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Aliases for CLEC4A Gene

Aliases for CLEC4A Gene

  • C-Type Lectin Domain Family 4 Member A 2 3 3 5
  • C-Type (Calcium Dependent, Carbohydrate-Recognition Domain) Lectin, Superfamily Member 6 2 3
  • C-Type Lectin Superfamily Member 6 3 4
  • Dendritic Cell Immunoreceptor 3 4
  • Lectin-Like Immunoreceptor 3 4
  • C-Type Lectin DDB27 3 4
  • CLECSF6 3 4
  • DCIR 3 4
  • LLIR 3 4
  • C-Type Lectin Domain Family 4, Member A 2
  • HDCGC13P 3
  • CD367 3
  • DDB27 3

External Ids for CLEC4A Gene

Previous HGNC Symbols for CLEC4A Gene

  • CLECSF6

Previous GeneCards Identifiers for CLEC4A Gene

  • GC12P008168
  • GC12P008169
  • GC12P008170
  • GC12P008277
  • GC12P008087
  • GC12P008278
  • GC12P008083

Summaries for CLEC4A Gene

Entrez Gene Summary for CLEC4A Gene

  • This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type 2 transmembrane protein may play a role in inflammatory and immune response. Multiple transcript variants encoding distinct isoforms have been identified for this gene. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLEC4A Gene

CLEC4A (C-Type Lectin Domain Family 4 Member A) is a Protein Coding gene. Diseases associated with CLEC4A include Inflammatory Bowel Disease 6. Among its related pathways are C-type lectin receptor signaling pathway and CLEC7A (Dectin-1) signaling. Gene Ontology (GO) annotations related to this gene include transmembrane signaling receptor activity and carbohydrate binding. An important paralog of this gene is CLEC4C.

UniProtKB/Swiss-Prot for CLEC4A Gene

  • May be involved in regulating immune reactivity. May play a role in modulating dendritic cells (DC) differentiation and/or maturation. May be involved via its ITIM motif (immunoreceptor tyrosine-based inhibitory motifs) in the inhibition of B-cell-receptor-mediated calcium mobilization and protein tyrosine phosphorylation.

Gene Wiki entry for CLEC4A Gene

Additional gene information for CLEC4A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLEC4A Gene

Genomics for CLEC4A Gene

GeneHancer (GH) Regulatory Elements for CLEC4A Gene

Promoters and enhancers for CLEC4A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J008123 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 650.7 +0.2 153 0.4 RUNX3 CLEC4A POU5F1P3 ENSG00000284697
GH12J008156 Enhancer 0.9 Ensembl ENCODE 20.6 +33.6 33569 2 PKNOX1 JUN ZNF766 ZNF316 POLR2A ZSCAN5C NFE2 MAFK ZNF639 ZNF197 ZNF705A CLEC4A NECAP1 ENSG00000284393 FAM66C
GH12J008179 Promoter/Enhancer 1.4 Ensembl ENCODE 12.3 +56.7 56681 1.4 HDGF SIN3A GLI4 ZNF2 YY1 GLIS2 ZNF213 ZNF143 KLF7 SP3 FAM66C CLEC4A LINC00612 ZNF705A ENSG00000276417
GH12J008087 Enhancer 1 Ensembl ENCODE dbSUPER 11.3 -35.3 -35251 2.1 PKNOX1 ZNF687 EBF1 MEF2B BATF IKZF1 TARDBP ZNF143 ETV6 RUNX3 NECAP1 C3AR1 CLEC4A FOXJ2 GC12P008091 ENSG00000284697
GH12J007969 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 6.1 -152.4 -152432 4.4 HDGF PKNOX1 SMAD1 ARNT SIN3A FEZF1 POLR2B ZNF207 ZNF143 FOS SLC2A3 NECAP1 CLEC4A FOXJ2 CLEC6A C3AR1 GC12P007976
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLEC4A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLEC4A gene promoter:
  • IRF-1
  • AML1a
  • POU3F2
  • Pax-2b
  • Pax-2a
  • Pax-2
  • Nkx3-1 v4
  • Nkx3-1 v3
  • Nkx3-1 v2
  • Nkx3-1 v1

Genomic Locations for CLEC4A Gene

Genomic Locations for CLEC4A Gene
chr12:8,123,632-8,138,607
(GRCh38/hg38)
Size:
14,976 bases
Orientation:
Plus strand
chr12:8,276,228-8,291,203
(GRCh37/hg19)
Size:
14,976 bases
Orientation:
Plus strand

