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CLEC1A Gene

protein-coding   GIFtS: 50
GCID: GC12M010222

C-Type Lectin Domain Family 1, Member A

  See related disease
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 1, Member A1 2
CLEC12 3 5
CLEC-12 3
C-Type Lectin Domain Family 1 Member A2
C-Type Lectin-Like Receptor-12
C-Type Lectin-Like Receptor 13

External Ids:    HGNC: 243551   Entrez Gene: 512672   Ensembl: ENSG000001500487   OMIM: 6067825   UniProtKB: Q8NC013   

Export aliases for CLEC1A gene to outside databases

Previous GC identifers: GC12M010115 GC12M009965


(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 CLEC1A Gene:
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 protein may play a role in
regulating dendritic cell function. Alternative splice variants have been described but their biological nature
has not been determined. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in
the natural killer gene complex region. (provided by RefSeq, Jul 2008)

GeneCards Summary for CLEC1A Gene:
CLEC1A (C-type lectin domain family 1, member A) is a protein-coding gene. Diseases associated with CLEC1A include endotheliitis. GO annotations related to this gene include transmembrane signaling receptor activity and carbohydrate binding. An important paralog of this gene is OLR1.

Gene Wiki entry for CLEC1A Gene


(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 CLEC1A gene promoter:
         SRF   Pax-5   MEF-2   SRF (504 AA)   USF-1:USF-2   CUTL1   MEF-2A   HSF2   USF-1   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLEC1A promoter sequence
   Search Chromatin IP Primers for CLEC1A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLEC1A


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

CLEC1A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLEC1A gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M010222:  view genomic region     (about GC identifiers)

Start:
10,222,153 bp from pter      End:
10,264,226 bp from pter
Size:
42,074 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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CLC1A_HUMAN, Q8NC01 (See protein sequence)
Recommended Name: C-type lectin domain family 1 member A  
Size: 280 amino acids; 31952 Da
Secondary accessions: Q8IUW7 Q9NZH3

Explore the universe of human proteins at neXtProt for CLEC1A: NX_Q8NC01

Explore proteomics data for CLEC1A at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn95, Asn169

  • See CLEC1A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_057595.2  
    ENSEMBL proteins: 
     ENSP00000326407   ENSP00000415048   ENSP00000417010   ENSP00000438408   ENSP00000396272  

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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

    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 Q8NC01

    ProtoNet protein and cluster: Q8NC01

    1 Blocks protein domain: IPB013600 Ly49-like N-terminal

    UniProtKB/Swiss-Prot: CLC1A_HUMAN, Q8NC01
    Similarity: Contains 1 C-type lectin domain


    CLEC1A 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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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004888transmembrane signaling receptor activity TAS10671229
    GO:0030246carbohydrate binding IEA--
         
    CLEC1A for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for CLEC1A:
     Increased cell number in G1, s 

         1 MGI phenotypic allele for Clec1a (no phenotypes)

    CLEC1A for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Clec1atm1Lex for CLEC1A

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CLEC1A
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CLEC1A

    miRNA
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    miRTarBase miRNAs that target CLEC1A:
    hsa-mir-1 (MIRT023827)

    Block miRNA regulation of human, mouse, rat CLEC1A using miScript Target Protectors
    4 qRT-PCR Assays for microRNAs that regulate CLEC1A:
    hsa-miR-138-1* hsa-miR-222* hsa-miR-138 hsa-miR-4299
    SwitchGear 3'UTR luciferase reporter plasmidCLEC1A 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat CLEC1A

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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLEC1A

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLEC1A


    (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
    CLC1A_HUMAN, Q8NC01: Membrane; Single-pass type II membrane protein (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    cytosol1
    nucleus1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular TAS10671229
    GO:0005887integral component of plasma membrane TAS10671229

    CLEC1A 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 CLEC1A
    Interactions:

        Search GeneGlobe Interaction Network for CLEC1A

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for CLEC1A (ENSP000003264074) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HDAC4ENSP000002646064STRING: ENSP00000264606
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006952defense response TAS10671229
    GO:0007166cell surface receptor signaling pathway TAS10671229

    CLEC1A 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 CLEC1A (CLC1A)



    (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,
    Conferences by KenesGroup, 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 CLEC1A gene: 
    NM_016511.2  

    Unigene Cluster for CLEC1A:

    C-type lectin domain family 1, member A
    Hs.29549  [show with all ESTs]
    Unigene Representative Sequence: BC067746
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000315330(uc001qxb.3) ENST00000457018(uc001qxd.3 uc010sgx.2)
    ENST00000420265 ENST00000544104 ENST00000414501
    miRNA
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    4 qRT-PCR Assays for microRNAs that regulate CLEC1A:
    hsa-miR-138-1* hsa-miR-222* hsa-miR-138 hsa-miR-4299
    SwitchGear 3'UTR luciferase reporter plasmidCLEC1A 3' UTR sequence
    Inhib. RNA
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    Primer
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    OriGene qPCR primer pairs and template standards for CLEC1A
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CLEC1A
      QuantiTect SYBR Green Assays in human, mouse, rat CLEC1A
      QuantiFast Probe-based Assays in human, mouse, rat CLEC1A

    Additional mRNA sequence: 

    AF200949.1 AK075114.1 AK091989.1 AK291584.1 AK300979.1 AK313589.1 AY358587.1 BC039072.1 
    BC067746.1 

    4 DOTS entries:

    DT.312167  DT.100018370  DT.100749659  DT.100782288 

    Selected AceView cDNA sequences (see all 71):

