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Ly6c1 lymphocyte antigen 6 complex, locus C1 [ Mus musculus (house mouse) ]

Gene ID: 17067, updated on 4-Nov-2022

Summary

Official Symbol
Ly6c1provided by MGI
Official Full Name
lymphocyte antigen 6 complex, locus 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 embryo mesenchyme; gut; liver; metanephros; and nasal cavity. Orthologous to human LY6H (lymphocyte antigen 6 family member H). [provided by Alliance of Genome Resources, Apr 2022]
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

See Ly6c1 in Genome Data Viewer
Location:
15 D3; 15 34.29 cM
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (74915867..74920764, 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 lymphocyte antigen 6 complex, locus A Neighboring gene predicted gene 5960 Neighboring gene lymphocyte antigen 6 complex, locus C2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables acetylcholine receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables acetylcholine receptor inhibitor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in acetylcholine receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

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_001252055.2NP_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
    P0CW02, Q91XG0
    Related
    ENSMUSP00000137401.2, ENSMUST00000179762.8
    Conserved Domains (1) summary
    cd00117
    Location:27104
    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_001252056.2NP_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:27104
    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_001252057.2NP_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
    A0A087WRG9
    Related
    ENSMUSP00000140622.2, ENSMUST00000185200.7
    Conserved Domains (1) summary
    cl10471
    Location:2966
    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_001252058.1NP_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
    A0A087WRG9
    Related
    ENSMUSP00000139948.2, ENSMUST00000185372.2
    Conserved Domains (1) summary
    cl10471
    Location:2966
    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_001411341.1NP_001398270.1  lymphocyte antigen 6C1 isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC124637
    UniProtKB/TrEMBL
    A0A087WRG9
  6. NM_001411351.1NP_001398280.1  lymphocyte antigen 6C1 isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC124637
    UniProtKB/TrEMBL
    A0A087WRG9
  7. NM_001411355.1NP_001398284.1  lymphocyte antigen 6C1 isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AC124637
    UniProtKB/Swiss-Prot
    Q91XG0
  8. NM_010741.4NP_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
    P0CW02, Q91XG0
    Related
    ENSMUSP00000066954.10, ENSMUST00000065408.16
    Conserved Domains (1) summary
    cd00117
    Location:27104
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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..74920764 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030248358.2XP_030104218.1  lymphocyte antigen 6C1 isoform X2

    Conserved Domains (1) summary
    cl10471
    Location:2966
    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. XM_036159199.1XP_036015092.1  lymphocyte antigen 6C1 isoform X2

    Conserved Domains (1) summary
    cl10471
    Location:2966
    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. XM_006520521.5XP_006520584.1  lymphocyte antigen 6C1 isoform X1

    UniProtKB/Swiss-Prot
    P0CW02
    Related
    ENSMUSP00000139799.2, ENSMUST00000187347.7
    Conserved Domains (1) summary
    cd00117
    Location:27104
    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 ...