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CLEC9A Gene

protein-coding   GIFtS: 43
GCID: GC12P010183

C-Type Lectin Domain Family 9, Member A

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(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 9, Member A1 2
DNGR12 5
HEEE93412
UNQ93412
C-Type Lectin Domain Family 9 Member A2

External Ids:    HGNC: 267051   Entrez Gene: 2834202   Ensembl: ENSG000001979927   OMIM: 6122525   UniProtKB: Q6UXN83   

Export aliases for CLEC9A gene to outside databases

Previous GC identifers: GC12P010075 GC12P009926


(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 CLEC9A Gene:
CLEC9A is a group V C-type lectin-like receptor (CTLR) that functions as an activation receptor and is expressed
on myeloid lineage cells (Huysamen et al., 2008 (PubMed 18408006)).(supplied by OMIM, Aug 2008)

GeneCards Summary for CLEC9A Gene:
CLEC9A (C-type lectin domain family 9, member A) is a protein-coding gene. GO annotations related to this gene include carbohydrate binding. An important paralog of this gene is OLR1.

UniProtKB/Swiss-Prot: CLC9A_HUMAN, Q6UXN8
Function: Functions as an endocytic receptor on a small subset of myeloid cells specialized for the uptake and
processing of material from dead cells. Recognizes filamentous form of actin in association with particular
actin-binding domains of cytoskeletal proteins, including spectrin, exposed when cell membranes are damaged, and
mediate the cross-presentation of dead-cell associated antigens in a Syk-dependent manner




(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 at NCBI GenBank:
NC_000012.11  NC_018923.2  NT_009714.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the CLEC9A gene promoter:
         AhR   STAT1   Sox5   C/EBPbeta   FOXD3   MyoD   FOXJ2 (long isoform)   Cart-1   FOXJ2   ITF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLEC9A promoter sequence
   Search Chromatin IP Primers for CLEC9A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLEC9A


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

Entrez Gene cytogenetic band: 12p13.2   Ensembl cytogenetic band:  12p13.2   HGNC cytogenetic band: 12p13.31

CLEC9A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLEC9A gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P010183:  view genomic region     (about GC identifiers)

Start:
10,183,276 bp from pter      End:
10,218,565 bp from pter
Size:
35,290 bases      Orientation:
plus 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CLC9A_HUMAN, Q6UXN8 (See protein sequence)
Recommended Name: C-type lectin domain family 9 member A  
Size: 241 amino acids; 27324 Da
Subunit: Homodimer
1 PDB 3D structure from and Proteopedia for CLEC9A:
3VPP (3D)    
Secondary accessions: B0ZBM2

Explore the universe of human proteins at neXtProt for CLEC9A: NX_Q6UXN8

Explore proteomics data for CLEC9A at MOPED

Post-translational modifications: 

  • N-glycosylated1
  • Glycosylation2 at Asn81, Asn223
  • Modification sites at PhosphoSitePlus

  • See CLEC9A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_997228.1  
    ENSEMBL proteins: 
     ENSP00000348074  

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    (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

    4 InterPro protein domains:
     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 Q6UXN8

    ProtoNet protein and cluster: Q6UXN8

    UniProtKB/Swiss-Prot: CLC9A_HUMAN, Q6UXN8
    Similarity: Contains 1 C-type lectin domain


    Find genes that share domains with CLEC9A           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CLC9A_HUMAN, Q6UXN8
    Function: Functions as an endocytic receptor on a small subset of myeloid cells specialized for the uptake and
    processing of material from dead cells. Recognizes filamentous form of actin in association with particular
    actin-binding domains of cytoskeletal proteins, including spectrin, exposed when cell membranes are damaged, and
    mediate the cross-presentation of dead-cell associated antigens in a Syk-dependent manner

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030246carbohydrate binding IEA--
         
    Find genes that share ontologies with CLEC9A           About GenesLikeMe


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Clec9a):
     immune system  no phenotypic analysis 

    Find genes that share phenotypes with CLEC9A           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Clec9atm1.1Kens for CLEC9A

       genOway: Develop your customized and physiologically relevant rodent model for CLEC9A

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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
    CLC9A_HUMAN, Q6UXN8: Membrane; Single-pass type II membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0009986cell surface IDA18408006
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with CLEC9A           About GenesLikeMe


    (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 CLEC9A
    Interactions:

        Search GeneGlobe Interaction Network for CLEC9A

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006898receptor-mediated endocytosis IDA18408006
    GO:0050715positive regulation of cytokine secretion IDA18408006

    Find genes that share ontologies with CLEC9A           About GenesLikeMe



    (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 CLEC9A (CLC9A)



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CLEC9A gene: 
    NM_207345.2  

    Unigene Cluster for CLEC9A:

    C-type lectin domain family 9, member A
    Hs.531189  [show with all ESTs]
    Unigene Representative Sequence: AY358265
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000355819(uc001qxa.3) ENST00000544751 ENST00000538482
    miRNA
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    hsa-miR-4273 hsa-miR-3137
    SwitchGear 3'UTR luciferase reporter plasmidCLEC9A 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat CLEC9A

    Additional mRNA sequence: 

    AK307335.1 AY358265.1 EU339276.1 

    2 DOTS entries:

    DT.101956961  DT.204169 

    10 AceView cDNA sequences:

    BX115613 NM_207345 BU568744 AY358265 AI949415 D78845 R23980 H02323 
    R78471 H02425 

    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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    CLEC9A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAATTAGCAA
    CLEC9A Expression
    About this image

    CLEC9A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLEC9A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.531189

    UniProtKB/Swiss-Prot: CLC9A_HUMAN, Q6UXN8
    Tissue specificity: In peripheral blood highly restricted on the surface of BDCA31(+) dendritic cells and on a
    small subset of CD14(+) and CD16(-) monocytes

