Tlr3 (toll-like receptor 3) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Tlr3 (toll-like receptor 3) Rattus norvegicus
Analyze
Symbol: Tlr3
Name: toll-like receptor 3
RGD ID: 735171
Description: Enables double-stranded RNA binding activity. Involved in several processes, including cellular response to cytokine stimulus; cellular response to exogenous dsRNA; and microglial cell activation. Located in cell surface. Used to study asthma. Biomarker of colitis; pancreatitis; perinatal necrotizing enterocolitis; peripheral nervous system disease; and pre-eclampsia. Human ortholog(s) of this gene implicated in several diseases, including hepatitis B; hepatitis C; human immunodeficiency virus infectious disease; liver cirrhosis; and type 1 diabetes mellitus. Orthologous to human TLR3 (toll like receptor 3); PARTICIPATES IN Toll-like receptor signaling pathway; hepatitis C pathway; influenza A pathway; INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21646,821,980 - 46,837,900 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1646,822,039 - 46,836,545 (+)Ensembl
Rnor_6.01650,016,466 - 50,031,011 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1650,016,857 - 50,031,214 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01649,739,814 - 49,753,968 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41650,112,910 - 50,126,371 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11650,112,984 - 50,126,440 (+)NCBI
Celera1644,813,138 - 44,826,566 (+)NCBICelera
Cytogenetic Map16q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-citrinin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
1-nitropyrene  (ISO)
17beta-estradiol  (ISO)
2,4-dinitrotoluene  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-phenylprop-2-enal  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-fluorouracil  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
aripiprazole  (ISO)
arsenous acid  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisdemethoxycurcumin  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (EXP)
cadmium selenide  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
chlorogenic acid  (ISO)
chloroquine  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cyanidin cation  (EXP,ISO)
cyclosporin A  (ISO)
deoxycholic acid  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
folic acid  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
GW 4064  (ISO)
hydroquinone  (ISO)
indole-3-methanol  (EXP)
indometacin  (ISO)
lipopolysaccharide  (ISO)
metam  (ISO)
metformin  (ISO)
methamphetamine  (ISO)
methotrexate  (EXP,ISO)
nickel sulfate  (ISO)
nitrates  (EXP)
o-anisidine  (ISO)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
poly(I:C)  (EXP,ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
pristane  (EXP)
pyrene  (ISO)
quinacrine  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium aurothiosulfate  (ISO)
streptozocin  (ISO)
Sunset Yellow FCF  (ISO)
tartrazine  (ISO)
testosterone  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular response to exogenous dsRNA  (IEP,IMP)
cellular response to interferon-beta  (IEP)
cellular response to interferon-gamma  (IEP)
cellular response to mechanical stimulus  (ISO)
cellular response to virus  (IEA,ISO)
cellular response to xenobiotic stimulus  (IEP)
defense response  (ISO)
defense response to virus  (ISO)
extrinsic apoptotic signaling pathway  (ISO)
I-kappaB phosphorylation  (ISO)
inflammatory response  (IBA)
JNK cascade  (IEA,ISO)
male gonad development  (IEP)
MAPK cascade  (ISO)
microglial cell activation  (IDA)
MyD88-independent toll-like receptor signaling pathway  (IEA)
necroptotic signaling pathway  (ISO)
positive regulation of angiogenesis  (ISO)
positive regulation of apoptotic process  (IEP)
positive regulation of chemokine production  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (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-12 production  (ISO)
positive regulation of interleukin-6 production  (ISO)
positive regulation of interleukin-8 production  (ISO)
positive regulation of JNK cascade  (ISO)
positive regulation of NF-kappaB transcription factor activity  (ISO)
positive regulation of NIK/NF-kappaB signaling  (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)
positive regulation of type I interferon production  (ISO)
positive regulation of type III interferon production  (ISO)
regulation of dendritic cell cytokine production  (ISO)
response to dsRNA  (IDA)
response to exogenous dsRNA  (ISO)
response to virus  (IEP,ISO)
toll-like receptor 3 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
1. Abou-Zeid AA and El-Sayegh HK, Scand J Clin Lab Invest. 2011 Oct;71(6):456-61. doi: 10.3109/00365513.2011.585660. Epub 2011 May 30.
