Tlr9 (toll-like receptor 9) - Rat Genome Database

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Gene: Tlr9 (toll-like receptor 9) Rattus norvegicus
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Symbol: Tlr9
Name: toll-like receptor 9
RGD ID: 631352
Description: Exhibits unmethylated CpG binding activity. Involved in several processes, including cellular response to lipopolysaccharide; male gonad development; and microglial cell activation. Localizes to plasma membrane. Biomarker of brain disease; mastitis; and perinatal necrotizing enterocolitis. Human ortholog(s) of this gene implicated in several diseases, including allergic bronchopulmonary aspergillosis; cystic fibrosis; glomerulonephritis (multiple); hepatitis B; and lung disease (multiple). Orthologous to human TLR9 (toll like receptor 9); PARTICIPATES IN Toll-like receptor signaling pathway; Chagas disease pathway; malaria pathway; INTERACTS WITH acrylamide; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
RGD Orthologs
Human
Mouse
Chinchilla
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28106,864,680 - 106,868,796 (+)NCBI
Rnor_6.0 Ensembl8114,916,122 - 114,920,171 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08114,916,122 - 114,920,171 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08114,279,020 - 114,283,069 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8106,185,754 - 106,189,869 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Achlorhydria  (ISO)
acute kidney failure  (ISO)
Acute Necrotizing Pancreatitis  (IEP)
adult respiratory distress syndrome  (ISO)
alcoholic liver cirrhosis  (ISO)
allergic bronchopulmonary aspergillosis  (ISO)
allergic conjunctivitis  (ISO)
allergic rhinitis  (ISO)
anogenital venereal wart  (ISO)
asthma  (ISO)
bacterial pneumonia  (ISO)
Brain Injuries  (ISO)
breast cancer  (ISO)
bronchiolitis obliterans  (ISO)
cardiovascular system disease  (ISO)
cervix uteri carcinoma in situ  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
chronic granulomatous disease  (ISO)
Chronic Hepatitis B  (ISO)
Chronic Hepatitis C  (ISO)
chronic kidney disease  (ISS)
Chronic Periodontitis  (ISO)
crescentic glomerulonephritis  (ISO)
Crohn's disease  (ISO)
cutaneous leishmaniasis  (ISO)
cystic fibrosis  (ISO)
dermatomyositis  (ISO)
Experimental Autoimmune Neuritis  (IEP)
Granuloma, Foreign-Body  (ISO)
Hearing Loss  (ISO)
hepatitis B  (ISO)
hepatitis C  (ISO)
hepatocellular carcinoma  (ISO)
Herpes Simplex Encephalitis  (IEP)
herpes simplex virus keratitis  (ISO)
Hypergammaglobulinemia  (ISO)
IgA glomerulonephritis  (ISO)
Inflammation  (ISO)
interstitial lung disease  (ISO)
Klebsiella Infections  (ISO)
Legionnaires' disease  (ISO)
Liver Injury  (ISO)
Lung Neoplasms  (ISO)
lung non-small cell carcinoma  (ISO)
lupus nephritis  (ISO)
Malarial Anemia  (ISO)
mastitis  (IEP)
membranoproliferative glomerulonephritis  (ISO)
non-alcoholic fatty liver disease  (ISO)
non-alcoholic steatohepatitis  (ISO)
Oral Lichen Planus  (ISO)
papillomavirus infectious disease  (ISO)
perinatal necrotizing enterocolitis  (IEP)
Pneumococcal Infections  (ISO)
Pneumococcal Meningitis  (ISO)
primary biliary cholangitis  (ISO)
proteinuria  (ISO)
pulmonary fibrosis  (ISO)
pulmonary tuberculosis  (ISO)
renal cell carcinoma  (ISO)
Respiratory Sounds  (ISO)
Respiratory Tract Granuloma  (ISO)
Schistosomiasis Mansoni  (ISO)
sinusitis  (ISO)
squamous cell carcinoma  (ISO)
systemic lupus erythematosus  (ISO)
Tracheoesophageal Fistula  (ISO)
Transplant Rejection  (ISO)
Triple Negative Breast Neoplasms  (ISO)
trypanosomiasis  (ISO)
ureteral obstruction  (ISO)
viral pneumonia  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of innate immune response  (ISO)
cellular response to chloroquine  (ISO)
cellular response to lipopolysaccharide  (IEP)
cellular response to metal ion  (IEP)
defense response to Gram-negative bacterium  (ISO)
defense response to virus  (IBA,IMP,ISO)
I-kappaB kinase/NF-kappaB signaling  (IBA,ISO)
I-kappaB phosphorylation  (ISO)
immune response  (IBA,ISO)
inflammatory response  (IEA)
innate immune response  (IEA)
maintenance of gastrointestinal epithelium  (ISO)
male gonad development  (IEP)
microglial cell activation  (IDA)
MyD88-dependent toll-like receptor signaling pathway  (ISO)
negative regulation of ATPase-coupled calcium transmembrane transporter activity  (ISO)
negative regulation of ERK1 and ERK2 cascade  (IEA,ISO)
negative regulation of interleukin-6 production  (ISO)
negative regulation of interleukin-8 production  (ISO)
negative regulation of NF-kappaB transcription factor activity  (ISO)
negative regulation of toll-like receptor signaling pathway  (ISO)
positive regulation of autophagy  (IDA)
positive regulation of B cell activation  (ISO)
positive regulation of B cell proliferation  (ISO)
positive regulation of chemokine production  (ISO)
positive regulation of cytokine production  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of granulocyte macrophage colony-stimulating factor production  (ISO)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (ISO)
positive regulation of immunoglobulin production  (ISO)
positive regulation of inflammatory response  (IEA)
positive regulation of interferon-alpha production  (ISO)
positive regulation of interferon-beta production  (ISO)
positive regulation of interferon-gamma production  (ISO)
positive regulation of interleukin-10 production  (ISO)
positive regulation of interleukin-12 production  (ISO)
positive regulation of interleukin-18 production  (ISO)
positive regulation of interleukin-6 production  (IBA,ISO)
positive regulation of interleukin-8 production  (ISO)
positive regulation of JUN kinase activity  (ISO)
positive regulation of MAPK cascade  (ISO)
positive regulation of NF-kappaB transcription factor activity  (IBA,ISO)
positive regulation of NIK/NF-kappaB signaling  (ISO)
positive regulation of nitric-oxide synthase biosynthetic process  (ISO)
positive regulation of toll-like receptor 9 signaling pathway  (ISO)
positive regulation of toll-like receptor signaling pathway  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of tumor necrosis factor production  (ISO)
regulation of B cell activation  (ISO)
regulation of B cell differentiation  (ISO)
regulation of dendritic cell cytokine production  (ISO)
regulation of inflammatory response  (ISO)
regulation of protein phosphorylation  (ISO)
regulation of toll-like receptor 9 signaling pathway  (ISO)
response to virus  (ISO)
toll-like receptor 9 signaling pathway  (IEA)
toll-like receptor signaling pathway  (IBA,IDA)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:11130078   PMID:12925853   PMID:14993594   PMID:15356140   PMID:15723075   PMID:16098606   PMID:16286015   PMID:16415873   PMID:17128265   PMID:17475835   PMID:18203139   PMID:18250457  
PMID:18305481   PMID:18820679   PMID:18931679   PMID:19047410   PMID:19740627   PMID:20847273   PMID:21402738   PMID:21747311   PMID:21864114   PMID:21870333   PMID:22427638   PMID:23109291  
PMID:23479602   PMID:23826189   PMID:23857366   PMID:24091496   PMID:24409285   PMID:24535292   PMID:24610369   PMID:24740015   PMID:25384124   PMID:25686612   PMID:25910936   PMID:25917084  
PMID:26934958   PMID:28647749   PMID:28990073   PMID:29128901   PMID:29348267   PMID:29445737   PMID:29929196   PMID:29992753   PMID:30106134   PMID:30577532  


