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    Slamf6 SLAM family member 6 [ Mus musculus (house mouse) ]

    Gene ID: 30925, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Slamf6provided by MGI
    Official Full Name
    SLAM family member 6provided by MGI
    Primary source
    MGI:MGI:1353620
    See related
    Ensembl:ENSMUSG00000015314 AllianceGenome:MGI:1353620
    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
    KAL1; NTBA; KAL1b; Ly108; NTB-A; SF2000
    Summary
    Involved in natural killer cell differentiation and natural killer cell proliferation. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. Orthologous to human SLAMF6 (SLAM family member 6). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in thymus adult (RPKM 5.3), spleen adult (RPKM 3.2) and 4 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Slamf6 in Genome Data Viewer
    Location:
    1 H3; 1 79.54 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (171745002..171776525)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (171917458..171948958)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene CD84 antigen Neighboring gene predicted gene, 51686 Neighboring gene STARR-seq mESC enhancer starr_03042 Neighboring gene STARR-seq mESC enhancer starr_03043 Neighboring gene STARR-seq mESC enhancer starr_03044 Neighboring gene predicted gene 52845 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:173849407-173849647 Neighboring gene STARR-positive B cell enhancer ABC_E3330 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:173851483-173851687 Neighboring gene predicted gene, 37065 Neighboring gene STARR-seq mESC enhancer starr_03046 Neighboring gene STARR-positive B cell enhancer ABC_E5850 Neighboring gene VISTA enhancer mm1677 Neighboring gene VANGL planar cell polarity 2 Neighboring gene STARR-positive B cell enhancer ABC_E9498 Neighboring gene nescient helix loop helix 1

    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. Alternative Splicing of the Inhibitory Immune Checkpoint Receptor SLAMF6 Generates a Dominant Positive Form, Boosting T-cell Effector Functions. Hajaj E, et al. Cancer Immunol Res, 2021 Jun. PMID 33762352
    2. SLAMF6​ deficiency augments tumor killing and skews toward an effector phenotype revealing it as a novel T cell checkpoint. Hajaj E, et al. Elife, 2020 Mar 3. PMID 32122464, Free PMC Article
    3. Cutting edge: the SLAM family receptor Ly108 controls T cell and neutrophil functions. Howie D, et al. J Immunol, 2005 May 15. PMID 15879084
    4. Characterization of Ly108-H1 Signaling Reveals Ly108-3 Expression and Additional Strain-Specific Differences in Lupus Prone Mice. Rietdijk S, et al. Int J Mol Sci, 2023 Mar 6. PMID 36902453, Free PMC Article
    5. SAP-regulated T Cell-APC adhesion and ligation-dependent and -independent Ly108-CD3ζ interactions. Chu C, et al. J Immunol, 2014 Oct 15. PMID 25217164

