Pdgfra (platelet derived growth factor receptor alpha) - Rat Genome Database

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Gene: Pdgfra (platelet derived growth factor receptor alpha) Rattus norvegicus
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Symbol: Pdgfra
Name: platelet derived growth factor receptor alpha
RGD ID: 3284
Description: Enables phosphatidylinositol 3-kinase binding activity and platelet-derived growth factor alpha-receptor activity. Involved in several processes, including animal organ development; cellular response to interleukin-1; and positive regulation of branching involved in lung morphogenesis. Located in several cellular components, including axon; nucleus; and plasma membrane. Used to study middle cerebral artery infarction. Biomarker of chronic ulcer of skin; hypertension; oligohydramnios; pulmonary fibrosis; and sciatic neuropathy. Human ortholog(s) of this gene implicated in hematologic cancer (multiple); hypereosinophilic syndrome; and pancreatic cancer. Orthologous to human PDGFRA (platelet derived growth factor receptor alpha); PARTICIPATES IN platelet-derived growth factor signaling pathway; calcium/calcium-mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alpha platelet-derived growth factor receptor; alpha-type platelet-derived growth factor receptor; APDGFR; CD140 antigen-like family member A; LOC102554024; PDGF-R-alpha; PDGFACE; PDGFR-alpha; platelet derived growth factor receptor, alpha polypeptide; platelet-derived growth factor alpha receptor; Platelet-derived growth factor receptor alpha; platelet-derived growth factor receptor alpha-like
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
mRatBN7.21433,005,838 - 33,054,347 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1433,005,839 - 33,054,335 (-)Ensembl
Rnor_6.01435,527,926 - 35,581,130 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1435,527,927 - 35,581,031 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01435,356,434 - 35,409,311 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41435,369,422 - 35,418,126 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11435,369,672 - 35,418,126 (-)NCBI
Celera1432,273,077 - 32,324,887 (-)NCBICelera
RH 3.4 Map14432.47RGD
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
B-lymphoblastic leukemia/lymphoma  (ISO)
Brain Injuries  (IEP)
brain stem glioma  (ISO)
breast carcinoma  (ISO)
Chronic Allograft Nephropathy  (IEP)
chronic ulcer of skin  (IEP)
cleft palate  (ISO)
colon carcinoma  (ISO)
congenital diaphragmatic hernia  (ISS)
congestive heart failure  (ISO)
Craniofacial Abnormalities  (ISO)
craniopharyngioma  (ISO)
Endometrioid Carcinomas  (ISO)
Eosinophilia  (ISO)
Experimental Autoimmune Encephalomyelitis  (IDA)
Experimental Colitis  (IEP)
Experimental Liver Cirrhosis  (IDA,ISO)
Fetal Death  (ISO)
gastrointestinal stromal tumor  (ISO)
Germ Cell and Embryonal Neoplasms  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
hypereosinophilic syndrome  (ISO)
Hyperoxia  (IEP)
hypertension  (IEP)
in situ carcinoma  (ISO)
isolated cleft palate  (ISO)
Kidney Reperfusion Injury  (IEP)
leukemia  (ISO)
Leydig cell tumor  (ISO)
lung disease  (ISO)
lung squamous cell carcinoma  (ISO)
medulloblastoma  (ISO)
melanoma  (ISO)
mesenchymal chondrosarcoma  (ISO)
middle cerebral artery infarction  (IDA)
Multiple Polyps and Recurrent Inflammatory Fibroid, Gastrointestinal  (ISO)
myeloid leukemia  (ISO)
myeloid sarcoma  (ISO)
Neointima  (IEP)
oligohydramnios  (IEP)
Ovarian Neoplasms  (ISO)
pancreatic cancer  (ISO)
Pdgfra-Associated Chronic Eosinophilic Leukemia  (ISO)
prostate adenocarcinoma  (ISO)
pulmonary fibrosis  (IEP)
renal cell carcinoma  (ISO)
Respiratory System Abnormalities  (ISO)
sciatic neuropathy  (IEP)
seminoma  (ISO)
spina bifida  (ISO)
Stroke  (IEP)
T-cell acute lymphoblastic leukemia  (ISO)
Uterine Neoplasms  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,2-(2-Chlorophenyl-4'-chlorophenyl)-1,1-dichloroethene  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
carbofuran  (EXP)
carbon nanotube  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (EXP)
Cuprizon  (ISO)
cyclosporin A  (ISO)
DDD  (ISO)
DDE  (ISO)
DDT  (EXP)
dermatan sulfate  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP)
dieldrin  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (EXP,ISO)
