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Aliases for CD9 Gene

Aliases for CD9 Gene

  • CD9 Molecule 2 3 5
  • Cell Growth-Inhibiting Gene 2 Protein 3 4
  • Motility Related Protein-1 2 3
  • Leukocyte Antigen MIC3 3 4
  • CD9 Antigen (P24) 2 3
  • Tetraspanin-29 3 4
  • 5H9 Antigen 3 4
  • CD9 Antigen 3 4
  • TSPAN29 3 4
  • MRP-1 3 4
  • MIC3 3 4
  • Motility-Related Protein 4
  • BA-2/P24 Antigen 3
  • Antigen CD9 3
  • TSPAN-29 3
  • Tspan-29 4
  • DRAP-27 3
  • BTCC-1 3
  • P24 4

External Ids for CD9 Gene

Previous HGNC Symbols for CD9 Gene

  • MIC3

Previous GeneCards Identifiers for CD9 Gene

  • GC12P006164
  • GC12P006284
  • GC12P006308

Summaries for CD9 Gene

Entrez Gene Summary for CD9 Gene

  • 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]

GeneCards Summary for CD9 Gene

CD9 (CD9 Molecule) is a Protein Coding gene. Diseases associated with CD9 include Cytomegalovirus Retinitis and Diphtheria. Among its related pathways are Fertilization and Uptake and actions of bacterial toxins. Gene Ontology (GO) annotations related to this gene include integrin binding. An important paralog of this gene is TSPAN2.

UniProtKB/Swiss-Prot for CD9 Gene

  • Involved in platelet activation and aggregation. Regulates paranodal junction formation. Involved in cell adhesion, cell motility and tumor metastasis. Required for sperm-egg fusion.

Gene Wiki entry for CD9 Gene

Additional gene information for CD9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CD9 Gene

Genomics for CD9 Gene

GeneHancer (GH) Regulatory Elements for CD9 Gene

Promoters and enhancers for CD9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J006197 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 +3.3 3287 11 SIN3A ZNF48 ZNF121 GLIS2 FOS SP3 REST NBN CTCF KLF1 CD9 ENO2 ING4 GC12M006235 ENSG00000202318
GH12J006177 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 653.3 -18.5 -18478 6.8 HDGF FOXA2 ARID4B DMAP1 GLI4 YY1 ZNF280A SLC30A9 FOS RUNX3 CD9 LOC105369623 ENSG00000247853 SPSB2 NCAPD2 ZNF384 ENSG00000219410 VWF
GH12J006138 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 23.6 -58.9 -58865 4.8 CTCF GTF2F1 NFATC3 MAX CEBPG ZIC2 E4F1 YY1 MTA3 POLR2A CD9 PLEKHG6 ENSG00000126749 VWF TAPBPL TNFRSF1A CHD4 VAMP1 IFFO1 PIR35613
GH12J006166 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 19.8 -31.6 -31625 3.9 PKNOX1 ATF1 ARNT TCF12 ZNF766 ZNF207 ZNF143 ATF7 FOS RUNX3 PIR38862 CD9 VWF ATN1 NTF3 TNFRSF1A TAPBPL VAMP1 PIR39839 LOC105369623
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CD9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CD9 gene promoter:
  • STAT3
  • NF-kappaB1
  • E2F-4
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-5
  • Egr-4

Genomic Locations for CD9 Gene

Genomic Locations for CD9 Gene
38,557 bases
Plus strand
38,557 bases
Plus strand

Genomic View for CD9 Gene

Genes around CD9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CD9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CD9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CD9 Gene

Proteins for CD9 Gene

  • Protein details for CD9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    CD9 antigen
    Protein Accession:
    Secondary Accessions:
    • D3DUQ9
    • Q5J7W6
    • Q96ES4

    Protein attributes for CD9 Gene

    228 amino acids
    Molecular mass:
    25416 Da
    Quaternary structure:
    • Forms both disulfide-linked homodimers and higher homooligomers as well as heterooligomers with other members of the tetraspanin family. Interacts with CD63. Identified in a complex with CD63 and ITGB3. Associates with CR2/CD21 and with PTGFRN/CD9P1. Interacts directly with IGSF8. Interacts with PDPN; this interaction is homophilic and attenuates platelet aggregation and pulmonary metastasis induced by PDPN (PubMed:18541721). Interacts (via the second extracellular domain) with integrin ITGAV:ITGB3 (PubMed:27993971).