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Characterization of Ly108-H1 Signaling Reveals Ly108-3 Expression and Additional Strain-Specific Differences in Lupus Prone Mice.
      Title: Characterization of Ly108-H1 Signaling Reveals Ly108-3 Expression and Additional Strain-Specific Differences in Lupus Prone Mice.
    2. Alternative Splicing of the Inhibitory Immune Checkpoint Receptor SLAMF6 Generates a Dominant Positive Form, Boosting T-cell Effector Functions.
      Title: Alternative Splicing of the Inhibitory Immune Checkpoint Receptor SLAMF6 Generates a Dominant Positive Form, Boosting T-cell Effector Functions.
    3. SLAMF6 deficiency augments tumor killing and skews toward an effector phenotype revealing it as a novel T cell checkpoint.
      Title: SLAMF6​ deficiency augments tumor killing and skews toward an effector phenotype revealing it as a novel T cell checkpoint.
    4. Critical Role for SLAM/SAP Signaling in the Thymic Developmental Programming of IL-17- and IFN-gamma-Producing gammadelta T Cells.
      Title: Critical Role for SLAM/SAP Signaling in the Thymic Developmental Programming of IL-17- and IFN-γ-Producing γδ T Cells.
    5. Authors found that seSLAMF6 reduced activation-induced cell death and had an antiapoptotic effect on tumor-infiltrating lymphocytes.
      Title: Soluble SLAMF6 Receptor Induces Strong CD8(+) T-cell Effector Function and Improves Anti-Melanoma Activity In Vivo.
    6. naive T cells regulate B cell survival in a SLAMF6-dependent manner
      Title: T Cells Regulate Peripheral Naive Mature B Cell Survival by Cell-Cell Contact Mediated through SLAMF6 and SAP.
    7. in addition to its established role in Invariant NKT(iNKT) cell ontogeny, Ly108 regulates iNKT cell function in mice and humans
      Title: Invariant NKT Cell Activation Is Potentiated by Homotypic trans-Ly108 Interactions.
    8. CRISPR-Mediated Slamf1Delta/Delta Slamf5Delta/Delta Slamf6Delta/Delta Triple Gene Disruption Reveals NKT Cell Defects but Not T Follicular Helper Cell Defects.
      Title: CRISPR-Mediated Slamf1Δ/Δ Slamf5Δ/Δ Slamf6Δ/Δ Triple Gene Disruption Reveals NKT Cell Defects but Not T Follicular Helper Cell Defects.
    9. In addition to their role in NK cell activation by hematopoietic cells, the SLAM-SAP-SHP1 pathways influence responsiveness toward nonhematopoietic targets by a process akin to NK cell 'education'.
      Title: A hematopoietic cell-driven mechanism involving SLAMF6 receptor, SAP adaptors and SHP-1 phosphatase regulates NK cell education.
    10. study establishes a central role for germinal center B cell-specific CD84 and Ly108 expression in maintaining B cell tolerance in germinal centers and in preventing autoimmunity
      Title: B cell-intrinsic CD84 and Ly108 maintain germinal center B cell tolerance.
    Submit: New GeneRIF Correction See all GeneRIFs (23)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (6)  1 citation

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    involved_in T cell activation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in T-helper 17 cell lineage commitment ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in natural killer cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in natural killer cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of interleukin-17 production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of natural killer cell mediated cytotoxicity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of type II interferon production ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SLAM family member 6
    Names
    lymphocyte antigen 108

    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_001347186.1 → NP_001334115.1  SLAM family member 6 isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AC091523, BC030031
      Consensus CDS
      CCDS83638.1
      UniProtKB/Swiss-Prot
      C6ESQ1, Q9ET39, Q9ET40
      UniProtKB/TrEMBL
      Q18PJ0, Q18PJ2
      Related
      ENSMUSP00000141448.2, ENSMUST00000195656.6

    2. NM_001347187.1 → NP_001334116.1  SLAM family member 6 isoform 3 precursor

      Status: VALIDATED

      Source sequence(s)
      AC091523, EU591721
      Consensus CDS
      CCDS83639.1
      UniProtKB/TrEMBL
      Q18PJ2
      Related
      ENSMUSP00000141944.2, ENSMUST00000194561.2

    3. NM_030710.3 → NP_109635.1  SLAM family member 6 isoform 1 precursor

      See identical proteins and their annotated locations for NP_109635.1

      Status: VALIDATED

      Source sequence(s)
      AC091523
      Consensus CDS
      CCDS15504.1
      UniProtKB/TrEMBL
      Q18PG5, Q18PJ2
      Related
      ENSMUSP00000130610.2, ENSMUST00000171330.7
      Conserved Domains (1) summary
      cl11960
      Location:44 → 142
      Ig; Immunoglobulin domain

    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_000067.7 Reference GRCm39 C57BL/6J

      Range
      171745002..171776525
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006496884.5 → XP_006496947.1  SLAM family member 6 isoform X1

      UniProtKB/TrEMBL
      Q18PJ2
      Conserved Domains (1) summary
      cl11960
      Location:44 → 142
      Ig; Immunoglobulin domain

    2. XM_006496886.5 → XP_006496949.1  SLAM family member 6 isoform X2

      UniProtKB/TrEMBL
      Q18PJ2
      Conserved Domains (1) summary
      cl11960
      Location:25 → 123
      Ig; Immunoglobulin domain

    3. XM_011238825.3 → XP_011237127.1  SLAM family member 6 isoform X3

    RNA

    1. XR_373611.5 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ET39.1 GenPept UniProtKB/Swiss-Prot:Q9ET39

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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