Tnfrsf1b (TNF receptor superfamily member 1B) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Tnfrsf1b (TNF receptor superfamily member 1B) Rattus norvegicus
Analyze
Symbol: Tnfrsf1b
Name: TNF receptor superfamily member 1B
RGD ID: 621238
Description: Enables tumor necrosis factor-activated receptor activity. Involved in several processes, including cellular response to growth factor stimulus; cellular response to tumor necrosis factor; and response to lipopolysaccharide. Located in several cellular components, including neuronal cell body; perinuclear region of cytoplasm; and varicosity. Used to study visual epilepsy. Biomarker of Crohn's disease; myocardial infarction; sciatic neuropathy; and ureteral obstruction. Human ortholog(s) of this gene implicated in several diseases, including Parkinsonism; acne; bone disease (multiple); glomerulonephritis (multiple); and lung disease (multiple). Orthologous to human TNFRSF1B (TNF receptor superfamily member 1B); PARTICIPATES IN tumor necrosis factor mediated signaling pathway; amyotrophic lateral sclerosis pathway; cytokine mediated signaling pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: p75; p80 TNF-alpha receptor; TNF-R2; TNF-RII; TNFR-II; Tnfr2; tumor necrosis factor receptor 2; tumor necrosis factor receptor superfamily member 1B; tumor necrosis factor receptor superfamily, member 1b; tumor necrosis factor receptor type II
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
mRatBN7.25157,070,642 - 157,104,216 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5157,070,642 - 157,104,206 (-)Ensembl
Rnor_6.05163,136,390 - 163,167,299 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5163,136,390 - 163,167,299 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05166,815,372 - 166,845,910 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45163,666,541 - 163,697,484 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15163,674,328 - 163,707,672 (-)NCBI
Celera5155,362,574 - 155,393,443 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acne  (ISO)
acquired immunodeficiency syndrome  (ISO)
Acute Experimental Pancreatitis  (IEP)
acute kidney failure  (ISO)
adult respiratory distress syndrome  (ISO)
allergic disease  (ISO)
Alzheimer's disease  (ISO)
ankylosing spondylitis  (ISO)
Anti-Neutrophil Cytoplasmic Antibody-Associated Vasculitis  (ISO)
autistic disorder  (ISO)
bacterial pneumonia  (ISO)
Bone Fractures  (ISO)
brain ischemia  (ISO)
Bronchial Spasm  (ISO)
cerebral malaria  (ISO)
chronic obstructive pulmonary disease  (ISO)
colon carcinoma  (ISO)
congestive heart failure  (ISO)
Crohn's disease  (IEP)
cryptogenic organizing pneumonia  (ISO)
Diabetic Nephropathies  (ISO)
end stage renal disease  (ISO)
endometrial cancer  (ISO)
endometriosis  (ISO)
Experimental Arthritis  (IDA,IEP,ISO)
Experimental Diabetes Mellitus  (ISO)
extrinsic allergic alveolitis  (ISO)
Fatigue  (ISO)
Fetal Death  (ISO)
focal segmental glomerulosclerosis  (ISO)
glomerulonephritis  (ISO)
glomerulosclerosis  (ISO)
Headache  (ISO)
Hyperalgesia  (IMP,ISO)
Hypoalbuminemia  (ISO)
IgA glomerulonephritis  (ISO)
Inflammation  (ISO)
Intervertebral Disc Displacement  (ISO)
kidney failure  (ISO)
Legionnaires' disease  (ISO)
liver cirrhosis  (ISO)
lupus nephritis  (ISO)
mycosis fungoides  (ISO)
myocardial infarction  (IEP)
Nasal Polyps  (ISO)
Neurogenic Inflammation  (IDA)
non-alcoholic fatty liver disease  (ISO)
nonprogressive cerebellar ataxia with mental retardation  (ISO)
obesity  (ISO)
osteoporosis  (ISO)
ovarian cancer  (ISO)
Parkinson's disease  (ISO)
Parkinsonism  (ISO)
pneumonia  (ISO)
polymyositis  (ISO)
pre-eclampsia  (ISO)
pulmonary sarcoidosis  (ISO)
renal cell carcinoma  (ISO)
retinal detachment  (ISO)
sciatic neuropathy  (IEP)
Sciatica  (IDA)
Sezary's disease  (ISO)
silicosis  (ISO)
Spinal Cord Compression  (IEP,ISO)
Systemic Inflammatory Response Syndrome  (IEP)
systemic lupus erythematosus  (ISO)
Transplant Rejection  (IEP)
tuberculosis  (ISO)
type 2 diabetes mellitus  (ISO)
ureteral obstruction  (IEP,ISO)
visual epilepsy  (IDA)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-butoxyethanol  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-butylphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
alfacalcidol  (ISO)
Aloe emodin  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aripiprazole  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
asbestos  (ISO)
bathocuproine disulfonic acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzoates  (ISO)
beta-D-glucosamine  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
bleomycin A2  (EXP,ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon monoxide  (ISO)
carbon nanotube  (ISO)
chloroquine  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
cocaine  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
DDE  (EXP)
dextran  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
dichromium trioxide  (ISO)
doxorubicin  (EXP,ISO)
ethanol  (ISO)
fluoranthene  (ISO)
furosemide  (EXP)
Fusarenone X  (ISO)
gefitinib  (ISO)
glyphosate  (EXP)
hopane  (ISO)
hydrogen peroxide  (ISO)
indole-3-methanol  (EXP)
ionomycin  (ISO)
ketoconazole  (EXP,ISO)
lead diacetate  (ISO)
lead nitrate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lenalidomide  (ISO)
lipopolysaccharide  (ISO)
melatonin  (ISO)
methyl methanesulfonate  (ISO)
Mitotane  (EXP)
monosodium L-glutamate  (ISO)
mycophenolic acid  (ISO)
N-acetyl-L-cysteine  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nitrogen dioxide  (ISO)
obeticholic acid  (ISO)
octreotide  (EXP)
oleanolic acid  (ISO)
osthole  (ISO)
oxidopamine  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorononanoic acid  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
prenyl diphosphate  (ISO)
procyanidin B3  (ISO)
progesterone  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (ISO)
quercitrin  (ISO)
resveratrol  (ISO)
sanguinarine  (ISO)
SB 203580  (ISO)
serpentine asbestos  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium stibogluconate  (ISO)
streptozocin  (ISO)
succimer  (ISO)
sulfur dioxide  (ISO)
temozolomide  (ISO)
terameprocol  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
thalidomide  (ISO)
titanium dioxide  (ISO)
uranium atom  (ISO)
valproic acid  (ISO)
vemurafenib  (ISO)
vinclozolin  (EXP)
WR-1065  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Aderka D, etal., Arthritis Rheum. 1993 Aug;36(8):1111-20.
