Pgf (placental growth factor) - Rat Genome Database

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Gene: Pgf (placental growth factor) Rattus norvegicus
Analyze
Symbol: Pgf
Name: placental growth factor
RGD ID: 619850
Description: Enables identical protein binding activity. Involved in several processes, including animal organ regeneration; positive regulation of angiogenesis; and positive regulation of endothelial cell proliferation. Located in extracellular space. Used to study congestive heart failure and myocardial infarction. Biomarker of diabetic retinopathy; end stage renal disease; pre-eclampsia; and status epilepticus. Human ortholog(s) of this gene implicated in several diseases, including brain ischemia; diabetic neuropathy; glioblastoma; myocardial infarction; and pancreatic endocrine carcinoma. Orthologous to human PGF (placental growth factor); PARTICIPATES IN vascular endothelial growth factor signaling pathway; ceramide signaling pathway; mTOR signaling pathway; INTERACTS WITH (S)-nicotine; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC93298; placenta growth factor; Plgf
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
mRatBN7.26104,816,102 - 104,826,685 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl6104,816,104 - 104,826,685 (-)Ensembl
Rnor_6.06108,994,016 - 109,004,598 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,994,018 - 109,004,598 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06116,552,660 - 116,563,242 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46109,215,540 - 109,226,122 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16109,218,997 - 109,229,578 (-)NCBI
Celera6102,639,061 - 102,649,643 (-)NCBICelera
RH 3.4 Map6731.99RGD
Cytogenetic Map6q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2-hydroxypropanoic acid  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
chromium atom  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP)
colforsin daropate hydrochloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP)
curcumin  (EXP)
cyclosporin A  (ISO)
DDT  (EXP)
Deguelin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (EXP)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP,ISO)
dieldrin  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
furosemide  (EXP)
genistein  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
Licochalcone B  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (EXP,ISO)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
N-nitrosodimethylamine  (ISO)
naphthalene  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
nicotine  (EXP)
organoselenium compound  (ISO)
oxaliplatin  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
pentanal  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
picoxystrobin  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
propanal  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
tebuconazole  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP)
thimerosal  (ISO)
titanium dioxide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc protoporphyrin  (ISO)
zinc(0)  (ISO)

