Pdgfd (platelet derived growth factor D) - Rat Genome Database

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Gene: Pdgfd (platelet derived growth factor D) Rattus norvegicus
Analyze
Symbol: Pdgfd
Name: platelet derived growth factor D
RGD ID: 621880
Description: Predicted to enable platelet-derived growth factor receptor binding activity. Involved in several processes, including cellular response to growth factor stimulus; positive regulation of cell migration; and positive regulation of cell population proliferation. Located in extracellular space. Used to study glomerulonephritis and mesangial proliferative glomerulonephritis. Biomarker of liver cirrhosis; mesangial proliferative glomerulonephritis; and myocardial infarction. Human ortholog(s) of this gene implicated in prostatic hypertrophy. Orthologous to human PDGFD (platelet derived growth factor D); PARTICIPATES IN platelet-derived growth factor signaling pathway; melanoma pathway; prostate cancer pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; aflatoxin B1.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: iris-expressed growth factor; PDGF-D; platelet-derived growth factor D; platelet-derived growth factor, D polypeptide; rSCDGF-B; SCDGF-B; Scdgfb; spinal cord-derived growth factor B; spinal-cord derived growth factor-B protein
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
mRatBN7.283,488,448 - 3,722,395 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl83,488,423 - 3,722,395 (+)Ensembl
Rnor_6.084,441,010 - 4,666,754 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl84,440,876 - 4,669,014 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.084,454,510 - 4,682,165 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.483,326,218 - 3,341,300 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.183,125,520 - 3,341,300 (+)NCBI
Celera85,067,751 - 5,287,344 (+)NCBICelera
Cytogenetic Map8q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
extracellular space  (IBA,IDA)
membrane  (IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. PDGF-D inhibition by CR002 ameliorates tubulointerstitial fibrosis following experimental glomerulonephritis. Boor P, etal., Nephrol Dial Transplant. 2007 May;22(5):1323-31. Epub 2007 Feb 17.
2. Pro-fibrogenic potential of PDGF-D in liver fibrosis. Borkham-Kamphorst E, etal., J Hepatol. 2007 Jun;46(6):1064-74. Epub 2007 Feb 23.
3. Expression patterns of PDGF-A, -B, -C and -D and the PDGF-receptors alpha and beta in activated rat hepatic stellate cells (HSC). Breitkopf K, etal., Cytokine. 2005 Sep 7;31(5):349-57.
4. PDGF-D contributes to neointimal hyperplasia in rat model of vessel injury. Chen J, etal., Biochem Biophys Res Commun. 2005 Apr 15;329(3):976-83.
5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Molecular cloning of SCDGF-B, a novel growth factor homologous to SCDGF/PDGF-C/fallotein. Hamada T, etal., Biochem Biophys Res Commun 2001 Jan 26;280(3):733-7.
7. The expression of SCDGF/PDGF-C/fallotein and SCDGF-B/PDGF-D in the rat central nervous system. Hamada T, etal., Mech Dev 2002 Mar;112(1-2):161-4.
8. A novel function for platelet-derived growth factor D: induction of osteoclastic differentiation for intraosseous tumor growth. Huang W, etal., Oncogene. 2012 Oct 18;31(42):4527-35. doi: 10.1038/onc.2011.573. Epub 2011 Dec 12.
9. Inducible platelet-derived growth factor D-chain expression by angiotensin II and hydrogen peroxide involves transcriptional regulation by Ets-1 and Sp1. Liu MY, etal., Blood. 2006 Mar 15;107(6):2322-9. Epub 2005 Sep 27.
10. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
11. Differential tumorigenic potential and matriptase activation between PDGF B versus PDGF D in prostate cancer. Najy AJ, etal., Mol Cancer Res. 2012 Aug;10(8):1087-97. doi: 10.1158/1541-7786.MCR-12-0071. Epub 2012 Jun 11.
12. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. A fully human monoclonal antibody (CR002) identifies PDGF-D as a novel mediator of mesangioproliferative glomerulonephritis. Ostendorf T, etal., J Am Soc Nephrol. 2003 Sep;14(9):2237-47.
14. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
15. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
16. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
18. Comprehensive gene review and curation RGD comprehensive gene curation
19. Angiotensin II-inducible platelet-derived growth factor-D transcription requires specific Ser/Thr residues in the second zinc finger region of Sp1. Tan NY, etal., Circ Res. 2008 Feb 29;102(4):e38-51. doi: 10.1161/CIRCRESAHA.107.167395. Epub 2008 Feb 7.
20. PDGF-A, -C, and -D but not PDGF-B increase TGF-beta1 and chronic rejection in rat cardiac allografts. Tuuminen R, etal., Arterioscler Thromb Vasc Biol. 2009 May;29(5):691-8. doi: 10.1161/ATVBAHA.108.178558. Epub 2009 Feb 12.
21. A novel signaling axis of matriptase/PDGF-D/ß-PDGFR in human prostate cancer. Ustach CV, etal., Cancer Res. 2010 Dec 1;70(23):9631-40. doi: 10.1158/0008-5472.CAN-10-0511. Epub 2010 Nov 23.
22. Induction of progressive glomerulonephritis by podocyte-specific overexpression of platelet-derived growth factor-D. van Roeyen CR, etal., Kidney Int. 2011 Dec;80(12):1292-305. doi: 10.1038/ki.2011.278. Epub 2011 Aug 24.
23. Platelet-derived growth factor-D promotes fibrogenesis of cardiac fibroblasts. Zhao T, etal., Am J Physiol Heart Circ Physiol. 2013 Jun 15;304(12):H1719-26. doi: 10.1152/ajpheart.00130.2013. Epub 2013 Apr 12.
24. Platelet-derived growth factor involvement in myocardial remodeling following infarction. Zhao W, etal., J Mol Cell Cardiol. 2011 Nov;51(5):830-8. doi: 10.1016/j.yjmcc.2011.06.023. Epub 2011 Jul 13.
Additional References at PubMed
PMID:11940581   PMID:15611105   PMID:20548288   PMID:23254481   PMID:23376485   PMID:24006456   PMID:25148874   PMID:30483778  


