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CD9 CD9 molecule [ Homo sapiens (human) ]

Gene ID: 928, updated on 9-Dec-2018

Summary

Official Symbol
CD9provided by HGNC
Official Full Name
CD9 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1709
See related
Ensembl:ENSG00000010278 MIM:143030
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
MIC3; MRP-1; BTCC-1; DRAP-27; TSPAN29; TSPAN-29
Summary
This gene encodes a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Tetraspanins are cell surface glycoproteins with four transmembrane domains that form multimeric complexes with other cell surface proteins. The encoded protein functions in many cellular processes including differentiation, adhesion, and signal transduction, and expression of this gene plays a critical role in the suppression of cancer cell motility and metastasis. [provided by RefSeq, Jan 2011]
Expression
Broad expression in esophagus (RPKM 210.8), prostate (RPKM 168.1) and 21 other tissues See more
Orthologs

Genomic context

See CD9 in Genome Data Viewer
Location:
12p13.31
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (6199707..6238271)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6309482..6347437)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene von Willebrand factor Neighboring gene RNA, 7SL, cytoplasmic 69, pseudogene Neighboring gene uncharacterized LOC105369623 Neighboring gene uncharacterized LOC105369622 Neighboring gene uncharacterized LOC105369625 Neighboring gene ATP synthase membrane subunit f pseudogene 5 Neighboring gene uncharacterized LOC105369624

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 identifies ephrin type A receptors implicated in paclitaxel induced peripheral sensory neuropathy.
NHGRI GWA Catalog
Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk.
NHGRI GWA Catalog
New gene functions in megakaryopoiesis and platelet formation.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Recruitment of Env to tetraspanin-enriched micro domains (TEMs) is required for cell-cell fusion repression by CD9 and CD63 PubMed
env Tetraspanin proteins, such as CD9, CD63, CD81, CD82, and CD231, are incorporated on the membrane of released virions in an HIV-1 envelope protein (Env)-independent manner and have the potential to inhibit HIV-1 Env-mediated infection PubMed
env Overexpression of CD81 and CD9 renders cells less susceptible to HIV-1 gp120/gp41-mediated syncytia formation; antibodies raised against CD9 and CD81 enhance syncytia formation PubMed
Pr55(Gag) gag HIV-1 Gag recruits and traps CD9 to Gag assembly sites at the plasma membrane, which is dependent upon Gag polymerization and the presence of cholesterol PubMed
gag HIV-1 Gag proteins co-localize with tetraspanins CD9, CD81, and CD82 in CD63-enriched micro domains PubMed
gag Env-mediated cell-cell fusion repression by CD9 and CD63 requires the presence of HIV-1 Gag PubMed
matrix gag HIV-1 MA co-localizes with CD9 in monocyte-derived macrophages PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Fertilization, organism-specific biosystem (from REACTOME)
    Fertilization, organism-specific biosystemMammalian fertilization comprises sperm migration through the female reproductive tract, biochemical and morphological changes to sperm, and sperm-egg interaction in the oviduct. Although the broad c...
  • Hematopoietic cell lineage, organism-specific biosystem (from KEGG)
    Hematopoietic cell lineage, organism-specific biosystemBlood-cell development progresses from a hematopoietic stem cell (HSC), which can undergo either self-renewal or differentiation into a multilineage committed progenitor cell: a common lymphoid proge...
  • Hematopoietic cell lineage, conserved biosystem (from KEGG)
    Hematopoietic cell lineage, conserved biosystemBlood-cell development progresses from a hematopoietic stem cell (HSC), which can undergo either self-renewal or differentiation into a multilineage committed progenitor cell: a common lymphoid proge...
  • Hemostasis, organism-specific biosystem (from REACTOME)
    Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...
  • Infectious disease, organism-specific biosystem (from REACTOME)
    Infectious disease, organism-specific biosystem
    Infectious disease
  • Platelet activation, signaling and aggregation, organism-specific biosystem (from REACTOME)
    Platelet activation, signaling and aggregation, organism-specific biosystemPlatelet activation begins with the initial binding of adhesive ligands and of the excitatory platelet agonists (released or generated at the sites of vascular trauma) to cognate receptors on the pla...
  • Platelet degranulation, organism-specific biosystem (from REACTOME)
    Platelet degranulation, organism-specific biosystemPlatelets function as exocytotic cells, secreting a plethora of effector molecules at sites of vascular injury. Platelets contain a number of distinguishable storage granules including alpha granules...
  • Reproduction, organism-specific biosystem (from REACTOME)
    Reproduction, organism-specific biosystemHuman reproduction mixes the genomes of two individuals creating a new organism. The offspring individuals produced by sexual reproduction differ from their parents and from their siblings. Reproduct...
  • Response to elevated platelet cytosolic Ca2+, organism-specific biosystem (from REACTOME)
    Response to elevated platelet cytosolic Ca2+, organism-specific biosystemActivation of phospholipase C enzymes results in the generation of second messengers of the phosphatidylinositol pathway. The events resulting from this pathway are a rise in intracellular calcium an...
  • Sperm:Oocyte Membrane Binding, organism-specific biosystem (from REACTOME)
    Sperm:Oocyte Membrane Binding, organism-specific biosystemAfter the acrosome reactome the sperm has passed through the cumulus cells and the zona pellucida. The membrane of the sperm head and the membrane of the oocyte are drawn together through the interac...
  • Uptake and actions of bacterial toxins, organism-specific biosystem (from REACTOME)
    Uptake and actions of bacterial toxins, organism-specific biosystemThe toxic effects of many bacteria on their human hosts are mediated by proteins released from the bacteria that enter human cells and disrupt critical cellular functions (Henkel et al. 2010). All of...
  • Uptake and function of diphtheria toxin, organism-specific biosystem (from REACTOME)
    Uptake and function of diphtheria toxin, organism-specific biosystemDiphtheria is a serious, often fatal human disease associated with damage to many tissues. Bacteria in infected individuals, however, are typically confined to the lining of the throat or to a skin l...
  • a6b1 and a6b4 Integrin signaling, organism-specific biosystem (from Pathway Interaction Database)
    a6b1 and a6b4 Integrin signaling, organism-specific biosystem
    a6b1 and a6b4 Integrin signaling

