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

Gene ID: 89886, updated on 5-Mar-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
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Genomic context

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Location:
1q23.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (159951492..159983984, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159088558..159121055, complement)
105.20220307 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 SLAM and SAP gene families control innate and adaptive immune responses. Calpe S, et al. Adv Immunol, 2008. PMID 18501771
  2. 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
  3. 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
  4. CD2F-10: a new member of the CD2 subset of the immunoglobulin superfamily. Fennelly JA, et al. Immunogenetics, 2001 Sep. PMID 11685473
  5. Identification and characterization of SF2000 and SF2001, two new members of the immune receptor SLAM/CD2 family. Fraser CC, et al. Immunogenetics, 2002 Feb. PMID 11862385

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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)

Genotypes

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

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in T cell activation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in biological_process ND
No biological Data available
more info
  
involved_in plasmacytoid dendritic cell cytokine production 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_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
    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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