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Aliases for CLEC4M Gene

Aliases for CLEC4M Gene

  • C-Type Lectin Domain Family 4, Member M 2 3
  • CD299 Antigen 2 3 4
  • CD209L 3 4 6
  • Dendritic Cell-Specific ICAM-3-Grabbing Non-Integrin 2 3 4
  • Liver/Lymph Node-Specific ICAM-3-Grabbing Non-Integrin 3 4
  • CD209 Antigen-Like Protein 1 3 4
  • DC-SIGN-Related Protein 3 4
  • DC-SIGN2 3 4
  • DC-SIGNR 3 4
  • DCSIGNR 3 6
  • L-SIGN 3 4
  • CD299 3 4
  • LSIGN 3 6
  • Liver/Lymph Node-Specific ICAM-3 Grabbing Non-Integrin 3
  • C-Type Lectin Domain Family 4 Member M 3
  • Mannose Binding C-Type Lectin DC-SIGNR 3
  • HP10347 3
  • CD209L1 4

External Ids for CLEC4M Gene

Previous Symbols for CLEC4M Gene

  • CD209L
  • CD299

Summaries for CLEC4M Gene

Entrez Gene Summary for CLEC4M Gene

  • This gene encodes a transmembrane receptor and is often referred to as L-SIGN because of its expression in the endothelial cells of the lymph nodes and liver. The encoded protein is involved in the innate immune system and recognizes numerous evolutionarily divergent pathogens ranging from parasites to viruses, with a large impact on public health. The protein is organized into three distinct domains: an N-terminal transmembrane domain, a tandem-repeat neck domain and C-type lectin carbohydrate recognition domain. The extracellular region consisting of the C-type lectin and neck domains has a dual function as a pathogen recognition receptor and a cell adhesion receptor by binding carbohydrate ligands on the surface of microbes and endogenous cells. The neck region is important for homo-oligomerization which allows the receptor to bind multivalent ligands with high avidity. Variations in the number of 23 amino acid repeats in the neck domain of this protein are common and have a significant impact on ligand binding ability. This gene is closely related in terms of both sequence and function to a neighboring gene (GeneID 30835; often referred to as DC-SIGN or CD209). DC-SIGN and L-SIGN differ in their ligand-binding properties and distribution. Alternative splicing results in multiple variants.[provided by RefSeq, Feb 2009]

GeneCards Summary for CLEC4M Gene

CLEC4M (C-Type Lectin Domain Family 4, Member M) is a Protein Coding gene. Diseases associated with CLEC4M include intrauterine infections and severe acute respiratory syndrome. Among its related pathways are Tuberculosis and Influenza A. GO annotations related to this gene include receptor activity and peptide antigen binding. An important paralog of this gene is CLEC4D.

UniProtKB/Swiss-Prot for CLEC4M Gene

  • Probable pathogen-recognition receptor involved in peripheral immune surveillance in liver. May mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, HCV E2, and human SARS coronavirus protein S. Is a receptor for ICAM3, probably by binding to mannose-like carbohydrates. Is presumably a coreceptor for the SARS coronavirus.

Gene Wiki entry for CLEC4M Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLEC4M Gene

Genomics for CLEC4M Gene

Genomic Location for CLEC4M Gene

Start:
7,763,133 bp from pter
End:
7,769,605 bp from pter
Size:
6,473 bases
Orientation:
Plus strand

Genomic View for CLEC4M Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLEC4M Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLEC4M Gene

Regulatory Elements for CLEC4M Gene

Proteins for CLEC4M Gene

  • Protein details for CLEC4M Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H2X3-CLC4M_HUMAN
    Recommended name:
    C-type lectin domain family 4 member M
    Protein Accession:
    Q9H2X3
    Secondary Accessions:
    • A6NKI4
    • A8K8B3
    • Q69F40
    • Q969M4
    • Q96QP3
    • Q96QP4
    • Q96QP5
    • Q96QP6
    • Q9BXS3
    • Q9H2Q9
    • Q9H8F0
    • Q9Y2A8

