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Aliases for CLEC4M Gene

Aliases for CLEC4M Gene

  • C-Type Lectin Domain Family 4 Member M 2 3 5
  • CD299 Antigen 2 3 4
  • Dendritic Cell-Specific ICAM-3-Grabbing Non-Integrin 2 3 4
  • Liver/Lymph Node-Specific ICAM-3-Grabbing Non-Integrin 3 4
  • C-Type Lectin Domain Family 4, Member M 2 3
  • CD209 Antigen-Like Protein 1 3 4
  • DC-SIGN-Related Protein 3 4
  • DC-SIGN2 3 4
  • DC-SIGNR 3 4
  • CD209L 3 4
  • L-SIGN 3 4
  • CD299 3 4
  • Liver/Lymph Node-Specific ICAM-3 Grabbing Non-Integrin 3
  • Mannose Binding C-Type Lectin DC-SIGNR 3
  • DCSIGNR 3
  • HP10347 3
  • CD209L1 4
  • LSIGN 3

External Ids for CLEC4M Gene

Previous HGNC Symbols for CLEC4M Gene

  • CD209L
  • CD299

Previous GeneCards Identifiers for CLEC4M Gene

  • GC19P007735
  • GC19P007828
  • GC19P007498

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 japanese encephalitis and severe acute respiratory syndrome. Among its related pathways are Influenza A and Phagosome. GO annotations related to this gene include receptor activity and calcium-dependent protein binding. An important paralog of this gene is CLEC6A.

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. Is a receptor for ICAM3, probably by binding to mannose-like carbohydrates.

  • (Microbial infection) Acts as an attachment receptor for ebola virus (PubMed:12050398, PubMed:12502850). Acts as an attachment receptor for hepatitis C virus (PubMed:15371595, PubMed:16816373). Acts as an attachment receptor for HIV-1 (PubMed:21277928, PubMed:12502850). Acts as an attachment receptor for human coronavirus 229E (PubMed:17037540). Acts as an attachment receptor for human cytomegalovirus/HHV-5 (PubMed:12433371). Acts as an attachment receptor for influenzavirus (PubMed:21191006). Acts as an attachment receptor for SARS coronavirus (PubMed:15479853). Acts as an attachment receptor for west-nile virus (PubMed:16415006). Acts as an attachment receptor for Japanese encephalitis virus (PubMed:24623090). Acts as an attachment receptor for Marburg virus glycoprotein (PubMed:15479853).

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

Regulatory Elements for CLEC4M Gene

Enhancers for CLEC4M Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around CLEC4M on UCSC Golden Path with GeneCards custom track

Genomic Location for CLEC4M Gene

Chromosome:
19
Start:
7,763,054 bp from pter
End:
7,770,558 bp from pter
Size:
7,505 bases
Orientation:
Plus strand

Genomic View for CLEC4M Gene

Genes around CLEC4M on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLEC4M Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLEC4M Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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.
    • (Microbial infection) Interacts with ebola virus glycoprotein (PubMed:12050398, PubMed:12502850).
    • (Microbial infection) Interacts with hepatitis C virus E1 and E2 protein (PubMed:15371595, PubMed:16816373).
    • (Microbial infection) Interacts with HIV-1 gp120 (PubMed:21277928, PubMed:12502850).
    • (Microbial infection) Interacts with human coronavirus 229E spike glycoprotein.
    • (Microbial infection) Interacts with human cytomegalovirus/HHV-5 gB protein.
    • (Microbial infection) Interacts with influenzavirus hemagglutinin.
    • (Microbial infection) Interacts with SARS coronavirus spike glycoprotein.
    • (Microbial infection) Interacts with west-nile virus envelope protein E.
    • (Microbial infection) Interacts with Japanese encephalitis virus E protein.
    • (Microbial infection) Interacts with Marburg virus glycoprotein.
    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 Asn 92 and Asn 361
  • Modification sites at PhosphoSitePlus

Antibody Products

  • R&D Systems Antibodies for CLEC4M (DC-SIGNR/CD299)
  • Cloud-Clone Corp. Antibodies for CLEC4M

No data available for DME Specific Peptides for CLEC4M Gene

Domains & Families for CLEC4M Gene

Gene Families for CLEC4M Gene

Graphical View of Domain Structure for InterPro Entry

Q9H2X3

UniProtKB/Swiss-Prot:

