Pdgfb (platelet derived growth factor subunit B) - Rat Genome Database

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Gene: Pdgfb (platelet derived growth factor subunit B) Rattus norvegicus
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Symbol: Pdgfb
Name: platelet derived growth factor subunit B
RGD ID: 3283
Description: Enables signaling receptor binding activity. Involved in several processes, including positive regulation of biosynthetic process; positive regulation of cell migration; and response to peptide hormone. Located in several cellular components, including basolateral plasma membrane; dendrite; and neuronal cell body. Used to study asthma; brain infarction; glomerulonephritis; and visual epilepsy. Biomarker of cholestasis; hypertension (multiple); liver cirrhosis; oligohydramnios; and ureteral obstruction. Human ortholog(s) of this gene implicated in basal ganglia calcification; clear cell renal cell carcinoma; connective tissue cancer (multiple); familial meningioma; and prostatic hypertrophy. Orthologous to human PDGFB (platelet derived growth factor subunit B); PARTICIPATES IN platelet-derived growth factor signaling pathway; sphingosine 1-phosphate signaling pathway; glioma pathway; INTERACTS WITH (+)-dihydromyricetin; (S)-nicotine; 11-deoxycorticosterone.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: c-sis; pdgf protein; PDGF subunit B; PDGF-2; platelet derived growth factor, B polypeptide; platelet derived growth factor-bb; Platelet-derived growth factor; platelet-derived growth factor B chain; platelet-derived growth factor beta polypeptide; platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog); Platelet-derived growth factor same as Sis (Simian sarcoma viral oncogene homologue c-sis); platelet-derived growth factor subunit B; Platelet-derived growth factor, same as Sis (Simian sarcoma viral oncogene homologue, c-sis); SIS
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
mRatBN7.27111,539,444 - 111,557,984 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7111,540,345 - 111,557,984 (-)Ensembl
Rnor_6.07121,215,458 - 121,233,092 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7121,214,628 - 121,232,741 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07121,205,505 - 121,223,140 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47118,244,385 - 118,262,021 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17118,279,553 - 118,295,832 (-)NCBI
Celera7107,869,873 - 107,887,412 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
AIDS Dementia Complex  (ISO)
Alzheimer's disease  (ISO)
asthma  (IMP,ISO)
background diabetic retinopathy  (ISO)
basal ganglia calcification  (ISS)
basal ganglia disease  (ISO)
brain infarction  (IMP)
Brain Injuries  (IEP)
calcinosis  (ISO)
cholestasis  (IEP)
choriocarcinoma  (ISO)
Chronic Allograft Nephropathy  (IEP)
clear cell renal cell carcinoma  (ISO)
COVID-19  (ISO)
dermatofibrosarcoma protuberans  (ISO)
Diabetic Nephropathies  (ISO)
essential thrombocythemia  (ISO)
Experimental Autoimmune Encephalomyelitis  (IDA)
Experimental Diabetes Mellitus  (IDA,IEP,ISO)
familial meningioma  (ISO)
Fetal Growth Retardation  (ISO)
Fibrosis  (ISO)
Gingival Hyperplasia  (ISO)
glioblastoma  (ISO)
glomerulonephritis  (IMP)
Graft vs Host Disease  (ISO)
Head Injuries, Penetrating  (IEP)
hepatocellular carcinoma  (ISO)
hereditary breast ovarian cancer syndrome  (ISO)
high grade glioma  (ISO)
Hyperoxic Lung Injury  (IEP)
hypertension  (IEP)
Hypoxia-Ischemia, Brain  (IEP)
Idiopathic Basal Ganglia Calcification 1  (ISO)
Idiopathic Basal Ganglia Calcification 5  (ISO)
Inflammation  (ISO)
inflammatory bowel disease  (ISO)
Kidney Reperfusion Injury  (IEP)
Kuhnt-Junius degeneration  (ISO)
leiomyoma  (ISO)
Leydig cell tumor  (ISO)
liver cirrhosis  (IEP)
Liver Injury  (IEP)
Lymphatic Metastasis  (ISO)
meningioma  (ISO)
Neointima  (IEP)
Neoplasm Metastasis  (ISO)
oligohydramnios  (IEP)
Optic Nerve Injuries  (IEP)
pancreatitis  (ISO)
Periapical Diseases  (IEP)
proliferative diabetic retinopathy  (ISO)
prostate carcinoma  (ISO)
prostatic hypertrophy  (ISO)
pulmonary fibrosis  (ISO)
pulmonary hypertension  (IEP,ISO)
retinal disease  (ISO)
rheumatoid arthritis  (ISO)
sinusitis  (ISO)
Spinal Cord Injuries  (ISO)
Tibial Fractures  (ISO)
ureteral obstruction  (IEP)
visual epilepsy  (IMP)
Wounds and Injuries  (IEP,ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-dihydromyricetin  (EXP)
(+)-taxifolin  (ISO)
(R)-mevalonic acid  (ISO)
(S)-nicotine  (EXP,ISO)
11-deoxycorticosterone  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-trans,6-trans,10-trans-geranylgeranyl diphosphate  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (EXP,ISO)
6,7-dimethoxy-2-phenylquinoxaline  (ISO)
6-propyl-2-thiouracil  (EXP)
9-cis-retinoic acid  (ISO)
acetylsalicylic acid  (ISO)
acrylamide  (EXP)
ADP  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
anagrelide  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arotinoid acid  (ISO)
arsenite(3-)  (ISO)
BAPTA  (EXP)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bivalirudin  (EXP)
buta-1,3-diene  (ISO)
butan-1-ol  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
carvedilol  (ISO)
chloroprene  (ISO)
choline  (ISO)
chondroitin sulfate  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clopidogrel  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
curcumin  (EXP)
cyanidin cation  (ISO)
cyclosporin A  (ISO)
Deguelin  (ISO)
delphinidin  (ISO)
desferrioxamine B  (EXP)
dextran sulfate  (ISO)
dibutyl phthalate  (ISO)
diethyl malate  (ISO)
dihydrolipoic acid  (EXP)
dimethyl fumarate  (ISO)
dioxygen  (ISO)
divanadium pentaoxide  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
emodin  (EXP)
endosulfan  (EXP)
ethanol  (ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (ISO)
fenhexamid  (ISO)
ferroheme b  (ISO)
folic acid  (ISO)
gadolinium trichloride  (EXP)
genistein  (ISO)
glycyrrhetinate  (ISO)
glycyrrhetinic acid  (ISO)
heme b  (ISO)
hemin  (ISO)
heparin  (EXP)
hydrogen peroxide  (EXP)
L-cysteine  (EXP)
L-methionine  (EXP,ISO)
Licochalcone B  (ISO)
lipopolysaccharide  (ISO)
lipoxin A4  (ISO)
losartan  (EXP)
luteolin  (EXP)
LY294002  (EXP,ISO)
mabuterol  (EXP)
malvidin  (ISO)
medroxyprogesterone acetate  (ISO)
mercury dibromide  (ISO)
methamphetamine  (EXP,ISO)
methotrexate  (ISO)
methoxychlor  (EXP)
methylmercury chloride  (ISO)
morphine  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodimethylamine  (EXP)
nebivolol  (ISO)
nickel atom  (EXP)
nickel dichloride  (ISO)
nicotine  (EXP,ISO)
nitrofen  (EXP)
oleic acid  (ISO)
ozone  (ISO)
palbociclib  (ISO)
Panaxynol  (EXP)
paraquat  (EXP)
peonidin  (ISO)
peonidin chloride  (ISO)
perindopril  (EXP)
phenobarbital  (EXP)
phenylmercury acetate  (ISO)
phenytoin  (EXP,ISO)
phorbol 13-acetate 12-myristate  (EXP,ISO)
phosgene  (ISO)
picoxystrobin  (ISO)
pioglitazone  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
pyrimidifen  (ISO)
quercetin  (ISO)
ramipril  (ISO)
reactive oxygen species  (EXP,ISO)
resveratrol  (ISO)
rotenone  (ISO)
Salvianolic acid A  (EXP)
salvianolic acid B  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
serpentine asbestos  (EXP,ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP,ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sorafenib  (ISO)
sunitinib  (ISO)
tetrachloromethane  (EXP,ISO)
thifluzamide  (ISO)
thioacetamide  (ISO)
titanium dioxide  (ISO)
trichloroethene  (ISO)
triclosan  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vildagliptin  (ISO)
warfarin  (EXP)
Y-27632  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin cytoskeleton organization  (ISO)
activation of protein kinase activity  (ISO,ISS)
activation of protein kinase B activity  (IEA,ISO,ISS)
blood vessel development  (ISO)
blood vessel morphogenesis  (ISO)
branching involved in salivary gland morphogenesis  (ISO)
cell chemotaxis  (ISO,ISS)
cell projection assembly  (ISO)
cellular response to angiotensin  (IEP)
cellular response to growth factor stimulus  (IEA,ISO)
cellular response to mechanical stimulus  (IEP)
cellular response to mycophenolic acid  (IDA)
embryonic placenta development  (ISO,ISS)
epithelial cell proliferation involved in salivary gland morphogenesis  (ISO)
eye photoreceptor cell development  (ISO)
glial cell development  (ISO)
heart development  (ISO,ISS)
hemopoiesis  (ISO,ISS)
interleukin-18-mediated signaling pathway  (IEA,ISO)
male gonad development  (IEP)
metanephric glomerular endothelium development  (ISO)
metanephric glomerular mesangial cell development  (ISO,ISS)
metanephric glomerular mesangial cell proliferation involved in metanephros development  (ISO)
monocyte chemotaxis  (IEA,ISO,ISS)
negative regulation of cell migration  (ISO)
negative regulation of gene expression  (IEA,ISO)
negative regulation of phosphatidylinositol biosynthetic process  (IEA,ISO,ISS)
negative regulation of platelet activation  (IEA,ISO,ISS)
negative regulation of pri-miRNA transcription by RNA polymerase II  (IEA,ISO)
negative regulation of protein binding  (IEA,ISO)
negative regulation of transcription, DNA-templated  (ISO,ISS)
negative regulation of vascular associated smooth muscle cell differentiation  (IEA,ISO)
neuron remodeling  (ISO)
paracrine signaling  (ISO,ISS)
peptidyl-serine phosphorylation  (IEA,ISO,ISS)
peptidyl-tyrosine phosphorylation  (IEA,ISO,ISS)
platelet-derived growth factor receptor signaling pathway  (IBA,IMP,ISO)
positive chemotaxis  (IEA)
positive regulation of blood vessel endothelial cell migration  (IEA,ISO,ISS)
positive regulation of calcium ion import  (IEA,ISO,ISS)
positive regulation of cell division  (IEA)
positive regulation of cell migration  (IBA,ISO)
positive regulation of cell population proliferation  (IBA,ISO,ISS)
positive regulation of cell-substrate adhesion  (IEA,ISO)
positive regulation of chemotaxis  (IEA,ISO,ISS)
positive regulation of collagen biosynthetic process  (IMP)
positive regulation of cyclin-dependent protein serine/threonine kinase activity  (IEA,ISO,ISS)
positive regulation of DNA biosynthetic process  (IEA,ISO,ISS)
positive regulation of DNA replication  (IMP)
positive regulation of endothelial cell proliferation  (IEA,ISO,ISS)
positive regulation of ERK1 and ERK2 cascade  (IBA,IEA,ISO,ISS)
positive regulation of fibroblast growth factor receptor signaling pathway  (ISO)
positive regulation of fibroblast proliferation  (IEA,ISO,ISS)
positive regulation of gene expression  (IEA,ISO)
positive regulation of glomerular filtration  (ISO,ISS)
positive regulation of glomerular mesangial cell proliferation  (IEA,ISO,ISS)
positive regulation of hepatic stellate cell activation  (IMP)
positive regulation of hepatic stellate cell proliferation  (IMP)
positive regulation of hyaluronan biosynthetic process  (IEA,ISO,ISS)
positive regulation of MAP kinase activity  (IBA,IDA,IEA,ISO)
positive regulation of MAPK cascade  (ISO,ISS)
positive regulation of metanephric mesenchymal cell migration  (IDA,ISO)
positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway  (IEA,ISO,ISS)
positive regulation of mitotic cell cycle, embryonic  (ISO)
positive regulation of mitotic nuclear division  (IEA,ISO,ISS)
positive regulation of peptidyl-tyrosine phosphorylation  (ISO)
positive regulation of phosphatidylinositol 3-kinase activity  (IEA,ISO,ISS)
positive regulation of phosphatidylinositol 3-kinase signaling  (IBA,IEA,ISO,ISS)
positive regulation of pri-miRNA transcription by RNA polymerase II  (IEA,ISO)
positive regulation of protein autophosphorylation  (IBA,IEA,ISO,ISS)
positive regulation of protein tyrosine kinase activity  (IEA,ISO,ISS)
positive regulation of reactive oxygen species metabolic process  (IEA,ISO,ISS)
positive regulation of smooth muscle cell migration  (IMP,ISO)
positive regulation of smooth muscle cell proliferation  (IMP,ISO)
positive regulation of transcription, DNA-templated  (IDA,ISO)
positive regulation of vascular associated smooth muscle cell dedifferentiation  (IEA,ISO)
positive regulation of vascular associated smooth muscle cell migration  (IEA,ISO)
positive regulation of vascular associated smooth muscle cell proliferation  (IEA,ISO)
protein kinase C signaling  (IEA,ISO)
protein phosphorylation  (ISO,ISS)
reactive oxygen species metabolic process  (IEA,ISO,ISS)
regulation of cell population proliferation  (IEP)
regulation of peptidyl-tyrosine phosphorylation  (ISO)
response to axon injury  (IEP)
response to estradiol  (IEP)
response to estrogen  (IEP)
response to human chorionic gonadotropin  (IEP)
response to hypoxia  (IEP)
response to insulin  (IEP)
response to organic cyclic compound  (IEP)
response to organic substance  (IEP)
response to wounding  (IEA,ISO,ISS)
response to xenobiotic stimulus  (IEP)
retina development in camera-type eye  (ISO)
retina vasculature development in camera-type eye  (ISO)
substrate-dependent cell migration  (ISO)
synapse assembly  (ISO)
wound healing  (IEP)

Cellular Component

References

References - curated
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95. Zhu L, etal., Oncol Rep. 2006 May;15(5):1217-23.
