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CLEC18B Gene

protein-coding   GIFtS: 32
GCID: GC16M074442

C-Type Lectin Domain Family 18, Member B

  Search for CLEC18B
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 18, Member B1 2     Mannose Receptor-Like 22
Mannose Receptor-Like Protein 12 3     Secretory Protein LOC4971902
MRCL22     MRLP13
C-Type Lectin Domain Family 18 Member B2     

External Ids:    HGNC: 338491   Entrez Gene: 4971902   Ensembl: ENSG000001408397   UniProtKB: Q6UXF73   

Export aliases for CLEC18B gene to outside databases

Previous GC identifer: GC16M073002


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for CLEC18B Gene:
CLEC18B (C-type lectin domain family 18, member B) is a protein-coding gene. GO annotations related to this gene include carbohydrate binding. An important paralog of this gene is CRISPLD2.


(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_000016.9  NT_010498.16  NC_018927.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CLEC18B gene promoter:
         GR   AML1a   GR-beta   Olf-1   STAT5A   C/EBPalpha   AREB6   USF-1   GR-alpha   ATF6   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for CLEC18B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLEC18B


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

Entrez Gene cytogenetic band: 16q22.3   Ensembl cytogenetic band:  16q23.1   HGNC cytogenetic band: 16q22.3

CLEC18B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLEC18B gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M074442:  view genomic region     (about GC identifiers)

Start:
74,442,529 bp from pter      End:
74,455,368 bp from pter
Size:
12,840 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: CL18B_HUMAN, Q6UXF7 (See protein sequence)
Recommended Name: C-type lectin domain family 18 member B precursor  
Size: 455 amino acids; 50490 Da
Secondary accessions: B4DF90
Alternative splicing: 2 isoforms:  Q6UXF7-1   Q6UXF7-2   

Explore the universe of human proteins at neXtProt for CLEC18B: NX_Q6UXF7

Explore proteomics data for CLEC18B at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn144

  • See CLEC18B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001011880.2  
    ENSEMBL proteins: 
     ENSP00000341051  

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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

    Selected InterPro protein domains (see all 8):
     IPR000742 EG-like_dom
     IPR014044 CAP_domain
     IPR001283 Allrgn_V5/Tpx1
     IPR016187 C-type_lectin_fold
     IPR018378 C-type_lectin_CS

    Graphical View of Domain Structure for InterPro Entry Q6UXF7

    ProtoNet protein and cluster: Q6UXF7

    UniProtKB/Swiss-Prot: CL18B_HUMAN, Q6UXF7
    Similarity: Contains 1 C-type lectin domain
    Similarity: Contains 1 EGF-like domain
    Similarity: Contains 1 SCP domain


    Find genes that share domains with CLEC18B           About GenesLikeMe


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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0030246carbohydrate binding IEA--
         
    Find genes that share ontologies with CLEC18B           About GenesLikeMe


    Animal Models:
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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
    CL18B_HUMAN, Q6UXF7: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    plasma membrane2
    cytosol1
    peroxisome1

    Gene Ontology (GO): 1 cellular component term:    About this table

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

    Find genes that share ontologies with CLEC18B           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 CLEC18B
    Interactions:

        Search GeneGlobe Interaction Network for CLEC18B

    (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 CLEC18B (CL18B)



    (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 CLEC18B gene: 
    NM_001011880.2  

    Unigene Clusters for CLEC18B:

    C-type lectin domain family 18, member B
    Hs.454670  [show with all ESTs], Hs.556045  [show with all ESTs]
    Unigene Representative Sequences: AK293982, NM_173619
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000339953(uc010vmv.1 uc002fct.3 uc002fcu.3 uc010vmw.1)
    ENST00000564842 ENST00000425714(uc010vmu.1)
    miRNA
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    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat CLEC18B

    Additional mRNA sequence: 

    AF448856.1 AY358373.1 BC062573.1 

    13 DOTS entries:

    DT.95373006  DT.408627  DT.101982772  DT.120684573  DT.120698532  DT.100813484  DT.120698507  DT.120698528 
    DT.97858387  DT.120684438  DT.120684456  DT.120684650  DT.120698518 

    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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    CLEC18B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AACCCCACGG
    CLEC18B Expression
    About this image

    CLEC18B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLEC18B Protein Expression

    SOURCE GeneReport for Unigene clusters: Hs.454670 Hs.556045
        Custom PCR Arrays for CLEC18B
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLEC18B

    (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 animals.

