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

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Gene: Pdgfb (platelet derived growth factor subunit B) Ictidomys tridecemlineatus
Analyze
Symbol: Pdgfb
Name: platelet derived growth factor subunit B
RGD ID: 12583545
Description: ENCODES a protein that exhibits signaling receptor binding (ortholog); INVOLVED IN actin cytoskeleton organization (ortholog); blood vessel development (ortholog); blood vessel morphogenesis (ortholog); PARTICIPATES IN platelet-derived growth factor signaling pathway; sphingosine 1-phosphate signaling pathway; ASSOCIATED WITH adenylosuccinase lyase deficiency (ortholog); AIDS Dementia Complex (ortholog); Alzheimer's disease (ortholog); FOUND IN basolateral plasma membrane (ortholog); cytoplasm (ortholog); dendrite (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: platelet-derived growth factor subunit B
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049459,343,420 - 9,358,195 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364922,353,841 - 2,368,573 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364922,353,840 - 2,368,573 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Pdgfb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049459,343,420 - 9,358,195 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364922,353,841 - 2,368,573 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364922,353,840 - 2,368,573 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDGFB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382239,223,359 - 39,244,982 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2239,223,359 - 39,244,982 (-)EnsemblGRCh38hg38GRCh38
GRCh372239,619,364 - 39,640,987 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362237,949,665 - 37,970,936 (-)NCBINCBI36Build 36hg18NCBI36
Build 342237,944,218 - 37,961,419NCBI
Celera2223,421,845 - 23,443,115 (-)NCBICelera
Cytogenetic Map22q13.1ENTREZGENE
HuRef2222,586,719 - 22,607,974 (-)NCBIHuRef
CHM1_12239,578,202 - 39,599,467 (-)NCBICHM1_1
T2T-CHM13v2.02239,694,033 - 39,715,652 (-)NCBIT2T-CHM13v2.0
Pdgfb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391579,880,066 - 79,899,178 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1579,880,075 - 79,899,178 (-)EnsemblGRCm39 Ensembl
GRCm381579,995,865 - 80,024,614 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1579,995,874 - 80,014,977 (-)EnsemblGRCm38mm10GRCm38
MGSCv371579,826,304 - 79,845,238 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361579,823,129 - 79,842,063 (-)NCBIMGSCv36mm8
Celera1582,118,153 - 82,136,874 (-)NCBICelera
Cytogenetic Map15E1NCBI
cM Map1537.85NCBI
Pdgfb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87113,419,882 - 113,438,343 (-)NCBIGRCr8
mRatBN7.27111,539,444 - 111,557,984 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7111,540,345 - 111,557,984 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7113,288,390 - 113,306,033 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07115,511,934 - 115,529,580 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07115,481,281 - 115,498,926 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17118,279,553 - 118,295,832 (-)NCBI
Celera7107,869,873 - 107,887,412 (-)NCBICelera
Cytogenetic Map7q34NCBI
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
NHGRI_mPanPan1-v22349,068,209 - 49,089,303 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12251,759,600 - 51,779,759 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02220,127,223 - 20,148,407 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12237,944,018 - 37,964,883 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2237,944,018 - 37,964,883 (-)Ensemblpanpan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01026,550,122 - 26,571,489 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1026,551,117 - 26,571,479 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11026,264,832 - 26,283,141 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01026,584,490 - 26,602,860 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01026,760,558 - 26,778,890 (+)NCBIUU_Cfam_GSD_1.0
PDGFB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl58,986,462 - 9,007,435 (+)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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1921,863,768 - 21,886,395 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666045103,877,990 - 103,890,183 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pdgfb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247529,072,512 - 9,088,593 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247529,072,471 - 9,088,289 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSSTOT00000021992   ⟹   ENSSTOP00000019197
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049364922,353,841 - 2,368,573 (+)Ensembl
RefSeq Acc Id: XM_040281797   ⟹   XP_040137731
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_0244049459,343,420 - 9,358,195 (+)NCBI
Protein Sequences
Protein RefSeqs XP_040137731 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000019197.2
GenBank Protein KAG3290909 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_040137731   ⟸   XM_040281797
Ensembl Acc Id: ENSSTOP00000019197   ⟸   ENSSTOT00000021992
Protein Domains
Platelet-derived growth factor (PDGF) family


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000022345 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000021992.2 UniProtKB/TrEMBL
Gene3D-CATH 2.10.90.10 UniProtKB/TrEMBL
InterPro Cystine-knot_cytokine UniProtKB/TrEMBL
  PD_growth_factor_CS UniProtKB/TrEMBL
  PDGF/VEGF_dom UniProtKB/TrEMBL
  PDGF_N UniProtKB/TrEMBL
NCBI Gene Pdgfb ENTREZGENE
PANTHER PLATELET-DERIVED GROWTH FACTOR UniProtKB/TrEMBL
  PTHR11633:SF2 UniProtKB/TrEMBL
Pfam PDGF UniProtKB/TrEMBL
  PDGF_N UniProtKB/TrEMBL
PROSITE PDGF_1 UniProtKB/TrEMBL
  PDGF_2 UniProtKB/TrEMBL
SMART PDGF UniProtKB/TrEMBL
Superfamily-SCOP SSF57501 UniProtKB/TrEMBL
UniProt I3N4A1_ICTTR UniProtKB/TrEMBL