References

References - curated
1. Agunanne EE, etal., Am J Nephrol. 2010;32(4):332-9. Epub 2010 Aug 19.
2. Bahtiyar MO, etal., Am J Obstet Gynecol. 2007 Jan;196(1):72.e1-6.
3. Bastek JA, etal., J Matern Fetal Neonatal Med. 2011 Apr;24(4):600-5. Epub 2010 Sep 7.
4. Batchelor TT, etal., J Clin Oncol. 2010 Jun 10;28(17):2817-23. Epub 2010 May 10.
5. Beck H, etal., J Neuropathol Exp Neurol. 2002 Apr;61(4):339-50.
6. Bennuru S, etal., Am J Trop Med Hyg. 2010 Oct;83(4):884-90.
7. Binsalamah ZM, etal., Int J Nanomedicine. 2011;6:2667-78. Epub 2011 Oct 31.
8. Bobic S, etal., Am J Respir Cell Mol Biol. 2012 Feb 3.
9. Brittain JE, etal., Blood. 2010 Mar 11;115(10):2014-20. Epub 2009 Dec 29.
10. Carnevale D, etal., Circulation. 2011 Sep 20;124(12):1337-50. Epub 2011 Sep 6.
11. Chaballe L, etal., Glia. 2011 Mar;59(3):379-96. doi: 10.1002/glia.21108. Epub 2010 Dec 6.
12. Chaiworapongsa T, etal., J Matern Fetal Neonatal Med. 2010 Feb;23(2):167-78.
13. Chang JD, etal., Proc Natl Acad Sci U S A. 2007 May 8;104(19):8077-82. Epub 2007 May 2.
14. Chen HW, etal., FASEB J. 2006 Nov;20(13):2393-5. Epub 2006 Oct 5.
15. Cheng L, etal., J Biol Chem. 2004 Jul 16;279(29):30654-61. Epub 2004 May 4.
16. Cho GJ, etal., J Korean Med Sci. 2003 Jun;18(3):402-8.
17. Choi WS, etal., J Vet Sci. 2005 Sep;6(3):179-83.
18. DiSalvo J, etal., J Biol Chem 1995 Mar 31;270(13):7717-23.
19. Duenas Pousa I, etal., Gastroenterol Hepatol. 2007 Nov;30(9):518-24.
20. Dunne JV, etal., Rheumatol Int. 2012 Mar 30.
21. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
22. Gmeiner M, etal., J Thorac Cardiovasc Surg. 2011 May;141(5):1238-45. Epub 2011 Feb 16.
23. He M, etal., Cancer Genet Cytogenet. 2006 Jul 15;168(2):150-4.
24. Hilfenhaus G, etal., Endocr Relat Cancer. 2013 May 20;20(3):305-19. doi: 10.1530/ERC-12-0223. Print 2013 Jun.
25. Hindryckx P, etal., Ann Rheum Dis. 2011 Nov;70(11):2044-8. Epub 2011 Aug 26.
26. Hindryckx P, etal., Lab Invest. 2010 Apr;90(4):566-76. Epub 2010 Feb 8.
27. Incio J, etal., Clin Cancer Res. 2016 Jun 15;22(12):2993-3004. doi: 10.1158/1078-0432.CCR-15-1839. Epub 2016 Feb 9.
28. Kanellakis P, etal., Br J Pharmacol. 2010 Aug;160(8):2085-96.
29. Khurana R, etal., Circulation. 2005 May 31;111(21):2828-36. Epub 2005 May 23.
30. Koh PO, etal., J Vet Med Sci. 2007 Sep;69(9):877-80.
31. Koh SH, etal., Exp Neurol. 2012 Jan;233(1):472-80. Epub 2011 Nov 19.
32. Kowalczuk L, etal., PLoS One. 2011 Mar 7;6(3):e17462.
33. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
34. Liu H, etal., Brain. 2006 Oct;129(Pt 10):2734-45. Epub 2006 Aug 10.
35. Maae E, etal., Breast Cancer Res Treat. 2012 May;133(1):257-65. Epub 2012 Jan 22.
36. Maes C, etal., J Clin Invest. 2006 May;116(5):1230-42. Epub 2006 Apr 13.
37. Matsumoto K, etal., Anticancer Res. 2003 Nov-Dec;23(6D):4953-8.
38. MGD data from the GO Consortium
39. Molvarec A, etal., Clin Chim Acta. 2011 Oct 9;412(21-22):1957-62. Epub 2011 Jul 6.
40. Murakami T, etal., Exp Neurol. 2011 Jan;227(1):195-202. Epub 2010 Nov 5.
41. Nakamura T, etal., Int J Cardiol. 2009 Jan 9;131(2):186-91. Epub 2008 Jan 14.
42. NCBI rat LocusLink and RefSeq merged data July 26, 2002
43. Olsson AK, etal., Nat Rev Mol Cell Biol. 2006 May;7(5):359-71.
44. Pilarczyk K, etal., Atherosclerosis. 2008 Jan;196(1):333-40. Epub 2006 Dec 8.
45. Pipeline to import KEGG annotations from KEGG into RGD
46. RGD automated data pipeline
47. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
48. RGD automated import pipeline for gene-chemical interactions
49. Robak E, etal., Lupus. 2009 Apr;18(4):332-41.
50. Roncal C, etal., Cardiovasc Res. 2010 Apr 1;86(1):29-36. Epub 2009 Dec 1.
51. Smadja DM, etal., Pediatr Cardiol. 2010 Jul;31(5):657-62. Epub 2010 Feb 27.
52. Suwaki N, etal., Am J Obstet Gynecol. 2006 Dec;195(6):1687-92. Epub 2006 Jun 12.
53. Theilade S, etal., Diabet Med. 2012 Mar;29(3):337-44. doi: 10.1111/j.1464-5491.2011.03482.x.
54. Tugues S, etal., Hepatology. 2007 Dec;46(6):1919-26.
55. Van Steenkiste C, etal., Hepatology. 2011 May;53(5):1629-40. doi: 10.1002/hep.24238.
56. Vanheule E, etal., Eur J Gastroenterol Hepatol. 2011 Jan;23(1):66-75.
57. Viglietto G, etal., Oncogene. 1997 Nov 27;15(22):2687-98.
58. Voros G, etal., Endocrinology. 2005 Oct;146(10):4545-54. Epub 2005 Jul 14.
59. Wang C, etal., Eur J Pharmacol. 2009 Jun 10;612(1-3):143-52. Epub 2009 Apr 6.
60. Wu Q, etal., Am J Nephrol. 2006;26(1):97-104. Epub 2006 Mar 14.
61. Xu Y, etal., Brain Res. 2012 Jan 6;1429:124-33. Epub 2011 Oct 6.
62. Xu Y, etal., Neurochem Res. 2012 Mar;37(3):665-70. Epub 2011 Dec 8.
63. Yano K, etal., J Exp Med. 2006 Jun 12;203(6):1447-58. Epub 2006 May 15.
64. Yoo SA, etal., Arthritis Rheum. 2009 Feb;60(2):345-54.
65. Zheng Y, etal., Arterioscler Thromb Vasc Biol. 2007 Mar;27(3):503-11. Epub 2006 Dec 28.
66. Zimpfer D, etal., J Thorac Cardiovasc Surg. 2009 Apr;137(4):963-70.
Additional References at PubMed
PMID:12477932   PMID:13678594   PMID:15489334   PMID:17997886   PMID:18421240   PMID:19048427   PMID:20860549   PMID:21123739   PMID:21215706   PMID:21266048   PMID:21911594   PMID:21969865  
PMID:23691181   PMID:24001991   PMID:25184477   PMID:25515701   PMID:26192016   PMID:27280587   PMID:29933759   PMID:30361676  