CLC4M_HUMAN :
  • The tandem repeat domain, also called neck domain, mediates oligomerization.
Domain:
  • The tandem repeat domain, also called neck domain, mediates oligomerization.
  • Contains 1 C-type lectin domain.
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. Is a receptor for ICAM3, probably by binding to mannose-like carbohydrates.
UniProtKB/Swiss-Prot Function:
(Microbial infection) Acts as an attachment receptor for ebola virus (PubMed:12050398, PubMed:12502850). Acts as an attachment receptor for hepatitis C virus (PubMed:15371595, PubMed:16816373). Acts as an attachment receptor for HIV-1 (PubMed:21277928, PubMed:12502850). Acts as an attachment receptor for human coronavirus 229E (PubMed:17037540). Acts as an attachment receptor for human cytomegalovirus/HHV-5 (PubMed:12433371). Acts as an attachment receptor for influenzavirus (PubMed:21191006). Acts as an attachment receptor for SARS coronavirus (PubMed:15479853). Acts as an attachment receptor for west-nile virus (PubMed:16415006). Acts as an attachment receptor for Japanese encephalitis virus (PubMed:24623090). Acts as an attachment receptor for Marburg virus glycoprotein (PubMed:15479853).

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

Animal Models for CLEC4M Gene

MGI Knock Outs for CLEC4M:

miRNA for CLEC4M Gene

miRTarBase miRNAs that target CLEC4M

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets 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 4
cytosol 1
endosome 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLEC4M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane TAS 11337487
genes like me logo Genes that share ontologies with CLEC4M: view

Pathways & Interactions for CLEC4M Gene

SuperPathways for CLEC4M Gene

Superpath Contained pathways
1 Influenza A
.35
2 Phagosome
3 Tuberculosis
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:0002250 adaptive immune response IEA --
GO:0006897 endocytosis IEA --
GO:0007159 leukocyte cell-cell adhesion NAS 11337487
GO:0030193 regulation of blood coagulation IMP 21810271
GO:0035556 intracellular signal transduction NAS 11337487
genes like me logo Genes that share ontologies with CLEC4M: view

No data available for SIGNOR curated interactions for CLEC4M Gene

Drugs & Compounds for CLEC4M Gene

(1) Drugs for CLEC4M Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0

(5) Additional Compounds for CLEC4M Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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 (x38.1).

Protein differential expression in normal tissues from HIPED for CLEC4M Gene

This gene is overexpressed in Testis (65.4).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with CLEC4M: view