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    In Situ
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    (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 CLEC9A gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clec9a1 , 5 C-type lectin domain family 9, member a1, 5 71.99(n)1
    60.08(a)1
      6 (63.30 cM)5
    2324141  NM_001205363.11  NP_001192292.11 
     1294088625 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    31(a)
    1 → many
    2(81818136-81823316)


    ENSEMBL Gene Tree for CLEC9A (if available)
    TreeFam Gene Tree for CLEC9A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLEC9A gene
    OLR12  CLEC1B2  CLEC7A2  CLEC12B2  CLEC12A2  CLEC1A2  
    2 SIMAP similar genes for CLEC9A using alignment to 1 protein entry:     CLC9A_HUMAN:
    CLEC2B    KLRD1

    Find genes that share paralogs with CLEC9A           About GenesLikeMe



    (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 CLEC9A (see all 699)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs563503031,2
    C--10181396(+) AGCATA/GGTATT 1 -- us2k13Minor allele frequency- G:0.08NA WA 240
    rs1885594161,2
    --10181450(+) TCTCAC/TCTCAC 1 -- us2k10--------
    rs768776311,2
    C,F--10181472(+) TTAACA/GAAAGA 1 -- us2k11Minor allele frequency- G:0.03NA 120
    rs1453498571,2
    C--10181482(+) ACAGGA/CGACCT 1 -- us2k10--------
    rs1172459781,2
    F--10181614(+) GTCTTT/GTGCTC 1 -- us2k11Minor allele frequency- G:0.01NA 120
    rs1930685371,2
    --10181665(+) AAAAGC/GCAGAC 1 -- us2k10--------
    rs1826569251,2
    --10181668(+) AGCCAA/GACGTA 1 -- us2k10--------
    rs1868854071,2
    --10181679(+) TATATA/TAATTA 1 -- us2k10--------
    rs1913699161,2
    --10181840(+) ATAGTA/GTGTGT 1 -- us2k10--------
    rs123082931,2
    C--10181858(+) TGTGTA/GTATAT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CLEC9A (10183276 - 10218565 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for CLEC9A:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv898755CNV Loss21882294
    nsv524870CNV Gain19592680
    esv9698OTHER Inversion19470904

    Site Specific Mutation Identification with 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.)
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    OMIM gene information: 612252    OMIM disorders: --


    Find genes that share disorders with CLEC9A           About GenesLikeMe

    Genetic Association Database (GAD): CLEC9A

    Export disorders for CLEC9A 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 CLEC9A gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with CLEC9A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The dendritic cell receptor Clec9A binds damaged cells via exposed actin filaments. (PubMed id 22483802)1, 2 Zhang J.G.... Lahoud M.H. (Immunity 2012)
    2. Tumor therapy in mice via antigen targeting to a novel, DC-restricted C-type lectin. (PubMed id 18497879)1, 2 Sancho D.... Reis e Sousa C. (J. Clin. Invest. 2008)
    3. CLEC9A is a novel activation C-type lectin-like receptor expressed on BDCA3+ dendritic cells and a subset of monocytes. (PubMed id 18408006)1, 2 Huysamen C.... Brown G.D. (J. Biol. Chem. 2008)
    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. (Genome Res. 2003)
    5. Increased tubulointerstitial recruitment of human CD141(hi) CLEC9A(+) and CD1c(+) myeloid dendritic cell subsets in renal fibrosis and chronic kidney disease. (PubMed id 24049150)1 Kassianos A.J....Wilkinson R. (Am. J. Physiol. Renal Physiol. 2013)
    6. F-actin is an evolutionarily conserved damage-associated molecular pattern recognized by DNGR-1, a receptor for dead cells. (PubMed id 22483800)1 Ahrens S....KjA ( 2012)
    7. The C-type lectin receptor CLEC9A mediates antigen uptake and (cross-)presentation by human blood BDCA3+ myeloid dendritic cells. (PubMed id 22234694)1 Schreibelt G....de Vries I.J. (Blood 2012)
    8. DNGR-1 is a specific and universal marker of mouse and human Batf3-dependent dendritic cells in lymphoid and nonlymphoid tissues. (PubMed id 22442345)1 Poulin L.F....Reis e Sousa C. (Blood 2012)
    9. Targeting antigen to mouse dendritic cells via Clec9A induces potent CD4 T cell responses biased toward a follicular helper phenotype. (PubMed id 21677141)1 Lahoud M.H....Caminschi I. (J. Immunol. 2011)
    10. Characterization of human DNGR-1+ BDCA3+ leukocytes as putative equivalents of mouse CD8alpha+ dendritic cells. (PubMed id 20479117)1 Poulin L.F....Reis e Sousa C. (J. Exp. Med. 2010)

    (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: 283420 HGNC: 26705 AceView: UNQ9341 Ensembl:ENSG00000197992 euGenes: HUgn283420
    ECgene: CLEC9A H-InvDB: CLEC9A

    (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 CLEC9A 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 CLEC9A gene:
    Search GeneIP for patents involving CLEC9A

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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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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     DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLEC9A Predesigned siRNA for gene silencing in human, mouse, rat CLEC9A
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     Search Tocris compounds for CLEC9A (CLC9A)
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     Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

     Novus Tissue Slides
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     Browse ESI BIO Cell Lines and PureStem Progenitors for CLEC9A
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     Browse compounds at ApexBio
     Search Addgene for plasmids for CLEC9A
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      eBioscience FlowRNA Probe Sets
     genOway: Develop your customized and physiologically relevant rodent model for CLEC9A
     antibodies-online antibodies for CLEC9A (30 products)
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     antibodies-online proteins for CLEC9A (3 products)
           
    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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