Pdgfa (platelet derived growth factor, alpha) - Rat Genome Database

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Gene: Pdgfa (platelet derived growth factor, alpha) Mus musculus
Analyze
Symbol: Pdgfa
Name: platelet derived growth factor, alpha
RGD ID: 11067
MGI Page MGI
Description: Predicted to enable several functions, including platelet-derived growth factor binding activity; protein dimerization activity; and signaling receptor binding activity. Involved in digestive tract development and embryonic lung development. Acts upstream of or within several processes, including animal organ development; positive regulation of mesenchymal cell proliferation; and regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling. Located in extracellular space and microvillus. Is expressed in several structures, including alimentary system; extraembryonic component; genitourinary system; nervous system; and sensory organ. 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; glioma pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: PDGF A-chain; PDGF subunit A; PDGF-1; platelet-derived growth factor A chain; platelet-derived growth factor A-chain; platelet-derived growth factor alpha polypeptide; platelet-derived growth factor subunit A
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal axial skeleton morphology  (IAGP)
abnormal craniofacial bone morphology  (IAGP)
abnormal epididymis epithelium morphology  (IAGP)
abnormal epididymis morphology  (IAGP)
abnormal kidney cortex morphology  (IAGP)
abnormal lung morphology  (IAGP)
abnormal myotome development  (IAGP)
abnormal pulmonary alveolar parenchyma morphology  (IAGP)
abnormal pulmonary alveolus morphology  (IAGP)
abnormal pulmonary elastic fiber morphology  (IAGP)
abnormal pulmonary interalveolar septum morphology  (IAGP)
abnormal scapula morphology  (IAGP)
abnormal small intestine morphology  (IAGP)
abnormal somite development  (IAGP)
abnormal spermatogenesis  (IAGP)
absent pulmonary alveoli  (IAGP)
arrest of spermatogenesis  (IAGP)
atelectasis  (IAGP)
blistering  (IAGP)
common atrium  (IAGP)
decreased body size  (IAGP)
decreased embryo size  (IAGP)
decreased fetal size  (IAGP)
decreased small intestinal villus number  (IAGP)
embryonic lethality during organogenesis, complete penetrance  (IAGP)
embryonic lethality during organogenesis, incomplete penetrance  (IAGP)
emphysema  (IAGP)
enlarged thoracic cavity  (IAGP)
fetal growth retardation  (IAGP)
heart right ventricle hypertrophy  (IAGP)
hydrops fetalis  (IAGP)
impaired lung alveolus development  (IAGP)
kyphosis  (IAGP)
lung hemorrhage  (IAGP)
midline facial cleft  (IAGP)
pericardial effusion  (IAGP)
pneumothorax  (IAGP)
postnatal growth retardation  (IAGP)
postnatal lethality, incomplete penetrance  (IAGP)
premature death  (IAGP)
respiratory failure  (IAGP)
rib bifurcation  (IAGP)
rib fusion  (IAGP)
short sternum  (IAGP)
spina bifida  (IAGP)
spina bifida occulta  (IAGP)
thick ventricular wall  (IAGP)
wavy neural tube  (IAGP)
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. Cao WH, etal., Zhonghua Shao Shang Za Zhi. 2005 Oct;21(5):359-62.
4. Chen CM, etal., Neonatology. 2007;92(3):187-93. Epub 2007 May 21.
5. Cook JL, etal., Brain Res Mol Brain Res. 1998 Mar 30;55(1):9-19.
6. Dembinski A, etal., J Physiol Pharmacol. 2006 Mar;57(1):39-58.
7. Fudge K, etal., Mod Pathol. 1994 Jun;7(5):549-54.
8. Heinig J, etal., Zentralbl Gynakol. 2000;122(8):413-8.
9. Katayose D, etal., Am J Physiol. 1993 Feb;264(2 Pt 1):L100-6.
10. Langham RG, etal., Nephrol Dial Transplant. 2003 Jul;18(7):1392-6.
11. Liang M, etal., Cancer Biol Ther. 2006 Jan;5(1):28-33. Epub 2006 Jan 12.
12. Liapis H, etal., Nephron. 1997;76(2):161-70.
13. MGD and Homologene mouse data transfer
14. MGD data from the GO Consortium
15. MGD IEA
16. Nazarenko I, etal., PLoS One. 2011 Apr 7;6(4):e18303. doi: 10.1371/journal.pone.0018303.
17. Pang H, etal., Clin Exp Pharmacol Physiol. 2007 May-Jun;34(5-6):393-8.
18. Pipeline to import KEGG annotations from KEGG into RGD
19. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
20. RGD automated import pipeline
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Savikko J, etal., Transplantation. 2002 Feb 27;73(4):506-11.
24. Wagner W and Wehrmann M, J Cell Mol Med. 2007 Nov-Dec;11(6):1342-51.
Additional References at PubMed
PMID:1292572   PMID:1302014   PMID:1324805   PMID:1340209   PMID:1451656   PMID:1535334   PMID:1611719   PMID:1683707   PMID:1879607   PMID:1986867   PMID:2155144   PMID:2996133  
PMID:6093261   PMID:7588258   PMID:7640655   PMID:7649812   PMID:7720681   PMID:7844163   PMID:7958864   PMID:8007964   PMID:8011581   PMID:8032683   PMID:8106451   PMID:8206913  
PMID:8654889   PMID:8662221   PMID:8681381   PMID:8689409   PMID:8706788   PMID:8786423   PMID:8889548   PMID:8900172   PMID:8901196   PMID:8933762   PMID:8954727   PMID:9142500  
PMID:9192668   PMID:9286595   PMID:9374392   PMID:9620692   PMID:9734598   PMID:9812194   PMID:9853970   PMID:9876175   PMID:9988218   PMID:10051313   PMID:10067860   PMID:10208749  
PMID:10331973   PMID:10349636   PMID:10362801   PMID:10383162   PMID:10395790   PMID:10419690   PMID:10666377   PMID:10806482   PMID:10831606   PMID:10903171   PMID:10922068   PMID:10926756  
PMID:10984614   PMID:11042159   PMID:11060232   PMID:11069109   PMID:11076861   PMID:11217851   PMID:11239463   PMID:11744381   PMID:11803579   PMID:11830569   PMID:11940581   PMID:12037011  
PMID:12101409   PMID:12176888   PMID:12466851   PMID:12477932   PMID:12651897   PMID:12812790   PMID:12904583   PMID:14514732   PMID:14522834   PMID:14523011   PMID:14610273   PMID:14963008  
PMID:15361870   PMID:15486046   PMID:15525682   PMID:15533830   PMID:15536133   PMID:15543606   PMID:15637050   PMID:15790963   PMID:15811134   PMID:15890262   PMID:15932761   PMID:15979417  
PMID:15987744   PMID:16141072   PMID:16141073   PMID:16344272   PMID:16387292   PMID:16462734   PMID:16481423   PMID:17560563   PMID:17852407   PMID:17916632   PMID:17994097   PMID:18194151  
PMID:18287559   PMID:18297729   PMID:18367558   PMID:18460333   PMID:18521186   PMID:18559345   PMID:18625210   PMID:18799693   PMID:18804439   PMID:18927153   PMID:19019919   PMID:19217431  
PMID:19272526   PMID:19498055   PMID:19501082   PMID:19734317   PMID:19752192   PMID:19998489   PMID:20412779   PMID:20487000   PMID:20619341   PMID:20643125   PMID:20981831   PMID:21187969  
PMID:21267068   PMID:21308778   PMID:21310900   PMID:21438071   PMID:21491542   PMID:21677750   PMID:21873635   PMID:21931722   PMID:21985298   PMID:22096492   PMID:22264326   PMID:22682244  
PMID:22730381   PMID:22949635   PMID:22964636   PMID:23266329   PMID:23274689   PMID:23465490   PMID:23525041   PMID:23529017   PMID:23733391   PMID:23748534   PMID:23819440   PMID:23938297  
PMID:24086166   PMID:24093435   PMID:24644058   PMID:24886827   PMID:24952961   PMID:25116623   PMID:25166724   PMID:25336526   PMID:25453829   PMID:25499914   PMID:25631042   PMID:25686533  
PMID:25975959   PMID:26049020   PMID:26764350   PMID:26769046   PMID:26988758   PMID:27746098   PMID:27816607   PMID:27829154   PMID:28098558   PMID:28323616   PMID:28887481   PMID:28947535  
PMID:29636361   PMID:30022023   PMID:30080858   PMID:30228991   PMID:30796970   PMID:30834523   PMID:30913328   PMID:31331942   PMID:32067289   PMID:32186397   PMID:32274496   PMID:32294451  
PMID:32295602   PMID:32394892   PMID:32497091   PMID:32768399   PMID:33057360   PMID:33168840   PMID:33707239  


Genomics

Comparative Map Data
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
(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
(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
(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
Pdgfa  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5G2UniSTS
cM Map582.0UniSTS
cM Map582.0UniSTS
Pdgfa  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5G2UniSTS
cM Map582.0UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301715Elmaz2_melevated maze behavior 2 (mouse)Not determined5125101165141714711Mouse
1301857Bglq14_mbody growth late QTL 14 (mouse)Not determined5118920110151834684Mouse
1301543Hypch_mhypercholesterolemia (mouse)Not determined5109090758139133150Mouse
1301986Bpq4_mblood pressure QTL 4 (mouse)Not determined5121556974151834684Mouse
1302079Lbw3_mlupus NZB x NZW 3 (mouse)Not determined5124714580151834684Mouse
4141081Nidd7k_mNidd7 on KK-A (mouse)Not determined119806972149423861Mouse
4141218Ath24_matherosclerosis 24 (mouse)Not determined129583274151834684Mouse
1301362Prnr1_mprion resistance 1 (mouse)Not determined589271017146851125Mouse
