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

CLEC5A Gene

protein-coding   GIFtS: 50
GCID: GC07M141627

C-type lectin domain family 5, member A

(Previous names: C-type (calcium dependent, carbohydrate-recognition domain)...)
(Previous symbol: CLECSF5)
 Explore 8 diseases affiliated with
CLEC5A via our new
 Human Malady Compendium 
Biological research products
for CLEC5A
    

(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 5, Member A1 2     Myeloid DAP12-Associating Lectin 12 3
CLECSF51 2 3 5     C-Type Lectin Superfamily Member 52 3
MDL-11 2 3     C-Type Lectin Domain Family 5 Member A2
MDL12 3 5     Myeloid DAP12-Associating Lectin-12
C-Type (Calcium Dependent, Carbohydrate-Recognition Domain) Lectin, Superfamily
Member 51 2
     

External Ids:    HGNC: 20541   Entrez Gene: 236012   Ensembl: ENSG000002582277   OMIM: 6049875   UniProtKB: Q9NY253   

Export aliases for CLEC5A gene to outside databases

Previous GC identifers: GC07M141081 GC07M141273 GC07M135923


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

Entrez Gene summary for CLEC5A:
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 II transmembrane protein
interacts with dnax-activation protein 12 and may play a role in cell activation. Alternative splice variants have
been described but their full-length sequence has not been determined. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: CLC5A_HUMAN, Q9NY25
Function: Functions as a positive regulator of osteoclastogenesis. Cell surface receptor that signals via TYROBP.
Regulates inflammatory responses. Acts as a key regulator of synovial injury and bone erosion during autoimmune joint
inflammation (By similarity). Critical macrophage receptor for dengue virus serotypes 1-4. The binding of dengue virus
to CLEC5A triggers signaling through the phosphylation of TYROBP, this interaction does not result in viral entry, but
stimulates proinflammatory cytokine release

Gene Wiki entry for CLEC5A


(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_000007.13  NC_018918.1  NT_007914.15  NT_079596.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CLEC5A gene promoter:
         Nkx3-1   Nkx3-1 v4   HOXA3   MEF-2   Nkx3-1 v1   Nkx3-1 v2   PPAR-gamma1   Nkx3-1 v3   PPAR-gamma2   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLEC5A promoter sequence
   Search SABiosciences Chromatin IP Primers for CLEC5A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLEC5A


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

Entrez Gene cytogenetic band: 7q33   Ensembl cytogenetic band:  7q34   HGNC cytogenetic band: 7q34

CLEC5A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLEC5A gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M141627:  view genomic region     (about GC identifiers)

Start:
141,627,157 bp from pter      End:
141,646,807 bp from pter
Size:
19,651 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 140,965,368-140,984,972     

(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: CLC5A_HUMAN, Q9NY25 (See protein sequence)
Recommended Name: C-type lectin domain family 5 member A  
Size: 188 amino acids; 21521 Da
Subunit: Monomer. Homodimer. The majority of CLEC5A is expressed as a monomeric form on macrophages. Interacts with
TYROBP/DAP12. The interaction with TYROBP is required for CLEC5 cell surface expression. Interacts with HCST/DAP10.
Forms an CLEC5A/TYROBP/HCST trimolecular complex depending almost solely on TYROBP
Subcellular location: Cell membrane; Single-pass type II membrane protein
1 PDB 3D structure from and Proteopedia for CLEC5A:
2YHF (3D)    
Secondary accessions: Q52M11 Q9UKQ0
Alternative splicing: 2 isoforms:  Q9NY25-1   Q9NY25-2   

Explore the universe of human proteins at neXtProt for CLEC5A: NX_Q9NY25

Post-translational modifications:

  • N-glycosylated. Contains sialic acid residues (By similarity)1
  • View neXtProt modification sites for NX_Q9NY25

  • CLEC5A Protein expression data from MOPED and PaxDb: --
    REFSEQ proteins: NP_037384.1  
    ENSEMBL proteins: 
     ENSP00000449999   ENSP00000392561   ENSP00000446890   ENSP00000395258   ENSP00000414897  
    Reactome Protein details: Q9NY25
    Human Recombinant Protein Products: 
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for CLEC5A

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887integral to plasma membrane TAS10449773
    GO:0009986cell surface ISS--


