RT1-Ba (RT1 class II, locus Ba) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: RT1-Ba (RT1 class II, locus Ba) Rattus norvegicus
Analyze
Symbol: RT1-Ba
Name: RT1 class II, locus Ba
RGD ID: 1595867
Description: Predicted to enable MHC class II protein complex binding activity and peptide antigen binding activity. Involved in cellular response to glucocorticoid stimulus and negative regulation of T cell proliferation. Predicted to be located in external side of plasma membrane and lysosome. Predicted to be part of MHC class II protein complex. Used to study uveitis. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); gastrointestinal system cancer (multiple); glomerulonephritis (multiple); hematologic cancer (multiple); and systemic scleroderma (multiple). Orthologous to several human genes including HLA-DQA1 (major histocompatibility complex, class II, DQ alpha 1); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; asthma pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: activated B cell RT1Bl alpha chain; BA1; MGC105667; MHC class I antigen; MHC class II antigen RT1.B alpha chain; Rano class II histocompatibility antigen, B alpha chain; RT1 class II antigen, Ba chain; RT1 class II, locus Ba (mapped); RT1-B alpha; RT1-Ba_mapped
RGD Orthologs
Human
Mouse
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,575,134 - 4,579,727 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl204,066,132 - 4,070,721 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0204,066,133 - 4,070,726 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0206,146,271 - 6,150,864 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,697,971 - 4,702,564 (+)NCBIRGSC3.4rn4RGSC3.4
Celera206,176,966 - 6,181,559 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
abdominal aortic aneurysm  (ISO)
achalasia  (ISO)
acute lymphoblastic leukemia  (ISO)
allergic disease  (ISO)
alopecia areata  (ISO)
Amyopathic Dermatomyositis  (ISO)
ankylosing spondylitis  (ISO)
antiphospholipid syndrome  (ISO)
aplastic anemia  (ISO)
arthritis  (ISO)
aspirin-induced respiratory disease  (ISO)
asthma  (ISO)
autoimmune disease  (ISO)
autoimmune myocarditis  (ISO)
autoimmune polyendocrine syndrome  (ISO)
autoimmune polyendocrine syndrome type 2  (ISO)
autoimmune thyroiditis  (ISO)
brain infarction  (ISO)
breast cancer  (ISO)
celiac disease  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
choreatic disease  (ISO)
chronic fatigue syndrome  (ISO)
Chronic Hepatitis B  (ISO)
Chronic Hepatitis C  (ISO)
chronic myeloid leukemia  (ISO)
colon carcinoma  (ISO)
congenital toxoplasmosis  (ISO)
Delayed Hypersensitivity  (IDA)
dermatitis  (ISO)
diffuse scleroderma  (ISO)
dilated cardiomyopathy 1H  (ISO)
Discoid Lupus Erythematosus  (ISO)
Drug Eruptions  (ISO)
eosinophilia-myalgia syndrome  (ISO)
Experimental Autoimmune Encephalomyelitis  (IDA,IMP)
Experimental Liver Cirrhosis  (EXP)
factor VIII deficiency  (ISO)
gastric adenocarcinoma  (ISO)
glucose intolerance  (ISO)
Graves' disease  (ISO)
Hashimoto Disease  (ISO)
Helicobacter Infections  (ISO)
Henoch-Schoenlein purpura  (ISO)
hepatitis B  (ISO)
hepatitis C  (ISO)
hepatocellular carcinoma  (ISO)
human immunodeficiency virus infectious disease  (ISO)
hypertension  (ISO)
juvenile rheumatoid arthritis  (ISO)
lepromatous leprosy  (ISO)
liver cirrhosis  (ISO)
lupus nephritis  (ISO)
MALT lymphoma  (ISO)
marginal zone B-cell lymphoma  (ISO)
melanoma  (ISO)
membranous glomerulonephritis  (ISO)
multiple sclerosis  (ISO)
myasthenia gravis  (ISO)
myositis  (ISO)
narcolepsy  (ISO)
Nasal Polyps  (ISO)
onchocerciasis  (ISO)
Oropharyngeal Neoplasms  (ISO)
pancreatitis  (ISO)
paroxysmal nocturnal hemoglobinuria  (ISO)
pemphigus  (ISO)
primary biliary cholangitis  (ISO)
proteinuria  (ISO)
Pseudomonas Infections  (ISO)
psoriasis  (ISO)
rheumatic fever  (ISO)
rheumatic heart disease  (ISO)
rheumatoid arthritis  (ISO)
rhinitis  (ISO)
rhinoscleroma  (ISO)
Schistosomiasis Japonica  (ISO)
Sjogren's syndrome  (ISO)
Spinal Tuberculoses  (ISO)
stomach cancer  (ISO)
Stroke  (ISO)
Sudden Hearing Loss  (ISO)
systemic lupus erythematosus  (ISO)
systemic scleroderma  (ISO)
thrombophilia  (ISO)
tuberculosis  (ISO)
Tubulointerstitial Nephritis and Uveitis  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
uveitis  (IMP)
visceral leishmaniasis  (ISO)
vitiligo  (ISO)
Vogt-Koyanagi-Harada disease  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dinitrobenzenesulfonic acid  (ISO)
2-butoxyethanol  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3,7-dihydropurine-6-thione  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
acetamide  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP)
auranofin  (ISO)
azathioprine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP)
bisphenol F  (ISO)
buspirone  (EXP)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
coumarin  (EXP)
DDT  (EXP)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dichloromethane  (EXP)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
ethylbenzene  (EXP)
flutamide  (EXP)
fluvastatin  (ISO)
folic acid  (ISO)
folpet  (ISO)
gentamycin  (EXP)
hydrazine  (ISO)
isoprenaline  (ISO)
lead diacetate  (ISO)
lumiracoxib  (ISO)
menadione  (ISO)
mercaptopurine  (ISO)
mercury atom  (ISO)
mercury dichloride  (EXP)
mercury(0)  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nimesulide  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
palladium  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
propanal  (ISO)
propiconazole  (ISO)
purine-6-thiol  (ISO)
quercetin  (ISO)
quercitrin  (ISO)
rotenone  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
tamoxifen  (EXP)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP)
tremolite asbestos  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
triptonide  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

References

References - curated
1. Adamus G, etal., Invest Ophthalmol Vis Sci. 2006 Jun;47(6):2555-61.
2. Amirzargar AA, etal., Pathol Oncol Res. 2007;13(1):47-51. Epub 2007 Mar 27.
3. Arnett FC, etal., Arthritis Rheum. 1996 Sep;39(9):1507-18.
4. Aron Y, etal., Am J Respir Crit Care Med. 1999 May;159(5 Pt 1):1464-8.
5. Azuma T, etal., Cancer. 1998 Mar 15;82(6):1013-8. doi: 10.1002/(sici)1097-0142(19980315)82:6<1013::aid-cncr2>3.0.co;2-f.
6. Barlow AB, etal., Clin Endocrinol (Oxf). 1996 Jan;44(1):73-7.
7. Book L, etal., Am J Med Genet. 2001 Jan 1;98(1):70-4.
8. Burrows GG, etal., J Immunol. 1998 Dec 1;161(11):5987-96.
9. Caliz R, etal., Rheumatology (Oxford). 2001 Jan;40(1):31-6.
10. Castro F, etal., Ann Rheum Dis. 2001 Aug;60(8):791-5.
11. Chen K, etal., PLoS One. 2013 Oct 28;8(10):e77315. doi: 10.1371/journal.pone.0077315. eCollection 2013.
12. Chen YW, etal., BMC Immunol. 2008 Jul 31;9:43.
13. Chinoy H, etal., Rheumatology (Oxford). 2007 Sep;46(9):1411-6. Epub 2007 Jun 22.
14. da Silva SA, etal., BMC Infect Dis. 2009 Aug 22;9:134.
15. De Angelis F, etal., Tissue Antigens. 2012 Feb;79(2):123-9. doi: 10.1111/j.1399-0039.2011.01811.x. Epub 2011 Nov 26.
16. De Block CE, etal., Aliment Pharmacol Ther. 2002 Feb;16(2):281-9.
17. de Graaf KL, etal., Eur J Immunol. 2008 Jan;38(1):299-308.
18. de Kauwe AL, etal., J Immunol. 2009 Jun 15;182(12):7440-50.
19. Eller E, etal., Genes Immun. 2007 Dec;8(8):628-33. Epub 2007 Aug 30.
20. Esmaeilzadeh H, etal., Am J Rhinol Allergy. 2015 May-Jun;29(3):e63-9. doi: 10.2500/ajra.2015.29.4154.
21. Fajardo-Dolci G, etal., Otolaryngol Head Neck Surg. 2006 Aug;135(2):243-7.
22. Fallahi P, etal., Gene. 2013 May 15;520(2):131-8. doi: 10.1016/j.gene.2013.02.032. Epub 2013 Feb 27.
23. Fischer GF, etal., Hum Immunol. 1994 Dec;41(4):280-4.
24. Friedl-Hajek R, etal., Clin Exp Allergy. 1999 Apr;29(4):478-87.
25. Gao J, etal., Chin Med J (Engl). 2003 Jul;116(7):1078-82.
26. Garza-González E, etal., J Gastroenterol. 2004 Dec;39(12):1138-42. doi: 10.1007/s00535-004-1462-2.
27. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
28. Gray LA, etal., J Infect Dis. 2017 Dec 12;216(11):1460-1470. doi: 10.1093/infdis/jix497.
29. Greenbaum CJ, etal., Diabetologia. 2005 Jan;48(1):68-74. Epub 2004 Dec 16.
30. Guo JC, etal., Zhongguo Zhong Xi Yi Jie He Za Zhi. 2016 May;36(5):539-43.
31. Guo X, etal., Zhonghua Jie He He Hu Xi Za Zhi. 2001 Mar;24(3):139-41.
32. Haas JP, etal., Autoimmunity. 2009 May;42(4):389-91.
33. Hallioglu O, etal., Clin Exp Rheumatol. 2005 Jan-Feb;23(1):117-20.
34. Hardie RA, etal., AIDS. 2008 Apr 23;22(7):807-16.
35. Hashimoto K, etal., Horm Res. 2005;64(5):253-60. Epub 2005 Oct 27.
36. Hay CR, etal., Thromb Haemost. 1997 Feb;77(2):234-7.
37. Henkes W and Reske K, Mol Immunol. 1989 Feb;26(2):171-9.
38. Huber SA, etal., J Virol. 1999 Jul;73(7):5630-6. doi: 10.1128/JVI.73.7.5630-5636.1999.
39. Ishibashi M, etal., Arch Virol. 2018 Apr;163(4):855-865. doi: 10.1007/s00705-017-3675-8. Epub 2017 Dec 16.
40. Jiang YG, etal., World J Gastroenterol. 2003 Oct;9(10):2221-5.
41. Jimenez BD, etal., Life Sci. 2002 Jun 7;71(3):311-23.
42. Karra VK, etal., Indian J Med Res. 2018 Jun;147(6):573-580. doi: 10.4103/ijmr.IJMR_1644_15.
43. Kawahara Y, etal., Clin Gastroenterol Hepatol. 2005 Sep;3(9):865-8.
44. Khosravi F, etal., Iran J Allergy Asthma Immunol. 2007 Sep;6(3):137-42.
45. Kokaraki G, etal., Tissue Antigens. 2009 Mar;73(3):199-205.
46. Kouri I, etal., J Neurol Sci. 2011 Jul 7.
47. Kozuka R, etal., J Gastroenterol Hepatol. 2019 May;34(5):937-946. doi: 10.1111/jgh.14454. Epub 2018 Sep 26.
48. Lambert NC, etal., Arthritis Rheum. 2000 Sep;43(9):2005-10.
49. Lara-Marquez ML, etal., Clin Exp Allergy 1999 Jan;29(1):60-71.
50. Larizza D, etal., J Pediatr. 2001 Nov;139(5):738-40.
51. LeishGEN Consortium, etal., Nat Genet. 2013 Feb;45(2):208-13. doi: 10.1038/ng.2518. Epub 2013 Jan 6.
52. Levinson RD, etal., Invest Ophthalmol Vis Sci. 2003 Feb;44(2):653-7.
53. Li HS, etal., Zhonghua Yu Fang Yi Xue Za Zhi. 2006 May;40(3):173-6.
54. Li S, etal., PLoS Genet. 2012;8(7):e1002791. doi: 10.1371/journal.pgen.1002791. Epub 2012 Jul 12.
55. Li X, etal., Yi Chuan Xue Bao. 1999;26(4):295-300.
56. Liu C and Cheng B, Int J Immunogenet. 2007 Oct;34(5):373-8. doi: 10.1111/j.1744-313X.2007.00702.x.
57. Liu Q, etal., Zhonghua Yan Ke Za Zhi. 1999 May;35(3):210-5.
58. Liu W, etal., Ann Hum Genet. 2005 Jul;69(Pt 4):382-8.
59. Liu W, etal., Chin Med J (Engl). 2004 Oct;117(10):1449-52.
60. Lu LP, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2006 Aug;23(4):427-30.
61. Luppi P, etal., J Biol Regul Homeost Agents. 1999 Jan-Mar;13(1):14-26.
62. Mignot E, etal., Am J Hum Genet. 2001 Mar;68(3):686-99. Epub 2001 Feb 13.
63. Molnar-Gabor E, etal., Laryngoscope. 2000 Mar;110(3 Pt 1):422-5.
64. Monsuur AJ, etal., PLoS One. 2008 May 28;3(5):e2270.
65. Movahedi M, etal., Iran J Allergy Asthma Immunol. 2008 Dec;7(4):215-20.
66. Mullarkey ME, etal., Tissue Antigens. 2005 Feb;65(2):199-205. doi: 10.1111/j.1399-0039.2005.00351.x.
67. Murray JA, etal., Clin Gastroenterol Hepatol. 2007 Dec;5(12):1406-12. Epub 2007 Oct 24.
68. Nakanishi K and Inoko H, Diabetes. 2006 Jun;55(6):1862-8.
69. Nakao S, etal., Blood. 1994 Dec 15;84(12):4257-61.
70. Nakken B, etal., Scand J Immunol. 2001 Oct;54(4):428-33.
71. O'Hanlon TP, etal., Medicine (Baltimore). 2006 Mar;85(2):111-27.
72. OMIM Disease Annotation Pipeline
73. Perri F, etal., Tissue Antigens. 2002 Jan;59(1):55-7. doi: 10.1034/j.1399-0039.2002.590112.x.
74. Pipeline to import KEGG annotations from KEGG into RGD
75. Planelles D, etal., Br J Dermatol. 2006 Feb;154(2):261-6.
76. Pratsidou-Gertsi P, etal., Eur J Immunogenet. 1999 Aug;26(4):299-310.
77. Reed AM and Stirling JD, Hum Immunol. 1995 Nov;44(3):131-5.
78. Reed AM, etal., J Immunol. 2004 Apr 15;172(8):5041-6.
79. Ren S, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2002 Feb;19(1):58-60.
80. Resic-Lindehammer S, etal., Acta Diabetol. 2008 Dec;45(4):231-5. Epub 2008 Sep 4.
81. RGD automated data pipeline
82. RGD automated import pipeline for gene-chemical interactions
83. RGD comprehensive gene curation
84. Rider LG, etal., Arthritis Rheum. 1998 Apr;41(4):710-9.
85. Ruiz-de-Leon A, etal., Dig Dis Sci. 2002 Jan;47(1):15-9.
86. Samimi-Rad K, etal., J Med Virol. 2015 Sep;87(9):1565-72. doi: 10.1002/jmv.24211. Epub 2015 May 12.
87. Sanchez-Marin LA, etal., Otolaryngol Head Neck Surg. 2007 Mar;136(3):481-3.
88. Sanchez-Velasco P, etal., Hum Immunol. 2005 Jul;66(7):818-25.
89. Sanjeevi CB, etal., Ann N Y Acad Sci. 2002 Apr;958:362-75.
90. Shams S, etal., J Clin Immunol. 2009 Mar;29(2):175-9. Epub 2008 Sep 9.
91. Sharma SK, etal., Am J Respir Crit Care Med. 2002 Oct 1;166(7):916-9. doi: 10.1164/rccm.2108091.
92. Shen J, etal., Med Sci Monit. 2018 May 24;24:3442-3449. doi: 10.12659/MSM.907864.
93. Shen N, etal., Zhonghua Yi Xue Za Zhi. 2001 Mar 25;81(6):352-5.
94. Shichishima T, etal., Blood. 2002 Jul 1;100(1):22-8.
95. Shimokawa PT, etal., Virulence. 2016 May 18;7(4):456-64. doi: 10.1080/21505594.2016.1150401. Epub 2016 Feb 8.
96. Singer JB, etal., Nat Genet. 2010 Aug;42(8):711-4. doi: 10.1038/ng.632. Epub 2010 Jul 18.
97. Smith J, etal., J Clin Pathol. 2005 Aug;58(8):860-3.
98. Spraggs CF, etal., J Clin Oncol. 2011 Feb 20;29(6):667-73. Epub 2011 Jan 18.
99. Stanescu HC, etal., N Engl J Med. 2011 Feb 17;364(7):616-26.
100. Stanevicha V, etal., Arthritis Res Ther. 2007;9(3):R58.
101. Sumnik Z, etal., Diabetes Care. 2006 Apr;29(4):858-63.
102. Sumnik Z, etal., J Pediatr Endocrinol Metab. 2003 Jul-Aug;16(6):851-8.
103. Suzuki K, etal., Tissue Antigens. 2005 May;65(5):459-66.
104. Taylor GM, etal., Br J Cancer. 1998 Sep;78(5):561-5.
105. Tibbs C, etal., Hepatology. 1996 Dec;24(6):1342-5. doi: 10.1053/jhep.1996.v24.pm0008938158.
106. Tromp G, etal., Ann N Y Acad Sci. 2006 Nov;1085:392-5.
107. Urabe Y, etal., J Hepatol. 2013 May;58(5):875-82. doi: 10.1016/j.jhep.2012.12.024. Epub 2013 Jan 12.
108. Ursum J, etal., J Rheumatol. 2010 Jul;37(7):1431-8. Epub 2010 May 15.
109. Wagner AM, etal., Diabetes Metab Res Rev. 2011 Jul;27(5):493-498. doi: 10.1002/dmrr.1189.
110. Wallaschofski H, etal., Horm Metab Res. 2003 Feb;35(2):120-4.
111. Wang M, etal., Otolaryngol Head Neck Surg. 2004 Feb;130(2):192-6.
112. Ward MM, etal., Arthritis Rheum. 2009 Jul 15;61(7):859-66.
113. Weinstock C, etal., Tissue Antigens. 2011 Apr;77(4):317-24. doi: 10.1111/j.1399-0039.2011.01634.x.
114. Xiao FL, etal., Arch Dermatol Res. 2005 Nov;297(5):201-9. Epub 2005 Nov 11.
115. Xun YH, etal., Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi. 2009 Dec;23(6):430-3.
116. Yang HY, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2005 Dec;22(6):702-4.
117. Yang S, etal., Int J Dermatol. 2005 Dec;44(12):1022-7.
118. Yen JH, etal., Kaohsiung J Med Sci. 2001 Apr;17(4):183-9.
119. Yeo SW, etal., Arch Otolaryngol Head Neck Surg. 2001 Aug;127(8):945-9.
120. Yousefipour GA, etal., Iran J Immunol. 2009 Jun;6(2):99-102.
121. Yu J, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2014 Feb;31(1):93-6. doi: 10.3760/cma.j.issn.1003-9406.2014.01.022.
122. Zang GQ, etal., World J Gastroenterol. 2004 Jul 15;10(14):2116-8. doi: 10.3748/wjg.v10.i14.2116.
123. Zavaglia C, etal., J Hepatol. 1998 Jan;28(1):1-7.
124. Zhang JH, etal., Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi. 2005 Feb 28;23(1):6-9.
125. Zhang X, etal., Int J Dermatol. 2004 Mar;43(3):181-7.
126. Zhang XY, etal., Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi. 2011 Feb;27(2):182-5.
Additional References at PubMed
PMID:2499874   PMID:3610254   PMID:6084802   PMID:6319276   PMID:7679955   PMID:7985028   PMID:8344727   PMID:8598040   PMID:8598041   PMID:8638109   PMID:9432982   PMID:9492004  
PMID:11027433   PMID:11069069   PMID:11148202   PMID:11465104   PMID:11685465   PMID:11714799   PMID:11854359   PMID:12477932   PMID:12879310   PMID:15517241   PMID:19946888   PMID:24586191  


Genomics

Comparative Map Data
RT1-Ba
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,575,134 - 4,579,727 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl204,066,132 - 4,070,721 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0204,066,133 - 4,070,726 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0206,146,271 - 6,150,864 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,697,971 - 4,702,564 (+)NCBIRGSC3.4rn4RGSC3.4
Celera206,176,966 - 6,181,559 (+)NCBICelera
Cytogenetic Map20p12NCBI
HLA-DQA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl632,628,179 - 32,647,062 (+)EnsemblGRCh38hg38GRCh38
GRCh38632,637,406 - 32,654,846 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37632,605,183 - 32,611,461 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,713,161 - 32,719,407 (+)NCBINCBI36hg18NCBI36
Build 34632,713,160 - 32,719,407NCBI
Cytogenetic Map6p21.32NCBI
HuRef632,346,937 - 32,353,106 (+)NCBIHuRef
CHM1_1632,607,658 - 32,613,904 (+)NCBICHM1_1
H2-Aa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,501,718 - 34,506,797 (-)NCBIGRCm39mm39
GRCm39 Ensembl1734,501,718 - 34,506,797 (-)Ensembl
GRCm381734,282,744 - 34,287,823 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,282,744 - 34,287,823 (-)EnsemblGRCm38mm10GRCm38
MGSCv371734,419,696 - 34,424,716 (-)NCBIGRCm37mm9NCBIm37
MGSCv361733,891,091 - 33,896,110 (-)NCBImm8
Celera1737,044,263 - 37,049,282 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.98NCBI
MHC-DQA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11739,422,445 - 39,428,777 (-)NCBI
ChlSab1.1 Ensembl1739,420,134 - 39,428,871 (-)Ensembl
Vero_WHO_p1.0NW_02366604432,455,961 - 32,462,315 (+)NCBI

Position Markers
D20Yum74  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,576,395 - 4,576,557 (-)MAPPERmRatBN7.2
Rnor_6.0204,069,303 - 4,069,464NCBIRnor6.0
Rnor_5.0206,149,441 - 6,149,602UniSTSRnor5.0
RGSC_v3.4204,699,233 - 4,699,394UniSTSRGSC3.4
Celera206,178,228 - 6,178,389UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
737973Pia21Pristane induced arthritis QTL 214.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2036216564606812Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7175099Tcs2T cell selection QTL 2T cell selectionexpression2045025574693102Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:188
Count of miRNA genes:133
Interacting mature miRNAs:148
Transcripts:ENSRNOT00000000523
Prediction methods:Microtar, 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 2 3
Medium 1 11 28 13 16 13 5 8 1 19 11 11 5
Low 14 15 14 14 3 3 28 10 22 3
Below cutoff 8 12 12 12 25 6 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001008831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF307302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH002251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493031 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493032 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ493035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ554214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY626199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY701537 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC086448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234577 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  K02815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC222945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L11341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M29311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X14879 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000000523   ⟹   ENSRNOP00000000523
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,066,132 - 4,070,721 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077143   ⟹   ENSRNOP00000070569
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,066,132 - 4,067,164 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091096
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,066,732 - 4,067,931 (-)Ensembl
RefSeq Acc Id: NM_001008831   ⟹   NP_001008831
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,575,134 - 4,579,727 (+)NCBI
Rnor_6.0204,066,133 - 4,070,726 (-)NCBI
Rnor_5.0206,146,271 - 6,150,864 (-)NCBI
RGSC_v3.4204,697,971 - 4,702,564 (+)RGD
Celera206,176,966 - 6,181,559 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001008831   ⟸   NM_001008831
- Peptide Label: precursor
- UniProtKB: Q6MGA0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070569   ⟸   ENSRNOT00000077143
RefSeq Acc Id: ENSRNOP00000000523   ⟸   ENSRNOT00000000523
Protein Domains
Ig-like   Ig-like C1-type

Transcriptome

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

Promoters
RGD ID:13701329
Promoter ID:EPDNEW_R11852
Type:initiation region
Name:RT1-Ba_1
Description:RT1 class II, locus Ba
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_6.0204,070,718 - 4,070,778EPDNEW

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:1595867 AgrOrtholog
Ensembl Genes ENSRNOG00000000451 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000523 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070569 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000523 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000077143 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.10.320.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7304077 IMAGE-MGC_LOAD
InterPro Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I/II-like_Ag-recog UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_a/b_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_a_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:309621 UniProtKB/TrEMBL
MGC_CLONE MGC:105667 IMAGE-MGC_LOAD
NCBI Gene 309621 ENTREZGENE
Pfam C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen RT1-Ba PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_MHC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IGc1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_II_alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54452 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JY95_RAT UniProtKB/TrEMBL
  HA2B_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q5UT85_RAT UniProtKB/TrEMBL
  Q6MGA0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-04-12 RT1-Ba  RT1 class II, locus Ba  RT1-Ba_mapped  RT1 class II, locus Ba (mapped)  Data Merged 737654 APPROVED
2006-11-20 RT1-Ba  RT1 class II, locus Ba      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 RT1-Ba_mapped  RT1 class II, locus Ba(mapped)  RT1-Ba  RT1 class II, locus Ba  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2004-02-11 RT1-Ba  RT1 class II, locus Ba      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 RT1-Ba  RT1 class II, locus Ba      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_mapping maps to the MHC RT1 complex 1300431
gene_physical_interaction alpha chain, with the RT1-Bb beta chain forms the Rt1-B MHC class II molecule 1300427