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ99568

Gene Ontology Provided by GOA

Function Evidence Code Pubs
integrin binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
brain development IEA
Inferred from Electronic Annotation
more info
 
cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
cell surface receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to low-density lipoprotein particle stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
fusion of sperm to egg plasma membrane involved in single fertilization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
fusion of sperm to egg plasma membrane involved in single fertilization IDA
Inferred from Direct Assay
more info
PubMed 
fusion of sperm to egg plasma membrane involved in single fertilization TAS
Traceable Author Statement
more info
 
negative regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cellular component movement IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of platelet aggregation IDA
Inferred from Direct Assay
more info
PubMed 
oligodendrocyte development IEA
Inferred from Electronic Annotation
more info
 
paranodal junction assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
paranodal junction assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
platelet activation NAS
Non-traceable Author Statement
more info
PubMed 
platelet degranulation TAS
Traceable Author Statement
more info
 
receptor internalization ISS
Inferred from Sequence or Structural Similarity
more info
 
response to water deprivation IEA
Inferred from Electronic Annotation
more info
 
sperm-egg recognition ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
apical plasma membrane IEA
Inferred from Electronic Annotation
more info
 
clathrin-coated endocytic vesicle membrane TAS
Traceable Author Statement
more info
 
endocytic vesicle membrane TAS
Traceable Author Statement
more info
 
external side of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space HDA PubMed 
extracellular vesicle HDA PubMed 
focal adhesion HDA PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane NAS
Non-traceable Author Statement
more info
PubMed 
membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
platelet alpha granule membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
CD9 antigen
Names
5H9 antigen
BA-2/p24 antigen
CD9 antigen (p24)
antigen CD9
cell growth-inhibiting gene 2 protein
leukocyte antigen MIC3
motility related protein-1
tetraspanin-29

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.

Genomic

  1. NG_055677.1 RefSeqGene

    Range
    5610..43565
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001330312.1NP_001317241.1  CD9 antigen isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AI003581, AL523128, X60111
    Consensus CDS
    CCDS81654.1
    UniProtKB/Swiss-Prot
    P21926
    UniProtKB/TrEMBL
    A6NNI4
    Related
    ENSP00000494858.1, ENST00000642746.1
  2. NM_001769.4NP_001760.1  CD9 antigen isoform 1

    See identical proteins and their annotated locations for NP_001760.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AI003581, BM763066, X60111
    Consensus CDS
    CCDS8540.1
    UniProtKB/Swiss-Prot
    P21926
    Related
    ENSP00000009180.4, ENST00000009180.9
    Conserved Domains (2) summary
    cd03152
    Location:111193
    CD9_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), CD9 family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans ...
    pfam00335
    Location:9221
    Tetraspannin; Tetraspanin family

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_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    6199707..6238271
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005253814.4XP_005253871.1  CD9 antigen isoform X1

    See identical proteins and their annotated locations for XP_005253871.1

    UniProtKB/TrEMBL
    B4DK09
    Conserved Domains (2) summary
    cl02781
    Location:111149
    tetraspanin_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the ...
    pfam00335
    Location:9147
    Tetraspannin; Tetraspanin family
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