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

    Gene ID: 17067, updated on 2-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 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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