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CLEC2A Gene

protein-coding   GIFtS: 41
GCID: GC12M010051

C-Type Lectin Domain Family 2, Member A

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
C-Type Lectin Domain Family 2, Member A1 2     PILAR2 3
Keratinocyte-Associated C-Type Lectin1 2 3     INPE57922
Proliferation-Induced Lymphocyte-Associated Receptor1 2 3     UNQ57922
KACL2 3     C-Type Lectin Domain Family 2 Member A2

External Ids:    HGNC: 241911   Entrez Gene: 3878362   Ensembl: ENSG000001883937   OMIM: 6120875   UniProtKB: Q6UVW93   

Export aliases for CLEC2A gene to outside databases

Previous GC identifers: GC12M009943 GC12U901034 GC12M009808


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CLEC2A Gene:
CLEC2A belongs to the CLEC2 family of activation-induced, natural killer gene complex-encoded C-type lectin-like
receptors (Spreu et al., 2007 (PubMed 18046548)).(supplied by OMIM, May 2008)

GeneCards Summary for CLEC2A Gene:
CLEC2A (C-type lectin domain family 2, member A) is a protein-coding gene. Diseases associated with CLEC2A include acrospiroma, and eccrine acrospiroma. GO annotations related to this gene include carbohydrate binding and protein homodimerization activity. An important paralog of this gene is CLEC2D.

UniProtKB/Swiss-Prot: CLC2A_HUMAN, Q6UVW9
Function: Plays a role in modulating the extent of T-cell expansion. Enhances the expansion of TCR-stimulated
T-cells by increasing their survival through enhanced expression of anti-apoptotic proteins. May modulate the
capacity of T-cells to home to lymph nodes through SELL. Facilitates dedicated immune recognition of
keratinocytes via interaction with its receptor KLRF2 by stimulating natural killer cell mediated cytotoxicity




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000012.12  NT_009714.18  NC_018923.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CLEC2A gene promoter:
         ISGF-3   AP-1   HNF-1A   FOXL1   Evi-1   POU2F1   FOXJ2 (long isoform)   HNF-1   POU2F1a   FOXJ2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLEC2A promoter sequence
   Search Chromatin IP Primers for CLEC2A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLEC2A


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

Entrez Gene cytogenetic band: 12p13.31   Ensembl cytogenetic band:  12p13.31   HGNC cytogenetic band: 12p13.31

CLEC2A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLEC2A gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M010051:  view genomic region     (about GC identifiers)

Start:
10,051,272 bp from pter      End:
10,084,980 bp from pter
Size:
33,709 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CLC2A_HUMAN, Q6UVW9 (See protein sequence)
Recommended Name: C-type lectin domain family 2 member A  
Size: 174 amino acids; 19972 Da
Subunit: Homodimer; non disulfide-linked. Interacts with KLRB1. Interacts with KLRF2
1 PDB 3D structure from and Proteopedia for CLEC2A:
4IOP (3D)    
Secondary accessions: A5Y4G5 A9QKS2 A9QKS3
Alternative splicing: 2 isoforms:  Q6UVW9-1   Q6UVW9-2   

Explore the universe of human proteins at neXtProt for CLEC2A: NX_Q6UVW9

Explore proteomics data for CLEC2A at MOPED

Post-translational modifications: 

  • N-glycosylated1
  • Glycosylation2 at Asn78, Asn130, Asn143

  • See CLEC2A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001124183.1  
    ENSEMBL proteins: 
     ENSP00000339732   ENSP00000396163  

    CLEC2A Human Recombinant Protein Products:

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    CLEC2A Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of CLEC2A
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    CLEC2A Assay Products:

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    Cloud-Clone Corp. CLIAs for CLEC2A


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    CLEC: C-type lectin domain containing

    3 InterPro protein domains:
     IPR016187 C-type_lectin_fold
     IPR016186 C-type_lectin-like
     IPR001304 C-type_lectin