disodium selenite  (EXP,ISO)
diuron  (EXP)
divanadium pentaoxide  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
folic acid  (ISO)
formaldehyde  (EXP,ISO)
fulvestrant  (ISO)
furan  (EXP)
furosemide  (EXP)
genistein  (EXP,ISO)
heparin  (ISO)
hydrogen peroxide  (EXP,ISO)
indometacin  (EXP,ISO)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
leflunomide  (EXP)
lovastatin  (EXP)
maneb  (ISO)
masitinib  (ISO)
melatonin  (ISO)
methamphetamine  (EXP)
methylisothiazolinone  (ISO)
microcystin-LR  (ISO)
mifepristone  (EXP)
monosodium L-glutamate  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (EXP)
nitrofen  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
ochratoxin A  (EXP)
okadaic acid  (ISO)
oxycodone  (EXP)
p-toluidine  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
PCB138  (ISO)
pentanal  (ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (EXP,ISO)
ponatinib  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
protein kinase inhibitor  (ISO)
quercetin  (EXP)
raloxifene  (ISO)
SB 431542  (ISO)
serpentine asbestos  (EXP,ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium chloride  (ISO)
sorafenib  (ISO)
streptozocin  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vismodegib  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adrenal gland development  (IEA,ISO)
aging  (IEP)
anatomical structure morphogenesis  (ISO)
animal organ morphogenesis  (ISO)
brain development  (IEP)
cardiac myofibril assembly  (IEA,ISO,ISS)
cell chemotaxis  (IEA,ISO,ISS)
cell migration  (ISO)
cellular response to amino acid stimulus  (IEA,ISO)
cellular response to fibroblast growth factor stimulus  (IEP)
cellular response to interleukin-1  (IEP)
cellular response to reactive oxygen species  (IEA,ISO)
embryonic cranial skeleton morphogenesis  (IBA,IEA,ISO,ISS)
embryonic digestive tract morphogenesis  (IEA,ISO,ISS)
embryonic skeletal system morphogenesis  (ISS)
estrogen metabolic process  (IEA,ISO)
extracellular matrix organization  (IEA,ISO)
face morphogenesis  (IEA,ISO)
female gonad development  (ISO)
hematopoietic progenitor cell differentiation  (IEA,ISO)
in utero embryonic development  (IEA,ISO)
inner ear development  (IEP)
Leydig cell differentiation  (IEA,ISO)
lung development  (IEA,ISO)
lung growth  (IMP)
luteinization  (IEA,ISO,ISS)
male genitalia development  (IEA,ISO)
male gonad development  (IEP)
metanephric glomerular capillary formation  (IEA,ISO,ISS)
negative regulation of platelet activation  (IEA,ISO,ISS)
odontogenesis of dentin-containing tooth  (IEA,ISO)
peptidyl-tyrosine phosphorylation  (IEA,ISO,ISS)
phosphatidylinositol-mediated signaling  (IEA,ISO,ISS)
platelet aggregation  (IEA,ISO,ISS)
platelet-derived growth factor receptor signaling pathway  (ISO,ISS)
platelet-derived growth factor receptor-alpha signaling pathway  (IEA,ISO)
positive regulation of branching involved in lung morphogenesis  (IMP)
positive regulation of cell migration  (IEA,ISO,ISS)
positive regulation of cell population proliferation  (IMP,ISO,ISS)
positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway  (IEA,ISO)
positive regulation of cytosolic calcium ion concentration  (IEA,ISO,ISS)
positive regulation of ERK1 and ERK2 cascade  (IEA,ISO,ISS)
positive regulation of fibroblast proliferation  (IEA,ISO,ISS)
positive regulation of kinase activity  (IBA)
positive regulation of peptidyl-tyrosine phosphorylation  (IDA)
positive regulation of phosphatidylinositol 3-kinase activity  (IEA,ISO,ISS)
positive regulation of phospholipase C activity  (IEA,ISO)
protein autophosphorylation  (IEA,ISO,ISS)
regulation of chemotaxis  (IEA,ISO)
regulation of mesenchymal stem cell differentiation  (IEA,ISO,ISS)
response to cytokine  (IEP)
response to estradiol  (IEP)
response to estrogen  (IEP)
response to formaldehyde  (IEP)
response to hormone  (IEP)
response to hyperoxia  (IEP)
response to inorganic substance  (IEP)
response to organic substance  (IEP)
retina vasculature development in camera-type eye  (IEA,ISO,ISS)
roof of mouth development  (IEA,ISO)
signal transduction involved in regulation of gene expression  (IEA,ISO)
skeletal system morphogenesis  (ISO)
transmembrane receptor protein tyrosine kinase signaling pathway  (IBA)
white fat cell differentiation  (IEA,ISO)
wound healing  (IEP,ISO)

Cellular Component

References

