Pdgfa (platelet derived growth factor subunit A) - Rat Genome Database

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Gene: Pdgfa (platelet derived growth factor subunit A) Rattus norvegicus
Analyze
Symbol: Pdgfa
Name: platelet derived growth factor subunit A
RGD ID: 3282
Description: Predicted to enable several functions, including platelet-derived growth factor binding activity; protein dimerization activity; and signaling receptor binding activity. Involved in several processes, including male gonad development; response to estradiol; and response to retinoic acid. Predicted to be located in cell surface and microvillus. Predicted to be active in extracellular space. Biomarker of chronic ulcer of skin; oligohydramnios; pancreatitis; pulmonary hypertension; and renovascular hypertension. Human ortholog(s) of this gene implicated in high grade glioma. Orthologous to human PDGFA (platelet derived growth factor subunit A); PARTICIPATES IN ceramide signaling pathway; platelet-derived growth factor signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH (S)-nicotine; 1-naphthyl isothiocyanate; 11-deoxycorticosterone.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: PDGF subunit A; PDGF-1; PDGFACP; platelet derived growth factor, alpha; Platelet-derived growth factor A chain; platelet-derived growth factor alpha polypeptide; platelet-derived growth factor subunit A
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
mRatBN7.21215,645,549 - 15,667,056 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1215,645,541 - 15,666,497 (+)Ensembl
Rnor_6.01217,734,141 - 17,756,186 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1217,734,133 - 17,755,285 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01219,727,672 - 19,749,009 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41216,151,045 - 16,172,412 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11216,180,972 - 16,202,334 (+)NCBI
Celera1217,398,134 - 17,419,591 (+)NCBICelera
Cytogenetic Map12q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (EXP)
1-naphthyl isothiocyanate  (EXP)
11-deoxycorticosterone  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (ISO)
aluminium oxide  (ISO)
ammonium chloride  (EXP)
amosite asbestos  (EXP)
amphibole asbestos  (EXP)
aristolochic acid  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
belinostat  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (EXP)
beta-naphthoflavone  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A5  (ISO)
bucladesine  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
cadmium sulfate  (ISO)
capsaicin  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
celecoxib  (EXP,ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
CU-O LINKAGE  (ISO)
cyanidin cation  (ISO)
cyclosporin A  (ISO)
cypermethrin  (EXP)
delphinidin  (ISO)
desferrioxamine B  (EXP)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
diazoxon  (ISO)
dibutyl phthalate  (EXP)
dichloroacetic acid  (ISO)
dieldrin  (EXP)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
divanadium pentaoxide  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
entinostat  (ISO)
estriol  (ISO)
estrone  (ISO)
estrone 3-sulfate  (ISO)
ethanol  (ISO)
fenhexamid  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
furan  (ISO)
gadolinium trichloride  (EXP)
geldanamycin  (ISO)
genistein  (EXP)
glyphosate  (ISO)
gossypol  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (EXP,ISO)
ibuprofen  (ISO)
indole-3-methanol  (EXP)
indometacin  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
L-methionine  (ISO)
leflunomide  (ISO)
Licochalcone B  (ISO)
lipopolysaccharide  (ISO)
losartan  (EXP)
malvidin  (ISO)
medroxyprogesterone acetate  (ISO)
methotrexate  (ISO)
methoxychlor  (EXP)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
naproxen  (EXP)
nebivolol  (ISO)
nickel sulfate  (ISO)
nicotine  (EXP)
nitrofen  (EXP)
NS-398  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraoxon  (ISO)
paraquat  (EXP,ISO)
parathion  (ISO)
peonidin  (ISO)
peonidin chloride  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (ISO)
phenytoin  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
potassium chromate  (ISO)
potassium dichromate  (EXP)
progesterone  (ISO)
prostaglandin E2  (ISO)
prostaglandin I2  (ISO)
ramipril  (ISO)
reactive oxygen species  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
serpentine asbestos  (EXP,ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
Sodium oleate  (ISO)
sulindac  (EXP)
sumatriptan  (EXP)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP,ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin cytoskeleton organization  (ISO,ISS)
angiogenesis  (ISO,ISS)
animal organ morphogenesis  (ISO,ISS)
bone development  (ISO)
cell projection assembly  (ISO,ISS)
cellular response to transforming growth factor beta stimulus  (IEP)
digestive tract development  (ISO)
embryonic lung development  (ISO)
hair follicle development  (ISO,ISS)
inner ear development  (IEP)
lung alveolus development  (ISO,ISS)
male gonad development  (IEP)
negative chemotaxis  (IEA,ISO,ISS)
negative regulation of phosphatidylinositol biosynthetic process  (IEA,ISO,ISS)
negative regulation of platelet activation  (IEA,ISO,ISS)
platelet-derived growth factor receptor signaling pathway  (IBA,ISO,ISS)
positive regulation of cell division  (IEA)
positive regulation of cell migration  (IBA,ISO,ISS)
positive regulation of cell population proliferation  (IBA,IMP,ISO,ISS)
positive regulation of ERK1 and ERK2 cascade  (IBA,IEA,ISO,ISS)
positive regulation of fibroblast proliferation  (IEA,ISO,ISS)
positive regulation of MAP kinase activity  (IBA,IEA,ISO,ISS)
positive regulation of MAPK cascade  (ISO,ISS)
positive regulation of mesenchymal cell proliferation  (ISO,ISS)
positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway  (IEA,ISO,ISS)
positive regulation of phosphatidylinositol 3-kinase signaling  (IBA,IEA,ISO,ISS)
positive regulation of protein autophosphorylation  (IBA,IEA,ISO,ISS)
positive regulation of protein kinase B signaling  (IEA,ISO,ISS)
regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling  (ISO,ISS)
regulation of DNA biosynthetic process  (ISO,ISS)
regulation of glomerular mesangial cell proliferation  (ISO,ISS)
regulation of peptidyl-tyrosine phosphorylation  (ISO,ISS)
regulation of smooth muscle cell migration  (IEA,ISO,ISS)
response to estradiol  (IEP)
response to hypoxia  (IEP)
response to inorganic substance  (IEP)
response to organic substance  (IEP)
response to retinoic acid  (IEP)
response to wounding  (IEA,ISO,ISS)
response to xenobiotic stimulus  (IEP)
skin development  (ISO,ISS)
wound healing  (IEP)