2. Aderka D, etal., Cancer Res. 1991 Oct 15;51(20):5602-7.
3. Al-Lamki RS, etal., Am J Pathol. 2010 Aug;177(2):943-54. doi: 10.2353/ajpath.2010.091218. Epub 2010 Jun 21.
4. Andrade P, etal., Brain Res. 2012 Apr 23;1450:24-32. doi: 10.1016/j.brainres.2012.02.033. Epub 2012 Feb 22.
5. Bader T and Nettesheim P, J Immunol 1996 Oct 1;157(7):3089-96.
6. Bethunaickan R, etal., Arthritis Rheum. 2012 Oct;64(10):3399-408. doi: 10.1002/art.34553.
7. Bower JE, etal., Psychosom Med. 2002 Jul-Aug;64(4):604-11.
8. Bruggeman LA, etal., Lab Invest. 2011 Mar;91(3):413-25. doi: 10.1038/labinvest.2010.199. Epub 2011 Jan 10.
9. Cayci T, etal., J Obstet Gynaecol Res. 2011 Apr 12. doi: 10.1111/j.1447-0756.2010.01482.x.
10. Chen B, etal., Eur Respir J. 2005 Jun;25(6):1039-43.
11. Chen H, etal., Rheumatol Int. 2013 May;33(5):1223-7. doi: 10.1007/s00296-012-2529-7. Epub 2012 Oct 2.
12. Chen KB, etal., Spine (Phila Pa 1976). 2011 Jan 8.
13. Cheng X, etal., J Alzheimers Dis. 2010;19(2):621-30. doi: 10.3233/JAD-2010-1253.
14. Cho HY, etal., Am J Physiol Lung Cell Mol Physiol. 2001 Mar;280(3):L537-46.
15. Constantin CE, etal., J Neurosci. 2008 May 7;28(19):5072-81.
16. Dobrzycka B, etal., Eur Cytokine Netw. 2009 Sep;20(3):131-4.
17. Dorr AD, etal., J Appl Physiol. 2011 Apr 21.
18. Dougados M, etal., Ann Rheum Dis. 2011 May;70(5):799-804. Epub 2011 Feb 13.
19. Dubey S, etal., Clin Rheumatol. 2009 Aug;28(8):989-92. Epub 2009 Apr 2.
20. Fernandez R, etal., Respir Physiol Neurobiol. 2011 Mar 15;175(3):336-48. Epub 2010 Dec 30.
21. Fujita M, etal., Cytokine. 2008 Nov;44(2):298-303. Epub 2008 Oct 5.
22. Gadducci A, etal., Anticancer Res. 1996 Sep-Oct;16(5B):3125-8.
23. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
24. GOA data from the GO Consortium
25. Gohda T, etal., J Am Soc Nephrol. 2012 Mar;23(3):516-24. doi: 10.1681/ASN.2011060628. Epub 2012 Jan 19.
26. Granell S, etal., Cytokine. 2004 Feb 21;25(4):187-91.
27. Guo G, etal., Am J Physiol. 1999 Nov;277(5 Pt 2):F766-72.
28. Guthmann F, etal., Exp Lung Res. 2009 Nov;35(9):770-80.
29. Gutkowska J, etal., J Hypertens. 2011 Apr 17.
30. Hadlock GC, etal., J Pharmacol Exp Ther. 2010 Oct;335(1):207-12. Epub 2010 Jul 9.
31. Hao S, etal., Neuropsychopharmacology. 2011 Feb;36(3):664-76. Epub 2010 Nov 10.
32. Hasegawa M, etal., Nephron Clin Pract. 2009;113(3):c222-33. doi: 10.1159/000235242. Epub 2009 Aug 18.
33. Hildebrandt MA, etal., PLoS One. 2010 Aug 25;5(8):e12402.
34. Hoffmann U, etal., Am J Transplant. 2009 Apr;9(4):675-86. doi: 10.1111/j.1600-6143.2008.02536.x. Epub 2008 Mar 2.
35. Horii M, etal., Spine (Phila Pa 1976). 2011 Jan 15;36(2):E80-5.
36. Hwang DY, etal., J Neurochem. 2009 Dec;111(5):1202-12. Epub 2009 Sep 24.
37. Iglesias J, etal., Am J Kidney Dis. 2003 Jan;41(1):62-75.
38. Ingaramo PI, etal., Mol Immunol. 2011 Apr 8.
39. Ishikawa T, etal., Spine (Phila Pa 1976). 2013 Jan 1;38(1):11-6. doi: 10.1097/BRS.0b013e3182610fa9.
40. Islimye M, etal., Eur J Obstet Gynecol Reprod Biol. 2011 Nov;159(1):184-9. doi: 10.1016/j.ejogrb.2011.06.029. Epub 2011 Jul 7.
41. Jiang H, etal., Mol Neurodegener. 2011 Oct 6;6:69. doi: 10.1186/1750-1326-6-69.
42. Kang YM, etal., Tohoku J Exp Med. 2010;222(4):251-63.
43. Koenig KF, etal., Cytokine. 2012 Nov;60(2):410-6. doi: 10.1016/j.cyto.2012.07.004. Epub 2012 Jul 28.
44. Kong SS, etal., Clin Exp Pharmacol Physiol. 2011 Mar 1. doi: 10.1111/j.1440-1681.2011.05505.x.
45. Lin J, etal., Kidney Int. 2006 Jan;69(2):336-42.
46. Liu KD, etal., Crit Care Med. 2007 Dec;35(12):2755-61.
47. Loza MJ, etal., Clin Vaccine Immunol. 2011 Apr 20.
48. Lu Y, etal., Arthritis Res Ther. 2011 Apr 4;13(2):R56.
49. Lung HL, etal., Life Sci. 2001 Mar 23;68(18):2081-91.
50. MGD data from the GO Consortium
51. Misaki T, etal., Am J Pathol. 2009 Jul;175(1):74-83. doi: 10.2353/ajpath.2009.080884. Epub 2009 Jun 18.
52. Moller M, etal., Am J Respir Crit Care Med. 2010 Feb 15;181(4):388-93. Epub 2009 Dec 10.
53. Nakazawa T, etal., Invest Ophthalmol Vis Sci. 2011 Mar 14;52(3):1384-91. Print 2011 Mar.
54. NCBI rat LocusLink and RefSeq merged data July 26, 2002
55. Nemec A, etal., Exp Lung Res. 2009 Sep;35(7):605-20.
56. Niewczas MA, etal., Clin J Am Soc Nephrol. 2009 Jan;4(1):62-70. Epub 2008 Dec 10.
57. Niewczas MA, etal., J Am Soc Nephrol. 2012 Mar;23(3):507-15. doi: 10.1681/ASN.2011060627. Epub 2012 Jan 19.
58. Osburg B, etal., Am J Physiol Endocrinol Metab 2002 Nov;283(5):E899-908.
59. Pfeifer E, etal., Eur Cytokine Netw. 2012 Mar 1;23(1):15-20. doi: 10.1684/ecn.2012.0299.
60. Pipeline to import KEGG annotations from KEGG into RGD
61. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
62. Pottelberge GR, etal., Am J Respir Crit Care Med. 2011 Apr 1;183(7):898-906. Epub 2010 Oct 29.
63. Ramesh G and Reeves WB, Am J Physiol Renal Physiol. 2003 Oct;285(4):F610-8. Epub 2003 Jul 15.
64. Renaud SJ, etal., J Immunol. 2011 Feb 1;186(3):1799-808. Epub 2010 Dec 27.
65. RGD automated data pipeline
66. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
67. RGD automated import pipeline for gene-chemical interactions
68. Riezzo I, etal., J Neurosci Res. 2010 Mar;88(4):905-16.
69. Rostkowska-Nadolska B, etal., Adv Med Sci. 2008;53(2):263-9.
70. Rostoker G, etal., Clin Exp Immunol. 1998 Dec;114(3):468-76.
71. Safranow K, etal., Tissue Antigens. 2009 Nov;74(5):386-92.
72. Sama DM, etal., PLoS One. 2012;7(5):e38170. doi: 10.1371/journal.pone.0038170. Epub 2012 May 29.
73. Shen CH, etal., Anesth Analg. 2011 Feb;112(2):454-9. Epub 2010 Nov 16.
74. Shi Y, etal., Chin J Integr Med. 2011 Mar;17(3):212-7. Epub 2011 Feb 27.
75. Shimizu T, etal., Clin Rheumatol. 2000;19(5):352-9.
76. Shubayev VI and Myers RR, J Neuroimmunol. 2001 Mar 1;114(1-2):48-56.
77. Singh P, etal., Am J Physiol Renal Physiol. 2013 Apr 1;304(7):F991-9. doi: 10.1152/ajprenal.00525.2012. Epub 2013 Feb 6.
78. Sippy BD, etal., J Acquir Immune Defic Syndr Hum Retrovirol. 1995 Dec 15;10(5):511-21.
79. Spicka I, etal., Cas Lek Cesk. 1998 May 4;137(9):267-70.
80. Stoelcker B, etal., Infect Immun. 2002 Oct;70(10):5857-9.
81. Sunil VR, etal., Toxicol Appl Pharmacol. 2011 Feb 1;250(3):245-55. Epub 2010 Nov 9.
82. Tian LM, etal., Dermatology. 2010;221(3):276-84. doi: 10.1159/000319851.
83. Tsuchiya N, etal., Genes Immun. 2001 Oct;2(6):317-22.
84. Vega A, etal., Dev Neurobiol. 2010 Dec;70(14):913-28. doi: 10.1002/dneu.20834.
85. Vielhauer V, etal., J Clin Invest. 2005 May;115(5):1199-209. Epub 2005 Apr 1.
86. Wajant H, etal., Cell Death Differ. 2003 Jan;10(1):45-65.
87. Weinberg MS, etal., Exp Neurol. 2013 Jan 16. pii: S0014-4886(13)00024-1. doi: 10.1016/j.expneurol.2013.01.011.
88. Xiong DH, etal., J Bone Miner Res. 2006 Nov;21(11):1678-95.
89. Yan P, etal., Exp Neurol 2003 Oct;183(2):286-97.
90. Yanik GA, etal., Blood. 2008 Oct 15;112(8):3073-81. Epub 2008 Jul 29.
91. Ye Q, etal., Respir Med. 2011 Feb;105(2):292-7. Epub 2010 Dec 8.
92. Yu B, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2011 Jun;31(6):1055-8.
93. Zhang XC, etal., Pain. 2011 Jan;152(1):140-9. Epub 2010 Oct 30.
94. Zhou QH, etal., J Pharmacol Exp Ther. 2011 Nov;339(2):618-23. doi: 10.1124/jpet.111.185876. Epub 2011 Aug 10.
95. Zwiech R J Korean Med Sci. 2013 Feb;28(2):261-7. doi: 10.3346/jkms.2013.28.2.261. Epub 2013 Jan 29.
96. Zwiech R, etal., Pol Arch Med Wewn. 2005 Apr;113(4):326-33.
Additional References at PubMed
PMID:1645445   PMID:7990930   PMID:9435233   PMID:9551933   PMID:10747083   PMID:11279055   PMID:11588035   PMID:12849708   PMID:15509749   PMID:15987482   PMID:17010968   PMID:17049356  
PMID:17242187   PMID:17873366   PMID:17917074   PMID:18205044   PMID:18990246   PMID:21692635   PMID:21871121   PMID:22480688   PMID:25378394   PMID:26491108   PMID:26504355   PMID:26732833  
PMID:27147664   PMID:27979472   PMID:28052249   PMID:29975930   PMID:30988334  


Genomics

Comparative Map Data
Tnfrsf1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25157,070,642 - 157,104,216 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5157,070,642 - 157,104,206 (-)Ensembl
Rnor_6.05163,136,390 - 163,167,299 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5163,136,390 - 163,167,299 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05166,815,372 - 166,845,910 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45163,666,541 - 163,697,484 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15163,674,328 - 163,707,672 (-)NCBI
Celera5155,362,574 - 155,393,443 (-)NCBICelera
Cytogenetic Map5q36NCBI
TNFRSF1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl112,166,991 - 12,209,228 (+)EnsemblGRCh38hg38GRCh38
GRCh38112,166,948 - 12,209,222 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37112,227,048 - 12,269,277 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36112,149,647 - 12,191,864 (+)NCBINCBI36hg18NCBI36
Build 34112,161,325 - 12,203,542NCBI
Celera111,340,352 - 11,382,470 (+)NCBI
Cytogenetic Map1p36.22NCBI
HuRef111,380,310 - 11,422,542 (+)NCBIHuRef
CHM1_1112,214,947 - 12,257,256 (+)NCBICHM1_1
Tnfrsf1b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394144,938,938 - 144,973,453 (-)NCBIGRCm39mm39
GRCm39 Ensembl4144,940,033 - 144,973,440 (-)Ensembl
GRCm384145,212,368 - 145,246,870 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4145,213,463 - 145,246,870 (-)EnsemblGRCm38mm10GRCm38
MGSCv374144,802,271 - 144,836,773 (-)NCBIGRCm37mm9NCBIm37
MGSCv364144,479,055 - 144,513,557 (-)NCBImm8
Celera4146,801,795 - 146,837,140 (-)NCBICelera
Cytogenetic Map4E1NCBI
cM Map478.17NCBI
Tnfrsf1b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554861,792,115 - 1,818,362 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554861,790,531 - 1,817,986 (-)NCBIChiLan1.0ChiLan1.0
TNFRSF1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1112,130,663 - 12,172,646 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl112,130,663 - 12,172,646 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0110,915,743 - 10,957,765 (+)NCBIMhudiblu_PPA_v0panPan3
TNFRSF1B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1284,140,179 - 84,151,219 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl284,141,911 - 84,157,191 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha280,674,178 - 80,701,012 (-)NCBI
ROS_Cfam_1.0284,802,376 - 84,828,308 (-)NCBI
UMICH_Zoey_3.1281,551,315 - 81,578,384 (-)NCBI
UNSW_CanFamBas_1.0282,551,181 - 82,578,413 (-)NCBI
UU_Cfam_GSD_1.0283,616,667 - 83,643,630 (-)NCBI
Tnfrsf1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505835,083,616 - 35,110,985 (+)NCBI
SpeTri2.0NW_004936474908,414 - 935,765 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFRSF1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl672,195,435 - 72,231,149 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1672,195,420 - 72,231,146 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TNFRSF1B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120119,590,621 - 119,633,562 (-)NCBI
