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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CLEC3A Gene

protein-coding   GIFtS: 46
GCID: GC16P078056

C-type lectin domain family 3, member A

(Previous names: C-type (calcium dependent, carbohydrate-recognition domain)...)
(Previous symbol: CLECSF1)
 Explore 6 diseases affiliated with
CLEC3A via our new
 Human Malady Compendium 
Biological research products
for CLEC3A
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
C-Type Lectin Domain Family 3, Member A1 2
CLECSF11 2 3
C-Type (Calcium Dependent, Carbohydrate-Recognition Domain) Lectin, Superfamily
Member 1 (Cartilage-Derived)1 2
C-Type Lectin Domain Family 3 Member A2
C-Type Lectin Superfamily Member 13
Cartilage-Derived C-Type Lectin3

External Ids:    HGNC: 20521   Entrez Gene: 101432   Ensembl: ENSG000001665097   OMIM: 6135885   UniProtKB: O755963   

Export aliases for CLEC3A gene to outside databases

Previous GC identifers: GC16P076614 GC16P063813


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: CLC3A_HUMAN, O75596
Function: Promotes cell adhesion to laminin-332 and fibronectin




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NC_018927.1  NT_010498.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CLEC3A gene promoter:
         p53   Pax-6   NRSF form 1   NRSF form 2   Evi-1   PPAR-gamma1   FOXJ2 (long isoform)   FOXO1a   PPAR-gamma2   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLEC3A promoter sequence
   Search SABiosciences Chromatin IP Primers for CLEC3A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLEC3A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16q23   Ensembl cytogenetic band:  16q23.1   HGNC cytogenetic band: 16q23

CLEC3A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLEC3A gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P078056:  view genomic region     (about GC identifiers)

Start:
78,056,412 bp from pter      End:
78,100,658 bp from pter
Size:
44,247 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CLC3A_HUMAN, O75596 (See protein sequence)
Recommended Name: C-type lectin domain family 3 member A precursor  
Size: 197 amino acids; 22233 Da
Subcellular location: Secreted
Sequence caution: Sequence=AAQ88742.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: B2R8C4 Q3SX91 Q6UXF5

Explore the universe of human proteins at neXtProt for CLEC3A: NX_O75596

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O75596

  • CLEC3A Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001231684.1  NP_005743.4  

    ENSEMBL proteins: 
     ENSP00000299642   ENSP00000457211   ENSP00000460682  

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    OriGene Protein Over-expression Lysate: CLEC3A
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    Novus Biologicals CLEC3A Protein
    Novus Biologicals CLEC3A Lysates
    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins
    Uscn Proteins for CLEC3A

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--


    CLEC3A for ontologies           About GeneDecksing



    CLEC3A Antibody Products: 
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    Uscn Antibodies for CLEC3A
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    Uscn ELISAs and CLIAs for CLEC3A


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    CLEC3A for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR016187 C-type_lectin_fold
     IPR018378 C-type_lectin_CS
     IPR016186 C-type_lectin-like
     IPR001304 C-type_lectin

    Graphical View of Domain Structure for InterPro Entry O75596

    ProtoNet protein and cluster: O75596

    UniProtKB/Swiss-Prot: CLC3A_HUMAN, O75596
    Similarity: Contains 1 C-type lectin domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: CLC3A_HUMAN, O75596
    Function: Promotes cell adhesion to laminin-332 and fibronectin

    miRNA
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    hsa-miR-100* hsa-miR-548p hsa-miR-383 hsa-miR-29c hsa-miR-29a hsa-miR-29b
    SwitchGear 3'UTR luciferase reporter plasmidCLEC3A 3' UTR sequence
    Inhib. RNA
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    OriGene shRNA RFP: CLEC3A
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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLEC3A

    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030246carbohydrate binding IEA--


    CLEC3A for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Clec3atm1Lex for CLEC3A
         1 MGI phenotypic allele for Clec3a (no phenotypes)

    CLEC3A for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CLEC3A

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001501skeletal system development TAS10524194


    CLEC3A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CLEC3A
    Search CenterWatch for drugs/clinical trials and news about CLEC3A / CLC3A 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CLEC3A gene (2 alternative transcripts): 
    NM_001244755.1  NM_005752.4  

    Unigene Cluster for CLEC3A:

    C-type lectin domain family 3, member A
    Hs.177936  [show with all ESTs]
    Unigene Representative Sequence: NM_005752
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000299642(uc002ffh.4 uc021tlr.1) ENST00000567430 ENST00000565808
    ENST00000575655

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat CLEC3A
    6 QIAGEN miScript miRNA Assays for microRNAs that regulate CLEC3A:
    hsa-miR-100* hsa-miR-548p hsa-miR-383 hsa-miR-29c hsa-miR-29a hsa-miR-29b
    SwitchGear 3'UTR luciferase reporter plasmidCLEC3A 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for CLEC3A (see all 7)
    OriGene shRNA RFP: CLEC3A
    OriGene siRNA: CLEC3A
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CLEC3A
    Clone
    Products:
         
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for CLEC3A (see all 3)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for CLEC3A
    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
    GenScript: all cDNA clones in your preferred vector: CLEC3A (NM_005752)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CLEC3A
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLEC3A 
    Primer
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    OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for CLEC3A
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CLEC3A
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CLEC3A

    Additional cDNA sequence: 