Cellular Component
cell surface  (IEA,ISO,ISS)
cellular_component  (ND)
extracellular space  (IBA,IEA,ISO,ISS)
membrane  (IEA)
microvillus  (ISO,ISS)

Molecular Function

References

References - curated
1. Anan K, etal., Surgery. 1996 Mar;119(3):333-9.
2. Basciani S, etal., J Clin Endocrinol Metab. 2002 May;87(5):2310-9.
3. Breitkopf K, etal., Cytokine. 2005 Sep 7;31(5):349-57.
4. Cao WH, etal., Zhonghua Shao Shang Za Zhi. 2005 Oct;21(5):359-62.
5. Chen CM, etal., Neonatology. 2007;92(3):187-93. Epub 2007 May 21.
6. Chen H, etal., J Huazhong Univ Sci Technolog Med Sci. 2004;24(3):226-8.
7. Cook JL, etal., Brain Res Mol Brain Res. 1998 Mar 30;55(1):9-19.
8. Dembinski A, etal., J Physiol Pharmacol. 2006 Mar;57(1):39-58.
9. Fecteau KA, etal., Histol Histopathol. 2006 Dec;21(12):1295-302.
10. Fudge K, etal., Mod Pathol. 1994 Jun;7(5):549-54.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. GOA data from the GO Consortium
13. Griffiths MM, etal., Arthritis Rheum 2000 Jun;43(6):1278-89
14. Heinig J, etal., Zentralbl Gynakol. 2000;122(8):413-8.
15. Herren B, etal., Biochim Biophys Acta 1993 Jun 25;1173(3):294-302.
16. Kalyanasundaram A, etal., J Vasc Surg. 2006 Jan;43(1):117-24.
17. Katayose D, etal., Am J Physiol. 1993 Feb;264(2 Pt 1):L100-6.
18. Langham RG, etal., Nephrol Dial Transplant. 2003 Jul;18(7):1392-6.
19. Lee YW, etal., Acta Otolaryngol. 2004 Jun;124(5):558-62.
20. Liang M, etal., Cancer Biol Ther. 2006 Jan;5(1):28-33. Epub 2006 Jan 12.
21. Liapis H, etal., Nephron. 1997;76(2):161-70.
22. Mangum JB, etal., Part Fibre Toxicol. 2006 Nov 29;3:15.
23. MGD data from the GO Consortium
24. Nazarenko I, etal., PLoS One. 2011 Apr 7;6(4):e18303. doi: 10.1371/journal.pone.0018303.
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. Pang H, etal., Clin Exp Pharmacol Physiol. 2007 May-Jun;34(5-6):393-8.
27. Pipeline to import KEGG annotations from KEGG into RGD
28. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
29. RGD automated data pipeline
30. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
31. RGD automated import pipeline for gene-chemical interactions
32. RGD comprehensive gene curation
33. Savikko J, etal., Transplantation. 2002 Feb 27;73(4):506-11.
34. Savolainen-Peltonen H, etal., Transplantation. 2004 Jan 15;77(1):35-42.
35. Sim FJ, etal., J Neurosci 2002 Apr 1;22(7):2451-9.
36. Szabo P, etal., Mech Ageing Dev 1993 Feb;67(1-2):79-89.
37. Usui S, etal., J Biol Chem 2004 Mar 26;279(13):12300-11. Epub 2004 Jan 07.
38. Uzumcu M, etal., Biol Reprod. 2002 Mar;66(3):745-53.
39. Wagner W and Wehrmann M, J Cell Mol Med. 2007 Nov-Dec;11(6):1342-51.
Additional References at PubMed
PMID:291037   PMID:2439522   PMID:2536956   PMID:2538439   PMID:2836953   PMID:3754619   PMID:7073684   PMID:8900172   PMID:9374392   PMID:9409235   PMID:10331973   PMID:10806482  
PMID:10903171   PMID:11788434   PMID:11803579   PMID:11940581   PMID:12070119   PMID:12101409   PMID:12176888   PMID:12477932   PMID:14522834   PMID:15115658   PMID:15361870   PMID:15466888  
PMID:16462734   PMID:17442164   PMID:17470632   PMID:17632272   PMID:18428026   PMID:18512152   PMID:18559345   PMID:18635661   PMID:19019919   PMID:19213942   PMID:19373754   PMID:19691150  
PMID:19734317   PMID:19738159   PMID:20498031   PMID:20534510   PMID:20972576   PMID:21559360   PMID:21953009   PMID:22922759   PMID:23938297   PMID:25148874   PMID:25200619   PMID:25899145  
PMID:26032503   PMID:26262503   PMID:28358926  