    Protein attributes for CLEC4M Gene

    Size:
    399 amino acids
    Molecular mass:
    45350 Da
    Quaternary structure:
    • Homotetramer. Binds to many viral surface glycoproteins such as HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, HCV E2, and human SARS coronavirus S protein.
    Miscellaneous:
    • In vitro, is a receptor for HIV-1 and transmits HIV-1 to permissive T-cells
    SequenceCaution:
    • Sequence=AAR04559.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CLEC4M Gene

    Alternative splice isoforms for CLEC4M Gene

neXtProt entry for CLEC4M Gene

Proteomics data for CLEC4M Gene at MOPED

Post-translational modifications for CLEC4M Gene

  • Glycosylation at Asn92 and Asn361

No data available for DME Specific Peptides for CLEC4M Gene

Domains for CLEC4M Gene

Gene Families for CLEC4M Gene

HGNC:
  • CD :CD molecules
  • CLEC :C-type lectin domain containing

UniProtKB/Swiss-Prot:

CLC4M_HUMAN
Domain:
  • The tandem repeat domain, also called neck domain, mediates oligomerization:
    • Q9H2X3
  • Contains 1 C-type lectin domain.:
    • Q9H2X3
genes like me logo Genes that share domains with CLEC4M: view

Function for CLEC4M Gene

Molecular function for CLEC4M Gene

UniProtKB/Swiss-Prot Function: Probable pathogen-recognition receptor involved in peripheral immune surveillance in liver. May mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, HCV E2, and human SARS coronavirus protein S. Is a receptor for ICAM3, probably by binding to mannose-like carbohydrates. Is presumably a coreceptor for the SARS coronavirus.

Gene Ontology (GO) - Molecular Function for CLEC4M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001618 virus receptor activity IMP 15496474
GO:0004872 receptor activity NAS 11257134
GO:0005537 mannose binding IEA --
GO:0030246 carbohydrate binding NAS 11337487
GO:0030369 ICAM-3 receptor activity NAS 11257134
genes like me logo Genes that share ontologies with CLEC4M: view

Phenotypes for CLEC4M Gene

genes like me logo Genes that share phenotypes with CLEC4M: view

Animal Models for CLEC4M Gene

MGI Knock Outs for CLEC4M:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for CLEC4M Gene

Localization for CLEC4M Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLEC4M Gene

Isoform 1: Cell membrane; Single-pass type II membrane protein.
Isoform 2: Cell membrane; Single-pass type II membrane protein.
Isoform 3: Cell membrane; Single-pass type II membrane protein.
Isoform 5: Secreted.
Isoform 6: Secreted.
Isoform 7: Secreted.
Isoform 10: Secreted.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CLEC4M Gene COMPARTMENTS Subcellular localization image for CLEC4M gene
Compartment Confidence
plasma membrane 5
extracellular 3
cytosol 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLEC4M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005737 cytoplasm NAS 11337487
GO:0005887 integral component of plasma membrane TAS 10072769
GO:0016020 membrane TAS 11337487
genes like me logo Genes that share ontologies with CLEC4M: view

Pathways for CLEC4M Gene

SuperPathways for CLEC4M Gene

Superpath Contained pathways
1 Tuberculosis
2 Influenza A
.34
3 Phagosome
genes like me logo Genes that share pathways with CLEC4M: view

Pathways by source for CLEC4M Gene

3 KEGG pathways for CLEC4M Gene

Gene Ontology (GO) - Biological Process for CLEC4M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006897 endocytosis IEA --
GO:0007159 leukocyte cell-cell adhesion NAS 11337487
GO:0009988 cell-cell recognition TAS 11337487
GO:0010468 regulation of gene expression IMP 21810271
GO:0019048 modulation by virus of host morphology or physiology TAS 11337487
genes like me logo Genes that share ontologies with CLEC4M: view

Compounds for CLEC4M Gene

(1) HMDB Compounds for CLEC4M Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2

(5) Novoseek inferred chemical compound relationships for CLEC4M Gene

Compound -log(P) Hits PubMed IDs
mannose 58.7 4
polysaccharide 52.1 6
carbohydrates 26.6 1
galactose 23.9 2
allergens 18.2 2
genes like me logo Genes that share compounds with CLEC4M: view

