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

Gene ID: 54106, updated on 12-Aug-2020

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
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

Genomic context

See TLR9 in Genome Data Viewer
Location:
3p21.2
Exon count:
2
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (52221080..52226163, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52255096..52260179, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ALDOA pseudogene 1 Neighboring gene 5'-aminolevulinate synthase 1 Neighboring gene Sharpr-MPRA regulatory region 10522 Neighboring gene twinfilin actin binding protein 2 Neighboring gene uncharacterized LOC101929054

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

NHGRI GWAS Catalog

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
interleukin-1 receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
pattern recognition receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
siRNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
transmembrane signaling receptor activity IEA
Inferred from Electronic Annotation
more info
 
unmethylated CpG binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
I-kappaB kinase/NF-kappaB signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
I-kappaB phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
MyD88-dependent toll-like receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
defense response to Gram-negative bacterium IMP
Inferred from Mutant Phenotype
more info
PubMed 
defense response to bacterium NAS
Non-traceable Author Statement
more info
PubMed 
defense response to virus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
innate immune response TAS
Traceable Author Statement
more info
PubMed 
maintenance of gastrointestinal epithelium ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of calcium-transporting ATPase activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of interleukin-6 production ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of interleukin-8 production IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of toll-like receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of B cell activation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of B cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of I-kappaB kinase/NF-kappaB signaling IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of JNK cascade IC
Inferred by Curator
more info
PubMed 
positive regulation of JUN kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of MAPK cascade IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of NF-kappaB transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of NIK/NF-kappaB signaling IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of chemokine production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of granulocyte macrophage colony-stimulating factor production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of immunoglobulin production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of inflammatory response IC
Inferred by Curator
more info
PubMed 
positive regulation of interferon-alpha production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interferon-beta production IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of interferon-beta production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interferon-beta production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interferon-gamma production IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of interferon-gamma production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-10 production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-12 production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-18 production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-6 production IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of interleukin-6 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-8 production IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of interleukin-8 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of nitric-oxide synthase biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of toll-like receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of tumor necrosis factor production ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of B cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cytokine secretion IEA
Inferred from Electronic Annotation
more info
 
regulation of toll-like receptor 9 signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
response to molecule of bacterial origin TAS
Traceable Author Statement
more info
PubMed 
toll-like receptor 9 signaling pathway TAS
Traceable Author Statement
more info
 
toll-like receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
toll-like receptor signaling pathway TAS
Traceable Author Statement
more info
 
tumor necrosis factor production IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tumor necrosis factor production IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi membrane TAS
Traceable Author Statement
more info
 
apical plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
basolateral plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
early phagosome ISS
Inferred from Sequence or Structural Similarity
more info
 
endolysosome ISS
Inferred from Sequence or Structural Similarity
more info
 
endolysosome membrane TAS
Traceable Author Statement
more info
 
endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
endosome ISS
Inferred from Sequence or Structural Similarity
more info
 
endosome membrane TAS
Traceable Author Statement
more info
 
extracellular region NAS
Non-traceable Author Statement
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
lysosome ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

NCBI Reference Sequences (RefSeq)

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
    5001..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
    Q9NR96
    Related
    ENSP00000353874.2, ENST00000360658.2
    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: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    52221080..52226163 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.
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