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    SLAMF1 signaling lymphocytic activation molecule family member 1 [ Homo sapiens (human) ]

    Gene ID: 6504, updated on 17-Jun-2024

    Summary

    Official Symbol
    SLAMF1provided by HGNC
    Official Full Name
    signaling lymphocytic activation molecule family member 1provided by HGNC
    Primary source
    HGNC:HGNC:10903
    See related
    Ensembl:ENSG00000117090 MIM:603492; AllianceGenome:HGNC:10903
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SLAM; CD150; CDw150
    Summary
    Enables SH2 domain binding activity and identical protein binding activity. Involved in several processes, including negative regulation of CD40 signaling pathway; negative regulation of cytokine production; and positive regulation of MAPK cascade. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in lymph node (RPKM 8.7), appendix (RPKM 6.0) and 11 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLAMF1 in Genome Data Viewer
    Location:
    1q23.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160608106..160647044, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159745198..159784140, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160577896..160616834, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1928 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:160460168-160461367 Neighboring gene SLAM family member 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1929 Neighboring gene uncharacterized LOC105371468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1930 Neighboring gene Sharpr-MPRA regulatory region 7182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1931 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1933 Neighboring gene CD84 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1934 Neighboring gene NANOG hESC enhancer GRCh37_chr1:160567464-160567965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1939 Neighboring gene uncharacterized LOC107985220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1940 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:160621837-160622647 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160622648-160623458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1942 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160635284-160635845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:160644012-160644628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1944 Neighboring gene endogenous retrovirus group K member 18 Env polyprotein Neighboring gene SET pseudogene 9 Neighboring gene CD48 molecule

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study of treatment refractory schizophrenia in Han Chinese.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SH2 domain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables antigen binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables cell adhesion mediator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transmembrane signaling receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables virus receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in leukocyte chemotaxis involved in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in myeloid dendritic cell activation involved in immune response IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in natural killer cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in natural killer cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of CD40 signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of T cell cytokine production IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of interleukin-12 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of interleukin-6 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of tumor necrosis factor production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of type II interferon production IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in phagocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of ERK1 and ERK2 cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of JNK cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of T-helper 1 cell cytokine production IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of activated T cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell population proliferation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of dendritic cell chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of macrophage chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of type II interferon production IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of vesicle fusion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in symbiont entry into host cell IEA
    Inferred from Electronic Annotation
    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 extracellular exosome HDA PubMed 
    located_in phagocytic vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    signaling lymphocytic activation molecule
    Names
    IPO-3
    SLAM family member 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001330754.2NP_001317683.1  signaling lymphocytic activation molecule isoform a precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AL121985, AL138930, KF471075
      Consensus CDS
      CCDS81389.1
      UniProtKB/Swiss-Prot
      Q13291
      Related
      ENSP00000438406.2, ENST00000538290.2
      Conserved Domains (1) summary
      pfam06214
      Location:1125
      SLAM; Signaling lymphocytic activation molecule (SLAM) protein
    2. NM_003037.5NP_003028.1  signaling lymphocytic activation molecule isoform b precursor

      See identical proteins and their annotated locations for NP_003028.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks an alternate coding exon compared to variant 5. The resulting isoform (b) has a shorter and distinct C-terminus compared to isoform a.
      Source sequence(s)
      AL121985, AL138930
      Consensus CDS
      CCDS1207.1
      UniProtKB/Swiss-Prot
      Q13291, Q5W172, Q9HBE8, W0HKK7
      UniProtKB/TrEMBL
      Q96QR3
      Related
      ENSP00000306190.6, ENST00000302035.11
      Conserved Domains (1) summary
      pfam06214
      Location:1125
      SLAM; Signaling lymphocytic activation molecule (SLAM) protein

    RNA

    1. NR_104399.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two internal exons compared to variant 5. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 5, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK304237, AL121985, AL138930
    2. NR_104400.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks three alternate internal exons compared to variant 5. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 5, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL121985, AL138930, BC144498
    3. NR_104401.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two alternate internal exons and uses an alternate splice junction compared to variant 5. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 5, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL121985, AL138930, BC144499

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      160608106..160647044 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005245456.5XP_005245513.1  signaling lymphocytic activation molecule isoform X2

      See identical proteins and their annotated locations for XP_005245513.1

      UniProtKB/TrEMBL
      B2RAL4, Q96QR3
      Conserved Domains (1) summary
      pfam06214
      Location:1125
      SLAM; Signaling lymphocytic activation molecule (SLAM) protein
    2. XM_017002130.3XP_016857619.1  signaling lymphocytic activation molecule isoform X1

      UniProtKB/TrEMBL
      Q96QR3
    3. XM_047428490.1XP_047284446.1  signaling lymphocytic activation molecule isoform X6

    4. XM_017002131.3XP_016857620.1  signaling lymphocytic activation molecule isoform X5

    5. XM_047428487.1XP_047284443.1  signaling lymphocytic activation molecule isoform X4

      UniProtKB/TrEMBL
      Q9HBE9
    6. XM_047428486.1XP_047284442.1  signaling lymphocytic activation molecule isoform X3

      UniProtKB/TrEMBL
      B4E2E4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      159745198..159784140 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338391.1XP_054194366.1  signaling lymphocytic activation molecule isoform X2

      UniProtKB/TrEMBL
      B2RAL4, Q96QR3
    2. XM_054338390.1XP_054194365.1  signaling lymphocytic activation molecule isoform X1

      UniProtKB/TrEMBL
      Q96QR3
    3. XM_054338395.1XP_054194370.1  signaling lymphocytic activation molecule isoform X6

    4. XM_054338394.1XP_054194369.1  signaling lymphocytic activation molecule isoform X5

    5. XM_054338393.1XP_054194368.1  signaling lymphocytic activation molecule isoform X4

      UniProtKB/TrEMBL
      Q9HBE9
    6. XM_054338392.1XP_054194367.1  signaling lymphocytic activation molecule isoform X3

      UniProtKB/TrEMBL
      B4E2E4