References - curated
1. Abe H, etal., Biochem Biophys Res Commun. 2007 May 11;356(3):610-5. Epub 2007 Mar 15.
2. Abe J, etal., Circulation. 1997 Sep 16;96(6):1906-13.
3. Adams SF, etal., Gynecol Oncol. 2007 Mar;104(3):524-8. Epub 2006 Oct 17.
4. Arefi M, etal., Int J Hematol. 2012 Sep;96(3):320-6. doi: 10.1007/s12185-012-1141-7. Epub 2012 Jul 18.
5. Ataca P, etal., World J Gastroenterol. 2013 Oct 7;19(37):6237-44. doi: 10.3748/wjg.v19.i37.6237.
6. Basciani S, etal., J Clin Endocrinol Metab. 2002 May;87(5):2310-9.
7. Becher OJ, etal., Cancer Res. 2010 Mar 15;70(6):2548-57. doi: 10.1158/0008-5472.CAN-09-2503. Epub 2010 Mar 2.
8. Biswas SK, etal., Invest Ophthalmol Vis Sci. 2008 Aug;49(8):3687-98. Epub 2008 Apr 17.
9. Bonello MR and Khachigian LM, J Biol Chem. 2004 Jan 23;279(4):2377-82. Epub 2003 Oct 30.
10. Bonner JC, etal., Am J Physiol. 1998 Jan;274(1 Pt 1):L72-80.
11. Breitkopf K, etal., Cytokine. 2005 Sep 7;31(5):349-57.
12. Cao WH, etal., Zhonghua Shao Shang Za Zhi. 2005 Oct;21(5):359-62.
13. Chen CM, etal., Neonatology. 2007;92(3):187-93. Epub 2007 May 21.
14. Chen QP and Giannobile WV, Am J Physiol Cell Physiol. 2002 Mar;282(3):C538-44.
15. Cook JL, etal., Brain Res Mol Brain Res. 1998 Mar 30;55(1):9-19.
16. Cools J, etal., Blood. 2004 Apr 1;103(7):2802-5. Epub 2003 Nov 20.
17. Cools J, etal., N Engl J Med. 2003 Mar 27;348(13):1201-14.
18. Dorrance AM, etal., Am J Physiol Regul Integr Comp Physiol. 2007 Jan;292(1):R415-22. Epub 2006 Aug 17.
19. Ebert M, etal., Int J Cancer. 1995 Sep 4;62(5):529-35.
20. Elling C, etal., Blood. 2011 Mar 10;117(10):2935-43. doi: 10.1182/blood-2010-05-286757. Epub 2011 Jan 11.
21. Fernandez M, etal., Proc Natl Acad Sci U S A. 2004 Nov 16;101(46):16363-8. Epub 2004 Nov 8.
22. Fudge K, etal., Mod Pathol. 1994 Jun;7(5):549-54.
23. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
24. GOA data from the GO Consortium
25. Henriksen R, etal., Cancer Res. 1993 Oct 1;53(19):4550-4.
26. Herren B, etal., Biochim Biophys Acta 1993 Jun 25;1173(3):294-302.
27. Hwang RF, etal., Clin Cancer Res. 2003 Dec 15;9(17):6534-44.
28. Ingram JL, etal., FASEB J. 2004 Jul;18(10):1132-4. Epub 2004 May 20.
29. Jankov RP, etal., Am J Physiol Lung Cell Mol Physiol. 2005 Jun;288(6):L1162-70. Epub 2005 Feb 18.
30. Jechlinger M, etal., J Clin Invest. 2006 Jun;116(6):1561-70.
31. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
32. Lee KH, etal., Mol Cell Biol 1990 May;10(5):2237-46.
33. Lee MH, etal., Toxicology. 2008 Jan 14;243(1-2):224-35. Epub 2007 Oct 22.
34. Lee YW, etal., Acta Otolaryngol. 2004 Jun;124(5):558-62.
35. Lindroos PM, etal., Am J Respir Cell Mol Biol. 1995 Oct;13(4):455-65.
36. Liu X, etal., Mult Scler. 2005 Aug;11(4):381-9.
37. Mangum JB, etal., Part Fibre Toxicol. 2006 Nov 29;3:15.
38. MGD data from the GO Consortium
39. Morioka I, etal., Kobe J Med Sci. 2004 Jan;50(1-2):21-30.
40. Mosselman S, etal., Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2884-8.
41. Nakagawa T, etal., Am J Pathol. 1999 Nov;155(5):1689-99.
42. NCBI rat LocusLink and RefSeq merged data July 26, 2002
43. Nishiyama A, etal., J Neurosci Res. 1996 Feb 1;43(3):299-314.
44. OMIM Disease Annotation Pipeline
45. Palumbo C, etal., J Pathol. 2002 Apr;196(4):467-77.
46. Pardanani A, etal., Blood. 2004 Nov 15;104(10):3038-45. Epub 2004 Jul 29.
47. Pipeline to import KEGG annotations from KEGG into RGD
48. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
49. Qu SQ, etal., Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2012 Oct;20(5):1216-20.
50. RGD automated data pipeline
51. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