Genomics

Candidate Gene Status
Pdgfa is a candidate Gene for QTL Cia12
Comparative Map Data
Pdgfa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21215,645,549 - 15,667,056 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1215,645,541 - 15,666,497 (+)Ensembl
Rnor_6.01217,734,141 - 17,756,186 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1217,734,133 - 17,755,285 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01219,727,672 - 19,749,009 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41216,151,045 - 16,172,412 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11216,180,972 - 16,202,334 (+)NCBI
Celera1217,398,134 - 17,419,591 (+)NCBICelera
Cytogenetic Map12q11NCBI
PDGFA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7497,258 - 520,296 (-)EnsemblGRCh38hg38GRCh38
GRCh387497,245 - 520,668 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh377536,895 - 559,483 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367503,421 - 526,007 (-)NCBINCBI36hg18NCBI36
Celera7505,832 - 559,337 (-)NCBI
Cytogenetic Map7p22.3NCBI
HuRef7455,023 - 477,393 (-)NCBIHuRef
CHM1_17535,640 - 589,379 (-)NCBICHM1_1
CRA_TCAGchr7v27598,080 - 651,496 (-)NCBI
Pdgfa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395138,961,769 - 138,986,336 (-)NCBIGRCm39mm39
GRCm39 Ensembl5138,961,769 - 138,983,125 (-)Ensembl
GRCm385138,976,014 - 139,000,792 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5138,976,014 - 138,997,370 (-)EnsemblGRCm38mm10GRCm38
MGSCv375139,452,925 - 139,470,907 (-)NCBIGRCm37mm9NCBIm37
MGSCv365139,230,613 - 139,248,595 (-)NCBImm8
Celera5136,032,139 - 136,049,986 (-)NCBICelera
Cytogenetic Map5G2NCBI
cM Map577.65NCBI
Pdgfa
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554608,326,891 - 8,346,550 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554608,328,400 - 8,346,755 (-)NCBIChiLan1.0ChiLan1.0
PDGFA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17872,204 - 888,870 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v07648,722 - 672,023 (-)NCBIMhudiblu_PPA_v0panPan3
PDGFA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1616,271,082 - 16,293,246 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl616,270,104 - 16,292,396 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha617,743,941 - 17,762,483 (+)NCBI
ROS_Cfam_1.0616,400,056 - 16,421,423 (+)NCBI
UMICH_Zoey_3.1616,204,088 - 16,222,628 (+)NCBI
UNSW_CanFamBas_1.0616,130,433 - 16,148,998 (+)NCBI
UU_Cfam_GSD_1.0616,420,378 - 16,438,910 (+)NCBI
Pdgfa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344144,181,428 - 144,201,439 (+)NCBI
SpeTri2.0NW_004936754808,894 - 828,554 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDGFA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3303,311 - 323,036 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13296,399 - 322,967 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23152,233 - 170,626 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDGFA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12821,044,549 - 21,068,411 (+)NCBI
ChlSab1.1 Ensembl2821,047,219 - 21,069,827 (+)Ensembl
Vero_WHO_p1.0NW_023666090605,283 - 628,542 (-)NCBI
Pdgfa
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474026,172,808 - 26,191,557 (-)NCBI

