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SIGLEC16 Gene

pseudogene   GIFtS: 37
GCID: GC19P050473

Sialic Acid Binding Ig-Like Lectin 16 (Gene/Pseudogene)

(Previous names: sialic acid binding Ig-like lectin, pseudogene 16)
(Previous symbol: SIGLECP16)
  Search for SIGLEC16
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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Sialic Acid Binding Ig-Like Lectin 16 (Gene/Pseudogene)1 2
SIGLECP161 2 3
Siglec-P162 3
Sialic Acid Binding Ig-Like Lectin, Pseudogene 161
Siglec-163

External Ids:    HGNC: 248511   Entrez Gene: 4007092   Ensembl: ENSG000001616437   UniProtKB: A6NMB13   
ORGUL members:         

Export aliases for SIGLEC16 gene to outside databases

Previous GC identifers: GC19P055168 GC19P046849


(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 SIGLEC16 Gene:
SIGLEC16 (sialic acid binding Ig-like lectin 16 (gene/pseudogene)) is a pseudogene, and is affiliated with the lncRNA class.

UniProtKB/Swiss-Prot: SIG16_HUMAN, A6NMB1
Function: Putative adhesion molecule that mediates sialic-acid dependent binding to cells (By similarity)




(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_000019.10  NC_018930.2  NT_011109.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the SIGLEC16 gene promoter:
         E2F-3a   E2F   E2F-1   FOXO1a   E2F-2   FOXO1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SIGLEC16

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SIGLEC16


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

Entrez Gene cytogenetic band: 19q13.33   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.33

SIGLEC16 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SIGLEC16 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P050473:  view genomic region     (about GC identifiers)

Start:
50,472,857 bp from pter      End:
50,479,076 bp from pter
Size:
6,220 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SIGLEC16

(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: SIG16_HUMAN, A6NMB1 (See protein sequence)
Recommended Name: Sialic acid-binding Ig-like lectin 16 precursor  
Size: 481 amino acids; 52992 Da
Caution: According to PubMed:18629938, the SIGLECP16 sequence, that was initially classified as a pseudogene, has
a 4 bp deletion when compared with the sequence shown in this entry. This deletion is a polymorphism with a
frequency of around 50% in the UK population. The frameshifted allele is non-functional whereas the sequence
displayed here seems to be functional. The functional allele has been named SIGLEC16 in PubMed:18629938

Explore the universe of human proteins at neXtProt for SIGLEC16: NX_A6NMB1

Explore proteomics data for SIGLEC16 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn43, Asn78, Asn338, Asn347

  • See SIGLEC16 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    Reactome Protein details: A6NMB1

    SIGLEC16 Human Recombinant Protein Products:

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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:
    SIGLEC: Sialic acid binding Ig-like lectins
    C2SET: Immunoglobulin superfamily / C2-set domain containing
    ISET: Immunoglobulin superfamily / I-set domain containing
    VSET: Immunoglobulin superfamily / V-set domain containing

    Selected InterPro protein domains (see all 8):
     IPR003598 Ig_sub2
     IPR013162 CD80_C2-set
     IPR013098 Ig_I-set
     IPR013783 Ig-like_fold
     IPR013106 Ig_V-set

    Graphical View of Domain Structure for InterPro Entry A6NMB1

    ProtoNet protein and cluster: A6NMB1

    UniProtKB/Swiss-Prot: SIG16_HUMAN, A6NMB1
    Similarity: Belongs to the immunoglobulin superfamily. SIGLEC (sialic acid binding Ig-like lectin) family
    Similarity: Contains 3 Ig-like C2-type (immunoglobulin-like) domains
    Similarity: Contains 1 Ig-like V-type (immunoglobulin-like) domain


    SIGLEC16 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: SIG16_HUMAN, A6NMB1
    Function: Putative adhesion molecule that mediates sialic-acid dependent binding to cells (By similarity)

    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
    SIG16_HUMAN, A6NMB1: Membrane; Single-pass type I membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    extracellular2
    cytosol1
    endoplasmic reticulum1
    golgi apparatus1
    lysosome1
    mitochondrion1
    nucleus1
    peroxisome1

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

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

    SIGLEC16 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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    SuperPaths for SIGLEC16 About    
    See pathways by source

    SuperPathContained pathways About
    1Signaling by FGFR
    DAP12 interactions0.89

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for SIGLEC16
        DAP12 interactions



    SIGLEC16 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SIGLEC16
    Interactions:

        Search GeneGlobe Interaction Network for SIGLEC16

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion IEA--
    GO:0045087innate immune response TAS--

    SIGLEC16 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 SIGLEC16 (SIG16)