52. RGD automated import pipeline for gene-chemical interactions
53. RGD comprehensive gene curation
54. Ricono JM, etal., Am J Physiol Renal Physiol. 2002 Feb;282(2):F211-9.
55. Sarzani R, etal., Hypertension. 1991 Nov;18(5 Suppl):III93-9.
56. Savikko J, etal., Transplantation. 2002 Feb 27;73(4):506-11.
57. Savolainen-Peltonen H, etal., Transplantation. 2004 Jan 15;77(1):35-42.
58. Souza P, etal., Am J Respir Cell Mol Biol. 1996 Oct;15(4):551-62.
59. Sulzbacher I, etal., Am J Clin Pathol. 2003 Jul;120(1):107-12.
60. Sun HI, etal., Neurosurgery. 2010 Apr;66(4):744-50; discussion 750. doi: 10.1227/01.NEU.0000367553.65099.14.
61. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
62. Uchida T, etal., Exp Hematol. 2014 May;42(5):369-379.e3. doi: 10.1016/j.exphem.2014.01.009. Epub 2014 Jan 31.
63. Uzumcu M, etal., Biol Reprod. 2002 Mar;66(3):745-53.
64. Wang F, etal., Oncotarget. 2015 Feb 20;6(5):2709-24. doi: 10.18632/oncotarget.2779.
65. Watson PA, etal., Endocrinology 2002 Aug;143(8):2922-9.
66. Wicklein D, etal., PLoS One. 2012;7(2):e30567. doi: 10.1371/journal.pone.0030567. Epub 2012 Feb 14.
67. Wilczynski SP, etal., Hum Pathol. 2005 Mar;36(3):242-9.
68. Wu Y, etal., Clin Cancer Res. 2012 Apr 1;18(7):1966-78. doi: 10.1158/1078-0432.CCR-11-1971. Epub 2012 Mar 23.
69. Yamazaki T, etal., J Peripher Nerv Syst. 2009 Sep;14(3):165-76. doi: 10.1111/j.1529-8027.2009.00228.x.
70. Zahner G, etal., J Biol Chem 2002 Mar 22;277(12):9763-71.
Additional References at PubMed
PMID:1646396   PMID:2536956   PMID:2542288   PMID:2554309   PMID:8188664   PMID:8889548   PMID:9226440   PMID:10331973   PMID:10734113   PMID:10806482   PMID:10903171   PMID:11239463  
PMID:11803579   PMID:12651897   PMID:15021824   PMID:15372073   PMID:15543606   PMID:15613744   PMID:16794827   PMID:17143286   PMID:17335807   PMID:17350578   PMID:17470632   PMID:18462699  
PMID:18801569   PMID:19056881   PMID:19213942   PMID:19373754   PMID:19665498   PMID:19691150   PMID:19738159   PMID:19946888   PMID:20036247   PMID:20110689   PMID:20333648   PMID:20548288  
PMID:20645409   PMID:21146513   PMID:21171332   PMID:21289081   PMID:21596750   PMID:21954875   PMID:22027834   PMID:22265737   PMID:23160237   PMID:23266329   PMID:23545158   PMID:24029230  
PMID:24190966   PMID:24420748   PMID:24427322   PMID:24735959   PMID:25159478   PMID:25899145   PMID:25937181   PMID:28245285   PMID:29174980   PMID:29237719   PMID:30180991  


Genomics

Comparative Map Data
Pdgfra
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21433,005,838 - 33,054,347 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1433,005,839 - 33,054,335 (-)Ensembl
Rnor_6.01435,527,926 - 35,581,130 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1435,527,927 - 35,581,031 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01435,356,434 - 35,409,311 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41435,369,422 - 35,418,126 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11435,369,672 - 35,418,126 (-)NCBI
Celera1432,273,077 - 32,324,887 (-)NCBICelera
RH 3.4 Map14432.47RGD
Cytogenetic Map14p11NCBI
PDGFRA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl454,229,280 - 54,298,245 (+)EnsemblGRCh38hg38GRCh38
GRCh38454,229,127 - 54,298,245 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37455,095,460 - 55,164,412 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36454,790,204 - 54,859,169 (+)NCBINCBI36hg18NCBI36
Build 34454,936,129 - 55,005,339NCBI
Celera452,596,023 - 52,665,170 (+)NCBI
Cytogenetic Map4q12NCBI
HuRef451,043,324 - 51,112,555 (+)NCBIHuRef
CHM1_1455,130,846 - 55,199,987 (+)NCBICHM1_1