Genomic View for CLEC4A Gene

Genes around CLEC4A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLEC4A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLEC4A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLEC4A Gene

Proteins for CLEC4A Gene

  • Protein details for CLEC4A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UMR7-CLC4A_HUMAN
    Recommended name:
    C-type lectin domain family 4 member A
    Protein Accession:
    Q9UMR7
    Secondary Accessions:
    • Q17R69
    • Q8WXW9
    • Q9H2Z9
    • Q9NS33
    • Q9UI34

    Protein attributes for CLEC4A Gene

    Size:
    237 amino acids
    Molecular mass:
    27512 Da
    Quaternary structure:
    • May interact with PTPN6 via its ITIM motif.
    SequenceCaution:
    • Sequence=AAL56016.1; Type=Frameshift; Positions=229; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CLEC4A Gene

    Alternative splice isoforms for CLEC4A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLEC4A Gene

Post-translational modifications for CLEC4A Gene

  • Glycosylation at posLast=185185
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for CLEC4A
  • Boster Bio Antibodies for CLEC4A
  • Santa Cruz Biotechnology (SCBT) Antibodies for CLEC4A

No data available for DME Specific Peptides for CLEC4A Gene

Domains & Families for CLEC4A Gene

Gene Families for CLEC4A Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for CLEC4A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UMR7

UniProtKB/Swiss-Prot:

CLC4A_HUMAN :
  • Contains 1 copy of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases.
Domain:
  • Contains 1 copy of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2-containing phosphatases.
genes like me logo Genes that share domains with CLEC4A: view

Function for CLEC4A Gene

Molecular function for CLEC4A Gene

UniProtKB/Swiss-Prot Function:
May be involved in regulating immune reactivity. May play a role in modulating dendritic cells (DC) differentiation and/or maturation. May be involved via its ITIM motif (immunoreceptor tyrosine-based inhibitory motifs) in the inhibition of B-cell-receptor-mediated calcium mobilization and protein tyrosine phosphorylation.
UniProtKB/Swiss-Prot Induction:
Isoform 2 mRNA expression is up-regulated by agonists of neutrophils CSF2/GM-CSF, IL3/interleukin-3, IL4/interleukin-4 and IL13/interleukin-13.

Gene Ontology (GO) - Molecular Function for CLEC4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004888 transmembrane signaling receptor activity TAS 10438934
GO:0030246 carbohydrate binding IEA --
genes like me logo Genes that share ontologies with CLEC4A: view
genes like me logo Genes that share phenotypes with CLEC4A: view

Animal Models for CLEC4A Gene

MGI Knock Outs for CLEC4A:

Animal Model Products

CRISPR Products

miRNA for CLEC4A Gene

miRTarBase miRNAs that target CLEC4A

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLEC4A

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLEC4A Gene

Localization for CLEC4A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLEC4A Gene

Membrane; Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
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 CLEC4A gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytosol 2
nucleus 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CLEC4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 10438934
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CLEC4A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLEC4A Gene

Pathways & Interactions for CLEC4A Gene

genes like me logo Genes that share pathways with CLEC4A: view

Pathways by source for CLEC4A Gene

Gene Ontology (GO) - Biological Process for CLEC4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002223 stimulatory C-type lectin receptor signaling pathway TAS --
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0007155 cell adhesion TAS 10438934
GO:0007166 cell surface receptor signaling pathway TAS 10438934
genes like me logo Genes that share ontologies with CLEC4A: view

No data available for SIGNOR curated interactions for CLEC4A Gene

Drugs & Compounds for CLEC4A Gene

(16) Drugs for CLEC4A Gene - From: HMDB and Novoseek

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

(8) Additional Compounds for CLEC4A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLEC4A: view

Transcripts for CLEC4A Gene

Unigene Clusters for CLEC4A Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLEC4A

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLEC4A Gene

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

Relevant External Links for CLEC4A Gene

GeneLoc Exon Structure for
CLEC4A
ECgene alternative splicing isoforms for
CLEC4A

Expression for CLEC4A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLEC4A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLEC4A Gene

This gene is overexpressed in Whole Blood (x25.5).

