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    SLAMF9 SLAM family member 9 [ Homo sapiens (human) ]

    Gene ID: 89886, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SLAMF9provided by HGNC
    Official Full Name
    SLAM family member 9provided by HGNC
    Primary source
    HGNC:HGNC:18430
    See related
    Ensembl:ENSG00000162723 MIM:608589; AllianceGenome:HGNC:18430
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CD2F10; CD84H1; SF2001; CD2F-10; CD84-H1
    Summary
    This gene encodes a member of the signaling lymphocytic activation molecule family. The encoded protein is a cell surface molecule that consists of two extracellular immunoglobulin domains, a transmembrane domain and a short cytoplasmic tail that lacks the signal transduction motifs found in other family members. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Apr 2009]
    Expression
    Biased expression in stomach (RPKM 3.8), small intestine (RPKM 2.6) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLAMF9 in Genome Data Viewer
    Location:
    1q23.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (159951492..159983984, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159088558..159121055, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (159921282..159924027, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904437 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:159893727-159894926 Neighboring gene transgelin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:159904768-159905268 Neighboring gene immunoglobulin superfamily member 9 Neighboring gene uncharacterized LOC124904438 Neighboring gene Sharpr-MPRA regulatory region 11999 Neighboring gene long intergenic non-protein coding RNA 1133 Neighboring gene Fc receptor like 6 pseudogene 1 Neighboring gene uncharacterized LOC124904436 Neighboring gene ribosomal protein L27a pseudogene 2 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class M

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. The prognostic and immune significance of SLAMF9 in pan-cancer and validation of its role in colorectal cancer. Zhao C, et al. Sci Rep, 2024 Aug 2. PMID 39095516, Free PMC Article
    2. The SLAM and SAP gene families control innate and adaptive immune responses. Calpe S, et al. Adv Immunol, 2008. PMID 18501771
    3. Genetic approach to insight into the immunobiology of human dendritic cells and identification of CD84-H1, a novel CD84 homologue. Zhang W, et al. Clin Cancer Res, 2001 Mar. PMID 11300479
    4. Signalling lymphocyte activation molecule family member 9 is found on select subsets of antigen-presenting cells and promotes resistance to Salmonella infection. Wilson TJ, et al. Immunology, 2020 Apr. PMID 31880316, Free PMC Article
    5. CD2F-10: a new member of the CD2 subset of the immunoglobulin superfamily. Fennelly JA, et al. Immunogenetics, 2001 Sep. PMID 11685473

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The prognostic and immune significance of SLAMF9 in pan-cancer and validation of its role in colorectal cancer.
      Title: The prognostic and immune significance of SLAMF9 in pan-cancer and validation of its role in colorectal cancer.
    2. SLAMF9 is found on select subsets of antigen-presenting cells and promotes resistance to Salmonella infection.
      Title: Signalling lymphocyte activation molecule family member 9 is found on select subsets of antigen-presenting cells and promotes resistance to Salmonella infection.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC88194

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in T cell activation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    SLAM family member 9
    Names
    CD2 family member 10
    CD84 homolog 1
    cluster of differentiation 2 antigen family member 10
    cluster of differentiation 84 homolog 1
    signaling lymphocytic activation molecule family member 2001
    signaling lymphocytic activation molecule family member 9

    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_001146172.2 → NP_001139644.1  SLAM family member 9 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AL513485, AY034613, AY358801, CB528634
      Consensus CDS
      CCDS53392.1
      UniProtKB/Swiss-Prot
      Q96A28
      Related
      ENSP00000357071.3, ENST00000368092.7
      Conserved Domains (1) summary
      cd05775
      Location:33 → 130
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like

    2. NM_001146173.2 → NP_001139645.1  SLAM family member 9 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting isoform (3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AY034613, BC070213, CB528634
      UniProtKB/Swiss-Prot
      Q96A28
      UniProtKB/TrEMBL
      Q6NSE6
      Related
      ENST00000489098.1
      Conserved Domains (2) summary
      cd00096
      Location:38 → 42
      Ig; Ig strand B [structural motif]
      cl11960
      Location:29 → 86
      Ig; Immunoglobulin domain

    3. NM_033438.4 → NP_254273.2  SLAM family member 9 isoform 1 precursor

      See identical proteins and their annotated locations for NP_254273.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL513485, AY034613, CB528634
      Consensus CDS
      CCDS1191.1
      UniProtKB/Swiss-Prot
      Q5JRQ9, Q5JRR0, Q6UWG1, Q96A28
      Related
      ENSP00000357072.3, ENST00000368093.4
      Conserved Domains (2) summary
      cd05775
      Location:33 → 130
      Ig_SLAM-CD84_like_N; N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84_like
      pfam13927
      Location:135 → 204
      Ig_3; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      159951492..159983984 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002756.2 → XP_016858245.1  SLAM family member 9 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      159088558..159121055 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339486.1 → XP_054195461.1  SLAM family member 9 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96A28.2 GenPept UniProtKB/Swiss-Prot:Q96A28

    Gene LinkOut

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

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