neXtProt entry for CD9 Gene

Post-translational modifications for CD9 Gene

  • Palmitoylated at a low, basal level in unstimulated platelets. The level of palmitoylation increases when platelets are activated by thrombin (in vitro). The protein exists in three forms with molecular masses between 22 and 27 kDa, and is known to carry covalently linked fatty acids.
  • Glycosylation at posLast=5353 and posLast=5252
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for CD9

No data available for DME Specific Peptides for CD9 Gene

Domains & Families for CD9 Gene

Gene Families for CD9 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • CD markers
  • Plasma proteins
  • Predicted membrane proteins
  • Transporters

Suggested Antigen Peptide Sequences for CD9 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the tetraspanin (TM4SF) family.
  • Belongs to the tetraspanin (TM4SF) family.
genes like me logo Genes that share domains with CD9: view

Function for CD9 Gene

Molecular function for CD9 Gene

UniProtKB/Swiss-Prot Function:
Involved in platelet activation and aggregation. Regulates paranodal junction formation. Involved in cell adhesion, cell motility and tumor metastasis. Required for sperm-egg fusion.
GENATLAS Biochemistry:
cell differentiation antigen CD9 (p34),24kDa,membrane glycoprotein,single chain,identified by monoclonal antibodies ALB6,BLI16,FMC56

Phenotypes From GWAS Catalog for CD9 Gene

Gene Ontology (GO) - Molecular Function for CD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005178 integrin binding IDA,IEA 27993971
GO:0005515 protein binding IPI 11278880
genes like me logo Genes that share ontologies with CD9: view
genes like me logo Genes that share phenotypes with CD9: view

Animal Models for CD9 Gene

MGI Knock Outs for CD9:
  • Cd9 Cd9<tm1Mek>
  • Cd9 Cd9<tm1Bcx>
  • Cd9 Cd9<tm1Kudo>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CD9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CD9 Gene

Localization for CD9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CD9 Gene

Membrane; Multi-pass membrane protein. Cell membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CD9 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 2
endosome 2
nucleus 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space HDA 16502470
GO:0005886 plasma membrane TAS,NAS --
GO:0005887 integral component of plasma membrane NAS,TAS 2037603
GO:0005925 focal adhesion HDA 21423176
GO:0009897 external side of plasma membrane IEA --
genes like me logo Genes that share ontologies with CD9: view

Pathways & Interactions for CD9 Gene

genes like me logo Genes that share pathways with CD9: view

Pathways by source for CD9 Gene

1 KEGG pathway for CD9 Gene

Gene Ontology (GO) - Biological Process for CD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002576 platelet degranulation TAS --
GO:0007155 cell adhesion IDA,IEA 7511626
GO:0007166 cell surface receptor signaling pathway IBA --
GO:0007338 single fertilization IEA --
GO:0007342 fusion of sperm to egg plasma membrane involved in single fertilization TAS --
genes like me logo Genes that share ontologies with CD9: view

No data available for SIGNOR curated interactions for CD9 Gene

Drugs & Compounds for CD9 Gene

(38) Drugs for CD9 Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
C31G Investigational Pharma Target 0

(30) Additional Compounds for CD9 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CD9: view

Transcripts for CD9 Gene

mRNA/cDNA for CD9 Gene

(3) REFSEQ mRNAs :
(12) Additional mRNA sequences :
(9) Selected AceView cDNA sequences:
(16) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CD9 Gene

CD9 molecule:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CD9

Alternative Splicing Database (ASD) splice patterns (SP) for CD9 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12
SP1: - - - -
SP2: - - -
SP3: - - - - -
SP4: - - -
SP5: - -
SP6: - - - - - - -
SP7: - - - -
SP8: - - - - -

Relevant External Links for CD9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CD9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CD9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CD9 Gene

This gene is overexpressed in Esophagus - Mucosa (x4.0).

Protein differential expression in normal tissues from HIPED for CD9 Gene

This gene is overexpressed in Nasal epithelium (12.9), Spinal cord (8.1), and Urine (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CD9 Gene

Protein tissue co-expression partners for CD9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CD9 Gene:


SOURCE GeneReport for Unigene cluster for CD9 Gene:


mRNA Expression by UniProt/SwissProt for CD9 Gene:

Tissue specificity: Detected in platelets (at protein level). Expressed by a variety of hematopoietic and epithelial cells.

