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Ly6a lymphocyte antigen 6 complex, locus A [ Mus musculus (house mouse) ]

Gene ID: 110454, updated on 8-Nov-2022

Summary

Official Symbol
Ly6aprovided by MGI
Official Full Name
lymphocyte antigen 6 complex, locus Aprovided by MGI
Primary source
MGI:MGI:107527
See related
Ensembl:ENSMUSG00000075602 AllianceGenome:MGI:107527
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
TAP; Sca1; Sca-1; Ly-6A.2; Ly-6A/E; Ly-6E.1
Summary
Predicted to enable acetylcholine receptor binding activity and acetylcholine receptor inhibitor activity. Acts upstream of or within response to bacterium. Located in external side of plasma membrane. Is expressed in alimentary system; hindlimb tendon; liver; metanephros; and physiological umbilical hernia. Used to study osteoporosis. Orthologous to human LY6H (lymphocyte antigen 6 family member H). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in kidney adult (RPKM 243.9), mammary gland adult (RPKM 162.3) and 15 other tissues See more
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Genomic context

See Ly6a in Genome Data Viewer
Location:
15 D3; 15 34.29 cM
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (74866726..74869880, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (74994877..74998031, complement)

Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene 28068 Neighboring gene predicted gene 8000 Neighboring gene predicted gene, 41348 Neighboring gene lymphocyte antigen 6 complex, locus C1 Neighboring gene predicted gene 5960

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)
  • Targeted (6)  1 citation
  • Endonuclease-mediated (5) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

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 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in acetylcholine receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within response to bacterium IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
located_in external side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in intracellular anatomical structure 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 6A-2/6E-1
Names
T-cell-activating protein
stem cell antigen 1

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_001271416.1NP_001258345.1  lymphocyte antigen 6A-2/6E-1 precursor

    See identical proteins and their annotated locations for NP_001258345.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
    Source sequence(s)
    AC124637
    Consensus CDS
    CCDS27540.1
    UniProtKB/Swiss-Prot
    P05533, Q8BPD0
    Related
    ENSMUSP00000140638.2, ENSMUST00000189068.7
    Conserved Domains (1) summary
    smart00134
    Location:27111
    LU; Ly-6 antigen / uPA receptor -like domain
  2. NM_001271417.1NP_001258346.1  lymphocyte antigen 6A-2/6E-1 precursor

    See identical proteins and their annotated locations for NP_001258346.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
    Source sequence(s)
    AC124637, BG085582
    Consensus CDS
    CCDS27540.1
    UniProtKB/Swiss-Prot
    P05533, Q8BPD0
    Related
    ENSMUSP00000140998.2, ENSMUST00000186526.7
    Conserved Domains (1) summary
    smart00134
    Location:27111
    LU; Ly-6 antigen / uPA receptor -like domain
  3. NM_001271418.1NP_001258347.1  lymphocyte antigen 6A-2/6E-1 precursor

    See identical proteins and their annotated locations for NP_001258347.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses two alternate splice sites in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
    Source sequence(s)
    AC124637
    Consensus CDS
    CCDS27540.1
    UniProtKB/Swiss-Prot
    P05533, Q8BPD0
    Conserved Domains (1) summary
    smart00134
    Location:27111
    LU; Ly-6 antigen / uPA receptor -like domain
  4. NM_001271419.1NP_001258348.1  lymphocyte antigen 6A-2/6E-1 precursor

    See identical proteins and their annotated locations for NP_001258348.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses two alternate splice sites in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
    Source sequence(s)
    AC124637, J03636
    Consensus CDS
    CCDS27540.1
    UniProtKB/Swiss-Prot
    P05533, Q8BPD0
    Related
    ENSMUSP00000140287.2, ENSMUST00000187994.7
    Conserved Domains (1) summary
    smart00134
    Location:27111
    LU; Ly-6 antigen / uPA receptor -like domain
  5. NM_001271446.1NP_001258375.1  lymphocyte antigen 6A-2/6E-1 precursor

    See identical proteins and their annotated locations for NP_001258375.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses two alternate splice sites in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
    Source sequence(s)
    AC124637
    Consensus CDS
    CCDS27540.1
    UniProtKB/Swiss-Prot
    P05533, Q8BPD0
    Conserved Domains (1) summary
    smart00134
    Location:27111
    LU; Ly-6 antigen / uPA receptor -like domain
  6. NM_010738.3NP_034868.1  lymphocyte antigen 6A-2/6E-1 precursor

    See identical proteins and their annotated locations for NP_034868.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR, compared to variant 1. Variants 1, 2, 3, 4, 5, and 6 encode the same protein.
    Source sequence(s)
    AC124637, BY228083
    Consensus CDS
    CCDS27540.1
    UniProtKB/Swiss-Prot
    P05533, Q8BPD0
    Related
    ENSMUSP00000140099.2, ENSMUST00000187171.2
    Conserved Domains (1) summary
    smart00134
    Location:27111
    LU; Ly-6 antigen / uPA receptor -like domain

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
    74866726..74869880 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)