Pik3ca (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha) - Rat Genome Database

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Gene: Pik3ca (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha) Rattus norvegicus
Analyze
Symbol: Pik3ca
Name: phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha
RGD ID: 620916
Description: Enables 1-phosphatidylinositol-3-kinase activity. Involved in several processes, including positive regulation of smooth muscle cell proliferation; response to dexamethasone; and response to leucine. Part of phosphatidylinositol 3-kinase complex. Biomarker of autosomal recessive polycystic kidney disease. Human ortholog(s) of this gene implicated in several diseases, including CLOVES syndrome; Cowden syndrome; breast cancer (multiple); cutaneous Paget's disease; and gastrointestinal system cancer (multiple). Orthologous to human PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha); PARTICIPATES IN adenosine signaling pathway; altered phosphatidylinositol 3-kinase signaling pathway; altered phosphatidylinositol 3-kinase-Akt signaling pathway; INTERACTS WITH (+)-taxifolin; 2,2',4,4'-Tetrabromodiphenyl ether; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: MGC116320; p110alpha; phosphatidylinositol 3-kinase, catalytic, alpha polypeptide; phosphatidylinositol 4,5-bisphosphate 3-kinase 110 kDa catalytic subunit alpha; phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform; phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform; phosphoinositide-3-kinase catalytic alpha polypeptide; phosphoinositide-3-kinase, catalytic, alpha polypeptide; PI3-kinase subunit alpha; PI3K-alpha; PI3Kalpha; ptdIns-3-kinase subunit alpha; ptdIns-3-kinase subunit p110-alpha; serine/threonine protein kinase PIK3CA
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22115,175,275 - 115,249,034 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2115,174,984 - 115,249,032 (+)Ensembl
Rnor_6.02118,831,350 - 118,861,456 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2118,831,350 - 118,861,454 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02138,491,967 - 138,521,934 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42118,640,277 - 118,672,440 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12118,603,330 - 118,613,969 (+)NCBI
Celera2110,329,861 - 110,360,075 (+)NCBICelera
Cytogenetic Map2q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
adenocarcinoma  (ISO)
adenoid cystic carcinoma  (ISO)
adrenocortical carcinoma  (ISO)
adult hepatocellular carcinoma  (ISO)
Agenesis of Corpus Callosum  (ISO)
autosomal recessive polycystic kidney disease  (IEP)
Bannayan-Riley-Ruvalcaba syndrome  (ISO)
basal cell carcinoma  (ISO)
bladder urothelial carcinoma  (ISO)
Brain Neoplasms  (ISO)
breast adenocarcinoma  (ISO)
breast cancer  (ISO)
Breast Cancer, Familial  (ISO)
Breast Neoplasms  (ISO)
Cardiovascular Abnormalities  (ISO)
CLAPO Syndrome  (ISO)
CLOVES syndrome  (ISO)
colon adenocarcinoma  (ISO)
colon cancer  (ISO)
colon carcinoma  (ISO)
colorectal cancer  (ISO)
colorectal carcinoma  (ISO)
Colorectal Neoplasms  (ISO)
complex cortical dysplasia with other brain malformations  (ISO)
congenital heart disease  (ISO)
Cowden syndrome  (ISO)
Cowden syndrome 5  (ISO)
Cowden-Like Syndrome  (ISO)
Currarino syndrome  (ISO)
cutaneous Paget's disease  (ISO)
diaphragmatic eventration  (ISO)
diffuse large B-cell lymphoma  (ISO)
disease of cellular proliferation  (ISO)
Disease Progression  (ISO)
endometrial carcinoma  (ISO)
Endometrial Neoplasms  (ISO)
epidermal nevus  (ISO)
esophageal carcinoma  (ISO)
esophagus adenocarcinoma  (ISO)
estrogen-receptor positive breast cancer  (ISO)
Facial Asymmetry  (ISO)
familial multiple nevi flammei  (ISO)
gallbladder cancer  (ISO)
gallbladder carcinoma  (ISO)
gastric adenocarcinoma  (ISO)
Gastrointestinal Neoplasms  (ISO)
genetic disease  (ISO)
glioblastoma  (ISO)
glycogen storage disease II  (ISO)
Growth Disorders  (ISO)
Head and Neck Neoplasms  (ISO)
head and neck squamous cell carcinoma  (ISO)
Hemimegalencephaly  (ISO)
hepatocellular carcinoma  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
high grade glioma  (ISO)
Hyperplasia  (ISO)
Hypertelorism  (ISO)
Klippel-Trenaunay syndrome  (ISO)
liver cancer  (ISO)
lung adenocarcinoma  (ISO)
lung cancer  (ISO,ISS)
lung carcinoma  (ISO)
Lung Neoplasms  (ISO)
lung non-small cell carcinoma  (ISO)
lung oat cell carcinoma  (ISO)
lung small cell carcinoma  (ISO)
lung squamous cell carcinoma  (ISO)
Lymphatic Metastasis  (ISO)
Macrocephaly  (ISO)
medulloblastoma  (ISO)
Megalencephaly - Cutis Marmorata Telangiectatica Congenita  (ISO)
Megalencephaly-Polymicrogyria-Polydactyly-Hydrocephalus Syndrome  (ISO)
Megalodactyly  (ISO)
melanoma  (ISO)
Mouth Neoplasms  (ISO)
multiple myeloma  (ISO)
Nasopharyngeal Neoplasms  (ISO)
Neoplasm Metastasis  (ISO)
neuroblastoma  (ISO)
non-Hodgkin lymphoma  (ISO)
ovarian cancer  (ISO)
Ovarian Neoplasms  (ISO)
ovarian serous cystadenocarcinoma  (ISO)
ovary epithelial cancer  (ISO)
pancreatic adenocarcinoma  (ISO)
papillary renal cell carcinoma  (ISO)
Paraproteinemias  (ISO)
Penile Neoplasms  (ISO)
plasma cell neoplasm  (ISO)
plasmacytoma  (ISO)
polycystic kidney disease  (ISO)
prostate adenocarcinoma  (ISO)
prostate cancer  (ISO)
Prostatic Neoplasms  (ISO)
PTEN hamartoma tumor syndrome  (ISO)
rectal benign neoplasm  (ISO)
renal cell carcinoma  (ISO)
Renal Cell Carcinoma 1  (ISO)
sarcoma  (ISO)
seborrheic keratosis  (ISO)
skin melanoma  (ISO)
Sporadic Papillary Renal Cell Carcinoma  (ISO)
squamous cell carcinoma  (ISO)
stomach cancer  (ISO,ISS)
Stomach Neoplasms  (ISO)
Stroke  (ISO)
Thyroid Neoplasms  (ISO)
transitional cell carcinoma  (ISO)
uterine cancer  (ISO)
uterine carcinosarcoma  (ISO)
Uterine Cervical Neoplasms  (ISO)
Vascular Malformations  (ISO)
Ventricular Dysfunction, Left  (ISO)
Weight Gain  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-taxifolin  (EXP)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,5-hexanedione  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
acrylamide  (EXP,ISO)
all-trans-retinoic acid  (EXP)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsenous acid  (ISO)
atorvastatin calcium  (ISO)
ATP  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
cadmium dichloride  (EXP)
calcitriol  (ISO)
cantharidin  (ISO)
carbamazepine  (ISO)
carvacrol  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
dactolisib  (ISO)
deguelin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP,ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ergothioneine  (EXP)
erlotinib hydrochloride  (ISO)
ethanol  (EXP)
geldanamycin  (ISO)
ginsenoside Rg1  (ISO)
hyaluronic acid  (ISO)
hydrogen peroxide  (ISO)
idelalisib  (ISO)
iron atom  (EXP)
iron dextran  (EXP)
iron(0)  (EXP)
ivermectin  (ISO)
lithium chloride  (ISO)
LY294002  (ISO)
metformin  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylmercury(1+)  (ISO)
naringin  (ISO)
niclosamide  (ISO)
nicotine  (ISO)
nitric oxide  (ISO)
nitrofen  (EXP)
ochratoxin A  (ISO)
oleanolic acid  (ISO)
omacetaxine mepesuccinate  (ISO)
orotic acid  (ISO)
ozone  (EXP)
paracetamol  (ISO)
perfluorononanoic acid  (EXP)
perfluorooctanoic acid  (EXP)
pioglitazone  (ISO)
pyrvinium  (ISO)
quercetin  (ISO)
quercetin 3-O-beta-D-glucofuranoside  (ISO)
quercetin 3-O-beta-D-glucopyranoside  (ISO)
resveratrol  (ISO)
rimonabant  (ISO)
SB 431542  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sorafenib  (ISO)
succimer  (ISO)
sucrose  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tetracycline  (ISO)
thalidomide  (ISO)
thimerosal  (ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
wortmannin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin cytoskeleton organization  (ISO)
activation of protein kinase activity  (IEA)
adipose tissue development  (ISO)
angiogenesis  (IEA)
cardiac muscle cell contraction  (ISO)
cell migration  (IBA)
cellular response to glucose stimulus  (ISO)
cellular response to hydrostatic pressure  (ISO)
energy homeostasis  (ISO)
glucose metabolic process  (ISO)
hypomethylation of CpG island  (ISO)
liver development  (ISO)
negative regulation of actin filament depolymerization  (ISO)
negative regulation of anoikis  (ISO)
negative regulation of fibroblast apoptotic process  (ISO)
negative regulation of gene expression  (IGI)
negative regulation of neuron apoptotic process  (ISO)
phagocytosis  (IEA)
phosphatidylinositol 3-kinase signaling  (IBA,ISO)
phosphatidylinositol phosphate biosynthetic process  (IBA,IDA)
phosphatidylinositol-3-phosphate biosynthetic process  (IBA)
phosphatidylinositol-mediated signaling  (IBA)
phosphorylation  (ISO)
positive regulation of peptidyl-serine phosphorylation  (ISO)
positive regulation of protein kinase B signaling  (ISO)
positive regulation of smooth muscle cell proliferation  (IMP)
protein kinase B signaling  (ISO)
protein phosphorylation  (IEA)
regulation of actin filament organization  (ISO)
regulation of cellular respiration  (ISO)
regulation of gene expression  (ISO)
regulation of genetic imprinting  (ISO)
regulation of multicellular organism growth  (ISO)
regulation of protein phosphorylation  (ISO)
relaxation of cardiac muscle  (ISO)
response to activity  (IEP)
response to butyrate  (IEP)
response to dexamethasone  (IEP)
response to leucine  (IEP)
response to muscle inactivity  (IEP)
response to muscle stretch  (ISO)
vascular endothelial growth factor signaling pathway  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
acute myeloid leukemia pathway  (IEA)
adenosine signaling pathway  (ISO)
aldosterone signaling pathway  (IEA)
altered phosphatidylinositol 3-kinase signaling pathway  (ISO)
altered phosphatidylinositol 3-kinase-Akt signaling pathway  (ISO)
apoptotic cell death pathway  (IEA)
B cell receptor signaling pathway  (IEA)
ceramide signaling pathway  (IEA)
Chagas disease pathway  (IEA)
chemokine mediated signaling pathway  (IEA)
chronic myeloid leukemia pathway  (IEA)
colorectal cancer pathway  (IEA)
E-cadherin signaling pathway  (ISO)
endometrial cancer pathway  (IEA,ISO)
Entamoebiasis pathway  (IEA)
ephrin - ephrin receptor bidirectional signaling axis  (ISO)
epidermal growth factor/neuregulin signaling pathway  (IEA,ISO)
FasL mediated signaling pathway  (ISO)
Fc epsilon receptor mediated signaling pathway  (IEA,ISO)
Fc gamma receptor mediated signaling pathway  (IEA)
fibroblast growth factor signaling pathway  (ISO)
glioma pathway  (IEA)
granulocyte-macrophage colony-stimulating factor signaling pathway  (ISO)
Hedgehog signaling pathway  (ISO)
hepatitis C pathway  (IEA)
influenza A pathway  (IEA)
inositol metabolic pathway  (ISO)
inositol phosphate metabolic pathway  (IEA)
insulin signaling pathway  (IEA,ISO)
insulin-like growth factor signaling pathway  (ISO)
interleukin-1 signaling pathway  (ISO)
interleukin-2 signaling pathway  (ISO)
interleukin-23 signaling pathway  (ISO)
interleukin-3 signaling pathway  (ISO)
interleukin-4 signaling pathway  (ISO)
interleukin-5 signaling pathway  (ISO)
interleukin-6 signaling pathway  (ISO)
Jak-Stat signaling pathway  (IEA)
measles pathway  (IEA)
melanoma pathway  (IEA)
mTOR signaling pathway  (IEA)
N-cadherin signaling pathway  (ISO)
neurotrophic factor signaling pathway  (IEA)
non-small cell lung carcinoma pathway  (IEA,ISO)
nuclear factor kappa B signaling pathway  (ISO)
pancreatic cancer pathway  (IEA)
phosphatidylinositol 3-kinase class I signaling pathway  (ISO)
phosphatidylinositol 3-kinase signaling pathway  (IEA)
phosphatidylinositol 3-kinase-Akt signaling pathway  (ISO)
phosphoinositide metabolic pathway  (ISO)
platelet-derived growth factor signaling pathway  (ISO)
prostate cancer pathway  (IEA,ISO)
Reelin signaling pathway  (ISO)
renal cell carcinoma pathway  (IEA)
small cell lung carcinoma pathway  (IEA)
T cell receptor signaling pathway  (IEA)
Toll-like receptor signaling pathway  (IEA)
toxoplasmosis pathway  (IEA)
Trail mediated signaling pathway  (ISO)
type 2 diabetes mellitus pathway  (IEA)
type II interferon signaling pathway  (ISO)
vascular endothelial growth factor signaling pathway  (IEA,ISO)

References

References - curated
1. Bansal N, etal., Cancer Control. 2009 Jan;16(1):8-13.
2. Baptista IL, etal., PLoS One. 2013 Oct 4;8(10):e76752. doi: 10.1371/journal.pone.0076752. eCollection 2013.
3. Barbieri CE, etal., Eur Urol. 2013 Oct;64(4):567-76. doi: 10.1016/j.eururo.2013.05.029. Epub 2013 May 18.
4. Chen J, etal., Physiol Rep. 2017 Sep;5(18). pii: 5/18/e13441. doi: 10.14814/phy2.13441.
5. Dong M, etal., Hum Pathol. 2016 Jul;53:25-34. doi: 10.1016/j.humpath.2016.02.007. Epub 2016 Mar 4.
6. Engelman JA, etal., Nat Rev Genet. 2006 Aug;7(8):606-19.
7. Franke TF Oncogene. 2008 Oct 27;27(50):6473-88.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Guo XN, etal., Cancer Res. 2007 Jun 15;67(12):5851-8.
11. Hare LM, etal., Dev Biol. 2015 Aug 1;404(1):14-26. doi: 10.1016/j.ydbio.2015.04.022. Epub 2015 May 7.
12. Hers I, etal., Biochem J 2002 Dec 15;368(Pt 3):875-84.
13. Hirsch E, etal., J Endocrinol. 2007 Aug;194(2):243-56.
14. Kang Z, etal., Mod Pathol. 2012 Aug;25(8):1160-8. doi: 10.1038/modpathol.2012.65. Epub 2012 Apr 20.
15. Kaplan-Albuquerque N, etal., J Biol Chem. 2003 Oct 10;278(41):39830-8. Epub 2003 Jul 25.
16. Kim DC, etal., APMIS. 2014 Oct;122(10):1001-6. doi: 10.1111/apm.12245. Epub 2014 Mar 28.
17. Kinross KM, etal., J Clin Invest. 2012 Feb;122(2):553-7. doi: 10.1172/JCI59309. Epub 2012 Jan 3.
18. Li HG, etal., Int J Clin Exp Pathol. 2015 Nov 1;8(11):15255-9. eCollection 2015.
19. Liang L, etal., Zhonghua Wai Ke Za Zhi. 2012 Nov;50(11):1007-10.
20. Lindhurst MJ, etal., Nat Genet. 2012 Jun 24;44(8):928-33. doi: 10.1038/ng.2332.
21. Ma Z, etal., Eur J Appl Physiol. 2013 Oct;113(10):2473-86. doi: 10.1007/s00421-013-2685-9. Epub 2013 Jun 28.
22. MGD data from the GO Consortium
23. Miyaki M, etal., Int J Cancer. 2007 Oct 1;121(7):1627-30. doi: 10.1002/ijc.22829.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. OMIM Disease Annotation Pipeline
26. Pao W and Girard N, Lancet Oncol. 2011 Feb;12(2):175-80.
27. Pipeline to import KEGG annotations from KEGG into RGD
28. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
29. Pipeline to import SMPDB annotations from SMPDB into RGD
30. Ren XS, etal., PLoS One. 2014 Jan 30;9(1):e87660. doi: 10.1371/journal.pone.0087660. eCollection 2014.
31. RGD automated data pipeline
32. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
33. RGD automated import pipeline for gene-chemical interactions
34. Sanders HR and Albitar M, Cancer Genet Cytogenet. 2010 Nov;203(1):7-15.
35. Seo AN, etal., Anticancer Res. 2019 Apr;39(4):2145-2154. doi: 10.21873/anticanres.13328.
36. Slattery ML, etal., Carcinogenesis. 2010 Sep;31(9):1604-11. Epub 2010 Jul 9.
37. Takeshita T, etal., Oncotarget. 2017 Jun 14;8(32):52142-52155. doi: 10.18632/oncotarget.18479. eCollection 2017 Aug 8.
38. Tanaka Y, etal., Oncogene. 2006 May 11;25(20):2950-2. doi: 10.1038/sj.onc.1209311.
39. Vantler M, etal., Arterioscler Thromb Vasc Biol. 2015 Jun;35(6):1434-44. doi: 10.1161/ATVBAHA.114.304887. Epub 2015 Apr 23.
40. Vargiu P, etal., Oncogene 2004 Jan 15;23(2):559-68.
41. Wen F, etal., Int J Clin Exp Pathol. 2014 Oct 15;7(11):8295-303. eCollection 2014.
42. Zhang L, etal., Cancer Res 2003 Jul 15;63(14):4225-31.
43. Zhang XF, etal., Hepatology. 2010 Sep;52(3):954-65. doi: 10.1002/hep.23747.
44. Zhou H, etal., Mol Med Rep. 2019 Mar;19(3):2125-2136. doi: 10.3892/mmr.2019.9886. Epub 2019 Jan 22.
Additional References at PubMed
PMID:2174051   PMID:7542745   PMID:8628286   PMID:8889548   PMID:10860857   PMID:11596118   PMID:12477932   PMID:12486171   PMID:12904469   PMID:14657280   PMID:15192701   PMID:16625210  
PMID:17475835   PMID:19202327   PMID:20514400   PMID:21047779   PMID:21127054   PMID:21736902   PMID:22402981   PMID:24006492   PMID:24577313   PMID:24691033   PMID:25327288   PMID:27322831  
PMID:27372651   PMID:27991911  


Genomics

Comparative Map Data
Pik3ca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22115,175,275 - 115,249,034 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2115,174,984 - 115,249,032 (+)Ensembl
Rnor_6.02118,831,350 - 118,861,456 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2118,831,350 - 118,861,454 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02138,491,967 - 138,521,934 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42118,640,277 - 118,672,440 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12118,603,330 - 118,613,969 (+)NCBI
Celera2110,329,861 - 110,360,075 (+)NCBICelera
Cytogenetic Map2q24NCBI
PIK3CA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3179,148,114 - 179,240,093 (+)EnsemblGRCh38hg38GRCh38
GRCh383179,148,114 - 179,240,093 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373178,866,145 - 178,957,881 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363180,349,005 - 180,435,194 (+)NCBINCBI36hg18NCBI36
Build 343180,349,012 - 180,435,197NCBI
Celera3177,295,797 - 177,383,366 (+)NCBI
Cytogenetic Map3q26.32NCBI
HuRef3176,269,843 - 176,355,772 (+)NCBIHuRef
CHM1_13178,829,221 - 178,915,414 (+)NCBICHM1_1
Pik3ca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39332,451,203 - 32,520,256 (+)NCBIGRCm39mm39
GRCm39 Ensembl332,451,820 - 32,522,635 (+)Ensembl
GRCm38332,397,065 - 32,466,112 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl332,397,671 - 32,468,486 (+)EnsemblGRCm38mm10GRCm38
MGSCv37332,335,073 - 32,367,408 (+)NCBIGRCm37mm9NCBIm37
MGSCv36332,627,755 - 32,654,380 (+)NCBImm8
Celera332,346,082 - 32,378,426 (+)NCBICelera
Cytogenetic Map3A3NCBI
cM Map315.7NCBI
Pik3ca
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554208,356,353 - 8,427,024 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554208,355,415 - 8,427,024 (+)NCBIChiLan1.0ChiLan1.0
PIK3CA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13184,355,789 - 184,441,997 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3184,355,785 - 184,441,977 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03176,182,765 - 176,272,024 (+)NCBIMhudiblu_PPA_v0panPan3
PIK3CA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13412,600,140 - 12,681,905 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3412,600,233 - 12,675,910 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3416,743,641 - 16,822,678 (+)NCBI
ROS_Cfam_1.03412,496,918 - 12,576,076 (+)NCBI
UMICH_Zoey_3.13412,551,928 - 12,630,858 (+)NCBI
UNSW_CanFamBas_1.03412,531,843 - 12,610,836 (+)NCBI
UU_Cfam_GSD_1.03412,771,120 - 12,850,124 (+)NCBI
Pik3ca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602109,269,676 - 109,296,792 (+)NCBI
SpeTri2.0NW_0049365663,924,013 - 3,951,052 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PIK3CA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13117,180,544 - 117,277,232 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113117,193,935 - 117,282,151 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213126,401,142 - 126,461,414 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PIK3CA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11510,218,034 - 10,304,874 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1510,218,805 - 10,294,316 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606319,096,074 - 19,187,036 (-)NCBIVero_WHO_p1.0
Pik3ca
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473056,895,065 - 56,970,563 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
BF399071  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22115,249,365 - 115,249,506 (+)MAPPERmRatBN7.2
Rnor_6.02118,861,788 - 118,861,928NCBIRnor6.0
Rnor_5.02138,522,266 - 138,522,406UniSTSRnor5.0
RGSC_v3.42118,672,772 - 118,672,912UniSTSRGSC3.4
Celera2110,360,407 - 110,360,547UniSTS
RH 3.4 Map2692.6UniSTS
Cytogenetic Map2q25UniSTS
AA963575  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22115,248,821 - 115,248,918 (+)MAPPERmRatBN7.2
Rnor_6.02118,861,244 - 118,861,340NCBIRnor6.0
Rnor_5.02138,521,722 - 138,521,818UniSTSRnor5.0
RGSC_v3.42118,672,228 - 118,672,324UniSTSRGSC3.4
Celera2110,359,863 - 110,359,959UniSTS
RH 3.4 Map2690.6UniSTS
Cytogenetic Map2q25UniSTS
RH138898  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22115,247,075 - 115,247,279 (+)MAPPERmRatBN7.2
Rnor_6.02118,859,523 - 118,859,726NCBIRnor6.0
Rnor_5.02138,520,001 - 138,520,204UniSTSRnor5.0
RGSC_v3.42118,670,483 - 118,670,686UniSTSRGSC3.4
Celera2110,358,118 - 110,358,321UniSTS
RH 3.4 Map2692.6UniSTS
Cytogenetic Map2q25UniSTS
RH141610  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22115,246,391 - 115,246,594 (-)MAPPERmRatBN7.2
mRatBN7.22115,246,391 - 115,246,594 (+)MAPPERmRatBN7.2
Rnor_6.02118,858,839 - 118,859,041NCBIRnor6.0
Rnor_6.0X23,242,695 - 23,242,897NCBIRnor6.0
Rnor_5.02138,519,317 - 138,519,519UniSTSRnor5.0
Rnor_5.0X23,654,956 - 23,655,158UniSTSRnor5.0
RGSC_v3.4X41,988,145 - 41,988,347UniSTSRGSC3.4
RGSC_v3.42118,669,799 - 118,670,001UniSTSRGSC3.4
Celera2110,357,434 - 110,357,636UniSTS
CeleraX21,844,948 - 21,845,150UniSTS
Cytogenetic MapXq21UniSTS
Cytogenetic Map2q25UniSTS
UniSTS:257082  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X23,245,316 - 23,245,841NCBIRnor6.0
Rnor_5.0X23,657,577 - 23,658,102UniSTSRnor5.0
RGSC_v3.4X41,990,766 - 41,991,291UniSTSRGSC3.4
CeleraX21,847,568 - 21,848,093UniSTS
Cytogenetic MapXq21UniSTS
Cytogenetic Map2q25UniSTS
UniSTS:257083  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X23,244,005 - 23,244,413NCBIRnor6.0
Rnor_5.0X23,656,266 - 23,656,674UniSTSRnor5.0
RGSC_v3.4X41,989,455 - 41,989,863UniSTSRGSC3.4
CeleraX21,846,257 - 21,846,665UniSTS
Cytogenetic MapXq21UniSTS
Cytogenetic Map2q25UniSTS
UniSTS:257081  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22115,218,994 - 115,219,253 (-)MAPPERmRatBN7.2
mRatBN7.22115,218,994 - 115,219,253 (+)MAPPERmRatBN7.2
Rnor_6.0X23,246,386 - 23,246,644NCBIRnor6.0
Rnor_6.02118,831,425 - 118,831,683NCBIRnor6.0
Rnor_5.0X23,658,647 - 23,658,905UniSTSRnor5.0
Rnor_5.02138,492,042 - 138,492,300UniSTSRnor5.0
Celera2110,329,936 - 110,330,194UniSTS
CeleraX21,848,638 - 21,848,896UniSTS
Cytogenetic Map2q25UniSTS
Cytogenetic MapXq21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1558648Smcn1Smooth muscle cell number QTL 10.039blood vessel smooth muscle cell quantity (VT:0010525)aorta smooth muscle cell count per unit vessel length (CMO:0001646)259134147127460910Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)259324377141596857Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1558653Prcr1Prostate cancer resistance QTL 15prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)272532993157142209Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)276539322150540526Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)278665616143657569Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
61392Bp6Blood pressure QTL 67arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)280270434125270434Rat
1598865Bp296Blood pressure QTL 2962.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)281018907126018907Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
1578772Stresp14Stress response QTL 1450.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)282345893130923501Rat
7207808Bmd89Bone mineral density QTL 894.1femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)288862519133862519Rat
2300165Bmd49Bone mineral density QTL 494.80.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)288862519133862519Rat
2300170Bmd45Bone mineral density QTL 4512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)288862519133862519Rat
2300185Bmd46Bone mineral density QTL 468.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)288862519133862519Rat
1598862Glom9Glomerulus QTL 93.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)292337601137337601Rat
1598863Cm65Cardiac mass QTL 652.3heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)292337601137337601Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2102803808147803808Rat
8662836Vetf8Vascular elastic tissue fragility QTL 80.66thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2104559726149559726Rat
1581552Pur12Proteinuria QTL 125.190.0009total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)2112103657148076632Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1354594Despr10Despair related QTL 100.00000249locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)2114654253159654253Rat
1359035Bp276Blood pressure QTL 276arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527143657569Rat
1359035Bp276Blood pressure QTL 276arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527143657569Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:612
Count of miRNA genes:302
Interacting mature miRNAs:373
Transcripts:ENSRNOT00000014527
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 36 39 23 19 23 8 10 74 35 36 11 8
Low 7 18 18 18 1 5
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_133399 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039101610 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF395897 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC086516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC099154 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BP500486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ203660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB793501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK366194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK366305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR754046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DV722574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DV728106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DY314099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM035395 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM096453 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000083720   ⟹   ENSRNOP00000072496
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2115,174,984 - 115,249,032 (+)Ensembl
Rnor_6.0 Ensembl2118,831,350 - 118,861,454 (+)Ensembl
RefSeq Acc Id: NM_133399   ⟹   NP_596890
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22115,218,920 - 115,249,034 (+)NCBI
Rnor_6.02118,831,350 - 118,861,456 (+)NCBI
Rnor_5.02138,491,967 - 138,521,934 (+)NCBI
Celera2110,329,861 - 110,360,075 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039101610   ⟹   XP_038957538
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22115,175,275 - 115,249,003 (+)NCBI
Protein Sequences
Protein RefSeqs NP_596890 (Get FASTA)   NCBI Sequence Viewer  
  XP_038957538 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A0A0G2K344 (Get FASTA)   NCBI Sequence Viewer  
  AAK83379 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_596890   ⟸   NM_133399
- UniProtKB: A0A0G2K344 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072496   ⟸   ENSRNOT00000083720
RefSeq Acc Id: XP_038957538   ⟸   XM_039101610
- Peptide Label: isoform X1
Protein Domains
C2 PI3K-type   PI3K-ABD   PI3K-RBD   PI3K/PI4K   PIK helical

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 (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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
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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)
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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)
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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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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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)
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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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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