Genomics

Comparative Map Data
Pgf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26104,816,102 - 104,826,685 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl6104,816,104 - 104,826,685 (-)Ensembl
Rnor_6.06108,994,016 - 109,004,598 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,994,018 - 109,004,598 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06116,552,660 - 116,563,242 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46109,215,540 - 109,226,122 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16109,218,997 - 109,229,578 (-)NCBI
Celera6102,639,061 - 102,649,643 (-)NCBICelera
RH 3.4 Map6731.99RGD
Cytogenetic Map6q31NCBI
PGF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1474,941,834 - 74,955,626 (-)EnsemblGRCh38hg38GRCh38
GRCh381474,941,830 - 74,955,764 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371475,408,533 - 75,422,467 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361474,478,290 - 74,492,044 (-)NCBINCBI36hg18NCBI36
Build 341474,478,292 - 74,492,044NCBI
Celera1455,446,919 - 55,460,674 (-)NCBI
Cytogenetic Map14q24.3NCBI
HuRef1455,576,546 - 55,590,481 (-)NCBIHuRef
CHM1_11475,347,700 - 75,361,635 (-)NCBICHM1_1
Pgf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391285,213,411 - 85,224,559 (-)NCBIGRCm39mm39
GRCm39 Ensembl1285,213,409 - 85,224,564 (-)Ensembl
GRCm381285,166,637 - 85,177,785 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1285,166,635 - 85,177,790 (-)EnsemblGRCm38mm10GRCm38
MGSCv371286,507,591 - 86,518,235 (-)NCBIGRCm37mm9NCBIm37
MGSCv361286,055,744 - 86,066,388 (-)NCBImm8
Celera1286,623,655 - 86,634,299 (-)NCBICelera
Cytogenetic Map12D1NCBI
cM Map1239.58NCBI
Pgf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955523616,154 - 627,713 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955523616,196 - 627,055 (+)NCBIChiLan1.0ChiLan1.0
PGF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11474,338,976 - 74,352,964 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1474,338,976 - 74,352,964 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01455,494,152 - 55,508,066 (-)NCBIMhudiblu_PPA_v0panPan3
PGF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1848,059,554 - 48,110,534 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl848,059,552 - 48,075,170 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha847,743,752 - 47,795,118 (-)NCBI
ROS_Cfam_1.0848,287,229 - 48,338,603 (-)NCBI
UMICH_Zoey_3.1847,958,057 - 48,009,418 (-)NCBI
UNSW_CanFamBas_1.0847,979,365 - 48,030,910 (-)NCBI
UU_Cfam_GSD_1.0848,377,990 - 48,429,367 (-)NCBI
Pgf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864027,957,791 - 27,970,740 (+)NCBI
SpeTri2.0NW_0049364884,098,187 - 4,111,108 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PGF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1798,149,510 - 98,162,784 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27103,993,598 - 104,006,849 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PGF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12452,160,904 - 52,174,493 (-)NCBI
ChlSab1.1 Ensembl2452,161,787 - 52,173,989 (-)Ensembl
Vero_WHO_p1.0NW_02366605340,391,564 - 40,405,145 (-)NCBI
Pgf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473426,751,986 - 26,764,154 (+)NCBI

