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 part of platelet-derived growth factor complex. 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
Previously 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 ...
Candidate Gene For: Cia12
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21215,645,549 - 15,667,056 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1215,645,541 - 15,666,497 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1216,456,582 - 16,477,579 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01217,080,317 - 17,101,307 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01216,102,867 - 16,123,854 (+)NCBIRnor_WKY
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
(1->4)-beta-D-glucan  (ISO)
(S)-nicotine  (EXP)
1-naphthyl isothiocyanate  (EXP)
11-deoxycorticosterone  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,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,IEP)
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 A  (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 B  (EXP)
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)
epoxiconazole  (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  (EXP,ISO)
paraoxon  (ISO)
paraquat  (EXP,ISO)
parathion  (ISO)
peonidin  (ISO)
peonidin chloride  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (ISO)
phenytoin  (ISO)
PhIP  (EXP,IEP)
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)
T-2 toxin  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
Tetramethylthiourea  (EXP)
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 population proliferation  (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,NAS)
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)
signal transduction  (IEA)
skin development  (ISO,ISS)

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Vascular endothelial growth factor and platelet-derived growth factor are potential angiogenic and metastatic factors in human breast cancer. Anan K, etal., Surgery. 1996 Mar;119(3):333-9.
2. Expression of platelet-derived growth factor-A (PDGF-A), PDGF-B, and PDGF receptor-alpha and -beta during human testicular development and disease. Basciani S, etal., J Clin Endocrinol Metab. 2002 May;87(5):2310-9.
3. Expression patterns of PDGF-A, -B, -C and -D and the PDGF-receptors alpha and beta in activated rat hepatic stellate cells (HSC). Breitkopf K, etal., Cytokine. 2005 Sep 7;31(5):349-57.
4. [The expression of platelet-derived growth factor-A and its receptor in acute radiation-induced skin ulcer in rats] Cao WH, etal., Zhonghua Shao Shang Za Zhi. 2005 Oct;21(5):359-62.
5. Oligohydramnios decreases platelet-derived growth factor expression in fetal rat lungs. Chen CM, etal., Neonatology. 2007;92(3):187-93. Epub 2007 May 21.
6. Effect of retinoic acid on platelet-derived growth factorand lung development in newborn rats. Chen H, etal., J Huazhong Univ Sci Technolog Med Sci. 2004;24(3):226-8.
7. Temporal changes in gene expression following cryogenic rat brain injury. Cook JL, etal., Brain Res Mol Brain Res. 1998 Mar 30;55(1):9-19.
8. Effect of ischemic preconditioning on pancreatic regeneration and pancreatic expression of vascular endothelial growth factor and platelet-derived growth factor-A in ischemia/reperfusion-induced pancreatitis. Dembinski A, etal., J Physiol Pharmacol. 2006 Mar;57(1):39-58.
9. Detection of platelet-derived growth factor-alpha (PDGF-A) protein in cells of Leydig lineage in the postnatal rat testis. Fecteau KA, etal., Histol Histopathol. 2006 Dec;21(12):1295-302.
10. Mechanism of platelet-derived growth factor (PDGF) AA, AB, and BB binding to alpha and beta PDGF receptor. Fretto LJ, etal., J Biol Chem. 1993 Feb 15;268(5):3625-31.
11. Immunohistochemistry analysis of platelet-derived growth factor A and B chains and platelet-derived growth factor alpha and beta receptor expression in benign prostatic hyperplasias and Gleason-graded human prostate adenocarcinomas. Fudge K, etal., Mod Pathol. 1994 Jun;7(5):549-54.
12. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
14. Identification of four new quantitative trait loci regulating arthritis severity and one new quantitative trait locus regulating autoantibody production in rats with collagen-induced arthritis. Griffiths MM, etal., Arthritis Rheum 2000 Jun;43(6):1278-89