2. Al-Qahtani A, etal., J Med Virol. 2012 Sep;84(9):1353-9. doi: 10.1002/jmv.23271.
3. Alexopoulou L, etal., Nature 2001 Oct 18;413(6857):732-8.
4. Biswas B, etal., Am J Reprod Immunol. 2009 Oct;62(4):243-52. Epub 2009 Aug 24.
5. Byun JS, etal., J Hepatol. 2013 Feb;58(2):342-9. doi: 10.1016/j.jhep.2012.09.016. Epub 2012 Sep 27.
6. Chew V, etal., J Natl Cancer Inst. 2012 Dec 5;104(23):1796-807. doi: 10.1093/jnci/djs436. Epub 2012 Nov 29.
7. Citores MJ, etal., Clin Transplant. 2016 Jul;30(7):810-8. doi: 10.1111/ctr.12754. Epub 2016 May 23.
8. Daud II, etal., Int J Cancer. 2011 Feb 15;128(4):879-86. doi: 10.1002/ijc.25400.
9. El-Bendary M, etal., Br J Biomed Sci. 2018 Oct;75(4):175-181. doi: 10.1080/09674845.2018.1492186. Epub 2018 Aug 23.
10. Fischer J, etal., Sci Rep. 2018 Aug 24;8(1):12737. doi: 10.1038/s41598-018-31065-6.
11. Fransson M, etal., Respir Res. 2005 Sep 7;6:100.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Ge L, etal., Int Immunopharmacol. 2019 May;70:477-485. doi: 10.1016/j.intimp.2019.02.021. Epub 2019 Mar 12.