    Graphical View of Domain Structure for InterPro Entry Q6UVW9

    ProtoNet protein and cluster: Q6UVW9

    UniProtKB/Swiss-Prot: CLC2A_HUMAN, Q6UVW9
    Similarity: Contains 1 C-type lectin domain


    CLEC2A for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CLC2A_HUMAN, Q6UVW9
    Function: Plays a role in modulating the extent of T-cell expansion. Enhances the expansion of TCR-stimulated
    T-cells by increasing their survival through enhanced expression of anti-apoptotic proteins. May modulate the
    capacity of T-cells to home to lymph nodes through SELL. Facilitates dedicated immune recognition of
    keratinocytes via interaction with its receptor KLRF2 by stimulating natural killer cell mediated cytotoxicity
    Induction: By phytohemagglutinin (PHA) in peripheral CD8(+) T cells

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
    GO:0030246carbohydrate binding IEA--
    GO:0042803protein homodimerization activity IDA--
         
    CLEC2A for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CLEC2A
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CLEC2A
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CLEC2A

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    Browse Sino Biological Human cDNA Clones
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    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat CLEC2A

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CLC2A_HUMAN, Q6UVW9: Cell membrane; Single-pass type II membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    cytoskeleton2
    cytosol2
    extracellular1
    nucleus1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016021integral component of membrane IEA--

    CLEC2A for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CLEC2A
    Interactions:

        Search GeneGlobe Interaction Network for CLEC2A

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0042267natural killer cell mediated cytotoxicity TAS--

    CLEC2A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CLEC2A (CLC2A)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for CLEC2A gene (2 alternative transcripts): 
    NM_001130711.1  NM_207375.1  

    Unigene Cluster for CLEC2A:

    C-type lectin domain family 2, member A
    Hs.527665
    Unigene Representative Sequence: EF127467
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000339766(uc009zhb.2) ENST00000455827(uc009zhc.2)
    miRNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CLEC2A
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    OriGene clones in human, mouse for CLEC2A (see all 4)
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    GenScript: all cDNA clones in your preferred vector: CLEC2A (NM_001130711)
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    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat CLEC2A
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat CLEC2A
      QuantiFast Probe-based Assays in human, mouse, rat CLEC2A

    Additional mRNA sequence: 

    AY359126.1 EF127467.1 EU095393.1 EU095394.1 

    2 AceView cDNA sequences:

    NM_207375 AY359126 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CLEC2A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAATTTTTGA
    CLEC2A Expression
    About this image

    CLEC2A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLEC2A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.527665

    UniProtKB/Swiss-Prot: CLC2A_HUMAN, Q6UVW9
    Tissue specificity: Mainly expressed in skin. Also expressed in keratinocytes, spleen, thymus, small intestine,
    peripheral blood monocytes, bone marrow, ovary, testis and skin. High expression in CD8(+), B-lymphocytes and
    naive CD4(+) T-cells. Restricted mostly to proliferating lymphocytes. Not detected in myeloid leukocytes or
    natural killer (NK) cells

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLEC2A

    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for CLEC2A gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clec2f1 C-type lectin domain family 2, member f 53.47(n)
    40.97(a)
      435921  NM_001277202.1  NP_001264131.1 
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    24(a)
    many ↔ many
    16(223503-225021)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 3)
    Uncharacterized protein
    (see all 3)
    28(a)
    25(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    GL343438.1(61100-123526)
    2(193112946-193126895)


    ENSEMBL Gene Tree for CLEC2A (if available)
    TreeFam Gene Tree for CLEC2A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLEC2A gene
    CLEC2D2  CLEC2L2  CLEC2B2  CD692  
    4 SIMAP similar genes for CLEC2A using alignment to 1 protein entry:     CLC2A_HUMAN:
    CD69    CLEC2D    CLEC2B    CLEC2L

    CLEC2A for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CLEC2A (see all 443)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1816275641,2
    --10065327(+) TAATCC/TCAGGT 1 -- ds50010--------
    rs128173141,2
    C,F,A--10065356(+) GGACCG/CTGCTC 1 -- ds50016Minor allele frequency- C:0.11NA WA 246
    rs1400499201,2
    C--10065682(+) TTCTTC/TCCTTT 1 -- ds50010--------
    rs1503766841,2
    --10065723(+) CACGAA/TCCTAC 1 -- ds50010--------
    rs1858282781,2
    --10065726(+) GAACCA/TACTAT 1 -- ds50010--------
    rs732554191,2
    C--10065761(+) CTAGTC/TTATAT 1 -- ds50012Minor allele frequency- T:0.08WA 120
    rs747151741,2
    C,F--10065926(+) TGATTA/TGTTCA 1 -- ut312Minor allele frequency- T:0.08NA EA 240
    rs1380705071,2
    --10065945(+) GAGCCA/GTAGTA 1 -- ut310--------
    rs1901038111,2
    --10066043(+) AACTAA/GAAAAT 1 -- ut310--------
    rs1137223351,2
    C,F--10066068(+) GGTTCC/TGTATT 1 -- ut311Minor allele frequency- T:0.50CSA 2

    HapMap Linkage Disequilibrium report for CLEC2A (10051272 - 10084980 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for CLEC2A:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv898755CNV Loss21882294
    nsv523050CNV Loss19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CLEC2A
    DNA2.0 Custom Variant and Variant Library Synthesis for CLEC2A

    (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.)
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    OMIM gene information: 612087    OMIM disorders: --

    14 diseases for CLEC2A:    
    About MalaCards
    acrospiroma    eccrine acrospiroma    leiomyoma cutis    epidermal appendage tumor
    malignant syringoma    spiradenoma    syringocystadenoma papilliferum    pilomatrixoma
    acanthoma    syringoma    hidradenoma    leiomyoma
    keratosis    alopecia

    12 diseases from the University of Copenhagen DISEASES database for CLEC2A:
    Acanthoma     Pilomatrixoma     Syringocystadenoma papilliferum     Leiomyoma
    Skin cancer     Keratosis     Leiomyoma cutis     Epidermal appendage tumor
    Eccrine acrospiroma     Hidradenoma     Spiradenoma     Alopecia

    CLEC2A for disorders           About GeneDecksing


    Export disorders for CLEC2A 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)
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    PubMed articles for CLEC2A gene integrated from 10 sources:
    (articles sorted by number of sources associating them with CLEC2A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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, 3 Clark H.F.... Gray A.M. (Genome Res. 2003)
    2. Interaction of C-type lectin-like receptors NKp65 and KACL facilitates dedicated immune recognition of human keratinocytes. (PubMed id 20194751)1, 2 Spreu J....Steinle A. (Proc. Natl. Acad. Sci. U.S.A. 2010)
    3. PILAR is a novel modulator of human T-cell expansion. (PubMed id 18550855)1, 2 Huarte E....Conejo-Garcia J.R. (Blood 2008)
    4. CLEC2A: a novel, alternatively spliced and skin-associated member of the NKC-encoded AICL-CD69-LLT1 family. (PubMed id 18046548)1, 2 Spreu J.... Steinle A. (Immunogenetics 2007)
    5. Structure of NKp65 bound to its keratinocyte ligand reveals basis for genetically linked recognition in natural killer gene complex. (PubMed id 23803857)2 Li Y.... Mariuzza R.A. (Proc. Natl. Acad. Sci. U.S.A. 2013)
    6. Novel interactions in platelet biology: CLEC-2/podoplanin and laminin/GPVI. (PubMed id 19630798)1 Ozaki Y....Inoue O. (J. Thromb. Haemost. 2009)
    7. Genome-scale RNAi screen for host factors required for HIV replication. (PubMed id 18976975)1 Zhou H....Espeseth A.S. (amp 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 387836 HGNC: 24191 AceView: UNQ5792 Ensembl:ENSG00000188393 euGenes: HUgn387836
    ECgene: CLEC2A H-InvDB: CLEC2A

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for CLEC2A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CLEC2A gene:
    Search GeneIP for patents involving CLEC2A

    GeneCards and IP:
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    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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