    Orthologs for CLEC18B gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clec18a1 C-type lectin domain family 18, member A 82.58(n)
    80.38(a)
      353287  NM_181549.3  NP_853527.2 
    chicken
    (Gallus gallus)
    Aves CLEC18A1 C-type lectin domain family 18, member A 72.4(n)
    69.25(a)
      431137  XM_428688.4  XP_428688.3 
    worm
    (Caenorhabditis elegans)
    Secernentea lon-16
    Protein LON-1, isoform a (lon-1) mRNA, complete cd...
    23(a)
    1 → many
    III(5474478-5478382) WBGene00003055


    ENSEMBL Gene Tree for CLEC18B (if available)
    TreeFam Gene Tree for CLEC18B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLEC18B gene
    CRISPLD22  CLEC18C2  PI162  GLIPR12  CRISP22  PI152  CRISP12  CRISPLD12  
    CRISP32  GLIPR1L12  CLEC18A2  GLIPR1L22  R3HDML2  
    2 SIMAP similar genes for CLEC18B using alignment to 1 protein entry:     CL18B_HUMAN:
    CLEC18A    CLEC18C

    Find genes that share paralogs with CLEC18B           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 CLEC18B (see all 241)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2002409291,2
    C,F--74442881(+) GCAGGC/GGAGGG 1 -- ut311Minor allele frequency- G:0.20EU 477
    rs2001023051,2
    C--74443272(+) TCATTA/GCCCCT 1 -- int10--------
    rs2022228251,2
    --74443413(+) GTCAGA/GGATCA 1 -- int10--------
    rs1996058601,2
    F--74443466(+) GTAACG/AGTTTC 2 /R /C mis11Minor allele frequency- A:0.00EU 1321
    rs2006761131,2
    C--74443490(+) CTGGTC/TGTTCC 2 N D mis11Minor allele frequency- T:0.00EU 697
    rs1465559141,2
    C,F--74443542(+) AACCTG/CCAGGC 1 -- int11Minor allele frequency- C:0.12EU 1261
    rs2019399211,2
    C--74443733(+) CTGGGG/TTAACA 1 -- int10--------
    rs1499617541,2
    C,F--74443750(+) CCTACC/TCCATG 2 E G mis12Minor allele frequency- T:0.00NA EU 5487
    rs1399080301,2
    C,F--74443772(+) CCACAC/TCAGCC 2 M V mis12Minor allele frequency- T:0.00NA EU 5785
    rs1472299261,2
    C--74443789(+) ATGGT-/GGGGGA 1 -- int10--------

    HapMap Linkage Disequilibrium report for CLEC18B (74442529 - 74455368 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for CLEC18B (see all 15):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv821530CNV Duplication20802225
    nsv509632CNV Insertion20534489
    nsv833278CNV Loss17160897
    dgv488n67CNV Loss20364138
    nsv819754CNV Loss19587683
    nsv833277CNV Loss17160897
    dgv2911n71CNV Gain21882294
    dgv2910n71CNV Gain21882294
    esv32572CNV Gain17666407
    nsv827736CNV Gain20364138

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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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      --

    (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 CLEC18B gene integrated from 10 sources:
    (articles sorted by number of sources associating them with CLEC18B)
        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 Clark H.F.... Gray A.M. (Genome Res. 2003)
    2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    3. The C-type lectin-like domain superfamily. (PubMed id 16336259)1 Zelensky A.N. and Gready J.E. (FEBS J. 2005)
    4. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)2 Martin J.... Pennacchio L.A. (Nature 2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

    (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: 497190 HGNC: 33849 Ensembl:ENSG00000140839 euGenes: HUgn497190 ECgene: CLEC18B
    H-InvDB: CLEC18B

    (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 CLEC18B 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 CLEC18B gene:
    Search GeneIP for patents involving CLEC18B

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



    (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, eBioscience, 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 inGenious Targeting Laboratory, genOway)
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