    (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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    Unigene Cluster for SIGLEC16:

    Sialic acid binding Ig-like lectin 16 (gene/pseudogene)
    Hs.568076  [show with all ESTs]
    Unigene Representative Sequence: AK301031
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000602139 ENST00000599858 ENST00000417280 ENST00000456956(uc002prf.3 uc010ybj.1 uc010ybk.1)

    miRNA
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    Additional mRNA sequence: 

    AK301031.1 BC030222.1 NR_002825.1 

    1 DOTS entry:

    DT.97792297 

    3 AceView cDNA sequences:

    BC030222 AI913240 BC039008 

    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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    SIGLEC16 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SIGLEC16 Expression
    About this image

    SIGLEC16 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SIGLEC16 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.568076

    UniProtKB/Swiss-Prot: SIG16_HUMAN, A6NMB1
    Tissue specificity: Expressed in bone marrow, fetal brain, fetal liver, lung and salivary gland. Detected in
    brain, macrophage, cancerous esophagus and lung at protein level

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SIGLEC16

    (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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    ENSEMBL Gene Tree for SIGLEC16 (if available)
    TreeFam Gene Tree for SIGLEC16 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SIGLEC16 gene
    10 SIMAP similar genes for SIGLEC16 using alignment to 2 protein entries:     SIG16_HUMAN (see all proteins):
    SIGLEC11    SIGLEC10    CD33    SIGLEC14    SIGLEC12    CEA
    SIGLEC9    SIGLEC7    SIGLEC5    SIGLEC6

    SIGLEC16 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 SIGLEC16 (see all 214)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1459753721,2
    --50470993(+) TGCTTA/GTCTTT 1 -- us2k10--------
    rs789189081,2
    F--50471051(+) AGTGTA/GTATGT 1 -- us2k11Minor allele frequency- G:0.01WA 118
    rs621151631,2
    C,F--50471178(+) AATTAC/AAAATA 1 -- us2k11Minor allele frequency- A:0.50NA 2
    rs1916725371,2
    --50471211(+) CATAAA/CACAAA 1 -- us2k10--------
    rs43109771,2
    C,F,A--50471300(+) tgcagT/Ggacgg 1 -- us2k18Minor allele frequency- G:0.24WA NA CSA EA 367
    rs1415650941,2
    --50471365(+) GTCTCC/GTGAGT 1 -- us2k10--------
    rs1842648171,2
    C--50471390(+) GTGAGC/TGCCAC 1 -- us2k10--------
    rs1881112911,2
    --50471431(+) GAGACA/GGGGTT 1 -- us2k10--------
    rs355469221,2
    C--50471710(+) AAAAA-/AGTGTA 1 -- us2k10--------
    rs118806381,2
    C,F,H--50471823(+) caagtA/Tcccat 1 -- us2k12Minor allele frequency- T:0.11NA WA 120

    HapMap Linkage Disequilibrium report for SIGLEC16 (50472857 - 50479076 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SIGLEC16:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv54n68CNV Loss17160897
    nsv9739CNV Gain+Loss18304495
    nsv7309OTHER Inversion18451855

    Human Gene Mutation Database (HGMD): SIGLEC16
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SIGLEC16
    DNA2.0 Custom Variant and Variant Library Synthesis for SIGLEC16

    (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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    SIGLEC16 for disorders           About GeneDecksing


    Export disorders for SIGLEC16 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 SIGLEC16 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SIGLEC16)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. SIGLEC16 encodes a DAP12-associated receptor expressed in macrophages that evolved from its inhibitory counterpart SIGLEC11 and has functional and non-functional alleles in humans. (PubMed id 18629938)1, 2, 3 Cao H....Barrow A.D. (Eur. J. Immunol. 2008)
    2. Cloning and characterization of human Siglec-11. A recently evolved signaling molecule that can interact with SHP-1 and SHP-2 and is expressed by tissue macrophages, including brain microglia. (PubMed id 11986327)1, 2, 3 Angata T....Varki A. (J. Biol. Chem. 2002)
    3. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (Nature 2004)
    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. (Genome Res. 2004)
    5. 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)
    6. A second uniquely human mutation affecting sialic acid biology. (PubMed id 11546777)1 Angata T.... Varki A. (J. Biol. Chem. 2001)

    (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: 400709 HGNC: 24851 AceView: LOC400709 Ensembl:ENSG00000161643 euGenes: HUgn400709
    ECgene: SIGLEC16 H-InvDB: SIGLEC16

    (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 SIGLEC16 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 SIGLEC16 gene:
    Search GeneIP for patents involving SIGLEC16

    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, 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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