Genomics

Comparative Map Data
Pdgfd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.283,488,448 - 3,722,395 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl83,488,423 - 3,722,395 (+)Ensembl
Rnor_6.084,441,010 - 4,666,754 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl84,440,876 - 4,669,014 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.084,454,510 - 4,682,165 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.483,326,218 - 3,341,300 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.183,125,520 - 3,341,300 (+)NCBI
Celera85,067,751 - 5,287,344 (+)NCBICelera
Cytogenetic Map8q11NCBI
PDGFD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811103,907,189 - 104,164,147 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl11103,907,189 - 104,164,379 (-)EnsemblGRCh38hg38GRCh38
GRCh3711103,777,917 - 104,034,875 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611103,283,124 - 103,540,237 (-)NCBINCBI36hg18NCBI36
Celera11100,938,918 - 101,198,288 (-)NCBI
Cytogenetic Map11q22.3NCBI
HuRef1199,706,933 - 99,964,618 (-)NCBIHuRef
CHM1_111103,660,854 - 103,917,997 (-)NCBICHM1_1
T2T-CHM13v2.011103,910,709 - 104,168,067 (-)NCBI
Pdgfd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3996,168,377 - 6,534,284 (+)NCBIGRCm39mm39
GRCm39 Ensembl96,168,584 - 6,378,850 (+)Ensembl
GRCm3896,168,363 - 6,534,284 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl96,168,584 - 6,378,850 (+)EnsemblGRCm38mm10GRCm38
MGSCv3796,168,612 - 6,377,519 (+)NCBIGRCm37mm9NCBIm37
MGSCv3696,168,612 - 6,377,519 (+)NCBImm8
Celera93,573,881 - 3,783,053 (+)NCBICelera
Cytogenetic Map9A1NCBI
Pdgfd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554126,866,869 - 7,093,998 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554126,868,995 - 7,093,353 (-)NCBIChiLan1.0ChiLan1.0
PDGFD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111102,337,099 - 102,593,741 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11102,357,079 - 102,593,273 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01198,852,652 - 99,110,147 (-)NCBIMhudiblu_PPA_v0panPan3
PDGFD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1527,863,739 - 28,092,376 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl527,863,591 - 28,089,936 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha527,797,064 - 28,031,427 (+)NCBI
ROS_Cfam_1.0527,910,756 - 28,139,449 (+)NCBI
ROS_Cfam_1.0 Ensembl527,910,863 - 28,139,447 (+)Ensembl
UMICH_Zoey_3.1527,944,599 - 28,172,420 (+)NCBI
UNSW_CanFamBas_1.0527,831,224 - 28,058,908 (+)NCBI
UU_Cfam_GSD_1.0528,005,540 - 28,233,502 (+)NCBI
Pdgfd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494787,338,657 - 87,562,388 (-)NCBI
SpeTri2.0NW_0049365513,974,140 - 4,197,852 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDGFD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl934,388,643 - 34,621,244 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1934,388,636 - 34,621,227 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2938,432,144 - 38,616,298 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PDGFD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1195,293,263 - 95,551,138 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl195,292,193 - 95,385,199 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604330,343,471 - 30,592,345 (+)NCBIVero_WHO_p1.0
Pdgfd
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249181,052,567 - 1,293,192 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046249181,052,640 - 1,293,138 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:28
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000049325
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 8 6 19 4
Low 2 43 36 28 18 28 8 10 74 29 21 7 8
Below cutoff 1 13 13 1 13 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000049325   ⟹   ENSRNOP00000039308
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl84,440,876 - 4,668,545 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076529   ⟹   ENSRNOP00000068187
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl83,488,423 - 3,722,395 (+)Ensembl
Rnor_6.0 Ensembl84,440,902 - 4,669,014 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076748   ⟹   ENSRNOP00000067974
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl83,488,614 - 3,719,910 (+)Ensembl
Rnor_6.0 Ensembl84,440,980 - 4,668,545 (+)Ensembl
RefSeq Acc Id: NM_023962   ⟹   NP_076452
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.283,488,614 - 3,722,395 (+)NCBI
Rnor_6.084,441,010 - 4,666,754 (+)NCBI
Rnor_5.084,454,510 - 4,682,165 (+)NCBI
RGSC_v3.483,326,218 - 3,341,300 (+)RGD
Celera85,067,751 - 5,287,344 (+)RGD
Sequence:
RefSeq Acc Id: XM_039082130   ⟹   XP_038938058
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.283,488,448 - 3,722,395 (+)NCBI
Protein Sequences
Protein RefSeqs NP_076452 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938058 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAB18920 (Get FASTA)   NCBI Sequence Viewer  
  EDL78544 (Get FASTA)   NCBI Sequence Viewer  
  EDL78545 (Get FASTA)   NCBI Sequence Viewer  
  Q9EQT1 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_076452   ⟸   NM_023962
- Peptide Label: precursor
- UniProtKB: Q9EQT1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039308   ⟸   ENSRNOT00000049325
RefSeq Acc Id: ENSRNOP00000067974   ⟸   ENSRNOT00000076748
RefSeq Acc Id: ENSRNOP00000068187   ⟸   ENSRNOT00000076529
RefSeq Acc Id: XP_038938058   ⟸   XM_039082130
- Peptide Label: isoform X1
Protein Domains
CUB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9EQT1-F1-model_v2 AlphaFold Q9EQT1 1-370 view protein structure