Additional References at PubMed
PMID:291037   PMID:1396586   PMID:2439522   PMID:2536956   PMID:2538439   PMID:2836953   PMID:7073684   PMID:7679113   PMID:8889548   PMID:8900172   PMID:9409235   PMID:9685360  
PMID:9693135   PMID:10375497   PMID:10644978   PMID:10734101   PMID:11264163   PMID:11788434   PMID:11903042   PMID:11940581   PMID:12070119   PMID:12171932   PMID:12176888   PMID:12753322  
PMID:14751865   PMID:15021824   PMID:15084468   PMID:15183724   PMID:15681847   PMID:15919073   PMID:16019429   PMID:16368696   PMID:16456542   PMID:16530387   PMID:16644864   PMID:16893901  
PMID:16971352   PMID:16990553   PMID:17324121   PMID:17442164   PMID:17533428   PMID:17654489   PMID:17893914   PMID:17942966   PMID:17991872   PMID:18180311   PMID:18483410   PMID:18559345  
PMID:18775895   PMID:18827006   PMID:19019919   PMID:19088079   PMID:19133316   PMID:19426591   PMID:19442606   PMID:19691150   PMID:19880494   PMID:20307544   PMID:20452974   PMID:20718713  
PMID:20860549   PMID:21092652   PMID:21158157   PMID:21245329   PMID:21245381   PMID:21321938   PMID:21351537   PMID:21435466   PMID:21451101   PMID:21792920   PMID:21803557   PMID:22488213  
PMID:22619279   PMID:23103565   PMID:23139410   PMID:23179587   PMID:23298764   PMID:23460471   PMID:23554459   PMID:23979707   PMID:24008408   PMID:24100802   PMID:24248537   PMID:24397990  
PMID:24472833   PMID:24591339   PMID:25089138   PMID:25224828   PMID:25684702   PMID:25899145   PMID:26262503   PMID:26311435   PMID:26493107   PMID:28738389   PMID:28791754   PMID:29786113  
PMID:30257103   PMID:32647179  


Genomics

Comparative Map Data
Pdgfb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27111,539,444 - 111,557,984 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl7111,540,345 - 111,557,984 (-)Ensembl
Rnor_6.07121,215,458 - 121,233,092 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7121,214,628 - 121,232,741 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07121,205,505 - 121,223,140 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47118,244,385 - 118,262,021 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17118,279,553 - 118,295,832 (-)NCBI
Celera7107,869,873 - 107,887,412 (-)NCBICelera
Cytogenetic Map7q34NCBI
PDGFB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2239,223,359 - 39,244,982 (-)EnsemblGRCh38hg38GRCh38
GRCh382239,223,359 - 39,244,982 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372239,619,364 - 39,640,987 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362237,949,665 - 37,970,936 (-)NCBINCBI36hg18NCBI36
Build 342237,944,218 - 37,961,419NCBI
Celera2223,421,845 - 23,443,115 (-)NCBI
Cytogenetic Map22q13.1ENTREZGENE
HuRef2222,586,719 - 22,607,974 (-)NCBIHuRef
CHM1_12239,578,202 - 39,599,467 (-)NCBICHM1_1
Pdgfb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391579,880,066 - 79,899,178 (-)NCBIGRCm39mm39
GRCm39 Ensembl1579,880,075 - 79,899,178 (-)Ensembl
GRCm381579,995,865 - 80,024,614 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1579,995,874 - 80,014,977 (-)EnsemblGRCm38mm10GRCm38
MGSCv371579,826,304 - 79,845,238 (-)NCBIGRCm37mm9NCBIm37
MGSCv361579,823,129 - 79,842,063 (-)NCBImm8
Celera1582,118,153 - 82,136,874 (-)NCBICelera
Cytogenetic Map15E1NCBI
cM Map1537.85NCBI
Pdgfb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541325,148,062 - 25,166,987 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541325,150,702 - 25,166,987 (-)NCBIChiLan1.0ChiLan1.0
PDGFB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12237,944,018 - 37,964,883 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2237,944,018 - 37,964,883 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02220,127,223 - 20,148,407 (-)NCBIMhudiblu_PPA_v0panPan3
PDGFB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11025,798,877 - 25,819,422 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1025,798,938 - 25,817,746 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1025,734,794 - 25,753,108 (+)NCBI
ROS_Cfam_1.01026,550,122 - 26,571,489 (+)NCBI
UMICH_Zoey_3.11026,264,832 - 26,283,141 (+)NCBI
UNSW_CanFamBas_1.01026,584,490 - 26,602,860 (+)NCBI
UU_Cfam_GSD_1.01026,760,558 - 26,778,890 (+)NCBI
Pdgfb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049459,343,420 - 9,358,195 (+)NCBI