1301363Pbwg13_mpostnatal body weight growth 13 (mouse)Not determined5125147702151834684Mouse
1300913Bwefm_mbody weight females and males day 10 (mouse)Not determined5109362284143362395Mouse
1301226Bbaa2_mB.burgdorferi-associated arthritis 2 (mouse)Not determined5115128044149128176Mouse
1300827Cora1_mcorrelation in cytokine production 1 (mouse)Not determined5115128044149128176Mouse
10043890Trigq4_mtriglyceride QTL 4 (mouse)Not determined5107829235141829348Mouse
10412191Bbaa24_mB.burgdorferi-associated arthritis 24 (mouse)Not determined5119806972141714711Mouse
10412197Bbaa25_mB.burgdorferi-associated arthritis 25 (mouse)Not determined5109090176143090317Mouse
4142473Chlq11_mcirculating hormone level QTL 11 (mouse)Not determined5107829235141829348Mouse
11049557Lmr26_mleishmaniasis resistance 26 (mouse)5134002093151834684Mouse
11528552Scram1_mspinal cord resistance to astrocytoma modifier 1 (mouse)5121457140151834684Mouse
12880406Jcdq2_mjoint cartilage degeneration QTL 2 (mouse)5129851021151834684Mouse
13464251Ahl21_mage related hearing loss, early onset 21 (mouse)5109090176143090317Mouse
13464243Ahl20_mage related hearing loss, early onset 20 (mouse)5107829235141829348Mouse
27226719Tibw6_mtibia width 6, proximal, 16 week (mouse)572700000140000000Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1335
Count of miRNA genes:503
Interacting mature miRNAs:606
Transcripts:ENSMUST00000046901, ENSMUST00000076095, ENSMUST00000110896, ENSMUST00000110897, ENSMUST00000124080, ENSMUST00000132051, ENSMUST00000144934
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


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001363271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_008808 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_156469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006504659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011240971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_030254198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_030254199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_036164870 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC117698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH004413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK017169 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK142653 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY324648 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC003817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M29464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000046901   ⟹   ENSMUSP00000038870
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5138,962,271 - 138,980,708 (-)Ensembl
GRCm38.p6 Ensembl5138,976,516 - 138,994,953 (-)Ensembl
RefSeq Acc Id: ENSMUST00000076095   ⟹   ENSMUSP00000075463
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5138,961,769 - 138,980,792 (-)Ensembl
GRCm38.p6 Ensembl5138,976,014 - 138,995,037 (-)Ensembl
RefSeq Acc Id: ENSMUST00000110896   ⟹   ENSMUSP00000106521
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5138,962,726 - 138,983,125 (-)Ensembl
GRCm38.p6 Ensembl5138,976,971 - 138,997,370 (-)Ensembl
RefSeq Acc Id: ENSMUST00000110897   ⟹   ENSMUSP00000106522
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5138,962,697 - 138,981,842 (-)Ensembl
GRCm38.p6 Ensembl5138,976,942 - 138,996,087 (-)Ensembl
RefSeq Acc Id: ENSMUST00000124080
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5138,972,025 - 138,980,239 (-)Ensembl
GRCm38.p6 Ensembl5138,986,270 - 138,994,484 (-)Ensembl
RefSeq Acc Id: ENSMUST00000132051
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5138,974,196 - 138,981,756 (-)Ensembl
GRCm38.p6 Ensembl5138,988,441 - 138,996,001 (-)Ensembl
RefSeq Acc Id: ENSMUST00000144934
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5138,962,900 - 138,980,036 (-)Ensembl
GRCm38.p6 Ensembl5138,977,145 - 138,994,281 (-)Ensembl
RefSeq Acc Id: NM_001363271   ⟹   NP_001350200
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395138,961,769 - 138,980,699 (-)NCBI
GRCm385138,976,014 - 138,994,944 (-)NCBI
Sequence:
RefSeq Acc Id: NM_008808   ⟹   NP_032834
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395138,961,769 - 138,980,699 (-)NCBI
GRCm385138,976,014 - 138,994,944 (-)NCBI
MGSCv375139,452,925 - 139,470,907 (-)RGD
