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    TLR9 toll like receptor 9 [ Homo sapiens (human) ]

    Gene ID: 54106, updated on 9-Dec-2024

    Summary

    Official Symbol
    TLR9provided by HGNC
    Official Full Name
    toll like receptor 9provided by HGNC
    Primary source
    HGNC:HGNC:15633
    See related
    Ensembl:ENSG00000239732 MIM:605474; AllianceGenome:HGNC:15633
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CD289
    Summary
    The protein encoded by this gene is a member of the Toll-like receptor (TLR) family, which plays a fundamental role in pathogen recognition and activation of innate immunity. TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. They recognize pathogen-associated molecular patterns (PAMPs) that are expressed on infectious agents, and mediate the production of cytokines necessary for the development of effective immunity. Studies in mice and human indicate that this receptor mediates cellular response to unmethylated CpG dinucleotides in bacterial DNA to mount an innate immune response. [provided by RefSeq, Aug 2017]
    Expression
    Broad expression in lymph node (RPKM 2.9), spleen (RPKM 1.9) and 16 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TLR9 in Genome Data Viewer
    Location:
    3p21.2
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52221080..52225645, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52253966..52258531, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52255096..52259661, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ALDOA pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19929 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14432 Neighboring gene 5'-aminolevulinate synthase 1 Neighboring gene Sharpr-MPRA regulatory region 10522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52259793-52260294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52260295-52260794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14433 Neighboring gene twinfilin actin binding protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52270765-52271306 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52271307-52271849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19933 Neighboring gene NANOG hESC enhancer GRCh37_chr3:52274848-52275376 Neighboring gene TWF2 divergent transcript

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 inhibits TLR9-mediated upregulation of CD83 and the secretion of inflammatory cytokines TNF-alpha and IL-6, and chemokine IP10 in plasmacytoid dendritic cells (pDC) PubMed
    env TLR-9-induced IFN-alpha production is inhibited by both monomeric and trimeric HIV-1 gp120 in plasmacytoid dendritic cells (pDC) PubMed
    env Treatment of HIV-1 gp120 to astroglia displays significant decreases in TLR9 PubMed
    Envelope surface glycoprotein gp160, precursor env Combined activation of TLR7/8 and TLR9 by TLR7/8 and TLR9 agonists induces the highest titers of binding, neutralizing, and antibody-dependent cellular cytotoxicity-mediating antibodies against HIV-1 Env/gp140 PubMed
    Tat tat Treatment of HIV-1 Tat to astroglia displays significant decreases in TLR9 expression PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: TWF2

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables interleukin-1 receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables pattern recognition receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables pattern recognition receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables siRNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables unmethylated CpG binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in MyD88-dependent toll-like receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in canonical NF-kappaB signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cellular response to chloroquine IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to lipopolysaccharide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to metal ion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in defense response to Gram-negative bacterium IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in defense response to bacterium NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in defense response to virus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in detection of molecule of bacterial origin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in innate immune response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in maintenance of gastrointestinal epithelium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in male gonad development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in microglial cell activation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of ATPase-coupled calcium transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of ERK1 and ERK2 cascade IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of B cell activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of B cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of JNK cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of MAPK cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of autophagy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of canonical NF-kappaB signal transduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of chemokine production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of granulocyte macrophage colony-stimulating factor production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of immunoglobulin production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of inflammatory response IC
    Inferred by Curator
    more info
    PubMed 
    involved_in positive regulation of interferon-alpha production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of interferon-beta production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of interferon-beta production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of interleukin-10 production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of interleukin-12 production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of interleukin-18 production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of interleukin-6 production IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of interleukin-6 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of positive regulation of interleukin-8 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of interleukin-8 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of intestinal epithelial cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of non-canonical NF-kappaB signal transduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of toll-like receptor 9 signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of tumor necrosis factor production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of type II interferon production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of B cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of dendritic cell cytokine production IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in toll-like receptor 9 signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in toll-like receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in toll-like receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
     
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in early phagosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endolysosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endolysosome membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in lysosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_033933.1 RefSeqGene

      Range
      5519..10084
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_017442.4NP_059138.1  toll-like receptor 9 precursor

      See identical proteins and their annotated locations for NP_059138.1

      Status: REVIEWED

      Source sequence(s)
      AF245704, AF259262, BC032713
      Consensus CDS
      CCDS2848.1
      UniProtKB/Swiss-Prot
      B3Y661, D1CS56, Q6UVZ2, Q9HD68, Q9HD69, Q9HD70, Q9NR96, Q9NYC2, Q9NYC3
      UniProtKB/TrEMBL
      B6CH46, C3W5P5, D1CS61, D1CS62
      Related
      ENSP00000353874.2, ENST00000360658.3
      Conserved Domains (4) summary
      cd00116
      Location:476739
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:476497
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:496555
      LRR_8; Leucine rich repeat
      cl23749
      Location:8701009
      TIR_2; TIR domain

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      52221080..52225645 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      52253966..52258531 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_138688.1: Suppressed sequence

      Description
      NM_138688.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.