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CD9 CD9 molecule [ Homo sapiens (human) ]

Gene ID: 928, updated on 27-Nov-2024

Summary

Official Symbol
CD9provided by HGNC
Official Full Name
CD9 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1709
See related
Ensembl:ENSG00000010278 MIM:143030; AllianceGenome:HGNC:1709
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
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Genomic context

See CD9 in Genome Data Viewer
Location:
12p13.31
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6199946..6238266)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6207556..6245881)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6309112..6347432)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6268183-6268756 Neighboring gene Sharpr-MPRA regulatory region 14257 Neighboring gene uncharacterized LOC105369623 Neighboring gene uncharacterized LOC105369622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6289294-6289864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6299563-6300248 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6300249-6300934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6308438-6309050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6309051-6309662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6310889-6311501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6311502-6312113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6319522-6320145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6320176-6320677 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6323515-6324018 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:6324019-6324520 and GRCh37_chr12:6324521-6325024 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:6327115-6328314 Neighboring gene Sharpr-MPRA regulatory region 3368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6332057-6332610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6332611-6333162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6333163-6333716 Neighboring gene uncharacterized LOC105369625 Neighboring gene Sharpr-MPRA regulatory region 10655 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6350388-6350888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6350889-6351389 Neighboring gene CRISPRi-validated cis-regulatory element chr12.283 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6378001-6378746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4158 Neighboring gene ATP synthase membrane subunit f pseudogene 5 Neighboring gene Sharpr-MPRA regulatory region 10601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6390295-6390794 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:6402555-6402765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:6404819-6405319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6418662-6419382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6427837-6428456 Neighboring gene pleckstrin homology and RhoGEF domain containing G6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6432098-6432639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6433181-6433722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6433723-6434262

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ99568

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables integrin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to low-density lipoprotein particle stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in fusion of sperm to egg plasma membrane involved in single fertilization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in glial cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in myoblast fusion involved in skeletal muscle regeneration ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of platelet aggregation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in paranodal junction assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in platelet activation NAS
Non-traceable Author Statement
more info
PubMed 
involved_in receptor internalization ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of macrophage migration IEA
Inferred from Electronic Annotation
more info
 
involved_in sperm-egg recognition ISS
Inferred from Sequence or Structural Similarity
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)

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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.

Genomic

  1. NG_055677.1 RefSeqGene

    Range
    5694..43560
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1189

mRNA and Protein(s)

  1. NM_001330312.2NP_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. Variants 2 and 11-14 all encode the same isoform (2).
    Source sequence(s)
    AI003581, AL523128, X60111
    Consensus CDS
    CCDS81654.1
    UniProtKB/TrEMBL
    A6NNI4, B4DPP0
    Related
    ENSP00000494858.1, ENST00000642746.1
    Conserved Domains (1) summary
    cd03152
    Location:42124
    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 ...
  2. NM_001413241.1NP_001400170.1  CD9 antigen isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC006057
    UniProtKB/TrEMBL
    A0A087WU13
    Related
    ENSP00000478288.2, ENST00000610354.5
  3. NM_001413242.1NP_001400171.1  CD9 antigen isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC006057
    UniProtKB/TrEMBL
    G8JLH6
    Related
    ENSP00000371959.5, ENST00000382519.9
  4. NM_001413243.1NP_001400172.1  CD9 antigen isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC006057
    UniProtKB/Swiss-Prot
    D3DUQ9, P21926, Q5J7W6, Q96ES4
    Related
    ENSP00000371958.1, ENST00000382518.6
  5. NM_001413244.1NP_001400173.1  CD9 antigen isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC006057
  6. NM_001413245.1NP_001400174.1  CD9 antigen isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC006057
  7. NM_001413246.1NP_001400175.1  CD9 antigen isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC006057
  8. NM_001413247.1NP_001400176.1  CD9 antigen isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC006057
  9. NM_001413248.1NP_001400177.1  CD9 antigen isoform 9

    Status: REVIEWED

    Source sequence(s)
    AC006057
  10. NM_001413249.1NP_001400178.1  CD9 antigen isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC006057
    UniProtKB/TrEMBL
    A6NNI4
    Related
    ENST00000676788.1
  11. NM_001413250.1NP_001400179.1  CD9 antigen isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC006057
    UniProtKB/TrEMBL
    A6NNI4
  12. NM_001413251.1NP_001400180.1  CD9 antigen isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC006057
    UniProtKB/TrEMBL
    A6NNI4
    Related
    ENSP00000371955.2, ENST00000382515.7
  13. NM_001413252.1NP_001400181.1  CD9 antigen isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC006057
    UniProtKB/TrEMBL
    A6NNI4
    Related
    ENSP00000495090.1, ENST00000646407.1
  14. 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 isoform 1. Variants 1 and 5 both encode the same isoform (1).
    Source sequence(s)
    AI003581, BM763066, X60111
    Consensus CDS
    CCDS8540.1
    UniProtKB/Swiss-Prot
    D3DUQ9, P21926, Q5J7W6, Q96ES4
    UniProtKB/TrEMBL
    A0A7I2V3T7
    Related
    ENSP00000009180.4, ENST00000009180.10
    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:10217
    Tetraspannin; Tetraspanin family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    6199946..6238266
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005253814.5XP_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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6207556..6245881
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373859.1XP_054229834.1  CD9 antigen isoform X1