Pdgfra
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39575,311,988 - 75,358,867 (+)NCBIGRCm39mm39
GRCm39 Ensembl575,312,953 - 75,358,876 (+)Ensembl
GRCm38575,151,322 - 75,198,206 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl575,152,292 - 75,198,215 (+)EnsemblGRCm38mm10GRCm38
MGSCv37575,548,316 - 75,594,229 (+)NCBIGRCm37mm9NCBIm37
MGSCv36575,434,045 - 75,479,893 (+)NCBImm8
Celera572,441,591 - 72,487,596 (+)NCBICelera
Cytogenetic Map5C3.3NCBI
cM Map539.55NCBI
Pdgfra
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544716,569,909 - 16,612,373 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544716,570,652 - 16,613,410 (-)NCBIChiLan1.0ChiLan1.0
PDGFRA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1476,200,871 - 76,271,105 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl476,199,382 - 76,271,097 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0469,639,081 - 69,709,870 (-)NCBIMhudiblu_PPA_v0panPan3
PDGFRA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11346,729,722 - 46,775,828 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1346,730,703 - 46,773,278 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1346,687,151 - 46,733,378 (+)NCBI
ROS_Cfam_1.01347,339,954 - 47,386,179 (+)NCBI
UMICH_Zoey_3.11347,012,519 - 47,058,684 (+)NCBI
UNSW_CanFamBas_1.01346,544,815 - 46,590,877 (+)NCBI
UU_Cfam_GSD_1.01347,418,193 - 47,464,247 (+)NCBI
Pdgfra
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528529,444,794 - 29,494,171 (-)NCBI
SpeTri2.0NW_00493648216,804,129 - 16,853,539 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDGFRA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl840,967,493 - 41,021,442 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1840,966,568 - 41,021,440 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2843,067,784 - 43,081,654 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDGFRA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1714,243,291 - 14,307,373 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl714,241,070 - 14,307,422 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606615,086,695 - 15,149,115 (-)NCBIVero_WHO_p1.0
Pdgfra
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476115,223,789 - 15,269,685 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D14Wox20  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21433,055,829 - 33,056,013 (+)MAPPERmRatBN7.2
Rnor_6.01435,582,526 - 35,582,709NCBIRnor6.0
Rnor_5.01435,410,806 - 35,410,989UniSTSRnor5.0
RGSC_v3.41435,419,622 - 35,419,807UniSTSRGSC3.4
Celera1432,326,366 - 32,326,549UniSTS
Cytogenetic Map14p11UniSTS
RH94451  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21433,006,129 - 33,006,285 (+)MAPPERmRatBN7.2
Rnor_6.01435,528,218 - 35,528,373NCBIRnor6.0
Rnor_5.01435,356,726 - 35,356,881UniSTSRnor5.0
RGSC_v3.41435,369,714 - 35,369,869UniSTSRGSC3.4
RH 3.4 Map14432.47UniSTS
Cytogenetic Map14p11UniSTS
M84607  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21433,008,692 - 33,008,866 (+)MAPPERmRatBN7.2
Rnor_6.01435,530,781 - 35,530,954NCBIRnor6.0
Rnor_5.01435,359,289 - 35,359,462UniSTSRnor5.0
RGSC_v3.41435,372,277 - 35,372,450UniSTSRGSC3.4
Celera1432,279,520 - 32,279,693UniSTS
Cytogenetic Map14p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:518
Count of miRNA genes:252
Interacting mature miRNAs:331
Transcripts:ENSRNOT00000003077
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 14 8 13 8 6 6 64 35 36 11 6
Low 43 33 6 33 2 5 10 5 2
