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ICAM3 intercellular adhesion molecule 3 [ Homo sapiens (human) ]

Gene ID: 3385, updated on 15-Apr-2019

Summary

Official Symbol
ICAM3provided by HGNC
Official Full Name
intercellular adhesion molecule 3provided by HGNC
Primary source
HGNC:HGNC:5346
See related
Ensembl:ENSG00000076662 MIM:146631
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
CD50; CDW50; ICAM-R
Summary
The protein encoded by this gene is a member of the intercellular adhesion molecule (ICAM) family. All ICAM proteins are type I transmembrane glycoproteins, contain 2-9 immunoglobulin-like C2-type domains, and bind to the leukocyte adhesion LFA-1 protein. This protein is constitutively and abundantly expressed by all leucocytes and may be the most important ligand for LFA-1 in the initiation of the immune response. It functions not only as an adhesion molecule, but also as a potent signalling molecule. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2016]
Expression
Biased expression in bone marrow (RPKM 55.9), spleen (RPKM 28.5) and 12 other tissues See more
Orthologs

Genomic context

See ICAM3 in Genome Data Viewer
Location:
19p13.2
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (10333776..10339834, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10444452..10450345, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ferredoxin 2 Neighboring gene ribonucleoprotein, PTB binding 1 Neighboring gene tyrosine kinase 2 Neighboring gene cell division cycle 37 Neighboring gene microRNA 1181

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 meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env AM3 inhibits the interaction of DC-SIGN with ICAM3 and HIV-1 gp120 protein and blocks the DC-SIGN-dependent capture of HIV virions and the HIV trans-infection capability of DC-SIGN transfectants PubMed
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with ICAM3; predicted interaction to be relevant to viral egress at plasma membrane/extracellular matrix PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • C-type lectin receptors (CLRs), organism-specific biosystem (from REACTOME)
    C-type lectin receptors (CLRs), organism-specific biosystemPathogen recognition is central to the induction of T cell differentiation. Groups of pathogens share similar structures known as pathogen-associated molecular patterns (PAMPs), which are recognised ...
  • CD209 (DC-SIGN) signaling, organism-specific biosystem (from REACTOME)
    CD209 (DC-SIGN) signaling, organism-specific biosystemCD209 (also called as DC-SIGN (DC-specific intracellular adhesion molecule-3-grabbing non-integrin)) is a type II transmembrane C-type lectin receptor preferentially expressed on dendritic cells (DCs...
  • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
    Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
    Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystem (from REACTOME)
    Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystemA number of receptors and cell adhesion molecules play a key role in modifying the response of cells of lymphoid origin (such as B-, T- and NK cells) to self and tumor antigens, as well as to pathoge...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
    Integrin cell surface interactions, organism-specific biosystemThe extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
integrin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integrin binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
phagocytosis IEA
Inferred from Electronic Annotation
more info
 
regulation of immune response TAS
Traceable Author Statement
more info
 
stimulatory C-type lectin receptor signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
intercellular adhesion molecule 3
Names
ICAM-3

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_001320605.1NP_001307534.1  intercellular adhesion molecule 3 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate internal exon, compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.
    Source sequence(s)
    AC114271, AK226023, BC040123, CR982084
    Conserved Domains (3) summary
    pfam03921
    Location:32114
    ICAM_N; Intercellular adhesion molecule (ICAM), N-terminal domain
    pfam13895
    Location:221300
    Ig_2; Immunoglobulin domain
    cl11960
    Location:117211
    Ig; Immunoglobulin domain
  2. NM_001320606.1NP_001307535.1  intercellular adhesion molecule 3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 3 which is shorter than isoform 1.
    Source sequence(s)
    AK309643, BC040123, CR982084
    Consensus CDS
    CCDS82290.1
    UniProtKB/TrEMBL
    K7ERN2
    Related
    ENSP00000468333.1, ENST00000589261.5
    Conserved Domains (4) summary
    smart00410
    Location:343399
    IG_like; Immunoglobulin like
    pfam03921
    Location:137
    ICAM_N; Intercellular adhesion molecule (ICAM), N-terminal domain
    pfam13895
    Location:240319
    Ig_2; Immunoglobulin domain
    cl11960
    Location:40134
    Ig; Immunoglobulin domain
  3. NM_001320608.1NP_001307537.1  intercellular adhesion molecule 3 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) retains an intron and initiates translation at a downstream start site, compared to variant 1. It encodes isoform 4 which is shorter than isoform 1.
    Source sequence(s)
    AC114271, BC034409, BC046121, CR982084
    Conserved Domains (3) summary
    smart00410
    Location:159215
    IG_like; Immunoglobulin like
    pfam13895
    Location:56135
    Ig_2; Immunoglobulin domain
    cl11960
    Location:160208
    Ig; Immunoglobulin domain
  4. NM_002162.5NP_002153.2  intercellular adhesion molecule 3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002153.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC114271, AK226023, BC040123, CR982084
    Consensus CDS
    CCDS12235.1
    UniProtKB/Swiss-Prot
    P32942
    UniProtKB/TrEMBL
    A0A024R7C1
    Related
    ENSP00000160262.3, ENST00000160262.10
    Conserved Domains (4) summary
    pfam03921
    Location:32114
    ICAM_N; Intercellular adhesion molecule (ICAM), N-terminal domain
    pfam13895
    Location:317396
    Ig_2; Immunoglobulin domain
    cd00096
    Location:420476
    Ig; Immunoglobulin domain
    cl11960
    Location:117211
    Ig; Immunoglobulin domain

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_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    10333776..10339834 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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