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

Gene ID: 6504, updated on 8-Dec-2018

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
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
Expression
Biased expression in lymph node (RPKM 8.7), appendix (RPKM 6.0) and 11 other tissues See more
Orthologs

Genomic context

See SLAMF1 in Genome Data Viewer
Location:
1q23.3
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (160608100..160647311, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160579891..160617081, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SLAM family member 6 Neighboring gene uncharacterized LOC105371468 Neighboring gene CD84 molecule Neighboring gene uncharacterized LOC107985220 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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Measles, organism-specific biosystem (from KEGG)
    Measles, organism-specific biosystemMeasles virus (MV) is highly contagious virus that leads infant death worldwide. Humans are the unique natural reservoir for this virus. It causes severe immunosuppression favouring secondary bacteri...
  • Measles, conserved biosystem (from KEGG)
    Measles, conserved biosystemMeasles virus (MV) is highly contagious virus that leads infant death worldwide. Humans are the unique natural reservoir for this virus. It causes severe immunosuppression favouring secondary bacteri...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
antigen binding TAS
Traceable Author Statement
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transmembrane signaling receptor activity TAS
Traceable Author Statement
more info
PubMed 
virus receptor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
lymphocyte activation IEA
Inferred from Electronic Annotation
more info
 
myeloid dendritic cell activation involved in immune response IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of CD40 signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of interleukin-12 production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of interleukin-6 production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of tumor necrosis factor production IDA
Inferred from Direct Assay
more info
PubMed 
phagocytosis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of ERK1 and ERK2 cascade IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of JNK cascade IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell proliferation TAS
Traceable Author Statement
more info
PubMed 
viral entry into host cell IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell surface IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
signaling lymphocytic activation molecule
Names
IPO-3
SLAM family member 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_001330754.1NP_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_003037.4NP_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, BC132792
    Consensus CDS
    CCDS1207.1
    UniProtKB/Swiss-Prot
    Q13291
    Related
    ENSP00000306190.6, ENST00000302035.10
    Conserved Domains (1) summary
    pfam06214
    Location:1125
    SLAM; Signaling lymphocytic activation molecule (SLAM) protein

RNA

  1. NR_104399.2 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_104400.2 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_104401.2 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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    160608100..160647311 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005245456.4XP_005245513.1  signaling lymphocytic activation molecule isoform X2

    See identical proteins and their annotated locations for XP_005245513.1

    UniProtKB/Swiss-Prot
    Q13291
    Conserved Domains (1) summary
    pfam06214
    Location:1125
    SLAM; Signaling lymphocytic activation molecule (SLAM) protein
  2. XM_017002130.2XP_016857619.1  signaling lymphocytic activation molecule isoform X1

  3. XM_011509905.3XP_011508207.1  signaling lymphocytic activation molecule isoform X4

  4. XM_017002131.2XP_016857620.1  signaling lymphocytic activation molecule isoform X3

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