Ctla4 (cytotoxic T-lymphocyte-associated protein 4) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ctla4 (cytotoxic T-lymphocyte-associated protein 4) Rattus norvegicus
Analyze
Symbol: Ctla4
Name: cytotoxic T-lymphocyte-associated protein 4
RGD ID: 61975
Description: Predicted to have signaling receptor activity. Involved in negative regulation of T cell proliferation and negative regulation of immune response. Predicted to localize to several cellular components, including clathrin-coated endocytic vesicle; external side of plasma membrane; and perinuclear region of cytoplasm. Used to study myocarditis. Human ortholog(s) of this gene implicated in several diseases, including carcinoma (multiple); hematologic cancer (multiple); hepatitis B; kidney disease (multiple); and primary immunodeficiency disease (multiple). Orthologous to human CTLA4 (cytotoxic T-lymphocyte associated protein 4); PARTICIPATES IN autoimmune thyroiditis pathway; rheumatoid arthritis pathway; T cell receptor signaling pathway; INTERACTS WITH 3H-1,2-dithiole-3-thione; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Cd152; CD152 antigen; CTLA-4; cytotoxic T-lymphocyte protein 4; sCTLA4; soluble form; transmembrane form
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2962,318,874 - 62,325,978 (+)NCBI
Rnor_6.0 Ensembl967,699,379 - 67,706,065 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0967,699,397 - 67,706,068 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0967,509,236 - 67,515,681 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4959,495,773 - 59,501,300 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1959,642,754 - 59,648,282 (+)NCBI
Celera959,742,231 - 59,747,758 (+)NCBICelera
Cytogenetic Map9q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute myeloid leukemia  (ISO)
adult T-cell leukemia  (ISO)
Alcoholic Liver Diseases  (ISO)
allergic rhinitis  (ISO)
alopecia areata  (ISO)
anogenital venereal wart  (ISO)
anti-basement membrane glomerulonephritis  (ISO)
Anti-Neutrophil Cytoplasmic Antibody-Associated Vasculitis  (ISO)
asthma  (ISO)
atopic dermatitis  (ISO)
autoimmune hemolytic anemia  (ISO)
autoimmune hepatitis  (ISO)
Autoimmune Hypothyroidism  (ISO)
Autoimmune Lymphoproliferative Syndrome, Type V  (ISO)
autoimmune thyroiditis  (ISO)
B-Cell Chronic Lymphocytic Leukemia  (ISO)
basal cell carcinoma  (ISO)
Behcet's disease  (ISO)
breast cancer  (ISO)
Bronchial Hyperreactivity  (ISO)
celiac disease  (ISO)
Chronic Bronchitis  (ISO)
Chronic Hepatitis B  (ISO)
Chronic Hepatitis C  (ISO)
chronic obstructive pulmonary disease  (ISO)
contact dermatitis  (ISO)
Cryptogenic Cirrhosis  (ISO)
cutaneous T cell lymphoma  (ISO)
Diabetic Nephropathies  (ISO)
end stage renal disease  (ISO)
Enterocolitis  (ISO)
Experimental Arthritis  (IMP,ISO)
Experimental Autoimmune Encephalomyelitis  (ISO)
Experimental Autoimmune Uveitis  (ISO)
Experimental Melanoma  (ISO)
genetic disease  (ISO)
Graft vs Host Disease  (ISO)
granulomatosis with polyangiitis  (ISO)
Graves Ophthalmopathy  (ISO)
Graves' disease  (ISO)
Hashimoto Disease  (ISO)
hepatitis A  (ISO)
hepatitis B  (ISO)
hepatocellular carcinoma  (ISO)
immunoglobulin alpha deficiency  (ISO)
Inflammation  (ISO)
iridocyclitis  (ISO)
juvenile rheumatoid arthritis  (ISO)
kidney disease  (ISO)
Kidney Reperfusion Injury  (ISO)
latent autoimmune diabetes in adults  (ISO)
lung disease  (ISO)
lupus nephritis  (ISO)
Lymphadenopathy  (ISO)
Lymphatic Metastasis  (ISO)
malaria  (ISO)
melanoma  (ISO)
monoclonal gammopathy of uncertain significance  (ISO)
multiple myeloma  (ISO)
multiple sclerosis  (ISO)
myocardial infarction  (ISO)
myocarditis  (IMP)
Neoplasm Metastasis  (ISO)
Neurodevelopmental Disorders  (ISO)
non-Hodgkin lymphoma  (ISO)
oral submucous fibrosis  (ISO)
peripheral nervous system disease  (ISO)
primary biliary cholangitis  (ISO)
primary immunodeficiency disease  (ISO)
Prostatic Neoplasms  (ISO)
psoriasis  (ISO)
Pulmonary Arterial Hypertension  (ISO)
renal cell carcinoma  (ISO)
rheumatoid arthritis  (ISO)
rhinitis  (ISO)
sarcoidosis  (ISO)
silicosis  (ISO)
Sjogren's syndrome  (ISO)
Splenomegaly  (ISO)
squamous cell carcinoma  (ISO)
systemic lupus erythematosus  (ISO)
Transplant Rejection  (IMP,ISO)
tropical spastic paraparesis  (ISO)
type 1 diabetes mellitus  (ISO)
type 1 diabetes mellitus 12  (ISO)
urinary schistosomiasis  (ISO)
vitiligo  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Abe S, etal., J Card Fail. 2005 Sep;11(7):557-64.
2. Abrams JR, etal., J Exp Med. 2000 Sep 4;192(5):681-94.
3. Agarwal K, etal., J Hepatol. 2000 Apr;32(4):538-41.
4. Aiba Y, etal., J Gastroenterol. 2011 Oct;46(10):1203-12. doi: 10.1007/s00535-011-0417-7. Epub 2011 May 19.
5. Baniasadi V, etal., Tissue Antigens. 2006 May;67(5):383-9.
6. Beck KE, etal., J Clin Oncol. 2006 May 20;24(15):2283-9. doi: 10.1200/JCO.2005.04.5716.
7. Berce V and Potocnik U, Biomarkers. 2010 Mar;15(2):158-66.
8. Beyer M, etal., Blood. 2005 Sep 15;106(6):2018-25. Epub 2005 May 24.
9. Blazar BR, etal., Blood. 1994 Jun 15;83(12):3815-25.
10. Blomhoff A, etal., Pigment Cell Res. 2005 Feb;18(1):55-8.
11. Bolstad AI, etal., Arthritis Rheum. 2003 Jan;48(1):174-85.
12. Braun J, etal., Tissue Antigens. 1998 May;51(5):563-6.
13. Chandraker A, etal., Kidney Int. 1997 Dec;52(6):1678-84.
14. Chandraker A, etal., Transplantation. 2005 Apr 27;79(8):897-903.
15. Chaouali M, etal., Genes Dis. 2017 Dec 30;5(3):256-262. doi: 10.1016/j.gendis.2017.12.006. eCollection 2018 Sep.
16. Chikuma S, etal., J Exp Med 2003 Jan 6;197(1):129-35.
17. Cho H, etal., Gut Liver. 2016 Mar;10(2):288-94. doi: 10.5009/gnl14368.
18. Cosentino A, etal., Ann N Y Acad Sci. 2002 Apr;958:337-40.
19. Cozar JM, etal., Hum Immunol. 2007 Aug;68(8):698-704. Epub 2007 Jun 6.
20. Cunnane G, etal., Arthritis Rheum. 2004 May;50(5):1539-48.
21. Daroszewski J, etal., Eur J Endocrinol. 2009 Nov;161(5):787-93. doi: 10.1530/EJE-09-0600. Epub 2009 Sep 4.
22. Demaria S, etal., Clin Cancer Res. 2005 Jan 15;11(2 Pt 1):728-34.
23. Deurloo DT, etal., Am J Respir Cell Mol Biol. 2001 Dec;25(6):751-60.
24. Deurloo DT, etal., Clin Exp Allergy. 2003 Sep;33(9):1297-304.
25. Djilali-Saiah I, etal., Gut 1998 Aug;43(2):187-9.
26. Domagala-Kulawik J, etal., Scand J Immunol. 2011 Jan;73(1):59-65. doi: 10.1111/j.1365-3083.2010.02474.x.
27. Donaldson P, etal., Clin Gastroenterol Hepatol. 2007 Jun;5(6):755-60. doi: 10.1016/j.cgh.2007.02.012. Epub 2007 May 7.
28. Donner H, etal., J Clin Endocrinol Metab 1997 Dec;82(12):4130-2.
29. Downie-Doyle S, etal., Arthritis Rheum. 2006 Aug;54(8):2434-40.
30. Dwivedi M, etal., Pigment Cell Melanoma Res. 2011 Aug;24(4):737-40. doi: 10.1111/j.1755-148X.2011.00892.x.
31. Erfani N, etal., Cancer Invest. 2010 Oct;28(8):828-32. doi: 10.3109/07357901003630934.
32. Furugaki K, etal., J Hum Genet. 2004;49(3):166-8. Epub 2004 Feb 20.
33. Gallon L, etal., J Immunol. 1997 Nov 1;159(9):4212-6.
34. Gao JW, etal., Transpl Immunol. 2012 Jun;26(4):207-11. doi: 10.1016/j.trim.2012.02.005. Epub 2012 Mar 6.
35. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
36. Giscombe R, etal., J Rheumatol. 2002 May;29(5):950-3.
37. GOA data from the GO Consortium
38. Greve B, etal., Mult Scler. 2008 Mar;14(2):153-8. Epub 2007 Oct 17.
39. Guo L, etal., Transpl Immunol. 2003 Oct-Nov;12(1):41-8.
40. Haimila K, etal., Genes Immun. 2009 Mar;10(2):151-61. doi: 10.1038/gene.2008.89. Epub 2008 Nov 20.
41. Han SZ, etal., Int J Immunogenet. 2006 Aug;33(4):281-7.
42. Handa T, etal., Sarcoidosis Vasc Diffuse Lung Dis. 2003 Oct;20(3):190-6.
43. Harbo HF, etal., Tissue Antigens 1999 Jan;53(1):106-10.
44. Heward JM, etal., Clin Endocrinol (Oxf). 1998 Sep;49(3):331-4.
45. Heward JM, etal., J Clin Endocrinol Metab. 1999 Jul;84(7):2398-401.
46. Hubeau C, etal., J Immunol. 2007 Feb 1;178(3):1477-87.
47. Idris ZM, etal., Genet Test Mol Biomarkers. 2012 Jun;16(6):488-92. doi: 10.1089/gtmb.2011.0209. Epub 2012 Jan 30.
48. Ikegami H, etal., J Clin Endocrinol Metab. 2006 Mar;91(3):1087-92. Epub 2005 Dec 13.
49. Jasek M, etal., Int Arch Allergy Immunol. 2006;141(3):223-9. Epub 2006 Aug 22.
50. Jones G, etal., Br J Dermatol. 2006 Mar;154(3):467-71.
51. Kamesh L, etal., Rheumatology (Oxford). 2009 Dec;48(12):1502-5. doi: 10.1093/rheumatology/kep280. Epub 2009 Oct 8.
52. Karabon L, etal., Immunology. 2009 Sep;128(1 Suppl):e787-96. doi: 10.1111/j.1365-2567.2009.03083.x. Epub 2009 Feb 17.
53. Kawasaki E, etal., Diabetes Care. 2008 Aug;31(8):1608-10. Epub 2008 Apr 28.
54. Kawayama T, etal., Respirology. 2008 Nov;13(7):1000-1007.
55. Kim HJ, etal., Transpl Immunol. 2010 Oct;24(1):40-4. doi: 10.1016/j.trim.2010.10.001. Epub 2010 Oct 19.
56. Knoerzer DB, etal., J Clin Invest. 1995 Aug;96(2):987-93.
57. Kurup SP, etal., Nat Med. 2017 Oct;23(10):1220-1225. doi: 10.1038/nm.4395. Epub 2017 Sep 11.
58. Kwon ED, etal., Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):8099-103.
59. Kwon ED, etal., Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):15074-9.
60. LaBerge GS, etal., J Invest Dermatol. 2008 Jul;128(7):1757-62. doi: 10.1038/sj.jid.5701233. Epub 2008 Jan 17.
61. Lai LW, etal., Kidney Int. 2012 May;81(10):983-92. doi: 10.1038/ki.2011.412. Epub 2011 Dec 21.
62. Lan KH, etal., Biochem Biophys Res Commun. 2013 Oct 18;440(2):222-8. doi: 10.1016/j.bbrc.2013.09.031. Epub 2013 Sep 13.
63. Lee SY, etal., Chest. 2002 Jul;122(1):171-6.
64. Li Q, etal., J Gastroenterol Hepatol. 2013 Aug;28(8):1397-402. doi: 10.1111/jgh.12165.
65. Liu F, etal., PLoS One. 2010 Nov 3;5(11):e15404.
66. Liu Y, etal., Hum Immunol. 2010 Nov;71(11):1141-6. Epub 2010 Aug 21.
67. Marron MP, etal., Hum Mol Genet 1997 Aug;6(8):1275-82.
68. Megiorni F, etal., Arch Dermatol Res. 2013 Sep;305(7):665-70. doi: 10.1007/s00403-013-1348-3. Epub 2013 Apr 9.
69. MGD data from the GO Consortium
70. Mohammad Alizadeh AH, etal., World J Gastroenterol. 2006 Jan 28;12(4):630-5.
71. Monne M, etal., Am J Hematol. 2004 May;76(1):14-8.
72. Motta M, etal., Leukemia. 2005 Oct;19(10):1788-93.
73. Munthe-Kaas MC, etal., J Allergy Clin Immunol. 2004 Aug;114(2):280-7.
74. Nakajima T, etal., J Immunol. 2010 May 15;184(10):5835-41. Epub 2010 Apr 12.
75. NCBI rat LocusLink and RefSeq merged data July 26, 2002
76. Nishikawa K, etal., Eur J Immunol. 1994 Jun;24(6):1249-54.
77. Nistico L, etal., Hum Mol Genet. 1996 Jul;5(7):1075-80.
78. Nuriya S, etal., J Invest Dermatol. 2001 May;116(5):764-8.
79. Oaks MK, etal., Cell Immunol 2000 May 1;201(2):144-53.
80. Oaks MK, etal., Immunogenetics 1996;43(3):173-4.
81. Oaks MK, etal., Immunogenetics 1996;43(3):173-4.
82. Oertelt S, etal., Clin Dev Immunol. 2005 Dec;12(4):259-63. doi: 10.1080/17402520500317859.
83. OMIM Disease Annotation Pipeline
84. Oracki SA, etal., J Immunol. 2010 Jan 15;184(2):757-63. doi: 10.4049/jimmunol.0804349. Epub 2009 Dec 4.
85. Park KS, etal., Tissue Antigens. 2009 Sep;74(3):222-7. doi: 10.1111/j.1399-0039.2009.01303.x. Epub 2009 Jun 25.
86. Pavkovic M, etal., Am J Hematol. 2003 Feb;72(2):147-9.
87. Pehlivan S, etal., Eur J Dermatol. 2009 Mar-Apr;19(2):126-8. doi: 10.1684/ejd.2008.0578. Epub 2009 Jan 7.
88. Perez-Garcia A, etal., Leukemia. 2009 Mar;23(3):486-91. doi: 10.1038/leu.2008.339. Epub 2008 Dec 18.
89. Petrone A, etal., Thyroid. 2005 Mar;15(3):232-8.
90. Pipeline to import KEGG annotations from KEGG into RGD
91. Queirolo P, etal., Cancer Invest. 2013 Jun;31(5):336-45. doi: 10.3109/07357907.2013.793699. Epub 2013 May 3.
92. Ramirez E, etal., Braz J Med Biol Res. 2010 Nov;43(11):1109-15. doi: 10.1590/s0100-879x2010007500107. Epub 2010 Oct 8.
93. Reynolds J, etal., J Clin Invest. 2000 Mar;105(5):643-51.
94. RGD automated data pipeline
95. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
96. RGD automated import pipeline for gene-chemical interactions
97. RGD comprehensive gene curation
98. Rutkowski R, etal., Pol Merkur Lekarski. 2006 Feb;20(116):139-44.
99. Sato J, etal., Int Arch Allergy Immunol. 1999 Jul;119(3):197-204.
100. Schott E, etal., Eur J Gastroenterol Hepatol. 2007 Nov;19(11):947-51. doi: 10.1097/MEG.0b013e3282efa240.
101. Schubert D, etal., Nat Med. 2014 Dec;20(12):1410-6. doi: 10.1038/nm.3746. Epub 2014 Oct 20.
102. Shao H, etal., Invest Ophthalmol Vis Sci. 2001 Aug;42(9):2016-21.
103. Shi HZ, etal., J Asthma. 2005 Mar;42(2):133-9.
104. Shi YJ, etal., Mol Med Rep. 2013 Aug;8(2):480-6. doi: 10.3892/mmr.2013.1511. Epub 2013 Jun 6.
105. Shiraishi T, etal., Am J Transplant. 2002 Mar;2(3):223-8.
106. Sohn MH, etal., Pediatr Pulmonol. 2007 Jun;42(6):542-7.
107. Spriewald BM, etal., Ann Rheum Dis. 2005 Mar;64(3):457-61.
108. Spriewald BM, etal., Ophthalmic Res. 2007;39(2):116-20. Epub 2007 Feb 8.
109. Sugimoto K, etal., Clin Exp Nephrol. 2008 Apr;12(2):149-54. doi: 10.1007/s10157-007-0019-0. Epub 2008 Jan 9.
110. Sun K, etal., Zhonghua Jie He He Hu Xi Za Zhi. 2006 Feb;29(2):109-12.
111. Takekubo M, etal., J Gene Med. 2008 Mar;10(3):290-7.
112. Takiguchi M, etal., J Vet Med Sci. 2000 Jan;62(1):29-36.
113. Thio CL, etal., J Virol. 2004 Oct;78(20):11258-62. doi: 10.1128/JVI.78.20.11258-11262.2004.
114. Vaidya B, etal., Clin Endocrinol (Oxf). 2003 Jun;58(6):732-5.
115. Vaidya B, etal., Hum Mol Genet 1999 Jul;8(7):1195-9.
116. Valenti L, etal., Alcohol Alcohol. 2004 Jul-Aug;39(4):276-80. doi: 10.1093/alcalc/agh047.
117. Verwaerde C, etal., Gene Ther. 2003 Nov;10(23):1970-81.
118. Wang JJ, etal., Pediatr Nephrol. 2012 Nov;27(11):2059-64. doi: 10.1007/s00467-012-2216-7. Epub 2012 Jun 15.
119. Wang L, etal., BMC Cancer. 2007 Sep 10;7:173.
120. Waterhouse P, etal., Science 1995 Nov 10;270(5238):985-8.
121. Welsh MM, etal., Cancer Res. 2009 Aug 1;69(15):6158-63. doi: 10.1158/0008-5472.CAN-09-0415. Epub 2009 Jul 21.
122. Wong CK, etal., J Clin Immunol. 2008 Jan;28(1):36-43. Epub 2007 Nov 17.
123. Wu P, etal., Int J Immunopathol Pharmacol. 2006 Apr-Jun;19(2):357-68.
124. Xu XY, etal., Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2011 Nov;29(11):816-9.
125. Yang JC, etal., J Immunother. 2007 Nov-Dec;30(8):825-30.
126. Yee LJ, etal., J Infect Dis. 2003 Apr 15;187(8):1264-71. doi: 10.1086/374561. Epub 2003 Apr 2.
127. Yesilkaya E, etal., Genet Test. 2008 Sep;12(3):461-4. doi: 10.1089/gte.2008.0053.
128. Yin X, etal., Thyroid. 2012 Jul;22(7):730-6. doi: 10.1089/thy.2012.0007. Epub 2012 Jun 4.
129. Yip HK, etal., Circ J. 2007 Aug;71(8):1213-8.
130. Zakrzewska A, etal., Med Wieku Rozwoj. 2007 Apr-Jun;11(2 Pt 1):129-34.
131. Zhang W, etal., Int Immunol. 2012 Jun;24(6):379-88. doi: 10.1093/intimm/dxs041. Epub 2012 Feb 21.
132. Zhao SX, etal., PLoS One. 2010 Mar 23;5(3):e9821. doi: 10.1371/journal.pone.0009821.
133. Zheng C, etal., Br J Haematol. 2001 Jan;112(1):216-8.
134. Zhou G, etal., Gastroenterology. 2017 Oct;153(4):1107-1119.e10. doi: 10.1053/j.gastro.2017.06.017. Epub 2017 Jun 23.
135. Zhu G, etal., Eur Respir J. 2009 Sep;34(3):598-604. Epub 2009 Apr 22.
Additional References at PubMed
PMID:7544393   PMID:15814706   PMID:16227984   PMID:17875758   PMID:18522879   PMID:18601859   PMID:18641304   PMID:18665051   PMID:19191906   PMID:21532411   PMID:22325471   PMID:28484017  


Genomics

Comparative Map Data
Ctla4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2962,318,874 - 62,325,978 (+)NCBI
Rnor_6.0 Ensembl967,699,379 - 67,706,065 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0967,699,397 - 67,706,068 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0967,509,236 - 67,515,681 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4959,495,773 - 59,501,300 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1959,642,754 - 59,648,282 (+)NCBI
Celera959,742,231 - 59,747,758 (+)NCBICelera
Cytogenetic Map9q32NCBI
CTLA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2203,867,771 - 203,873,965 (+)EnsemblGRCh38hg38GRCh38
GRCh382203,867,771 - 203,873,965 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372204,732,494 - 204,738,688 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362204,440,754 - 204,446,928 (+)NCBINCBI36hg18NCBI36
Build 342204,558,016 - 204,564,189NCBI
Celera2198,487,330 - 198,493,462 (+)NCBI
Cytogenetic Map2q33.2NCBI
HuRef2196,579,809 - 196,585,939 (+)NCBIHuRef
CHM1_12204,739,066 - 204,745,196 (+)NCBICHM1_1
Ctla4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39160,948,184 - 60,954,991 (+)NCBIGRCm39mm39
GRCm39 Ensembl160,926,159 - 60,954,991 (+)Ensembl
GRCm38160,909,025 - 60,915,832 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl160,887,000 - 60,915,832 (+)EnsemblGRCm38mm10GRCm38
MGSCv37160,965,869 - 60,972,674 (+)NCBIGRCm37mm9NCBIm37
MGSCv36160,853,571 - 60,860,376 (+)NCBImm8
Celera161,424,040 - 61,430,841 (+)NCBICelera
Cytogenetic Map1C2NCBI
cM Map130.58NCBI
Ctla4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545711,028,698 - 11,073,460 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545711,028,707 - 11,034,898 (-)NCBIChiLan1.0ChiLan1.0
CTLA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B209,239,417 - 209,244,498 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B209,239,417 - 209,244,498 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B91,054,917 - 91,106,234 (+)NCBIMhudiblu_PPA_v0panPan3
CTLA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13712,647,712 - 12,653,874 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3712,634,563 - 12,653,874 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3713,530,863 - 13,537,025 (+)NCBI
ROS_Cfam_1.03712,584,278 - 12,590,425 (+)NCBI
UMICH_Zoey_3.13712,541,354 - 12,547,516 (+)NCBI
UNSW_CanFamBas_1.03712,504,724 - 12,510,894 (+)NCBI
UU_Cfam_GSD_1.03712,505,745 - 12,511,890 (+)NCBI
Ctla4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303160,849,279 - 160,854,996 (+)NCBI
SpeTri2.0NW_004936631484,356 - 489,643 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CTLA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15107,282,926 - 107,289,103 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115107,283,081 - 107,288,041 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215118,627,675 - 118,632,732 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CTLA4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11089,637,176 - 89,644,436 (+)NCBI
ChlSab1.1 Ensembl1089,638,314 - 89,642,344 (+)Ensembl
Ctla4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476512,449,205 - 12,454,324 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96081029882732466Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)96173092382890620Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92569237370692373Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93238513377385133Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
1598849Memor17Memory QTL 172.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)95488504176677636Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
1578659Tspe1Trichinella spiralis expulsion QTL 14.8parasite quantity (VT:0010441)logarithm of the intestinal adult Trichinella spiralis count (CMO:0002024)96675744471010122Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:61
Count of miRNA genes:60
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000013941
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 1
Low 3 7 18 22 3 4 7
Below cutoff 14 17 12 12 2 2 46 26 23 4 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000088183   ⟹   ENSRNOP00000069885
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl967,699,515 - 67,705,042 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091237   ⟹   ENSRNOP00000073071
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl967,699,379 - 67,706,065 (+)Ensembl
RefSeq Acc Id: NM_031674   ⟹   NP_113862
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2962,319,436 - 62,324,963 (+)NCBI
Rnor_6.0967,699,515 - 67,705,042 (+)NCBI
Rnor_5.0967,509,236 - 67,515,681 (+)NCBI
RGSC_v3.4959,495,773 - 59,501,300 (+)RGD
Celera959,742,231 - 59,747,758 (+)RGD
Sequence:
RefSeq Acc Id: XM_006245036   ⟹   XP_006245098
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2962,318,874 - 62,325,978 (+)NCBI
Rnor_6.0967,699,397 - 67,706,068 (+)NCBI
Rnor_5.0967,509,236 - 67,515,681 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_113862   ⟸   NM_031674
- Peptide Label: precursor
- UniProtKB: Q62859 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245098   ⟸   XM_006245036
- Peptide Label: isoform X1
- UniProtKB: G3V7D2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073071   ⟸   ENSRNOT00000091237
RefSeq Acc Id: ENSRNOP00000069885   ⟸   ENSRNOT00000088183
Protein Domains
Ig-like

Transcriptome

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


Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61975 AgrOrtholog
Ensembl Genes ENSRNOG00000054129 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069885 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073071 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000088183 UniProtKB/TrEMBL
  ENSRNOT00000091237 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro CTLA4 UniProtKB/TrEMBL
  CTLA4/CD28 UniProtKB/TrEMBL
  Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
KEGG Report rno:63835 UniProtKB/TrEMBL
NCBI Gene 63835 ENTREZGENE
PANTHER PTHR11494 UniProtKB/TrEMBL
  PTHR11494:SF8 UniProtKB/TrEMBL
Pfam V-set UniProtKB/TrEMBL
PharmGKB CTLA4 RGD
PhenoGen Ctla4 PhenoGen
PRINTS CTLANTIGEN4 UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
SMART IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A096MJE4_RAT UniProtKB/TrEMBL
  G3V7D2 ENTREZGENE, UniProtKB/TrEMBL
  Q62859 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Ctla4  cytotoxic T-lymphocyte-associated protein 4  Cd152  CD152 antigen  Symbol and Name updated 1299863 APPROVED
2002-06-10 Cd152  CD152 antigen      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_transcript alternatively spliced transcripts lack the exon 3 encoded transmembrane domain 634642