ChlSab1.1 Ensembl20119,590,325 - 119,633,497 (-)Ensembl
Vero_WHO_p1.0NW_02366605423,447,248 - 23,490,475 (-)NCBI
Tnfrsf1b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624818894,470 - 922,806 (-)NCBI

Position Markers
AU048745  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q32UniSTS
Cytogenetic Map13q24UniSTS
Cytogenetic Map6q32UniSTS
Cytogenetic Map17p12UniSTS
Cytogenetic Map16p14UniSTS
Cytogenetic Map13q26UniSTS
Cytogenetic Map10q22UniSTS
Cytogenetic Map7q11UniSTS
Cytogenetic Map8q24UniSTS
Cytogenetic Map5q21UniSTS
Cytogenetic Map4q24UniSTS
Cytogenetic Map2q11UniSTS
Cytogenetic Map1q54UniSTS
Cytogenetic Map1q36UniSTS
Cytogenetic Map18p11UniSTS
Cytogenetic Map13q13UniSTS
Cytogenetic Map10q24UniSTS
Cytogenetic Map8q31UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map13p13UniSTS
Cytogenetic Map1q21UniSTS
Cytogenetic Map11q23UniSTS
Cytogenetic Map10q31UniSTS
Cytogenetic Map16q12.2UniSTS
Cytogenetic Map3q24UniSTS
Cytogenetic Map5q36UniSTS
Cytogenetic Map3p13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5143799107158428037Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5144358090157869054Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5144377876161317411Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5151006154161165494Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5151113452164465185Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:530
Count of miRNA genes:258
Interacting mature miRNAs:340
Transcripts:ENSRNOT00000022478
Prediction methods:Miranda, 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 3 34 20 19 20 5 7 11
Low 43 23 21 21 8 11 72 30 33 8
Below cutoff 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022478   ⟹   ENSRNOP00000022478
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5157,070,642 - 157,104,206 (-)Ensembl
Rnor_6.0 Ensembl5163,136,390 - 163,167,299 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103500   ⟹   ENSRNOP00000094197
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5157,070,642 - 157,087,912 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119924   ⟹   ENSRNOP00000078858
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5157,070,642 - 157,104,206 (-)Ensembl
RefSeq Acc Id: NM_130426   ⟹   NP_569110
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25157,073,045 - 157,104,206 (-)NCBI
Rnor_6.05163,136,390 - 163,167,299 (-)NCBI
Rnor_5.05166,815,372 - 166,845,910 (-)NCBI
RGSC_v3.45163,666,541 - 163,697,484 (-)RGD
Celera5155,362,574 - 155,393,443 (-)RGD
Sequence:
RefSeq Acc Id: XM_039109197   ⟹   XP_038965125
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25157,070,642 - 157,104,216 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_569110   ⟸   NM_130426
- Peptide Label: precursor
- UniProtKB: Q80WY6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022478   ⟸   ENSRNOT00000022478
RefSeq Acc Id: XP_038965125   ⟸   XM_039109197
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000078858   ⟸   ENSRNOT00000119924
RefSeq Acc Id: ENSRNOP00000094197   ⟸   ENSRNOT00000103500

Transcriptome

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

Promoters
RGD ID:13694248
Promoter ID:EPDNEW_R4773
Type:multiple initiation site
Name:Tnfrsf1b_1
Description:TNF receptor superfamily member 1B
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_6.05163,167,299 - 163,167,359EPDNEW

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:621238 AgrOrtholog
Ensembl Genes ENSRNOG00000016575 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000022478 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000022478 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro TNFR/NGFR_Cys_rich_reg UniProtKB/Swiss-Prot
  TNFR_1B UniProtKB/Swiss-Prot
  TNFRSF1B_N UniProtKB/Swiss-Prot
KEGG Report rno:156767 UniProtKB/Swiss-Prot
NCBI Gene 156767 ENTREZGENE
Pfam TNFR_c6 UniProtKB/Swiss-Prot
PharmGKB TNFRSF1B RGD
PhenoGen Tnfrsf1b PhenoGen
PRINTS TNFACTORR1B UniProtKB/Swiss-Prot
PROSITE TNFR_NGFR_1 UniProtKB/Swiss-Prot
  TNFR_NGFR_2 UniProtKB/Swiss-Prot
SMART TNFR UniProtKB/Swiss-Prot
UniProt Q80WY6 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5YLP0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-05 Tnfrsf1b  TNF receptor superfamily member 1B  Tnfrsf1b  tumor necrosis factor receptor superfamily, member 1b  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Tnfrsf1b  tumor necrosis factor receptor superfamily, member 1b      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Tnfrsf1b  tumor necrosis factor receptor superfamily, member 1b      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_function binds to tumor necrosis factor (TNF)-alpha 628388