Evidence on tissue expression from TISSUES for CD9 Gene

  • Blood(4.6)
  • Nervous system(4.4)
  • Intestine(4.1)
  • Lung(3.9)
  • Skin(3.6)
  • Pancreas(3)
  • Stomach(3)
  • Kidney(2.9)
  • Spleen(2.8)
  • Bone marrow(2.7)
  • Heart(2.7)
  • Lymph node(2.7)
  • Muscle(2.6)
  • Liver(2.4)
  • Thyroid gland(2.3)
  • Adrenal gland(2.2)
genes like me logo Genes that share expression patterns with CD9: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CD9 Gene

Orthologs for CD9 Gene

This gene was present in the common ancestor of animals.

Orthologs for CD9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CD9 34 33
  • 99.56 (n)
(Canis familiaris)
Mammalia CD9 34 33
  • 88.41 (n)
(Bos Taurus)
Mammalia CD9 34 33
  • 87.32 (n)
(Rattus norvegicus)
Mammalia Cd9 33
  • 86.43 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 86 (a)
-- 34
  • 70 (a)
-- 34
  • 55 (a)
(Mus musculus)
Mammalia Cd9 16 34 33
  • 85.99 (n)
(Ornithorhynchus anatinus)
Mammalia CD9 34
  • 75 (a)
(Gallus gallus)
Aves CD9 34 33
  • 72.2 (n)
(Anolis carolinensis)
Reptilia CD9 34
  • 50 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cd9 33
  • 70.06 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.24740 33
(Danio rerio)
Actinopterygii cd9a 34 33
  • 67.11 (n)
cd9b 34
  • 55 (a)
Dr.27131 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9244 33
fruit fly
(Drosophila melanogaster)
Insecta Tsp96F 34
  • 24 (a)
(Caenorhabditis elegans)
Secernentea tsp-9 34
  • 26 (a)
Species where no ortholog for CD9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CD9 Gene

Gene Tree for CD9 (if available)
Gene Tree for CD9 (if available)
Evolutionary constrained regions (ECRs) for CD9: view image

Paralogs for CD9 Gene

(14) SIMAP similar genes for CD9 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with CD9: view

Variants for CD9 Gene

Sequence variations from dbSNP and Humsavar for CD9 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000194472 -- 6,229,866(+) C/A intron_variant
rs1000202979 -- 6,200,937(+) A/T intron_variant
rs1000208242 -- 6,226,876(+) C/T intron_variant
rs1000231455 -- 6,237,024(+) G/C genic_downstream_transcript_variant, intron_variant
rs1000285382 -- 6,230,828(+) A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CD9 Gene

Variant ID Type Subtype PubMed ID
nsv470263 CNV gain 18288195
nsv557253 CNV gain 21841781
nsv832320 CNV loss 17160897
nsv832321 CNV gain+loss 17160897

Variation tolerance for CD9 Gene

Residual Variation Intolerance Score: 47.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.28; 6.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CD9 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CD9 Gene

Disorders for CD9 Gene

MalaCards: The human disease database

(11) MalaCards diseases for CD9 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
cytomegalovirus retinitis
  • cmv retinitis
  • corynebacterium infection
hemangioma of spleen
  • splenic hemangioma
  • vaginal enterocele
testicular leukemia
- elite association - COSMIC cancer census association via MalaCards
Search CD9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CD9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CD9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CD9 Gene

Publications for CD9 Gene

  1. Tetraspanin family member CD9 inhibits Aggrus/podoplanin-induced platelet aggregation and suppresses pulmonary metastasis. (PMID: 18541721) Nakazawa Y … Fujita N (Blood 2008) 3 4 22 58
  2. Evidence for specific tetraspanin homodimers: inhibition of palmitoylation makes cysteine residues available for cross-linking. (PMID: 14556650) Kovalenko OV … Hemler ME (The Biochemical journal 2004) 3 4 22 58
  3. Organization of the human CD9 gene. (PMID: 8486348) Rubinstein E … Boucheix C (Genomics 1993) 3 4 22 58
  4. The CD9, CD81, and CD151 EC2 domains bind to the classical RGD-binding site of integrin αvβ3. (PMID: 27993971) Yu J … Takada Y (The Biochemical journal 2017) 3 4 58
  5. Distinct regions of the large extracellular domain of tetraspanin CD9 are involved in the control of human multinucleated giant cell formation. (PMID: 25551757) Hulme RS … Monk PN (PloS one 2014) 3 4 58

Products for CD9 Gene

  • Addgene plasmids for CD9

Sources for CD9 Gene

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