    CR614400 BX380079 BX379905 BX337172 NM_016511 AA441845 AI050791 CR619172 
    CR591145 BC039072 BX380212 CR591231 AI149025 BX339075 CR604680 CR606141 
    CR598502 AK075114 AY358587 AA058519 CB993235 BX324788 CB997137 BQ722745 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for CLEC1A    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d
    SP1:                          -           -                                             
    SP2:                          -                                                         
    SP3:                                      -                                             
    SP4:                          -     -     -                                             
    SP5:                          -     -     -     -                                       


    ECgene alternative splicing isoforms for CLEC1A

    (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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    CLEC1A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCGTTTCCCA
    CLEC1A Expression
    About this image


    CLEC1A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Pre-Granulosa Cells Primordial Follicle
     
     Blood (Hematopoietic System)
             Hematopoietic Stem Cells Hematopoietic Bone Marrow
     
     Placenta (Extraembryonic Tissues)
    CLEC1A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLEC1A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.29549

    UniProtKB/Swiss-Prot: CLC1A_HUMAN, Q8NC01
    Tissue specificity: Expressed preferentially in dendritic cells

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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 CLEC1A gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clec1a1 , 5 C-type lectin domain family 1, member a1, 5 76.95(n)1
    69.89(a)1
      6 (63.32 cM)5
    2436531  NM_175526.31  NP_780735.21 
     1294266845 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    39(a)
    1 → many
    2(81818136-81823316)


    ENSEMBL Gene Tree for CLEC1A (if available)
    TreeFam Gene Tree for CLEC1A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLEC1A gene
    OLR12  CLEC9A2  CLEC1B2  CLEC7A2  CLEC12B2  CLEC12A2  
    8 SIMAP similar genes for CLEC1A using alignment to 6 protein entries:     CLC1A_HUMAN (see all proteins):
    C15orf40    GBP3    LRRC36    KLRK1    CLEC1B    KLRD1
    CLEC12B    CLEC12A

    CLEC1A for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for CLEC1A
    PGOHUM00000240535


    (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 CLEC1A (see all 684)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1884812731,2
    --10222596(+) TTATAA/GTGTTA 1 -- ds50010--------
    rs1917708261,2
    --10222615(+) AGCATA/TAAACC 1 -- ds50010--------
    rs1416684081,2
    C--10222652(+) ATAAA-/CTTGGT 1 -- ds50010--------
    rs1830610671,2
    --10222684(+) AATGAG/TCCCTG 1 -- ds50010--------
    rs47642281,2
    C,F,H--10222710(+) GAGTCA/GTCTCA 1 -- ds5001 ese321Minor allele frequency- G:0.09NS EA NA WA CSA 1559
    rs177347991,2
    C,F,H--10222786(+) CTGACT/CGGAAA 1 -- ds5001 ese315Minor allele frequency- C:0.09NA NS EA WA 2024
    rs47642291,2
    C,F,H--10222905(+) CAACAT/CGTATT 1 -- ds5001 ese321Minor allele frequency- C:0.10NS EA NA WA CSA 1567
    rs1459427571,2
    --10222935(+) TCCAGA/GTAATC 1 -- ds50010--------
    rs1385055071,2
    --10222990(+) GCACAA/GTCAAA 1 -- ds50010--------
    rs1493301401,2
    C--10223188(+) GAAGAC/GGCTCA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for CLEC1A (10222153 - 10264226 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for CLEC1A:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2275947CNV Deletion18987734
    esv2745532CNV Deletion23290073
    esv271248CNV Insertion20981092
    esv1181821CNV Insertion17803354
    esv2431271CNV Insertion19546169
    esv273949CNV Insertion20981092
    nsv826239CNV Loss20364138
    nsv898757CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CLEC1A
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 606782    OMIM disorders: --

    1 disease for CLEC1A:    
    About MalaCards
    endotheliitis


    CLEC1A for disorders           About GeneDecksing


    Export disorders for CLEC1A 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 CLEC1A gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with CLEC1A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular characterization of two novel C-type lectin-like receptors, one of which is selectively expressed in human dendritic cells. (PubMed id 10671229)1, 2, 3, 9 Colonna M.... Angman L. (Eur. J. Immunol. 2000)
    2. A novel cluster of lectin-like receptor genes expressed in monocytic, dendritic and endothelial cells maps close to the NK receptor genes in the human NK gene complex. (PubMed id 11745369)1, 3, 9 Sobanov Y.... Hofer E. (Eur. J. Immunol. 2001)
    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. (Genome Res. 2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. 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)
    6. The human C-type lectin-like receptor CLEC-1 is upregulated by TGF-I^ and primarily localized in the endoplasmic membrane compartment. (PubMed id 22117783)1 Sattler S....Hofer E. (Scand. J. Immunol. 2012)
    7. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1 Otsuki T....Isogai T. (DNA Res. 2005)
    8. Evolutionary analysis reveals collective properties and specificity in the C-type lectin and lectin-like domain superfamily. (PubMed id 12945048)1 Ebner S....Ben-Tal N. (Proteins 2003)
    9. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    10. C-type lectin-like domains. (PubMed id 10508765)1 Drickamer K. (Curr. Opin. Struct. Biol. 1999)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 51267 HGNC: 24355 AceView: CLEC1 Ensembl:ENSG00000150048 euGenes: HUgn51267
    ECgene: CLEC1A H-InvDB: CLEC1A

    (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 CLEC1A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CLEC1A gene:
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