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Ly9 lymphocyte antigen 9 [ Mus musculus (house mouse) ]

Gene ID: 17085, updated on 8-May-2016
Official Symbol
Ly9provided by MGI
Official Full Name
lymphocyte antigen 9provided by MGI
Primary source
MGI:MGI:96885
See related
Ensembl:ENSMUSG00000004707 Vega:OTTMUSG00000016916
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Ly-9; T100; CD229; Lgp100; SLAMF3; AI893573
Orthologs
Location:
1 H3; 1 79.54 cM
Exon count:
10
Annotation release Status Assembly Chr Location
105 current GRCm38.p3 (GCF_000001635.23) 1 NC_000067.6 (171588613..171607410, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (173518744..173537491, complement)

Chromosome 1 - NC_000067.6Genomic Context describing neighboring genes Neighboring gene predicted gene, 35200 Neighboring gene predicted gene, 39703 Neighboring gene CD244 natural killer cell receptor 2B4 Neighboring gene SLAM family member 7 Neighboring gene microRNA 7683 Neighboring gene nuclear encoded tRNA histidine 1 (anticodon ATG)

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Markers

Homology

Gene Ontology Provided by MGI

Process Evidence Code Pubs
T-helper 17 cell lineage commitment ISO
Inferred from Sequence Orthology
more info
 
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
immune system process IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
positive regulation of interleukin-17 production ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane ISO
Inferred from Sequence Orthology
more info
 
Preferred Names
T-lymphocyte surface antigen Ly-9
Names
SLAM family member 3
cell surface molecule Ly-9
signaling lymphocytic activation molecule 3

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_001277968.1NP_001264897.1  T-lymphocyte surface antigen Ly-9 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC083892, AF244131, AK134106
    Consensus CDS
    CCDS69978.1
    UniProtKB/Swiss-Prot
    Q01965
    UniProtKB/TrEMBL
    E9PX73
    Related
    ENSMUSP00000004827, OTTMUSP00000023737, ENSMUST00000004827, OTTMUST00000050707
    Conserved Domains (2) summary
    pfam13927
    Location:251320
    Ig_3; Immunoglobulin domain
    cl11960
    Location:148246
    Ig; Immunoglobulin domain
  2. NM_008534.3NP_032560.2  T-lymphocyte surface antigen Ly-9 isoform 1 precursor

    See identical proteins and their annotated locations for NP_032560.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC083892, AF244131, AK134106
    Consensus CDS
    CCDS35779.1
    UniProtKB/Swiss-Prot
    Q01965
    Related
    ENSMUSP00000069319, OTTMUSP00000018387, ENSMUST00000068878, OTTMUST00000041044
    Conserved Domains (4) summary
    cd05775
    Location:57151
    Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
    smart00410
    Location:52129
    IG_like; Immunoglobulin like
    pfam13927
    Location:361430
    Ig_3; Immunoglobulin domain
    cl11960
    Location:258356
    Ig; Immunoglobulin domain

RNA

  1. NR_102726.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC083892, AK134106
    Related
    ENSMUST00000143463, OTTMUST00000050708

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 105 details...

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

Reference GRCm38.p3 C57BL/6J

Genomic

  1. NC_000067.6 Reference GRCm38.p3 C57BL/6J

    Range
    171588613..171607410 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Mm_Celera

Genomic

  1. AC_000023.1 Alternate Mm_Celera

    Range
    174446275..174465039 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)