Celera5136,032,139 - 136,049,986 (-)RGD
cM Map5 ENTREZGENE
Sequence:
RefSeq Acc Id: NR_156469
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395138,961,769 - 138,980,036 (-)NCBI
GRCm385138,976,014 - 138,994,281 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006504659   ⟹   XP_006504722
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395138,962,136 - 138,981,896 (-)NCBI
GRCm385138,976,381 - 138,996,125 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011240971   ⟹   XP_011239273
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395138,962,136 - 138,986,336 (-)NCBI
GRCm385138,976,381 - 139,000,792 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030254198   ⟹   XP_030110058
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395138,962,136 - 138,981,896 (-)NCBI
GRCm385138,976,381 - 138,996,134 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030254199   ⟹   XP_030110059
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395138,962,136 - 138,986,336 (-)NCBI
GRCm385138,976,381 - 139,000,792 (-)NCBI
Sequence:
RefSeq Acc Id: XM_036164870   ⟹   XP_036020763
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395138,962,136 - 138,986,336 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_032834   ⟸   NM_008808
- Peptide Label: isoform 1 precursor
- UniProtKB: P20033 (UniProtKB/Swiss-Prot),   Q99L56 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006504722   ⟸   XM_006504659
- Peptide Label: isoform X1
- UniProtKB: G5E891 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011239273   ⟸   XM_011240971
- Peptide Label: isoform X1
- UniProtKB: G5E891 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001350200   ⟸   NM_001363271
- Peptide Label: isoform 2 precursor
RefSeq Acc Id: XP_030110059   ⟸   XM_030254199
- Peptide Label: isoform X2
RefSeq Acc Id: XP_030110058   ⟸   XM_030254198
- Peptide Label: isoform X2
RefSeq Acc Id: ENSMUSP00000038870   ⟸   ENSMUST00000046901
RefSeq Acc Id: ENSMUSP00000106521   ⟸   ENSMUST00000110896
RefSeq Acc Id: ENSMUSP00000106522   ⟸   ENSMUST00000110897
RefSeq Acc Id: ENSMUSP00000075463   ⟸   ENSMUST00000076095
RefSeq Acc Id: XP_036020763   ⟸   XM_036164870
- Peptide Label: isoform X1
Protein Domains
PDGF_2

Promoters
RGD ID:6888534
Promoter ID:EPDNEW_M7718
Type:initiation region
Name:Pdgfa_1
Description:Mus musculus platelet derived growth factor, alpha , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm385138,994,944 - 138,995,004EPDNEW
RGD ID:6838036
Promoter ID:MM_KWN:44578
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6
Transcripts:AK147342_6330403L08RIK,   OTTMUST00000061873,   OTTMUST00000061887,   OTTMUST00000061891,   OTTMUST00000061892
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv365139,469,986 - 139,476,192 (-)MPROMDB
RGD ID:6838020
Promoter ID:MM_KWN:44579
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   ES_Cell,   Lung,   MEF_B4,   MEF_B6
Transcripts:ENSMUST00000110897,   OTTMUST00000061890
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv365139,471,696 - 139,472,196 (-)MPROMDB
RGD ID:6838019
Promoter ID:MM_KWN:44580
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lung,   MEF_B6
Transcripts:ENSMUST00000110896
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv365139,473,004 - 139,473,504 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:97527 AgrOrtholog
Ensembl Genes ENSMUSG00000025856 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000038870 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000075463 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000106521 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000106522 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000046901 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000076095 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000110896 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000110897 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.10.90.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 mmu:18590 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:97527 ENTREZGENE
NCBI Gene 18590 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 G5E891 ENTREZGENE, UniProtKB/TrEMBL
  P20033 ENTREZGENE, UniProtKB/Swiss-Prot
  Q3UQ96_MOUSE UniProtKB/TrEMBL
  Q7TPH7_MOUSE UniProtKB/TrEMBL
  Q99L56 ENTREZGENE, UniProtKB/TrEMBL
  Q9CU96_MOUSE UniProtKB/TrEMBL