14. Greidinger EL, etal., Arthritis Rheum. 2006 Feb;54(2):661-9.
15. Guo LH, etal., Biochem Biophys Res Commun. 2006 Oct 27;349(3):1156-62. Epub 2006 Sep 1.
16. Hamdy S, etal., Arch Virol. 2018 Sep;163(9):2433-2442. doi: 10.1007/s00705-018-3893-8. Epub 2018 Jun 2.
17. Harii N, etal., Mol Endocrinol. 2005 May;19(5):1231-50. Epub 2005 Jan 20.
18. Hayashida K and Eisenach JC, J Pain. 2011 Jan;12(1):94-100.
19. Horvath KM, etal., Am J Respir Cell Mol Biol. 2010 Oct 8.
20. Huang X, etal., Gene. 2015 Sep 15;569(2):218-24. doi: 10.1016/j.gene.2015.05.054. Epub 2015 May 27.
21. Hutchens M, etal., J Immunol. 2008 Jan 1;180(1):483-91.
22. Jeon SG, etal., J Allergy Clin Immunol. 2007 Oct;120(4):803-12. Epub 2007 Jul 5.
23. Joshi AD, etal., Eur J Immunol. 2008 Dec;38(12):3436-49.
24. Kang JW, etal., J Pineal Res. 2011 Feb 28. doi: 10.1111/j.1600-079X.2011.00858.x.
25. Kang MJ, etal., J Clin Invest. 2008 Aug;118(8):2771-84.
26. Kar P, etal., J Med Virol. 2017 Dec;89(12):2165-2172. doi: 10.1002/jmv.24849. Epub 2017 Sep 4.
27. Kumar H, etal., Int Rev Immunol. 2011 Feb;30(1):16-34.
28. Le Goffic R, etal., PLoS Pathog. 2006 Jun;2(6):e53. Epub 2006 Jun 9.
29. Lee SO, etal., Transpl Infect Dis. 2013 Apr;15(2):111-9. doi: 10.1111/tid.12033. Epub 2012 Dec 13.
30. Liu X, etal., Invest Ophthalmol Vis Sci. 2013 Sep 5;54(9):6012-7. doi: 10.1167/iovs.13-12159.
31. Liu Y, etal., Am J Physiol Gastrointest Liver Physiol. 2009 Sep;297(3):G442-50. Epub 2009 Jul 16.
32. Mansson A, etal., Int Arch Allergy Immunol. 2010;151(2):118-28. Epub 2009 Sep 15.
33. McKernan DP, etal., PLoS One. 2009 Dec 9;4(12):e8226.
34. Meng L, etal., Arthritis Res Ther. 2010;12(3):R103. Epub 2010 May 25.
35. Meng L, etal., PLoS One. 2011 Feb 25;6(2):e17252.
36. MGD data from the GO Consortium
37. Mosaad YM, etal., Immunol Invest. 2019 Apr;48(3):321-332. doi: 10.1080/08820139.2018.1527851. Epub 2018 Oct 15.
38. Murray LA, etal., Am J Respir Crit Care Med. 2008 Dec 15;178(12):1227-37. Epub 2008 Oct 10.
39. Noguchi E, etal., Clin Exp Allergy. 2004 Feb;34(2):177-83.
40. Nojiri K, etal., Oncol Rep. 2013 May;29(5):1737-43. doi: 10.3892/or.2013.2322. Epub 2013 Mar 4.
41. No├žon AL, etal., J Virol. 2014 Jan;88(1):679-89. doi: 10.1128/JVI.02094-13. Epub 2013 Oct 30.
42. Obata K, etal., J Neurochem. 2008 Jun 1;105(6):2249-59.
43. OMIM Disease Annotation Pipeline
44. Pipeline to import KEGG annotations from KEGG into RGD
45. Pirie FJ, etal., Tissue Antigens. 2005 Aug;66(2):125-30.
46. Qian F, etal., Clin Vaccine Immunol. 2013 Feb;20(2):146-55. doi: 10.1128/CVI.00530-12. Epub 2012 Dec 5.
47. Qian NS, etal., Mol Pain. 2011 Feb 22;7(1):15.
48. Ranjith-Kumar CT, etal., J Biol Chem. 2007 Jun 15;282(24):17696-705. Epub 2007 Apr 13.
49. Rasschaert J, etal., J Biol Chem. 2005 Oct 7;280(40):33984-91. Epub 2005 Jul 15.
50. Redfern RL, etal., Invest Ophthalmol Vis Sci. 2013 Feb 28;54(2):1554-63. doi: 10.1167/iovs.12-10739.
51. RGD automated data pipeline
52. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
53. RGD automated import pipeline for gene-chemical interactions
54. RGD comprehensive gene curation
55. Rojo-Botello NR, etal., J Periodontal Res. 2012 Feb;47(1):62-73. doi: 10.1111/j.1600-0765.2011.01405.x. Epub 2011 Aug 17.
56. Rong Y, etal., Inflammation. 2013 Apr;36(2):413-8. doi: 10.1007/s10753-012-9560-4.
57. Rudd BD, etal., J Immunol. 2006 Feb 1;176(3):1937-42.
58. Sato A, etal., J Gastroenterol Hepatol. 2006 Mar;21(3):521-30.
59. Scumpia PO, etal., Glia. 2005 Nov 1;52(2):153-62.
60. Seo W, etal., Hepatology. 2016 Aug;64(2):616-31. doi: 10.1002/hep.28644. Epub 2016 Jun 29.
61. Shi YJ, etal., Mol Med Rep. 2013 Aug;8(2):480-6. doi: 10.3892/mmr.2013.1511. Epub 2013 Jun 6.
62. Tinsley JH, etal., Am J Hypertens. 2009 Dec;22(12):1314-9. Epub 2009 Sep 24.
63. Wood LG, etal., Clin Exp Allergy. 2010 Dec 3. doi: 10.1111/j.1365-2222.2010.03669.x.
64. Yan MH, etal., Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi. 2010 Oct;26(10):966-8, 972.
65. Yuki N, etal., J Viral Hepat. 2010 Feb 1;17(2):130-8. doi: 10.1111/j.1365-2893.2009.01155.x. Epub 2009 Aug 5.
66. Zhu Y, etal., Mol Vis. 2013 Aug 6;19:1826-33. eCollection 2013.
Additional References at PubMed
PMID:12054664   PMID:12855817   PMID:14993594   PMID:15356140   PMID:16111635   PMID:16260493   PMID:16286015   PMID:17008311   PMID:17027917   PMID:17128265   PMID:17897319   PMID:18172197  
PMID:18207576   PMID:18223009   PMID:18250457   PMID:18261938   PMID:18592153   PMID:19047410   PMID:19115402   PMID:19593445   PMID:19734906   PMID:19740627   PMID:20692254   PMID:20848777  
PMID:21266579   PMID:21708001   PMID:21737330   PMID:22647506   PMID:22681877   PMID:22702720   PMID:23155421   PMID:23558035   PMID:23817958   PMID:23965176   PMID:23981041   PMID:24091496  
PMID:24416163   PMID:24423102   PMID:24621600   PMID:24729619   PMID:24914679   PMID:25204797   PMID:25217833   PMID:25533241   PMID:25754930   PMID:25815475   PMID:26062413   PMID:26417991  
PMID:26934179   PMID:28000161   PMID:28726298   PMID:29445737   PMID:34015428  


Genomics

Comparative Map Data
Tlr3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21646,821,980 - 46,837,900 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1646,822,039 - 46,836,545 (+)Ensembl
Rnor_6.01650,016,466 - 50,031,011 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1650,016,857 - 50,031,214 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01649,739,814 - 49,753,968 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41650,112,910 - 50,126,371 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11650,112,984 - 50,126,440 (+)NCBI
Celera1644,813,138 - 44,826,566 (+)NCBICelera
Cytogenetic Map16q11NCBI
TLR3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl4186,069,155 - 186,088,073 (+)EnsemblGRCh38hg38GRCh38
GRCh384186,069,156 - 186,088,073 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh374186,990,310 - 187,009,227 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364187,227,303 - 187,243,246 (+)NCBINCBI36hg18NCBI36
Build 344187,365,457 - 187,381,399NCBI
Celera4184,312,848 - 184,328,791 (+)NCBI
Cytogenetic Map4q35.1NCBI
HuRef4182,742,451 - 182,758,393 (+)NCBIHuRef
CHM1_14186,966,756 - 186,982,686 (+)NCBICHM1_1
Tlr3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39845,848,702 - 45,864,112 (-)NCBIGRCm39mm39
GRCm39 Ensembl845,848,702 - 45,864,117 (-)Ensembl
GRCm38845,395,665 - 45,411,075 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl845,395,665 - 45,411,080 (-)EnsemblGRCm38mm10GRCm38
MGSCv37846,481,019 - 46,495,893 (-)NCBIGRCm37mm9NCBIm37
MGSCv36846,894,482 - 46,909,356 (-)NCBImm8
Celera848,083,156 - 48,098,074 (-)NCBICelera
Cytogenetic Map8B1.1NCBI
Tlr3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540322,979,120 - 23,001,467 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540322,977,882 - 23,001,392 (-)NCBIChiLan1.0ChiLan1.0
TLR3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14190,446,487 - 190,462,728 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4190,446,487 - 190,462,728 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04178,238,352 - 178,256,264 (+)NCBIMhudiblu_PPA_v0panPan3
TLR3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11644,617,012 - 44,633,591 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1644,550,846 - 44,653,247 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1645,103,720 - 45,132,454 (-)NCBI
ROS_Cfam_1.01646,830,974 - 46,859,705 (-)NCBI
UMICH_Zoey_3.11644,798,956 - 44,827,679 (-)NCBI
UNSW_CanFamBas_1.01645,411,963 - 45,440,690 (-)NCBI
UU_Cfam_GSD_1.01645,543,452 - 45,571,950 (-)NCBI
Tlr3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494334,721,792 - 34,740,517 (+)NCBI
SpeTri2.0NW_0049365543,370,766 - 3,388,125 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TLR3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1546,966,040 - 47,058,734 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11546,966,262 - 46,977,774 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21553,839,254 - 53,852,671 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TLR3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.17131,991,068 - 132,014,366 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl7131,991,029 - 132,016,232 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037112,309,987 - 112,333,459 (+)NCBIVero_WHO_p1.0
Tlr3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476916,925,969 - 16,945,250 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D16Rat67  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21646,825,402 - 46,825,624 (+)MAPPERmRatBN7.2
Rnor_6.01650,019,871 - 50,020,090NCBIRnor6.0
Rnor_5.01649,742,828 - 49,743,047UniSTSRnor5.0