Position Markers
AW525445  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21215,645,190 - 15,645,360 (+)MAPPERmRatBN7.2
Rnor_6.01217,733,783 - 17,733,952NCBIRnor6.0
Rnor_5.01219,727,314 - 19,727,483UniSTSRnor5.0
RGSC_v3.41216,150,687 - 16,150,856UniSTSRGSC3.4
Celera1217,397,776 - 17,397,945UniSTS
RH 3.4 Map12245.9UniSTS
Cytogenetic Map12q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12119611090Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1600391Edcs2Endometrial carcinoma susceptibility QTL23.50.01uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)12683319017870186Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)12931821632103380Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121107382524234895Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382528064557Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
7204484Bp358Blood pressure QTL 3580.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121300829619212979Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121363552330827399Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121363552335682913Rat
61443Btemp2Thermal response to stress QTL 23.30.000094body temperature trait (VT:0005535)core body temperature (CMO:0001036)121502518320794014Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121555082638478808Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:88
Count of miRNA genes:77
Interacting mature miRNAs:83
Transcripts:ENSRNOT00000001775, ENSRNOT00000042117
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 34 2 1 4 46 35 28 11 1
Low 9 53 37 17 37 7 7 28 13 7
Below cutoff 4 4 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001775   ⟹   ENSRNOP00000001775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1215,648,635 - 15,666,497 (+)Ensembl
Rnor_6.0 Ensembl1217,735,740 - 17,755,285 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000042117   ⟹   ENSRNOP00000040116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1215,645,541 - 15,666,456 (+)Ensembl
Rnor_6.0 Ensembl1217,734,133 - 17,755,232 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091476   ⟹   ENSRNOP00000074787
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1215,647,691 - 15,666,467 (+)Ensembl
Rnor_6.0 Ensembl1217,736,287 - 17,755,243 (+)Ensembl
RefSeq Acc Id: NM_012801   ⟹   NP_036933
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21215,645,549 - 15,666,475 (+)NCBI
Rnor_6.01217,734,141 - 17,755,251 (+)NCBI
Rnor_5.01219,727,672 - 19,749,009 (+)NCBI
RGSC_v3.41216,151,045 - 16,172,412 (+)RGD
Celera1217,398,134 - 17,419,591 (+)RGD
Sequence:
RefSeq Acc Id: XM_039089104   ⟹   XP_038945032
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21215,647,068 - 15,667,056 (+)NCBI
RefSeq Acc Id: XM_039089105   ⟹   XP_038945033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21215,646,825 - 15,667,056 (+)NCBI
RefSeq Acc Id: XM_039089106   ⟹   XP_038945034
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21215,647,798 - 15,667,056 (+)NCBI
RefSeq Acc Id: XM_039089107   ⟹   XP_038945035
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21215,645,620 - 15,667,056 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036933   ⟸   NM_012801
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000040116   ⟸   ENSRNOT00000042117
RefSeq Acc Id: ENSRNOP00000074787   ⟸   ENSRNOT00000091476
RefSeq Acc Id: ENSRNOP00000001775   ⟸   ENSRNOT00000001775
RefSeq Acc Id: XP_038945035   ⟸   XM_039089107
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945033   ⟸   XM_039089105
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038945032   ⟸   XM_039089104
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945034   ⟸   XM_039089106
- Peptide Label: isoform X2
Protein Domains
PDGF_2

Transcriptome

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

Promoters
RGD ID:13698473
Promoter ID:EPDNEW_R8998
Type:initiation region
Name:Pdgfa_1
Description:platelet derived growth factor subunit A
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_6.01217,736,584 - 17,736,644EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3282 AgrOrtholog
Ensembl Genes ENSRNOG00000001312 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001775 UniProtKB/Swiss-Prot
  ENSRNOP00000040116 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000074787 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001775 UniProtKB/Swiss-Prot
  ENSRNOT00000042117 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000091476 UniProtKB/TrEMBL
Gene3D-CATH 2.10.90.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5598667 IMAGE-MGC_LOAD
InterPro Cystine-knot_cytokine UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PD_growth_factor_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDGF/VEGF_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDGF_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25266 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72268 IMAGE-MGC_LOAD
NCBI Gene 25266 ENTREZGENE
Pfam PDGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDGF_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pdgfa PhenoGen
PROSITE PDGF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PDGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57501 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt P28576 ENTREZGENE, UniProtKB/Swiss-Prot
  Q6P7C3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-25 Pdgfa  platelet derived growth factor subunit A  Pdgfa  platelet-derived growth factor alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-08-29 Pdgfa  platelet-derived growth factor alpha polypeptide  Pdgfa  platelet derived growth factor, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Pdgfa  Platelet-derived growth factor A chain      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in oligodendrocyte progenitor cells 625458
gene_regulation expression upregulated in oligodendrocyte progenitor cells by demyelination of CNS 625458
gene_regulation increased mRNA expression in oligodendrocyte progenitor cells is delayed following the induction of lysolecithin-induced demyelination in the spinal cord of old adults compared with young adults 625458