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Aliases for CLEC3A Gene

Aliases for CLEC3A Gene

  • C-Type Lectin Domain Family 3 Member A 2 3 5
  • C-Type (Calcium Dependent, Carbohydrate-Recognition Domain) Lectin, Superfamily Member 1 (Cartilage-Derived) 2 3
  • CLECSF1 3 4
  • C-Type Lectin Domain Family 3, Member A 2
  • C-Type Lectin Superfamily Member 1 4
  • Cartilage-Derived C-Type Lectin 4

External Ids for CLEC3A Gene

Previous HGNC Symbols for CLEC3A Gene


Previous GeneCards Identifiers for CLEC3A Gene

  • GC16P076614
  • GC16P063813

Summaries for CLEC3A Gene

GeneCards Summary for CLEC3A Gene

CLEC3A (C-Type Lectin Domain Family 3 Member A) is a Protein Coding gene. GO annotations related to this gene include carbohydrate binding. An important paralog of this gene is CLEC3B.

UniProtKB/Swiss-Prot for CLEC3A Gene

  • Promotes cell adhesion to laminin-332 and fibronectin.

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLEC3A Gene

Genomics for CLEC3A Gene

Regulatory Elements for CLEC3A Gene

Enhancers for CLEC3A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16G078098 1.2 ENCODE 17.8 +77.2 77171 2.1 CREB3L1 MLX AGO1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 CLEC3A WWOX GC16M078111
GH16G077990 0.9 Ensembl ENCODE 23.1 -29.5 -29463 4.6 ZNF133 MNT CHD7 JUND POLR2A ZNF239 POU5F1 FOS FOSL2 CLEC3A VAT1L WWOX LOC105371351
GH16G077966 0.9 ENCODE 19.5 -55.1 -55078 3.4 PKNOX1 NFIB GLI4 FEZF1 RAD21 YY1 HSF1 ZNF143 THAP11 MIXL1 CLEC3A WWOX NUDT7 VAT1L LOC105371351
GH16G078002 1.1 Ensembl ENCODE 13.5 -19.3 -19315 0.8 PKNOX1 NFIB FEZF1 GLI4 ZNF2 RAD21 HSF1 ZNF143 FOS MIXL1 CLEC3A WWOX LOC105371351
GH16G077961 0.9 ENCODE 15.9 -59.7 -59692 3.6 PKNOX1 FOXA2 MLX WRNIP1 RARA CBX5 FOS ETV6 RCOR1 CREM CLEC3A NUDT7 VAT1L WWOX LOC105371351
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLEC3A on UCSC Golden Path with GeneCards custom track

Genomic Location for CLEC3A Gene

78,022,515 bp from pter
78,066,761 bp from pter
44,247 bases
Plus strand

Genomic View for CLEC3A Gene

Genes around CLEC3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLEC3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLEC3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLEC3A Gene

Proteins for CLEC3A Gene

  • Protein details for CLEC3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    C-type lectin domain family 3 member A
    Protein Accession:
    Secondary Accessions:
    • B2R8C4
    • Q3SX91
    • Q6UXF5

    Protein attributes for CLEC3A Gene

    197 amino acids
    Molecular mass:
    22233 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAQ88742.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for CLEC3A Gene

Post-translational modifications for CLEC3A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLEC3A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLEC3A Gene

Domains & Families for CLEC3A Gene

Gene Families for CLEC3A Gene

Protein Domains for CLEC3A Gene

Suggested Antigen Peptide Sequences for CLEC3A Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CLEC3A: view

No data available for UniProtKB/Swiss-Prot for CLEC3A Gene

Function for CLEC3A Gene

Molecular function for CLEC3A Gene

UniProtKB/Swiss-Prot Function:
Promotes cell adhesion to laminin-332 and fibronectin.

Gene Ontology (GO) - Molecular Function for CLEC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030246 carbohydrate binding IEA --
genes like me logo Genes that share ontologies with CLEC3A: view
genes like me logo Genes that share phenotypes with CLEC3A: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CLEC3A

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CLEC3A Gene

Localization for CLEC3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLEC3A Gene


Subcellular locations from

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 CLEC3A gene
Compartment Confidence
extracellular 5
cytosol 1

Gene Ontology (GO) - Cellular Components for CLEC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
genes like me logo Genes that share ontologies with CLEC3A: view

Pathways & Interactions for CLEC3A Gene

SuperPathways for CLEC3A Gene

No Data Available

Interacting Proteins for CLEC3A Gene

Selected Interacting proteins: O75596-CLC3A_HUMAN for CLEC3A Gene via IID

Gene Ontology (GO) - Biological Process for CLEC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 10524194
genes like me logo Genes that share ontologies with CLEC3A: view

No data available for Pathways by source and SIGNOR curated interactions for CLEC3A Gene

Drugs & Compounds for CLEC3A Gene

No Compound Related Data Available

Transcripts for CLEC3A Gene

mRNA/cDNA for CLEC3A Gene

(2) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(15) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CLEC3A Gene

C-type lectin domain family 3, member A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLEC3A Gene

No ASD Table

Relevant External Links for CLEC3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLEC3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLEC3A Gene

mRNA differential expression in normal tissues according to GTEx for CLEC3A Gene

This gene is overexpressed in Bladder (x23.8).