Transcripts for CLEC4M Gene

Unigene Clusters for CLEC4M Gene

C-type lectin domain family 4, member M:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CLEC4M Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b ^ 8
SP1: - -
SP2: - -
SP3:
SP4: - -
SP5: - - -

Relevant External Links for CLEC4M Gene

GeneLoc Exon Structure for
CLEC4M
ECgene alternative splicing isoforms for
CLEC4M

Expression for CLEC4M Gene

mRNA expression in normal human tissues for CLEC4M Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLEC4M Gene

This gene is overexpressed in Liver (38.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for CLEC4M Gene

SOURCE GeneReport for Unigene cluster for CLEC4M Gene Hs.421437

mRNA Expression by UniProt/SwissProt for CLEC4M Gene

Q9H2X3-CLC4M_HUMAN
Tissue specificity: Predominantly highly expressed in liver sinusoidal endothelial cells and in lymph node. Found in placental endothelium but not in macrophages. Expressed in type II alveolar cells and lung endothelial cells.
genes like me logo Genes that share expressions with CLEC4M: view

Orthologs for CLEC4M Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLEC4M Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLEC4M 37
  • 87 (a)
OneToOne
LOC100611969 36
  • 98.21 (n)
  • 96.6 (a)
cow
(Bos Taurus)
Mammalia CD209 37
  • 36 (a)
OneToMany
dog
(Canis familiaris)
Mammalia CD209 37
  • 42 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Cd209a 36
  • 64.62 (n)
  • 54.79 (a)
Cd209a 37
  • 55 (a)
ManyToMany
Cd209b 37
  • 41 (a)
ManyToMany
Cd209c 37
  • 57 (a)
ManyToMany
Cd209d 16
Cd209d 37
  • 57 (a)
ManyToMany
Cd209e 37
  • 58 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 41 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Cd209a 36
  • 67.06 (n)
  • 55.95 (a)
zebrafish
(Danio rerio)
Actinopterygii BX936386.1 37
  • 27 (a)
ManyToMany
CABZ01029886.1 37
  • 33 (a)
ManyToMany
CABZ01036814.1 37
  • 13 (a)
ManyToMany
cd209 37
  • 15 (a)
ManyToMany
CR847844.1 37
  • 24 (a)
ManyToMany
CR847844.2 37
  • 23 (a)
ManyToMany
CR847844.3 37
  • 25 (a)
ManyToMany
CR847844.4 37
  • 23 (a)
ManyToMany
CR847844.6 37
  • 17 (a)
ManyToMany
CU695221.2 37
  • 28 (a)
ManyToMany
illr1 37
  • 25 (a)
ManyToMany
illr2 37
  • 23 (a)
ManyToMany
illr3 37
  • 21 (a)
ManyToMany
illr4 37
  • 22 (a)
ManyToMany
si:ch211-133n4.11 37
  • 28 (a)
ManyToMany
si:ch211-133n4.12 37
  • 22 (a)
ManyToMany
si:ch211-133n4.7 37
  • 21 (a)
ManyToMany
si:ch211-154o6.6 37
  • 22 (a)
ManyToMany
si:ch211-170d8.8 37
  • 18 (a)
ManyToMany
si:ch211-214k5.3 37
  • 20 (a)
ManyToMany
si:ch211-232p21.6 37
  • 19 (a)
ManyToMany
si:ch73-111e15.1 37
  • 21 (a)
ManyToMany
si:ch73-122g19.1 37
  • 19 (a)
ManyToMany
si:ch73-343l4.1 37
  • 39 (a)
ManyToMany
si:ch73-343l4.2 37
  • 17 (a)
ManyToMany
si:ch73-343l4.3 37
  • 34 (a)
ManyToMany
si:ch73-343l4.4 37
  • 36 (a)
ManyToMany
si:ch73-343l4.5 37
  • 36 (a)
ManyToMany
si:ch73-343l4.6 37
  • 13 (a)
ManyToMany
si:ch73-343l4.8 37
  • 24 (a)
ManyToMany
si:dkey-12f6.5 37
  • 32 (a)
ManyToMany
si:dkey-181c13.1 37
  • 28 (a)
ManyToMany
si:dkey-187i8.2 37
  • 12 (a)
ManyToMany
zgc:174904 36
  • 49.36 (n)
  • 38.93 (a)
zgc:174904 37
  • 25 (a)
ManyToMany
Species with no ortholog for CLEC4M:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLEC4M Gene