RGSC_v3.41650,115,924 - 50,116,143UniSTSRGSC3.4
RGSC_v3.41650,115,923 - 50,116,143RGDRGSC3.4
RGSC_v3.11650,115,998 - 50,116,218RGD
Celera1644,816,145 - 44,816,364UniSTS
RH 3.4 Map16462.8RGD
RH 3.4 Map16462.8UniSTS
RH 2.0 Map16520.1RGD
SHRSP x BN Map1618.13RGD
FHH x ACI Map1623.2999RGD
Cytogenetic Map16q11UniSTS
RH128714  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21646,835,522 - 46,835,740 (+)MAPPERmRatBN7.2
Rnor_6.01650,029,989 - 50,030,206NCBIRnor6.0
Rnor_5.01649,752,946 - 49,753,163UniSTSRnor5.0
RGSC_v3.41650,126,042 - 50,126,259UniSTSRGSC3.4
Celera1644,826,237 - 44,826,454UniSTS
RH 3.4 Map16460.9UniSTS
Cytogenetic Map16q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162173597566735975Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)163195152060148445Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
631833Sach2Saccharin preference QTL 240.01consumption behavior trait (VT:0002069)calculated saccharin drink intake rate (CMO:0001613)164302484250166018Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:29
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000035781
Prediction methods:Miranda, Rnahybrid, Targetscan
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 2 27 17 13 17 28 21 11
Low 1 43 30 24 6 24 8 11 70 7 20 8
Below cutoff 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035781   ⟹   ENSRNOP00000036680
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1646,822,039 - 46,836,545 (+)Ensembl
Rnor_6.0 Ensembl1650,016,857 - 50,030,312 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087986   ⟹   ENSRNOP00000070415
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1646,824,940 - 46,836,545 (+)Ensembl
Rnor_6.0 Ensembl1650,022,998 - 50,031,214 (+)Ensembl
RefSeq Acc Id: NM_198791   ⟹   NP_942086
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21646,822,389 - 46,835,852 (+)NCBI
Rnor_6.01650,016,857 - 50,030,318 (+)NCBI
Rnor_5.01649,739,814 - 49,753,968 (+)NCBI
RGSC_v3.41650,112,910 - 50,126,371 (+)RGD
Celera1644,813,138 - 44,826,566 (+)RGD
Sequence:
RefSeq Acc Id: XM_008771266   ⟹   XP_008769488
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21646,821,980 - 46,836,545 (+)NCBI
Rnor_6.01650,016,466 - 50,030,783 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771267   ⟹   XP_008769489
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21646,822,284 - 46,836,545 (+)NCBI
Rnor_6.01650,016,466 - 50,030,783 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039094720   ⟹   XP_038950648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21646,822,343 - 46,836,545 (+)NCBI
RefSeq Acc Id: XR_005494652
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21646,822,343 - 46,836,545 (+)NCBI
RefSeq Acc Id: XR_005494653
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21646,822,343 - 46,837,900 (+)NCBI
Protein Sequences
Protein RefSeqs NP_942086 (Get FASTA)   NCBI Sequence Viewer  
  XP_008769488 (Get FASTA)   NCBI Sequence Viewer  
  XP_008769489 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950648 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAO62340 (Get FASTA)   NCBI Sequence Viewer  
  BAC81504 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_942086   ⟸   NM_198791
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_008769489   ⟸   XM_008771267
- Peptide Label: isoform X1
- UniProtKB: F1LN63 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769488   ⟸   XM_008771266
- Peptide Label: isoform X1
- UniProtKB: F1LN63 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000036680   ⟸   ENSRNOT00000035781
RefSeq Acc Id: ENSRNOP00000070415   ⟸   ENSRNOT00000087986
RefSeq Acc Id: XP_038950648   ⟸   XM_039094720
- Peptide Label: isoform X1
Protein Domains
TIR

Transcriptome

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

Promoters
RGD ID:13700107
Promoter ID:EPDNEW_R10631
Type:initiation region
Name:Tlr3_1
Description:toll-like receptor 3
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_6.01650,016,833 - 50,016,893EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: 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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:735171 AgrOrtholog
Ensembl Genes ENSRNOG00000021726 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036680 UniProtKB/TrEMBL
  ENSRNOP00000070415 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035781 UniProtKB/TrEMBL
  ENSRNOT00000087986 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10140 UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/TrEMBL
  L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  TIR_dom UniProtKB/TrEMBL
  TLR3 UniProtKB/TrEMBL
  TLR3_TMD UniProtKB/TrEMBL
  Toll-like_receptor UniProtKB/TrEMBL
  Toll_tir_struct_dom_sf UniProtKB/TrEMBL
KEGG Report rno:364594 UniProtKB/TrEMBL
NCBI Gene 364594 ENTREZGENE
PANTHER PTHR24365 UniProtKB/TrEMBL
  PTHR24365:SF524 UniProtKB/TrEMBL
Pfam LRR_1 UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
  TIR UniProtKB/TrEMBL
  Tlr3_TMD UniProtKB/TrEMBL
PhenoGen Tlr3 PhenoGen
PROSITE LRR UniProtKB/TrEMBL
  TIR UniProtKB/TrEMBL
SMART LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
  TIR UniProtKB/TrEMBL
Superfamily-SCOP TIR UniProtKB/TrEMBL
UniProt F1LN63 ENTREZGENE, UniProtKB/TrEMBL
  Q7TNI8_RAT UniProtKB/TrEMBL
  Q80Z88_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Tlr3  toll-like receptor 3      Symbol and Name status set to approved 1299863 APPROVED