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012802 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250879 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CA505634 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CA512174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB738013 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB801421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK475090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK475330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK477487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK478629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DV719360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M63837 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z14118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000003077   ⟹   ENSRNOP00000003077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1433,005,839 - 33,054,335 (-)Ensembl
Rnor_6.0 Ensembl1435,527,927 - 35,581,031 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118506   ⟹   ENSRNOP00000081799
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1433,005,839 - 33,044,103 (-)Ensembl
RefSeq Acc Id: NM_012802   ⟹   NP_036934
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21433,005,838 - 33,054,335 (-)NCBI
Rnor_6.01435,527,926 - 35,581,031 (-)NCBI
Rnor_5.01435,356,434 - 35,409,311 (-)NCBI
RGSC_v3.41435,369,422 - 35,418,126 (-)RGD
Celera1432,273,077 - 32,324,887 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250879   ⟹   XP_006250941
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21433,005,838 - 33,051,026 (-)NCBI
Rnor_6.01435,527,926 - 35,577,277 (-)NCBI
Rnor_5.01435,356,434 - 35,409,311 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250880   ⟹   XP_006250942
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21433,005,838 - 33,054,347 (-)NCBI
Rnor_6.01435,527,926 - 35,581,130 (-)NCBI
Rnor_5.01435,356,434 - 35,409,311 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250881   ⟹   XP_006250943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21433,005,838 - 33,051,604 (-)NCBI
Rnor_6.01435,527,926 - 35,578,317 (-)NCBI
Rnor_5.01435,356,434 - 35,409,311 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091625   ⟹   XP_038947553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21433,005,838 - 33,051,284 (-)NCBI
RefSeq Acc Id: XM_039091626   ⟹   XP_038947554
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21433,005,838 - 33,053,311 (-)NCBI
RefSeq Acc Id: XM_039091627   ⟹   XP_038947555
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21433,005,838 - 33,051,386 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_036934   ⟸   NM_012802
- Peptide Label: precursor
- UniProtKB: P20786 (UniProtKB/Swiss-Prot),   G3V6A0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250942   ⟸   XM_006250880
- Peptide Label: isoform X1
- UniProtKB: G3V6A0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250943   ⟸   XM_006250881
- Peptide Label: isoform X1
- UniProtKB: G3V6A0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250941   ⟸   XM_006250879
- Peptide Label: isoform X1
- UniProtKB: G3V6A0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003077   ⟸   ENSRNOT00000003077
RefSeq Acc Id: XP_038947554   ⟸   XM_039091626
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947555   ⟸   XM_039091627
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947553   ⟸   XM_039091625
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000081799   ⟸   ENSRNOT00000118506
Protein Domains
Ig-like   Ig-like C2-type   Protein kinase

Transcriptome

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

Promoters
RGD ID:13699281
Promoter ID:EPDNEW_R9806
Type:initiation region