ENSEMBL:
Gene Tree for CLEC4M (if available)
TreeFam:
Gene Tree for CLEC4M (if available)

Paralogs for CLEC4M Gene

genes like me logo Genes that share paralogs with CLEC4M: view

Variants for CLEC4M Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for CLEC4M Gene

Q9H2X3-CLC4M_HUMAN
The number of repeats in the tandem repeat domain is shown to vary between 3 and 9 per allele thus contributing to a further variability in addition to alternative splicing. The shown 7 repeat-containing form has been shown to be the most frequent one (53.9%) in a study with 350 Caucasian individuals

Sequence variations from dbSNP and Humsavar for CLEC4M Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type MAF
rs15282 -- 7,769,388(-) AAAAG(A/G)GTGCA utr-variant-3-prime, nc-transcript-variant, downstream-variant-500B
rs475896 -- 7,766,543(+) TCCAC(C/G)CAACA intron-variant, nc-transcript-variant
rs479448 -, - 7,766,175(-) CTTGA(C/T)AGATT reference, missense, intron-variant, nc-transcript-variant
rs488449 -- 7,762,313(-) AATTT(A/C)AAGAA upstream-variant-2KB
rs538442 -- 7,764,278(-) tctca(A/G)ttgaa intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLEC4M Gene

Variant ID Type Subtype PubMed ID
esv2751809 CNV Gain 17911159
nsv833732 CNV Gain 17160897
esv2718107 CNV Deletion 23290073
esv2718108 CNV Deletion 23290073
esv1300284 CNV Deletion 17803354

Relevant External Links for CLEC4M Gene

HapMap Linkage Disequilibrium report
CLEC4M
Human Gene Mutation Database (HGMD)
CLEC4M

Disorders for CLEC4M Gene

(1) University of Copenhagen DISEASES for CLEC4M Gene

(8) Novoseek inferred disease relationships for CLEC4M Gene

Disease -log(P) Hits PubMed IDs
immunodeficiency 54.9 15
hepatitis c 42.8 11
virus infection 40.4 5
hiv infections 21.8 6
autoimmunity 17.1 1

Relevant External Links for CLEC4M

Genetic Association Database (GAD)
CLEC4M
Human Genome Epidemiology (HuGE) Navigator
CLEC4M
genes like me logo Genes that share disorders with CLEC4M: view

No data available for UniProtKB/Swiss-Prot for CLEC4M Gene

Publications for CLEC4M Gene

  1. DC-SIGN, a related gene, DC-SIGNR, and CD23 form a cluster on 19p13. (PMID: 10975799) Soilleux E.J. … Trowsdale J. (J. Immunol. 2000) 3 4 23
  2. DC-SIGNR, a DC-SIGN homologue expressed in endothelial cells, binds to human and simian immunodeficiency viruses and activates infection in trans. (PMID: 11226297) Poehlmann S. … Doms R.W. (Proc. Natl. Acad. Sci. U.S.A. 2001) 3 4 23
  3. A dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN)-related protein is highly expressed on human liver sinusoidal endothelial cells and promotes HIV-1 infection. (PMID: 11257134) Bashirova A.A. … Carrington M. (J. Exp. Med. 2001) 3 4 23
  4. Extensive repertoire of membrane-bound and soluble dendritic cell- specific ICAM-3-grabbing nonintegrin 1 (DC-SIGN1) and DC-SIGN2 isoforms. Inter-individual variation in expression of DC-SIGN transcripts. (PMID: 11337487) Mummidi S. … Ahuja S.K. (J. Biol. Chem. 2001) 3 4 23
  5. A novel mechanism of carbohydrate recognition by the C-type lectins DC-SIGN and DC-SIGNR. Subunit organization and binding to multivalent ligands. (PMID: 11384997) Mitchell D.A. … Drickamer K. (J. Biol. Chem. 2001) 3 4 23

Products for CLEC4M Gene

Sources for CLEC4M Gene

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