    AK313316.1 AY358376.1 BC104414.2 BC104415.2 

    2 DOTS entries:

    DT.70103606  DT.99993476 

    15 AceView cDNA sequences:

    BM992309 AA398015 CA413540 AI867547 BX099834 AA399390 CN480293 AY358376 
    BQ181694 AI927004 NM_005752 AI085849 CN480352 BE872674 BQ309604 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CLEC3A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTTGGAATTA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    CLEC3A expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    HyStem+BMP4-induced 4D20.8 cells (Chondrogenic inducti...)Bone, Cartilage
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See CLEC3A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CLEC3A

    SOURCE GeneReport for Unigene cluster: Hs.177936

    UniProtKB/Swiss-Prot: CLC3A_HUMAN, O75596
    Tissue specificity: Restricted to cartilage and breast. Also expressed in breast cancers

        SABiosciences Custom PCR Arrays for CLEC3A
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLEC3A

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for CLEC3A gene from 3/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves CLEC3A1 C-type lectin domain family 3, member A 74.09(n)
    75.65(a)
      425961  XM_423644.3  XP_423644.1 
    lizard
    (Anolis carolinensis)
    Reptilia CLEC3A6
    --
    73(a)
    1 ↔ 1
    GL343446.1(77550-85433)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1003301221 c-type lectin domain family 3 member A-like 61.5(n)
    57.75(a)
      100330122  XM_002667565.2  XP_002667611.2 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CLEC3A gene
    CLEC3B2  CLEC11A2  
    2 SIMAP similar genes for CLEC3A using alignment to 4 protein entries:     CLC3A_HUMAN (see all proteins):
    DKFZp686H17246    CLEC3B

    CLEC3A for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/349 NCBI SNPs in CLEC3A are shown (see all 349    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1162263701,2
    F,--78054454(+) TTGCGC/GTAAGT 1 -- us2k11Minor allele frequency- G:0.03WA 118
    rs1491609491,2
    --78054516(+) CATTCC/GTAGCC 1 -- us2k10--------
    rs1883328711,2
    --78054551(+) TTATAC/GAGGTT 1 -- us2k10--------
    rs785262591,2
    C,F,--78054553(+) ATAGAG/AGTTTA 1 -- us2k11Minor allele frequency- A:0.04WA 118
    rs1926181561,2
    --78054589(+) AAGCGA/GTAGGT 1 -- us2k10--------
    rs1853089331,2
    --78054610(+) GCTCAC/GCCTGT 1 -- us2k10--------
    rs1464472721,2
    --78054615(+) GCCTGC/TCTTCA 1 -- us2k10--------
    rs1889218541,2
    --78054674(+) GTCAAC/TACCGG 1 -- us2k10--------
    rs1390315771,2
    --78054677(+) AACACC/TGGAGG 1 -- us2k10--------
    rs1414960211,2
    --78054746(+) GGTCTC/TACTAT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CLEC3A (78056412 - 78100658 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for CLEC3A
         2 CNVs: 9765 77425

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    CLEC3A for disorders           About GeneDecksing

    OMIM gene information: 613588    OMIM disorders: --

    6 diseases for CLEC3A:    About MalaCards
    lown-ganong-levine syndrome    mycobacterial infection    botulism    breast cancer
    cholesterol    hepatitis

    1 disease from the University of Copenhagen DISEASES database for CLEC3A:
    Methylmalonic acidemia
    Human Genome Epidemiology (HuGE) Navigator: CLEC3A (1 document)

    Export disorders for CLEC3A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for CLEC3A gene integrated from 9 sources:
    (articles sorted by number of sources associating them with CLEC3A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The cartilage-derived, C-type lectin (CLECSF1): structure of the gene and chromosomal location. (PubMed id 10524194)1, 2, 3, 9 Neame P.J.... Grimm D.R. (1999)
    2. Matrilysin (MMP-7) cleaves C-type lectin domain family 3 member A (CLEC3A) on tumor cell surface and modulates its cell adhesion activity. (PubMed id 19173304)1, 2, 9 Tsunezumi J....Miyazaki K. (2009)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
    5. Fine mapping and association studies of a high-densit y lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian su bjects. (PubMed id 19844255)1 Dastani Z....Genest J. (2010)
    6. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    9. Role of C-type lectins in mycobacterial infections. (PubMed id 18288961)9 Torrelles J.B....Schlesinger L.S. (2008)
    10. A lectin (CfLec-2) aggregating Staphylococcus haemolyticus from scallop Chlamys farreri. (PubMed id 18203621)9 Zheng P....Xing K. (2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 10143 HGNC: 2052 AceView: CLECSF1 Ensembl:ENSG00000166509 euGenes: HUgn10143
    ECgene: CLEC3A H-InvDB: CLEC3A

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CLEC3A Pharmacogenomics, SNPs, Pathways
    Functional Glycomics Gateway - Glycan Bindinghttp://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_258

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for CLEC3A gene:
    Search GeneIP for patents involving CLEC3A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    In Situ Hybridization Assays from
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     Browse OriGene Antibodies   OriGene shRNA RFP for CLEC3A  
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     CLEC3A Proteins, Antibodies, CLIAs, and ELISAs
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     SwitchGear 3'UTR luciferase reporter plasmids for CLEC3A
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     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLEC3A
           
    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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