SpeTri2.0NW_0049364922,353,840 - 2,368,573 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDGFB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl58,986,461 - 9,007,446 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa10.256,330,898 - 6,333,239 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDGFB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11921,865,792 - 21,888,068 (-)NCBI
ChlSab1.1 Ensembl1921,863,768 - 21,886,395 (-)Ensembl
Vero_WHO_p1.0NW_023666045103,877,990 - 103,890,183 (+)NCBI
Pdgfb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247529,072,471 - 9,088,289 (+)NCBI


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)780221299112308525Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)769736356112729554Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)794811085116738842Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:253
Count of miRNA genes:170
Interacting mature miRNAs:194
Transcripts:ENSRNOT00000023196
Prediction methods:Microtar, 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 23 3 1 4 50 29 18 11 1
Low 3 20 50 34 16 34 7 7 24 6 23 7
Below cutoff 7 7 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000023196   ⟹   ENSRNOP00000023196
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7111,540,345 - 111,557,984 (-)Ensembl
Rnor_6.0 Ensembl7121,214,628 - 121,232,741 (-)Ensembl
RefSeq Acc Id: NM_031524   ⟹   NP_113712
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27111,540,344 - 111,557,984 (-)NCBI
Rnor_6.07121,215,458 - 121,233,092 (-)NCBI
Rnor_5.07121,205,505 - 121,223,140 (-)NCBI
RGSC_v3.47118,244,385 - 118,262,021 (-)RGD
Celera7107,869,873 - 107,887,412 (-)RGD
Sequence:
RefSeq Acc Id: XM_039078420   ⟹   XP_038934348
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27111,539,444 - 111,549,272 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113712   ⟸   NM_031524
- Peptide Label: precursor
- UniProtKB: Q05028 (UniProtKB/Swiss-Prot),   G3V882 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023196   ⟸   ENSRNOT00000023196
RefSeq Acc Id: XP_038934348   ⟸   XM_039078420
- Peptide Label: isoform X1
Protein Domains
PDGF_2

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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)
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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
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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
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)
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
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)
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
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)
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)
SS/JrHsdMcwi (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
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)
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/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
WKY/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
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)
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
WN/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
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3283 AgrOrtholog
Ensembl Genes ENSRNOG00000017197 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000023196 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023196 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
  PDGF_suB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24628 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 24628 ENTREZGENE
PANTHER PTHR11633:SF2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PDGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDGF_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pdgfb 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 G3V882 ENTREZGENE, UniProtKB/TrEMBL
  PDGFB_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-25 Pdgfb  platelet derived growth factor subunit B  Pdgfb  platelet-derived growth factor beta polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-02 Pdgfb  platelet-derived growth factor beta polypeptide  Pdgfb  platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-08-29 Pdgfb  platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)  Pdgfb  platelet derived growth factor, B polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Pdgfb  Platelet-derived growth factor      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process increases the expression and mRNA stability of Ramp3 631307