Protein differential expression in normal tissues from HIPED for CLEC3A Gene

This gene is overexpressed in Kidney (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLEC3A Gene

Protein tissue co-expression partners for CLEC3A Gene

NURSA nuclear receptor signaling pathways regulating expression of CLEC3A Gene:


SOURCE GeneReport for Unigene cluster for CLEC3A Gene:


mRNA Expression by UniProt/SwissProt for CLEC3A Gene:

Tissue specificity: Restricted to cartilage and breast. Also expressed in breast cancers.
genes like me logo Genes that share expression patterns with CLEC3A: view

Primer Products

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLEC3A Gene

Orthologs for CLEC3A Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLEC3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLEC3A 34 35
  • 99.32 (n)
(Canis familiaris)
Mammalia CLEC3A 34 35
  • 91.16 (n)
(Bos Taurus)
Mammalia CLEC3A 34 35
  • 89.51 (n)
(Rattus norvegicus)
Mammalia Clec3a 34
  • 87.41 (n)
(Mus musculus)
Mammalia Clec3a 34 16 35
  • 86.05 (n)
(Monodelphis domestica)
Mammalia CLEC3A 35
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia CLEC3A 35
  • 79 (a)
(Gallus gallus)
Aves CLEC3A 34 35
  • 74.27 (n)
(Anolis carolinensis)
Reptilia CLEC3A 35
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clec3a 34
  • 69.43 (n)
(Danio rerio)
Actinopterygii LOC100330122 34
  • 62.15 (n)
  • 57 (a)
Species where no ortholog for CLEC3A 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)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLEC3A Gene

Gene Tree for CLEC3A (if available)
Gene Tree for CLEC3A (if available)

Paralogs for CLEC3A Gene

Paralogs for CLEC3A Gene

(2) SIMAP similar genes for CLEC3A Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with CLEC3A: view

Variants for CLEC3A Gene

Sequence variations from dbSNP and Humsavar for CLEC3A Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs1000055292 -- 78,025,309(+) CTGAT(C/G)TCTCC intron-variant
rs1000415948 -- 78,022,176(+) CACAC(A/G)CACGC upstream-variant-2KB
rs1000488111 -- 78,022,317(+) TTTAA(A/G)TTTAA upstream-variant-2KB
rs1000716427 -- 78,027,396(+) GCTAA(A/G)AATAC intron-variant, upstream-variant-2KB
rs1000751192 -- 78,023,065(+) ATCTG(C/G)TGTTA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLEC3A Gene

Variant ID Type Subtype PubMed ID
dgv3031n100 CNV gain 25217958
dgv3032n100 CNV loss 25217958
dgv5216n54 CNV loss 21841781
esv2760418 CNV gain+loss 21179565
esv3582336 CNV loss 25503493
esv3582337 CNV loss 25503493
esv3639185 CNV loss 21293372
esv3639186 CNV loss 21293372
esv3639187 CNV gain 21293372
nsv1056016 CNV loss 25217958
nsv1056561 CNV gain 25217958
nsv1058985 CNV loss 25217958
nsv817742 CNV gain 17921354
nsv833293 CNV gain 17160897

Variation tolerance for CLEC3A Gene

Residual Variation Intolerance Score: 55% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.05; 68.73% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLEC3A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLEC3A Gene

Disorders for CLEC3A Gene

Relevant External Links for CLEC3A

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for CLEC3A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLEC3A Gene

Publications for CLEC3A Gene

  1. The cartilage-derived, C-type lectin (CLECSF1): structure of the gene and chromosomal location. (PMID: 10524194) Neame P.J. … Grimm D.R. (Biochim. Biophys. Acta 1999) 2 3 4 22 64
  2. Matrilysin (MMP-7) cleaves C-type lectin domain family 3 member A (CLEC3A) on tumor cell surface and modulates its cell adhesion activity. (PMID: 19173304) Tsunezumi J. … Miyazaki K. (J. Cell. Biochem. 2009) 3 4 22 64
  3. Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects. (PMID: 19844255) Dastani Z. … Genest J. (Eur. J. Hum. Genet. 2010) 3 46 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 2003) 3 4 64

Products for CLEC3A Gene

Sources for CLEC3A Gene

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