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

Gene ID: 110454, updated on 2-Oct-2018

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 Vega:OTTMUSG00000045110
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
Expression
Broad expression in kidney adult (RPKM 243.9), mammary gland adult (RPKM 162.3) and 15 other tissues See more

Genomic context

See Ly6a in Genome Data Viewer
Location:
15 D3; 15 34.29 cM
Exon count:
4
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 15 NC_000081.6 (74994877..74998031, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 15 NC_000081.5 (74825307..74828318, complement)

Chromosome 15 - NC_000081.6Genomic 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 FunctionsWhat's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
response to bacterium IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
anchored component of membrane IEA
Inferred from Electronic Annotation
more info
 
external side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
intracellular IDA
Inferred from Direct Assay
more info
PubMed 
membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
lymphocyte antigen 6A-2/6E-1
Names
T-cell-activating protein
stem cell antigen 1

NCBI Reference Sequences (RefSeq)

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
    Related
    ENSMUSP00000140638.1, OTTMUSP00000066168, ENSMUST00000189068.6, OTTMUST00000118546
    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
    Related
    ENSMUSP00000140998.1, OTTMUSP00000066171, ENSMUST00000186526.6, OTTMUST00000118549
    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
    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
    Related
    ENSMUSP00000140287.1, OTTMUSP00000066169, ENSMUST00000187994.6, OTTMUST00000118547
    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
    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
    Related
    ENSMUSP00000140099.1, OTTMUSP00000066170, ENSMUST00000187171.1, OTTMUST00000118548
    Conserved Domains (1) summary
    smart00134
    Location:27111
    LU; Ly-6 antigen / uPA receptor -like domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000081.6 Reference GRCm38.p4 C57BL/6J

    Range
    74994877..74998031 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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