Protein differential expression in normal tissues from HIPED for CLEC4A Gene

This gene is overexpressed in Monocytes (34.7), Plasma (20.0), and Neutrophil (12.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLEC4A Gene



NURSA nuclear receptor signaling pathways regulating expression of CLEC4A Gene:

CLEC4A

SOURCE GeneReport for Unigene cluster for CLEC4A Gene:

Hs.504657

mRNA Expression by UniProt/SwissProt for CLEC4A Gene:

Q9UMR7-CLC4A_HUMAN
Tissue specificity: Expressed in dendritic cells, myeloid cells, B-cells and HL-60 cells (at protein level). TNF alpha, IL-1 alpha, and LPS, down-regulated expression at the surface of neutrophils (at protein level). Expressed preferentially in hematopoietic tissues. Expressed in peripheral blood leukocytes, neutrophils, moderate quantities in spleen, lymph node, and bone marrow, and at very low levels in thymus. Expressed in Ag-presenting cells (DC, monocytes, macrophages and B-cells), as well as on granulocytes. Expression was decreased in DC by signals inducing its maturation (e.g. CD40 ligand, LPS, and TNF alpha).

Evidence on tissue expression from TISSUES for CLEC4A Gene

  • Lung(4.2)
  • Spleen(2.4)
  • Blood(2.3)
  • Lymph node(2.3)
genes like me logo Genes that share expression patterns with CLEC4A: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLEC4A Gene

Orthologs for CLEC4A Gene

This gene was present in the common ancestor of mammals.

Orthologs for CLEC4A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLEC4A 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CLEC4A 33
  • 77.54 (n)
cow
(Bos Taurus)
Mammalia CLEC4A 34 33
  • 75.54 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Clec4a 33
  • 72.08 (n)
mouse
(Mus musculus)
Mammalia Clec4a2 16 34 33
  • 70.07 (n)
Clec4a1 34
  • 51 (a)
OneToMany
Clec4a4 34
  • 51 (a)
OneToMany
Clec4a3 34
  • 49 (a)
OneToMany
Clec4b1 34
  • 45 (a)
OneToMany
Clec4b2 34
  • 44 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 42 (a)
OneToMany
Species where no ortholog for CLEC4A was found in the sources mined by GeneCards:
  • 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)
  • zebrafish (Danio rerio)

Evolution for CLEC4A Gene

ENSEMBL:
Gene Tree for CLEC4A (if available)
TreeFam:
Gene Tree for CLEC4A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLEC4A: view image

Paralogs for CLEC4A Gene

Paralogs for CLEC4A Gene

(5) SIMAP similar genes for CLEC4A Gene using alignment to 2 proteins:

  • CLC4A_HUMAN
  • H0YGF9_HUMAN
genes like me logo Genes that share paralogs with CLEC4A: view

Variants for CLEC4A Gene

Sequence variations from dbSNP and Humsavar for CLEC4A Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000027759 -- 8,108,370(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000075788 -- 8,124,926(+) T/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000082410 -- 8,114,345(+) C/A/T genic_upstream_transcript_variant, intron_variant
rs1000215200 -- 8,105,421(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000287176 -- 8,132,462(+) T/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CLEC4A Gene

Variant ID Type Subtype PubMed ID
esv2759877 CNV gain+loss 17122850
nsv428270 CNV gain 18775914
nsv976563 CNV duplication 23825009

Variation tolerance for CLEC4A Gene

Residual Variation Intolerance Score: 76.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.76; 33.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLEC4A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLEC4A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLEC4A Gene

Disorders for CLEC4A Gene

MalaCards: The human disease database

(1) MalaCards diseases for CLEC4A Gene - From: DISEASES

Disorder Aliases PubMed IDs
inflammatory bowel disease 6
  • ibd6
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CLEC4A

genes like me logo Genes that share disorders with CLEC4A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLEC4A Gene

Publications for CLEC4A Gene

  1. APCs express DCIR, a novel C-type lectin surface receptor containing an immunoreceptor tyrosine-based inhibitory motif. (PMID: 10438934) Bates EE … Saeland S (Journal of immunology (Baltimore, Md. : 1950) 1999) 2 3 4 22 58
  2. The expression pattern of the ITIM-bearing lectin CLECSF6 in neutrophils suggests a key role in the control of inflammation. (PMID: 11994513) Richard M … Beaulieu AD (Journal of leukocyte biology 2002) 3 4 22 58
  3. Cloning and characterization of a novel ITIM containing lectin-like immunoreceptor LLIR and its two transmembrane region deletion variants. (PMID: 11178971) Huang X … Cao X (Biochemical and biophysical research communications 2001) 3 4 22 58
  4. Association of arthritis with a gene complex encoding C-type lectin-like receptors. (PMID: 17665455) Lorentzen JC … Fossum S (Arthritis and rheumatism 2007) 3 22 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for CLEC4A Gene

Sources for CLEC4A Gene

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