Position Markers
RH94485  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26104,816,740 - 104,816,847 (+)MAPPERmRatBN7.2
Rnor_6.06108,994,655 - 108,994,761NCBIRnor6.0
Rnor_5.06116,562,497 - 116,562,603UniSTSRnor5.0
RGSC_v3.46109,216,179 - 109,216,285UniSTSRGSC3.4
Celera6102,639,700 - 102,639,806UniSTS
RH 3.4 Map6731.99UniSTS
Cytogenetic Map6q31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)672202632117202632Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)673463459109394713Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)682523650110548006Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)683190345106747639Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)684130881129130881Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)685140138130140138Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)685140138130140138Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)689762877106752806Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)693701310128713626Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6104085867128713626Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:370
Count of miRNA genes:191
Interacting mature miRNAs:218
Transcripts:ENSRNOT00000007790
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 4 11
Low 3 42 24 8 16 8 8 11 74 31 23 11 8
Below cutoff 1 25 25 3 25 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007790   ⟹   ENSRNOP00000007790
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6104,816,104 - 104,826,685 (-)Ensembl
Rnor_6.0 Ensembl6108,994,018 - 109,004,598 (-)Ensembl
RefSeq Acc Id: NM_053595   ⟹   NP_446047
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26104,816,102 - 104,826,685 (-)NCBI
Rnor_6.06108,994,016 - 109,004,598 (-)NCBI
Rnor_5.06116,552,660 - 116,563,242 (+)NCBI
RGSC_v3.46109,215,540 - 109,226,122 (-)RGD
Celera6102,639,061 - 102,649,643 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446047 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA97426 (Get FASTA)   NCBI Sequence Viewer  
  AAH87006 (Get FASTA)   NCBI Sequence Viewer  
  EDL81554 (Get FASTA)   NCBI Sequence Viewer  
  EDL81555 (Get FASTA)   NCBI Sequence Viewer  
  Q63434 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446047   ⟸   NM_053595
- Peptide Label: precursor
- UniProtKB: Q63434 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007790   ⟸   ENSRNOT00000007790

Transcriptome

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

Promoters
RGD ID:13694736
Promoter ID:EPDNEW_R5261
Type:single initiation site
Name:Pgf_1
Description:placental growth factor
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_6.06109,004,612 - 109,004,672EPDNEW

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)
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
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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
LE/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
LE/Stm (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/Crl (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
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)
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
LEXF10A/StmMcwi (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
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/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
LEXF1C/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
LEXF2B/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
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/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
M520/NRrrcMcwi (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
MHS/Gib (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
MNS/Gib (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
MR/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
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)
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
PVG/Seac (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
SBH/Ygl (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: 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)
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: 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)
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/OlalpcvMcwi (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
SHRSP/A3NCrl (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
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)
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
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)
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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/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)
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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)
SS/JrHsdMcwi (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/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)
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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
WKY/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
WKY/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
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)
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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
WKY/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
WN/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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619850 AgrOrtholog
Ensembl Genes ENSRNOG00000005650 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000007790 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000007790 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.10.90.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7193034 IMAGE-MGC_LOAD
InterPro Cystine-knot_cytokine UniProtKB/Swiss-Prot
  PD_growth_factor_CS UniProtKB/Swiss-Prot
  PDGF/VEGF_dom UniProtKB/Swiss-Prot
KEGG Report rno:94203 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93298 IMAGE-MGC_LOAD
NCBI Gene 94203 ENTREZGENE
Pfam PDGF UniProtKB/Swiss-Prot
PhenoGen Pgf PhenoGen
PROSITE PDGF_1 UniProtKB/Swiss-Prot
  PDGF_2 UniProtKB/Swiss-Prot
SMART PDGF UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57501 UniProtKB/Swiss-Prot
UniProt PLGF_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Pgf  placental growth factor      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pgf  placental growth factor      Symbol and Name status set to provisional 70820 PROVISIONAL