Primer Products

In Situ Assay Products

No data available for Protein tissue co-expression partners for CLEC4M Gene

Orthologs for CLEC4M Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLEC4M Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
Mammalia Cd209a 35
  • 64.62 (n)
  • 54.79 (a)
Cd209a 16
Cd209a 36
  • 55 (a)
ManyToMany
Cd209b 36
  • 41 (a)
ManyToMany
Cd209c 36
  • 57 (a)
ManyToMany
Cd209d 36
  • 57 (a)
ManyToMany
Cd209e 36
  • 58 (a)
ManyToMany
chimpanzee
(Pan troglodytes)
Mammalia LOC100611969 35
  • 98.21 (n)
  • 96.6 (a)
CLEC4M 36
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cd209a 35
  • 67.06 (n)
  • 55.95 (a)
cow
(Bos Taurus)
Mammalia CD209 36
  • 36 (a)
OneToMany
dog
(Canis familiaris)
Mammalia CD209 36
  • 42 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 41 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii zgc:174904 35
  • 49.36 (n)
  • 38.93 (a)
BX936386.1 36
  • 27 (a)
ManyToMany
CABZ01029886.1 36
  • 33 (a)
ManyToMany
CABZ01036814.1 36
  • 13 (a)
ManyToMany
cd209 36
  • 15 (a)
ManyToMany
CR847844.1 36
  • 24 (a)
ManyToMany
CR847844.2 36
  • 23 (a)
ManyToMany
CR847844.3 36
  • 25 (a)
ManyToMany
CR847844.4 36
  • 23 (a)
ManyToMany
CR847844.6 36
  • 17 (a)
ManyToMany
CU695221.2 36
  • 28 (a)
ManyToMany
illr1 36
  • 25 (a)
ManyToMany
illr2 36
  • 23 (a)
ManyToMany
illr3 36
  • 21 (a)
ManyToMany
illr4 36
  • 22 (a)
ManyToMany
si:ch211-133n4.11 36
  • 28 (a)
ManyToMany
si:ch211-133n4.12 36
  • 22 (a)
ManyToMany
si:ch211-133n4.7 36
  • 21 (a)
ManyToMany
si:ch211-154o6.6 36
  • 22 (a)
ManyToMany
si:ch211-170d8.8 36
  • 18 (a)
ManyToMany
si:ch211-214k5.3 36
  • 20 (a)
ManyToMany
si:ch211-232p21.6 36
  • 19 (a)
ManyToMany
si:ch73-111e15.1 36
  • 21 (a)
ManyToMany
si:ch73-122g19.1 36
  • 19 (a)
ManyToMany
si:ch73-343l4.1 36
  • 39 (a)
ManyToMany
si:ch73-343l4.2 36
  • 17 (a)
ManyToMany
si:ch73-343l4.3 36
  • 34 (a)
ManyToMany
si:ch73-343l4.4 36
  • 36 (a)
ManyToMany
si:ch73-343l4.5 36
  • 36 (a)
ManyToMany
si:ch73-343l4.6 36
  • 13 (a)
ManyToMany
si:ch73-343l4.8 36
  • 24 (a)
ManyToMany
si:dkey-12f6.5 36
  • 32 (a)
ManyToMany
si:dkey-181c13.1 36
  • 28 (a)
ManyToMany
si:dkey-187i8.2 36
  • 12 (a)
ManyToMany
zgc:174904 36
  • 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
rs2277998 - 7,766,742(+) GGCAC(A/G)ACTCC nc-transcript-variant, reference, missense
rs11465376 - 7,765,914(+) GACCC(A/G)GCTGA intron-variant, nc-transcript-variant, reference, missense
rs479448 -, - 7,766,175(-) CTTGA(C/T)AGATT intron-variant, nc-transcript-variant, reference, missense
rs12977324 -- 7,764,243(+) aagca(C/T)attac intron-variant
rs12979429 -- 7,764,294(+) attac(A/G)tcatt 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

Variation tolerance for CLEC4M Gene

Residual Variation Intolerance Score: 82.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.02; 60.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLEC4M Gene

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

Disorders for CLEC4M Gene

MalaCards: The human disease database

(7) MalaCards diseases for CLEC4M Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
japanese encephalitis
  • japanese b encephalitis
severe acute respiratory syndrome
  • sars
encephalitis
hepatitis c virus
  • hepatitic c virus
west nile virus
  • west nile virus, susceptibility to
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for CLEC4M

Genetic Association Database (GAD)
CLEC4M
Human Genome Epidemiology (HuGE) Navigator
CLEC4M
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLEC4M
genes like me logo Genes that share disorders with CLEC4M: view

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

Publications for CLEC4M Gene

  1. Selection of cDNAs encoding putative type II membrane proteins on the cell surface from a human full-length cDNA bank. (PMID: 10072769) Yokoyama-Kobayashi M. … Kato S. (Gene 1999) 2 3 4 67
  2. HIV-1 transmission by dendritic cell-specific ICAM-3-grabbing nonintegrin (DC-SIGN) is regulated by determinants in the carbohydrate recognition domain that are absent in liver/lymph node-SIGN (L-SIGN). (PMID: 19833723) Chung N.P. … Kewalramani V.N. (J. Biol. Chem. 2010) 3 23
  3. Influence of polymorphism in dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin-related (DC-SIGNR) gene on HIV-1 trans-infection. (PMID: 20152818) Zhu D. … Kitamura Y. (Biochem. Biophys. Res. Commun. 2010) 3 23
  4. Autonomous tetramerization domains in the glycan-binding receptors DC-SIGN and DC-SIGNR. (PMID: 19249311) Yu Q.D. … Taylor M.E. (J. Mol. Biol. 2009) 3 23
  5. Capture and transmission of HIV-1 by the C-type lectin L-SIGN (DC-SIGNR) is inhibited by carbohydrate-binding agents and polyanions. (PMID: 19514109) Auwerx J. … Balzarini J. (Antiviral Res. 2009) 3 23

Products for CLEC4M Gene

Sources for CLEC4M Gene

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