulatory Ym1(+)Ly6C(hi) monocytes during recovery phase of tissue injury.
  8. TCR-dependent and cytokine-mediated signals that modulate T cell expression of Ly6C and Sca-1 in vitro and in vivo during infection.
    Title: Cytokine- and TCR-Mediated Regulation of T Cell Expression of Ly6C and Sca-1.
  9. Splenic Ly6C(hi) monocytes contribute to adverse late post-ischemic left ventricular remodeling in heme oxygenase-1 deficient mice.
    Title: Splenic Ly6C(hi) monocytes contribute to adverse late post-ischemic left ventricular remodeling in heme oxygenase-1 deficient mice.
  10. CX3CL1 is upregulated in both human and murine tumors following VEGF signaling blockade, resulting in recruitment of CX3CR1+Ly6Clo monocytes into the tumor
    Title: Ly6Clo monocytes drive immunosuppression and confer resistance to anti-VEGFR2 cancer therapy.
Submit: New GeneRIF Correction See all GeneRIFs (40)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables acetylcholine receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables acetylcholine receptor inhibitor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in acetylcholine receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cell surface IDA
Inferred from Direct Assay
more info
 PubMed 
located_in external side of plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
lymphocyte antigen 6C1
Names
Lymphocyte antigen Ly-6C
lymphocyte antigen 6 complex, locus C
lymphocyte antigen 6 complex, locus C1

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_001252055.2 → NP_001238984.1  lymphocyte antigen 6C1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001238984.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an additional segment in the 5' UTR, compared to variant 1. Variants 1, 2 and 8 encode the same isoform (1).
    Source sequence(s)
    AC124637
    Consensus CDS
    CCDS27541.1
    UniProtKB/Swiss-Prot
    P09568, P0CW02, Q58E40, Q8C2D8, Q91XG0
    UniProtKB/TrEMBL
    A0A087WRP7
    Related
    ENSMUSP00000137401.2, ENSMUST00000179762.8
    Conserved Domains (1) summary
    cd00117
    Location:27 → 104
    LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...

  2. NM_001252056.2 → NP_001238985.1  lymphocyte antigen 6C1 isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (3) has a longer and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC124637
    Consensus CDS
    CCDS79375.1
    UniProtKB/TrEMBL
    A0A087WNZ5
    Related
    ENSMUSP00000139559.2, ENSMUST00000188845.7
    Conserved Domains (1) summary
    cd00117
    Location:27 → 104
    LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...

  3. NM_001252057.2 → NP_001238986.1  lymphocyte antigen 6C1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001238986.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC124637
    Consensus CDS
    CCDS79376.1
    UniProtKB/TrEMBL
    A0A087WPW7, A0A087WRG9
    Related
    ENSMUSP00000140622.2, ENSMUST00000185200.7
    Conserved Domains (1) summary
    cl10471
    Location:29 → 66
    LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...

  4. NM_001252058.1 → NP_001238987.1  lymphocyte antigen 6C1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001238987.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' and 3' UTRs as well as in the 3' coding region, compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus, compared to isoform 1. Variants 4 and 5 encode the same isoform 3.
    Source sequence(s)
    AC124637, BE448813
    Consensus CDS
    CCDS79376.1
    UniProtKB/TrEMBL
    A0A087WPW7, A0A087WRG9
    Related
    ENSMUSP00000139948.2, ENSMUST00000185372.2
    Conserved Domains (1) summary
    cl10471
    Location:29 → 66
    LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...

  5. NM_001411341.1 → NP_001398270.1  lymphocyte antigen 6C1 isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC124637
    UniProtKB/TrEMBL
    A0A087WRG9

  6. NM_001411351.1 → NP_001398280.1  lymphocyte antigen 6C1 isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC124637
    UniProtKB/TrEMBL
    A0A087WRG9

  7. NM_001411355.1 → NP_001398284.1  lymphocyte antigen 6C1 isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AC124637
    UniProtKB/Swiss-Prot
    P09568, P0CW02, Q58E40, Q8C2D8, Q91XG0
    Related
    ENSMUSP00000139799.2, ENSMUST00000187347.7

  8. NM_010741.4 → NP_034871.2  lymphocyte antigen 6C1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_034871.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) is the predominant transcript and encodes isoform 1.
    Source sequence(s)
    AC124637
    Consensus CDS
    CCDS27541.1
    UniProtKB/Swiss-Prot
    P09568, P0CW02, Q58E40, Q8C2D8, Q91XG0
    UniProtKB/TrEMBL
    A0A087WRP7
    Related
    ENSMUSP00000066954.10, ENSMUST00000065408.16
    Conserved Domains (1) summary
    cd00117
    Location:27 → 104
    LU; Ly-6 antigen / uPA receptor -like domain; occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family,CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. Topology of these ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000081.7 Reference GRCm39 C57BL/6J

    Range
    74915867..74920690 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P0CW02.1 GenPept UniProtKB/Swiss-Prot:P0CW02

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