    CLEC5A for ontologies           About GeneDecksing



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

    CLEC5A for domains           About GeneDecksing

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

    Graphical View of Domain Structure for InterPro Entry Q9NY25

    ProtoNet protein and cluster: Q9NY25

    UniProtKB/Swiss-Prot: CLC5A_HUMAN, Q9NY25
    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: CLC5A_HUMAN, Q9NY25
    Function: Functions as a positive regulator of osteoclastogenesis. Cell surface receptor that signals via TYROBP.
    Regulates inflammatory responses. Acts as a key regulator of synovial injury and bone erosion during autoimmune joint
    inflammation (By similarity). Critical macrophage receptor for dengue virus serotypes 1-4. The binding of dengue virus
    to CLEC5A triggers signaling through the phosphylation of TYROBP, this interaction does not result in viral entry, but
    stimulates proinflammatory cytokine release

    miRNA
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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001618viral receptor activity IDA18496526
    GO:0005488binding ----
    GO:0005515protein binding ----
    GO:0030246carbohydrate binding IEA--


    CLEC5A for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for CLEC5A:
     Increased S DNA content  Increased number of mitotic ce  Large nuclei 

    Animal Models:
         Mouse knock-out Clec5atm1Cua for CLEC5A
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Clec5a):
     immune system  skeleton 

    CLEC5A 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

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Immune System
    Immune System1.00
    Innate Immune System0.46
    2Signaling by FGFR
    DAP12 interactions0.76

    Pathway sources
    See GeneCards unified pathways
    Show all pathways


    3        Reactome Pathways for CLEC5A
        DAP12 interactions
    Immune System
    Innate Immune System



    CLEC5A for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for CLEC5A

    1 Interacting protein for CLEC5A (Q9NY253) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TYROBPO439143I2D: score=1 
    About this table

    Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002076osteoblast development ISS--
    GO:0006968cellular defense response TAS10449773
    GO:0007165signal transduction TAS10449773
    GO:0009615response to virus IDA18496526
    GO:0019048virus-host interaction IEA--


    CLEC5A 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 CLEC5A

    1 HMDB Compound for CLEC5A    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    Search CenterWatch for drugs/clinical trials and news about CLEC5A / CLC5A 

    (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 CLEC5A gene: 
    NM_013252.2  

    Unigene Cluster for CLEC5A:

    C-type lectin domain family 5, member A
    Hs.446235  [show with all ESTs]
    Unigene Representative Sequence: NM_013252
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000546910(uc011krm.1 uc003vwv.1 uc003vww.1 uc010lnq.1 uc010lnr.1)
    ENST00000418498 ENST00000551012 ENST00000439991 ENST00000438351 ENST00000470595
    ENST00000481301

    miRNA
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    hsa-miR-3618 hsa-miR-136 hsa-miR-4254 hsa-miR-934 hsa-miR-548e hsa-miR-578 hsa-miR-373* hsa-miR-1270
    SwitchGear 3'UTR luciferase reporter plasmidCLEC5A 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for CLEC5A (see all 7)
    OriGene shRNA RFP: CLEC5A
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    Clone
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CLEC5A
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    Additional cDNA sequence: 

    AF139768.1 AJ271684.1 AK292766.1 AK295200.1 AK307095.1 AK313703.1 BC093714.1 BC112099.1 
    BC113098.1 BC113099.1 BC143392.1 

    2 DOTS entries:

    DT.40126468  DT.95110725 

    24/33 AceView cDNA sequences (see all 33):

    AI653660 AI932965 AI732898 AI635614 AI418484 AW292460 CD678553 AI394308 
    BQ446122 AL601652 NM_013252 AA722475 CD641133 BU198156 AI393074 AW076117 
    BQ005467 AJ271684 CD364647 BX282186 BE466448 AV715134 BF905853 BQ335025 

    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

    CLEC5A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

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

    About this image
    Genevestigator expression for CLEC5A

    SOURCE GeneReport for Unigene cluster: Hs.446235

    UniProtKB/Swiss-Prot: CLC5A_HUMAN, Q9NY25
    Tissue specificity: Expressed in peripheral blood monocytes and in the monocyte/macrophage cell lines U-937 and
    Mono-Mac-6, but not in cell lines of other origins. Expression is down-regulated when monocytes differentiate into
    dendritic cells

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLEC5A

    (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
      --

    ENSEMBL Gene Tree for CLEC5A (if available)
    TreeFam Gene Tree for CLEC5A (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CLEC5A gene
    CLEC2L2  CLEC2A2  CLEC2B2  KLRF22  KLRG22  CD692  CLEC2D2  KLRF12  
    KLRG12  KLRB12  
    5 SIMAP similar genes for CLEC5A using alignment to 5 protein entries:     CLC5A_HUMAN (see all proteins):
    CLECSF5    CLEC4C    KLRC2    CLEC4M    CLEC7A