15. Determination of cytokine mRNA-expression in term human placenta of patients with gestational hypertension, intrauterine growth retardation and gestational diabetes mellitus using polymerase chain reaction. Heinig J, etal., Zentralbl Gynakol. 2000;122(8):413-8.
16. Conservation in sequence and affinity of human and rodent PDGF ligands and receptors. Herren B, etal., Biochim Biophys Acta 1993 Jun 25;1173(3):294-302.
17. Simvastatin suppresses experimental aortic aneurysm expansion. Kalyanasundaram A, etal., J Vasc Surg. 2006 Jan;43(1):117-24.
18. Increased expression of PDGF A- and B-chain genes in rat lungs with hypoxic pulmonary hypertension. Katayose D, etal., Am J Physiol. 1993 Feb;264(2 Pt 1):L100-6.
19. Over-expression of platelet-derived growth factor in human diabetic nephropathy. Langham RG, etal., Nephrol Dial Transplant. 2003 Jul;18(7):1392-6.
20. Expression of platelet-derived growth factor in the developing cochlea of rats. Lee YW, etal., Acta Otolaryngol. 2004 Jun;124(5):558-62.
21. Expression and functional analysis of platelet-derived growth factor in uterine leiomyomata. Liang M, etal., Cancer Biol Ther. 2006 Jan;5(1):28-33. Epub 2006 Jan 12.
22. Increased expression of platelet-derived growth factor A and collagenous matrix proteins in congenital multicystic renal dysplasia. Liapis H, etal., Nephron. 1997;76(2):161-70.
23. Single-walled carbon nanotube (SWCNT)-induced interstitial fibrosis in the lungs of rats is associated with increased levels of PDGF mRNA and the formation of unique intercellular carbon structures that bridge alveolar macrophages in situ. Mangum JB, etal., Part Fibre Toxicol. 2006 Nov 29;3:15.
24. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
25. Brain abnormalities and glioma-like lesions in mice overexpressing the long isoform of PDGF-A in astrocytic cells. Nazarenko I, etal., PLoS One. 2011 Apr 7;6(4):e18303. doi: 10.1371/journal.pone.0018303.
26. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
27. Protective role of a novel erythrocyte-derived depressing factor on blood vessels of renovascular hypertensive rats. Pang H, etal., Clin Exp Pharmacol Physiol. 2007 May-Jun;34(5-6):393-8.
28. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
29. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
30. GOA pipeline RGD automated data pipeline
31. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
33. Comprehensive gene review and curation RGD comprehensive gene curation
34. The effect of acute rejection and cyclosporin A-treatment on induction of platelet-derived growth factor and its receptors during the development of chronic rat renal allograft rejection. Savikko J, etal., Transplantation. 2002 Feb 27;73(4):506-11.
35. Estrogen regulates insulin-like growth factor 1, platelet-derived growth factor A and B, and their receptors in the vascular wall. Savolainen-Peltonen H, etal., Transplantation. 2004 Jan 15;77(1):35-42.
36. cDNA microarray profiling of rat mammary gland carcinomas induced by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine and 7,12-dimethylbenzanthracene. Shan L, etal., Carcinogenesis. 2002 Oct;23(10):1561-8.
37. Global gene expression profiling of chemically induced rat mammary gland carcinomas and adenomas. Shan L, etal., Toxicol Pathol. 2005;33(7):768-75.
38. The age-related decrease in CNS remyelination efficiency is attributable to an impairment of both oligodendrocyte progenitor recruitment and differentiation. Sim FJ, etal., J Neurosci 2002 Apr 1;22(7):2451-9.
39. The age-dependent proliferation of rat aortic smooth muscle cells is independent of differential splicing of PDGF A-chain mRNA. Szabo P, etal., Mech Ageing Dev 1993 Feb;67(1-2):79-89.
40. Blood lipid mediator sphingosine 1-phosphate potently stimulates platelet-derived growth factor-A and -B chain expression through S1P1-Gi-Ras-MAPK-dependent induction of Kruppel-like factor 5. Usui S, etal., J Biol Chem 2004 Mar 26;279(13):12300-11. Epub 2004 Jan 07.
41. Inhibition of platelet-derived growth factor actions in the embryonic testis influences normal cord development and morphology. Uzumcu M, etal., Biol Reprod. 2002 Mar;66(3):745-53.
42. Differential cytokine activity and morphology during wound healing in the neonatal and adult rat skin. 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   PMID:34265313  