Genomics

Comparative Map Data
Tlr9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28106,864,680 - 106,868,796 (+)NCBI
Rnor_6.0 Ensembl8114,916,122 - 114,920,171 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08114,916,122 - 114,920,171 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08114,279,020 - 114,283,069 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8106,185,754 - 106,189,869 (+)NCBICelera
Cytogenetic Map8q32NCBI
TLR9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl352,221,080 - 52,225,645 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl352,221,080 - 52,226,163 (-)EnsemblGRCh38hg38GRCh38
GRCh38352,221,080 - 52,225,645 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37352,255,096 - 52,259,661 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36352,230,138 - 52,235,219 (-)NCBINCBI36hg18NCBI36
Build 34352,230,137 - 52,233,247NCBI
Celera352,234,410 - 52,239,491 (-)NCBI
Cytogenetic Map3p21.2NCBI
HuRef352,317,258 - 52,322,341 (-)NCBIHuRef
CHM1_1352,207,624 - 52,212,707 (-)NCBICHM1_1
Tlr9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399106,099,797 - 106,104,075 (+)NCBIGRCm39mm39
GRCm39 Ensembl9106,099,797 - 106,104,082 (+)Ensembl
GRCm389106,222,598 - 106,226,876 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9106,222,598 - 106,226,883 (+)EnsemblGRCm38mm10GRCm38
MGSCv379106,124,929 - 106,129,207 (+)NCBIGRCm37mm9NCBIm37
MGSCv369106,080,699 - 106,084,977 (+)NCBImm8
Celera9105,848,890 - 105,853,167 (+)NCBICelera
Cytogenetic Map9F1NCBI
Tlr9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555323,828,645 - 3,832,699 (-)NCBIChiLan1.0ChiLan1.0
TLR9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12037,529,322 - 37,547,117 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2037,542,340 - 37,547,114 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2037,529,401 - 37,539,957 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2037,510,887 - 37,521,504 (+)NCBI
Dog10K_Boxer_Tasha2037,523,889 - 37,528,666 (+)NCBI
ROS_Cfam_1.02037,879,856 - 37,897,682 (+)NCBI
UMICH_Zoey_3.12037,256,577 - 37,261,354 (+)NCBI
UMICH_Zoey_3.12037,243,558 - 37,254,192 (+)NCBI
UNSW_CanFamBas_1.02037,652,111 - 37,662,740 (+)NCBI
UNSW_CanFamBas_1.02037,665,125 - 37,669,902 (+)NCBI
UU_Cfam_GSD_1.02037,936,949 - 37,947,576 (+)NCBI
UU_Cfam_GSD_1.02037,950,172 - 37,954,949 (+)NCBI
TLR9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11334,353,444 - 34,370,990 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21337,634,343 - 37,652,036 (+)NCBISscrofa10.2Sscrofa10.2susScr3

Position Markers
PMC133006P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08114,919,768 - 114,920,086NCBIRnor6.0
Rnor_5.08114,282,666 - 114,282,984UniSTSRnor5.0
Celera8106,189,400 - 106,189,718UniSTS
PMC55404P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08114,919,810 - 114,920,069NCBIRnor6.0
Rnor_5.08114,282,708 - 114,282,967UniSTSRnor5.0
Celera8106,189,442 - 106,189,701UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)844458129118087517Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)850529480128036471Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)850529480128036471Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)855435004115812386Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)865717449128033050Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)872849686117849686Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight as a percentage of body weight (CMO:0000654)874917593121080545Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)876103982127182642Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)878805083123805083Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)878805083123805083Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)878805083123805083Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)878805083123805083Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)880697934125697934Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)883894304128894304Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
8693654Alc32Alcohol consumption QTL 3220.755drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)895319530115625029Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)895963141122354314Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8107769005129956433Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8110212979116947981Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:58
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000074194
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 5
Low 1 2 12 13 16 11 8 11
Below cutoff 1 31 39 35 1 35 7 10 56 24 30 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000074194   ⟹   ENSRNOP00000066453
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8114,916,122 - 114,920,171 (+)Ensembl
RefSeq Acc Id: NM_198131   ⟹   NP_937764
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28106,864,680 - 106,868,796 (+)NCBI
Rnor_6.08114,916,122 - 114,920,171 (+)NCBI
Rnor_5.08114,279,020 - 114,283,069 (+)NCBI
Celera8106,185,754 - 106,189,869 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_937764 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAO62342 (Get FASTA)   NCBI Sequence Viewer  
  AAO91938 (Get FASTA)   NCBI Sequence Viewer  
  AAO93109 (Get FASTA)   NCBI Sequence Viewer  
  AAW50953 (Get FASTA)   NCBI Sequence Viewer  
  EDL77326 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_937764   ⟸   NM_198131
- Peptide Label: precursor
- UniProtKB: Q6Y1S0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066453   ⟸   ENSRNOT00000074194
Protein Domains
TIR

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696246
Promoter ID:EPDNEW_R6770
Type:initiation region
Name:Tlr9_1
Description:toll-like receptor 9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08114,916,122 - 114,916,182EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:631352 AgrOrtholog
Ensembl Genes ENSRNOG00000048161 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000066453 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074194 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10140 UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/TrEMBL
InterPro Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRR_12 UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/TrEMBL
  TIR_dom UniProtKB/TrEMBL
  TLR9 UniProtKB/TrEMBL
  Toll_tir_struct_dom_sf UniProtKB/TrEMBL
KEGG Report rno:338457 UniProtKB/TrEMBL
NCBI Gene 338457 ENTREZGENE
PANTHER PTHR47410:SF3 UniProtKB/TrEMBL
Pfam LRR_12 UniProtKB/TrEMBL
  LRR_6 UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
  TIR UniProtKB/TrEMBL
PhenoGen Tlr9 PhenoGen
PROSITE LRR UniProtKB/TrEMBL
  TIR UniProtKB/TrEMBL
SMART LRR_TYP UniProtKB/TrEMBL
  TIR UniProtKB/TrEMBL
Superfamily-SCOP TIR UniProtKB/TrEMBL
UniProt M0RAA8_RAT UniProtKB/TrEMBL
  Q6Y1S0 ENTREZGENE, UniProtKB/TrEMBL
  Q80XA5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-11 Tlr9  toll-like receptor 9      Symbol and Name status set to approved 625702 APPROVED