    CLEC5A 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

    10/480 NCBI SNPs in CLEC5A are shown (see all 480    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1906208561,2
    --141626673(+) ACACCA/CCACGA 1 -- ds50010--------
    rs1126710441,2
    --141626690(+) CTGGTG/ATGTGA 1 -- ds50011Minor allele frequency- A:0.50CSA 2
    rs12859321,2
    C,F,A,--141626754(+) GAGAAC/TATGTG 1 -- ds50014Minor allele frequency- T:0.38NA 8
    rs1809740581,2
    --141626759(+) TATGTG/TGTGTT 1 -- ds50010--------
    rs1835714321,2
    --141626965(+) TGCCAA/CAATAA 1 -- ds50010--------
    rs1491336301,2
    --141626984(+) GTGCAA/TGTGTC 1 -- ds50010--------
    rs1114164241,2
    C,--141627053(+) TCAAAC/TGGTAT 1 -- ds50011Minor allele frequency- T:0.50WA 2
    rs1160327211,2
    F,--141627085(+) GAATCG/ACCACA 1 -- ds50013Minor allele frequency- A:0.03WA NA EA 358
    rs12859331,2
    C,F,A,H,--141627149(+) CAGGGG/AGCTGA 1 -- ds500127Minor allele frequency- A:0.45NS EA NA WA CSA 2772
    rs77800671,2
    C,F,H,--141627150(+) aggggG/Tctgaa 1 -- ds50014Minor allele frequency- T:0.01NS NA 506

    HapMap Linkage Disequilibrium report for CLEC5A (141627157 - 141646807 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for CLEC5A
         1 CNV: 36625

    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CLEC5A
    DNA2.0 Custom Variant and Variant Library Synthesis for CLEC5A

    (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

    CLEC5A for disorders           About GeneDecksing

    OMIM gene information: 604987    OMIM disorders: --

    8 diseases for CLEC5A:    About MalaCards
    dengue shock syndrome    viral encephalitis    dengue disease    hepatitis b
    vaginitis    encephalitis    hepatitis    arthritis

    1 disease from the University of Copenhagen DISEASES database for CLEC5A:
    Dengue disease
    Human Genome Epidemiology (HuGE) Navigator: CLEC5A (1 document)

    Export disorders for CLEC5A 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 CLEC5A gene, integrated from 9 sources (see all 22):
    (articles sorted by number of sources associating them with CLEC5A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Myeloid DAP12-associating lectin (MDL)-1 is a cell surface receptor involved in the activation of myeloid cells. (PubMed id 10449773)1, 2, 3 Bakker A.B.H.... Lanier L.L. (1999)
    2. CLEC5A is critical for dengue-virus-induced lethal disease. (PubMed id 18496526)1, 2, 9 Chen S.T....Hsieh S.L. (2008)
    3. Structural flexibility of the macrophage dengue virus receptor CLEC5A: Implications for ligand binding and signaling. (PubMed id 21566123)1, 2 Watson A.A.... O'Callaghan C.A. (2011)
    4. 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)
    5. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (2003)
    6. Crystallization and X-ray diffraction analysis of hum an CLEC5A (MDL-1), a dengue virus receptor. (PubMed id 20057064)1, 9 Watson A.A. and O'Callaghan C.A. (2010)
    7. Lack of association between CLEC5A gene single-nucleot ide polymorphisms and Kawasaki disease in Taiwanese children. (PubMed id 22536019)1 Yang Y.L....Chang W.C. (2012)
    8. Genomic association analysis identifies multiple loci influencing antihypertensive response to an angiotensin II receptor blocker. (PubMed id 22566498)1 Turner S.T....Boerwinkle E. (2012)
    9. CLEC5A (MDL-1) is a novel PU.1 transcriptional target during myeloid differentiation. (PubMed id 21094529)1 Batliner J....Tschan M.P. (2011)
    10. New genetic associations detected in a host response study to hepatitis B vaccine. (PubMed id 20237496)1 Davila S....Seielstad M. (2010)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 23601 HGNC: 2054 AceView: CLECSF5 Ensembl:ENSG00000258227 euGenes: HUgn23601
    ECgene: CLEC5A H-InvDB: CLEC5A

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for CLEC5A Pharmacogenomics, SNPs, Pathways
    Functional Glycomics Gateway - Glycan Bindinghttp://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_244

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    Patent Information for CLEC5A gene:
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