Genomics

Comparative Map Data
Pdgfa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21215,645,549 - 15,667,056 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1215,645,541 - 15,666,497 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1216,456,582 - 16,477,579 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01217,080,317 - 17,101,307 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01216,102,867 - 16,123,854 (+)NCBIRnor_WKY
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh387497,258 - 520,700 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl7497,258 - 520,296 (-)EnsemblGRCh38hg38GRCh38
GRCh377536,895 - 560,337 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367503,421 - 526,007 (-)NCBINCBI36Build 36hg18NCBI36
Celera7505,832 - 559,337 (-)NCBICelera
Cytogenetic Map7p22.3NCBI
HuRef7455,023 - 477,393 (-)NCBIHuRef
CHM1_17535,640 - 589,379 (-)NCBICHM1_1
T2T-CHM13v2.07598,210 - 621,677 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27598,080 - 651,496 (-)NCBI
Pdgfa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395138,961,769 - 138,986,336 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5138,961,769 - 138,983,125 (-)EnsemblGRCm39 Ensembl
GRCm385138,976,014 - 139,000,792 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5138,976,014 - 138,997,370 (-)EnsemblGRCm38mm10GRCm38
MGSCv375139,452,925 - 139,470,907 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365139,230,613 - 139,248,595 (-)NCBIMGSCv36mm8
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
NHGRI_mPanPan1753,757,065 - 53,780,484 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07648,722 - 672,023 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17872,204 - 888,870 (-)NCBIpanpan1.1PanPan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0616,400,056 - 16,421,423 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl616,400,113 - 16,420,573 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1616,204,088 - 16,222,628 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0616,130,433 - 16,148,998 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0616,420,378 - 16,438,910 (+)NCBIUU_Cfam_GSD_1.0
Pdgfa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344144,181,428 - 144,201,439 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936754808,213 - 828,613 (-)EnsemblSpeTri2.0
SpeTri2.0NW_004936754808,894 - 828,554 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDGFA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3301,584 - 321,712 (-)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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2821,047,219 - 21,069,827 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666090605,283 - 628,542 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pdgfa
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474026,169,064 - 26,188,866 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474026,172,808 - 26,191,557 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pdgfa
69 total Variants
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.


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

Markers in Region
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


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
- UniProtKB: Q6P7C3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038945033   ⟸   XM_039089105
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038945032   ⟸   XM_039089104
- Peptide Label: isoform X1
- UniProtKB: Q6P7C3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038945034   ⟸   XM_039089106
- Peptide Label: isoform X2
Protein Domains
Platelet-derived growth factor (PDGF) family

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P28576-F1-model_v2 AlphaFold P28576 1-204 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3282 AgrOrtholog
BioCyc Gene G2FUF-19876 BioCyc
Ensembl Genes ENSRNOG00000001312 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001775.7 UniProtKB/TrEMBL
  ENSRNOP00000040116 ENTREZGENE
  ENSRNOP00000040116.4 UniProtKB/Swiss-Prot
  ENSRNOP00000074787 ENTREZGENE
  ENSRNOP00000074787.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001775.7 UniProtKB/TrEMBL
  ENSRNOT00000042117 ENTREZGENE
  ENSRNOT00000042117.7 UniProtKB/Swiss-Prot
  ENSRNOT00000091476 ENTREZGENE
  ENSRNOT00000091476.2 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
PANTHER PLATELET-DERIVED GROWTH FACTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLATELET-DERIVED GROWTH FACTOR SUBUNIT A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 A0A8L2UH95_RAT UniProtKB/TrEMBL
  P28576 ENTREZGENE, UniProtKB/Swiss-Prot
  Q6P7C3 ENTREZGENE, 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