Name:Pdgfra_1
Description:platelet derived growth factor receptor alpha
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_6.01435,581,034 - 35,581,094EPDNEW

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)
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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
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/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
LE/Stm (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
LEW/Crl (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
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/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
LEXF1C/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
LEXF2B/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
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/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
M520/NRrrcMcwi (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
MHS/Gib (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
MNS/Gib (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
MR/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
MR/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
MWF/Hsd (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
PVG/Seac (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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SHRSP/Gcrc (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
SR/JrHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/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
WKY/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
WKY/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
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)
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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
WN/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
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:3284 AgrOrtholog
Ensembl Genes ENSRNOG00000002244 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003077 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003077 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDGFRA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_rcpt_3_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25267 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 25267 ENTREZGENE
Pfam I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase_Tyr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PDGFRA RGD
PhenoGen Pdgfra PhenoGen
PIRSF Alpha-PDGF_receptor UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_TYR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RECEPTOR_TYR_KIN_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TyrKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC217151
UniProt G3V6A0 ENTREZGENE, UniProtKB/TrEMBL
  P20786 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Pdgfra  platelet derived growth factor receptor alpha  LOC102554024  platelet-derived growth factor receptor alpha-like  Data Merged 737654 PROVISIONAL
2016-01-25 Pdgfra  platelet derived growth factor receptor alpha  Pdgfra  platelet derived growth factor receptor, alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-18 LOC102554024  platelet-derived growth factor receptor alpha-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Pdgfra  Platelet-derived growth factor receptor alpha      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation mRNA expression decreased by the transcription factor cAMP response element-binding protein (CREB) in vascular smooth muscle cells (SMCs) 625715