Transcriptome

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

Promoters
RGD ID:13695736
Promoter ID:EPDNEW_R6252
Type:single initiation site
Name:Pdgfd_1
Description:platelet derived growth factor D
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.084,440,902 - 4,440,962EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
BUF/N (2020)
Visual CSV TAB Printer
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
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
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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
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
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
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/Stm (2019)
Visual CSV TAB Printer
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
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
LEW/Crl (2019)
Visual CSV TAB Printer
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
LEXF10A/StmMcwi (2020)
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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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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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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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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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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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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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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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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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/NRrrcMcwi (2019)
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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
MR/N (2020)
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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
MWF/Hsd (2019)
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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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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
SHR/OlalpcvMcwi (2019)
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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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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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
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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/N (2020)
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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/NCrl (2019)
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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
WN/N (2020)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621880 AgrOrtholog
BioCyc Gene G2FUF-31804 BioCyc
Ensembl Genes ENSRNOG00000029148 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000067974.1 UniProtKB/TrEMBL
  ENSRNOP00000068187 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000076529 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000076748.2 UniProtKB/TrEMBL
Gene3D-CATH 2.10.90.10 UniProtKB/Swiss-Prot
  2.60.120.290 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CUB_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cystine-knot_cytokine UniProtKB/Swiss-Prot
  PDGF/VEGF_dom UniProtKB/Swiss-Prot
  PDGFD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sperma_CUB_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:66018 UniProtKB/Swiss-Prot
NCBI Gene 66018 ENTREZGENE
PANTHER PTHR11633:SF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CUB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDGF UniProtKB/Swiss-Prot
PhenoGen Pdgfd PhenoGen
PROSITE CUB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDGF_2 UniProtKB/Swiss-Prot
SMART CUB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDGF UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49854 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57501 UniProtKB/Swiss-Prot
UniProt A0A096MJ33_RAT UniProtKB/TrEMBL
  PDGFD_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-05 Pdgfd  platelet derived growth factor D  Pdgfd  platelet-derived growth factor, D polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Pdgfd  platelet-derived growth factor, D polypeptide  Scdgfb  spinal-cord derived growth factor-B protein  Symbol and Name updated 1299863 APPROVED
2002-08-07 Scdgfb  spinal-cord derived growth factor-B protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains two regions homologous to CUB and PDGF/vascular endothelial growth factor (VEGF) domains 68286
gene_homology member of the PDGF/VEGF superfamily 68286