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    SIGLEC16 sialic acid binding Ig like lectin 16 (gene/pseudogene) [ Homo sapiens (human) ]

    Gene ID: 400709, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SIGLEC16provided by HGNC
    Official Full Name
    sialic acid binding Ig like lectin 16 (gene/pseudogene)provided by HGNC
    Primary source
    HGNC:HGNC:24851
    See related
    Ensembl:ENSG00000161643 AllianceGenome:HGNC:24851
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SIGLECP16; Siglec-P16
    Summary
    Predicted to enable sialic acid binding activity. Involved in positive regulation of defense response to bacterium and positive regulation of interleukin-6 production. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Annotation information
    Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
    Expression
    Biased expression in ovary (RPKM 40.2) and spleen (RPKM 10.4) See more
    Orthologs
    all
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    Genomic context

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    See SIGLEC16 in Genome Data Viewer
    Location:
    19q13.33
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (49969664..49975814)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (52969773..52975922)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (50472921..50479071)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U3 Neighboring gene sialic acid binding Ig like lectin 11 Neighboring gene uncharacterized LOC124904745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50474918-50475418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14970 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:50490479-50490646 Neighboring gene VRK serine/threonine kinase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50497521-50498022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50498023-50498522 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10949 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:50527935-50528436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14973 Neighboring gene zinc finger protein 473 Neighboring gene uncharacterized LOC124904744

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Proinflammatory Macrophage Activation by the Polysialic Acid-Siglec-16 Axis Is Linked to Increased Survival of Patients with Glioblastoma. Thiesler H, et al. Clin Cancer Res, 2023 Jun 13. PMID 37058255, Free PMC Article
    2. Evolution of siglec-11 and siglec-16 genes in hominins. Wang X, et al. Mol Biol Evol, 2012 Aug. PMID 22383531, Free PMC Article
    3. 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. Cao H, et al. Eur J Immunol, 2008 Aug. PMID 18629938
    4. A human-specific gene in microglia. Hayakawa T, et al. Science, 2005 Sep 9. PMID 16151003
    5. Paired Siglec receptors generate opposite inflammatory responses to a human-specific pathogen. Schwarz F, et al. EMBO J, 2017 Mar 15. PMID 28100677, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Proinflammatory Macrophage Activation by the Polysialic Acid-Siglec-16 Axis Is Linked to Increased Survival of Patients with Glioblastoma.
      Title: Proinflammatory Macrophage Activation by the Polysialic Acid-Siglec-16 Axis Is Linked to Increased Survival of Patients with Glioblastoma.
    2. The authors demonstrated that the human-specific pathogen Escherichia coli K1 uses its polysialic acid capsule as a molecular mimic to engage Siglec-11 and escape killing. In contrast, engagement of the activating counterpart Siglec-16 increases elimination of bacteria.
      Title: Paired Siglec receptors generate opposite inflammatory responses to a human-specific pathogen.
    3. 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.
      Title: 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.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sialic acid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of defense response to bacterium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of interleukin-6 production IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    sialic acid-binding Ig-like lectin 16
    Names
    sialic acid binding Ig-like lectin 16
    sialic acid binding Ig-like lectin, pseudogene 16
    sialic acid-binding immunoglobulin-like lectin 16
    siglec-16

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001348364.2 → NP_001335293.2  sialic acid-binding Ig-like lectin 16 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the functional allele encoding the full-length protein.
      Source sequence(s)
      AC011452, AK301031, BC030222
      UniProtKB/Swiss-Prot
      A6NMB1
      Related
      ENSP00000502223.2, ENST00000602139.6
      Conserved Domains (2) summary
      cd05712
      Location:22 → 141
      Ig_Siglec_N; Immunoglobulin (Ig) domain at the N terminus of Siglec (sialic acid-binding Ig-like lectins)
      smart00410
      Location:247 → 323
      IG_like; Immunoglobulin like

    RNA

    1. NR_145574.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1, noncoding) represents the reference genome allele, which does not encode a full-length protein and is predicted to be non-functional.
      Source sequence(s)
      AC011452, AK301031, BC030222

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      49969664..49975814
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      52969773..52975922
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NG_024269.1: Suppressed sequence

      Description
      NG_024269.1: This RefSeq was permanently suppressed because it is now thought that this pseudogene is transcribed.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6NMB1.3 GenPept UniProtKB/Swiss-Prot:A6NMB1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials