Tlr1 (toll-like receptor 1) - Rat Genome Database

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Gene: Tlr1 (toll-like receptor 1) Rattus norvegicus
Analyze
Symbol: Tlr1
Name: toll-like receptor 1
RGD ID: 1309975
Description: Exhibits lipopeptide binding activity. Involved in microglial cell activation; response to bacterial lipoprotein; and toll-like receptor signaling pathway. Predicted to localize to Golgi apparatus; Toll-like receptor 1-Toll-like receptor 2 protein complex; and membrane raft. Biomarker of perinatal necrotizing enterocolitis. Human ortholog(s) of this gene implicated in several diseases, including IgA glomerulonephritis; aspergillosis; leprosy; pyelonephritis; and tuberculosis. Orthologous to human TLR1 (toll like receptor 1); PARTICIPATES IN Toll-like receptor signaling pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC305354; rCG56938-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21443,384,127 - 43,396,765 (+)NCBI
Rnor_6.0 Ensembl1445,062,662 - 45,081,991 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01445,062,662 - 45,065,014 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01444,871,931 - 44,874,283 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41446,114,913 - 46,124,820 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1442,538,240 - 42,540,804 (+)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Adhikary S, etal., J Neurotrauma. 2011 Dec;28(12):2417-27. doi: 10.1089/neu.2011.1853. Epub 2011 Oct 4.
2. Banas MC, etal., J Am Soc Nephrol. 2008 Apr;19(4):704-13. doi: 10.1681/ASN.2007040395. Epub 2008 Feb 6.
3. Ben-Ali M, etal., Hum Mutat. 2011 Jun;32(6):643-52. doi: 10.1002/humu.21486.
4. Chang JS, etal., J Immunol. 2006 Mar 1;176(5):3010-8.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Guo LH, etal., Biochem Biophys Res Commun. 2006 Oct 27;349(3):1156-62. Epub 2006 Sep 1.
8. Hawn TR, etal., PLoS One. 2009 Jun 22;4(6):e5990. doi: 10.1371/journal.pone.0005990.
9. Johnson CM, etal., J Immunol. 2007 Jun 15;178(12):7520-4.
10. Kesh S, etal., Ann N Y Acad Sci. 2005 Dec;1062:95-103.
11. Kormann MS, etal., J Allergy Clin Immunol. 2008 Jul;122(1):86-92, 92.e1-8. Epub 2008 Jun 10.
12. Kumar H, etal., Int Rev Immunol. 2011 Feb;30(1):16-34.
13. Lee JS, etal., Int J Immunogenet. 2011 Apr;38(2):133-8. doi: 10.1111/j.1744-313X.2010.00978.x. Epub 2010 Nov 25.
14. Liu Y, etal., Am J Physiol Gastrointest Liver Physiol. 2009 Sep;297(3):G442-50. Epub 2009 Jul 16.
15. Ma X, etal., PLoS One. 2007 Dec 19;2(12):e1318.
16. OMIM Disease Annotation Pipeline
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12077222   PMID:12091878   PMID:15294986   PMID:15632090   PMID:16880211   PMID:17889651   PMID:19931471   PMID:22198949   PMID:23155421   PMID:24091496   PMID:28822965   PMID:32329822  


Genomics

Comparative Map Data
Tlr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21443,384,127 - 43,396,765 (+)NCBI
Rnor_6.0 Ensembl1445,062,662 - 45,081,991 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01445,062,662 - 45,065,014 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01444,871,931 - 44,874,283 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41446,114,913 - 46,124,820 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1442,538,240 - 42,540,804 (+)NCBICelera
Cytogenetic Map14p11NCBI
TLR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl438,790,677 - 38,856,817 (-)EnsemblGRCh38hg38GRCh38
GRCh38438,791,055 - 38,806,262 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37438,797,876 - 38,806,412 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36438,474,271 - 38,482,807 (-)NCBINCBI36hg18NCBI36
Build 34438,620,443 - 38,628,978NCBI
Cytogenetic Map4p14NCBI
HuRef438,122,243 - 38,130,779 (-)NCBIHuRef
CHM1_1438,797,457 - 38,805,993 (-)NCBICHM1_1
Tlr1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39565,082,023 - 65,090,945 (-)NCBIGRCm39mm39
GRCm39 Ensembl565,082,022 - 65,090,906 (-)Ensembl
GRCm38564,924,680 - 64,933,600 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl564,924,679 - 64,933,563 (-)EnsemblGRCm38mm10GRCm38
MGSCv37565,316,073 - 65,323,938 (-)NCBIGRCm37mm9NCBIm37
MGSCv36565,203,969 - 65,211,834 (-)NCBImm8
Celera562,197,667 - 62,205,494 (-)NCBICelera
Cytogenetic Map5C3.1NCBI
cM Map533.53NCBI
Tlr1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554438,447,956 - 8,450,382 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554438,442,419 - 8,450,318 (+)NCBIChiLan1.0ChiLan1.0
TLR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1438,973,623 - 38,981,413 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl438,979,006 - 38,981,366 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0433,119,485 - 33,133,541 (-)NCBIMhudiblu_PPA_v0panPan3
TLR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1373,504,359 - 73,544,822 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl373,539,715 - 73,544,624 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha376,089,340 - 76,091,709 (+)NCBI
ROS_Cfam_1.0374,285,167 - 74,325,228 (+)NCBI
UMICH_Zoey_3.1373,588,991 - 73,591,359 (+)NCBI
UNSW_CanFamBas_1.0373,735,203 - 73,737,572 (+)NCBI
UU_Cfam_GSD_1.0374,115,278 - 74,117,647 (+)NCBI
Tlr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528539,707,097 - 39,715,850 (+)NCBI
SpeTri2.0NW_0049364826,582,430 - 6,591,128 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TLR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl830,147,621 - 30,155,466 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1830,147,600 - 30,155,454 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2831,627,675 - 31,660,825 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TLR1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12711,482,307 - 11,490,847 (+)NCBI
ChlSab1.1 Ensembl2711,488,294 - 11,490,654 (+)Ensembl
Tlr1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248407,287,772 - 7,349,282 (-)NCBI

Position Markers
RH131387  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01445,064,807 - 45,064,991NCBIRnor6.0
Rnor_5.01444,874,076 - 44,874,260UniSTSRnor5.0
RGSC_v3.41446,124,614 - 46,124,798UniSTSRGSC3.4
Celera1442,540,597 - 42,540,781UniSTS
Cytogenetic Map14p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)142018938665189386Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)142145756566457565Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143303991261783215Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143316331673391571Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)144031561085315610Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)144031561085315610Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)144031561085315610Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)144031561085315610Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)144163756980841518Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1442442731108833671Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1443910761105074364Rat


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 8
Low 3 1 55 39 11 39 14 35 26 11
Below cutoff 38 2 2 2 5 6 60 12 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000059124   ⟹   ENSRNOP00000055898
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1445,062,662 - 45,081,991 (+)Ensembl
RefSeq Acc Id: NM_001172120   ⟹   NP_001165591
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21443,394,182 - 43,396,746 (+)NCBI
Rnor_6.01445,062,662 - 45,065,014 (+)NCBI
Rnor_5.01444,871,931 - 44,874,283 (+)NCBI
Celera1442,538,240 - 42,540,804 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039091925   ⟹   XP_038947853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21443,384,127 - 43,396,765 (+)NCBI
RefSeq Acc Id: XM_039091926   ⟹   XP_038947854
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21443,384,127 - 43,396,765 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001165591 (Get FASTA)   NCBI Sequence Viewer  
  XP_038947853 (Get FASTA)   NCBI Sequence Viewer  
  XP_038947854 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL90081 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001165591   ⟸   NM_001172120
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000055898   ⟸   ENSRNOT00000059124
RefSeq Acc Id: XP_038947854   ⟸   XM_039091926
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947853   ⟸   XM_039091925
- Peptide Label: isoform X1
Protein Domains
TIR

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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)
ACI/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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/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
FHL/EurMcwi (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)
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)
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)
GK/Ox (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
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)
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/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
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)
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
MNS/Gib (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
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)
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: 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)
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: 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)
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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
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)
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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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
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)
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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/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
WKY/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
WKY/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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309975 AgrOrtholog
Ensembl Genes ENSRNOG00000038722 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000055898 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000059124 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10140 UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/TrEMBL
  TIR_dom UniProtKB/TrEMBL
  TLR1 UniProtKB/TrEMBL
  Toll-like_receptor UniProtKB/TrEMBL
  Toll_tir_struct_dom_sf UniProtKB/TrEMBL
NCBI Gene 305354 ENTREZGENE
PANTHER PTHR24365 UniProtKB/TrEMBL
  PTHR24365:SF261 UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
  TIR UniProtKB/TrEMBL
PhenoGen Tlr1 PhenoGen
PIRSF Toll-like_receptor UniProtKB/TrEMBL
PROSITE LRR UniProtKB/TrEMBL
  TIR UniProtKB/TrEMBL
SMART LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
  TIR UniProtKB/TrEMBL
Superfamily-SCOP SSF52200 UniProtKB/TrEMBL
UniProt E9PTL5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Tlr1  toll-like receptor 1  LOC100363942  rCG56938-like  Data Merged 1643240 APPROVED
2013-05-24 Tlr1  toll-like receptor 1  LOC100363038  rCG56938-like  Data Merged 1643240 APPROVED
2010-05-06 LOC100363942  rCG56938-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-06 LOC100363038  rCG56938-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Tlr1  toll-like receptor 1   Tlr1_predicted  toll-like receptor 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tlr1_predicted  toll-like receptor 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED