Ptn (pleiotrophin) - Rat Genome Database

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Gene: Ptn (pleiotrophin) Rattus norvegicus
Analyze
Symbol: Ptn
Name: pleiotrophin
RGD ID: 3444
Description: Enables several functions, including glycosaminoglycan binding activity; growth factor activity; and syndecan binding activity. Involved in several processes, including animal organ development; nervous system development; and regulation of epithelial cell proliferation. Located in several cellular components, including basement membrane; neuromuscular junction; and perinuclear region of cytoplasm. Is active in postsynapse and presynapse. Used to study Parkinson's disease. Biomarker of several diseases, including extrahepatic cholestasis; liver cirrhosis; sciatic neuropathy; transient cerebral ischemia; and visual epilepsy. Human ortholog(s) of this gene implicated in adrenal carcinoma. Orthologous to human PTN (pleiotrophin); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: HARP; HB-GAM; HBBM; HBGF-8; Hbnf; heparin affine regulatory peptide; heparin binding factor; heparin-binding brain mitogen; heparin-binding growth factor 8; heparin-binding growth-associated molecule; heparin-binding neurotrophic factor; heparin-binding neutrophic factor; OSF-1; osteoblast-specific factor 1; Pleiotrophin (Heparine binding factor, Hbnf, in the mouse)
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
mRatBN7.2465,293,731 - 65,375,572 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl465,293,734 - 65,375,456 (-)Ensembl
Rnor_6.0464,239,156 - 64,330,996 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl464,239,158 - 64,330,996 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0464,063,952 - 64,156,123 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4464,078,755 - 64,160,135 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1464,354,886 - 64,436,265 (-)NCBI
Celera460,333,929 - 60,415,522 (-)NCBICelera
Cytogenetic Map4q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-acetamidofluorene  (EXP)
2-amino-2-deoxy-D-galactopyranose  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP,ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-naphthoflavone  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
calcitriol  (EXP,ISO)
chondroitin sulfate  (ISO)
cocaine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
cycloheximide  (ISO)
cyclosporin A  (ISO)
dermatan sulfate  (ISO)
diazinon  (EXP)
dichlorine  (EXP)
dieldrin  (EXP)
diethylstilbestrol  (ISO)
dizocilpine maleate  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ellagic acid  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
folic acid  (ISO)
furan  (EXP)
furosemide  (EXP)
L-ascorbic acid  (ISO)
miconazole  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nickel atom  (ISO)
okadaic acid  (ISO)
oxaliplatin  (EXP)
ozone  (EXP)
p-chloromercuribenzoic acid  (ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
perfluorooctanoic acid  (EXP)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
progesterone  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP)
topotecan  (EXP)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
bone mineralization  (ISO)
brain development  (IEP)
cellular response to hypoxia  (IEP)
cellular response to organic cyclic compound  (IEP)
cellular response to platelet-derived growth factor stimulus  (IEP)
cellular response to UV  (IEP)
cellular response to vitamin D  (IEP)
cerebellum development  (IEP)
decidualization  (ISO,ISS)
dendrite arborization  (ISO,ISS)
dendrite regeneration  (IDA)
endothelial cell differentiation  (IEP)
estrous cycle  (IEP,ISO,ISS)
heart development  (IEP)
hindbrain development  (IEP)
integrin-mediated signaling pathway  (ISO,ISS)
learning  (IEP,ISO,ISS)
leukocyte chemotaxis involved in inflammatory response  (ISO,ISS)
liver development  (IEP)
long-term synaptic potentiation  (IEP)
lung development  (IEP)
memory  (ISO,ISS)
negative regulation of angiogenesis  (IMP)
negative regulation of catalytic activity  (IEA)
negative regulation of cell migration  (IMP)
negative regulation of epithelial cell proliferation  (IDA)
negative regulation of glial cell proliferation  (IMP)
negative regulation of long-term synaptic potentiation  (ISO,ISS)
negative regulation of membrane potential  (IDA)
negative regulation of mesenchymal cell proliferation  (IDA)
negative regulation of neuroblast proliferation  (ISO,ISS)
negative regulation of neuromuscular junction development  (IDA)
oogenesis  (ISO,ISS)
ossification  (ISO)
ossification involved in bone remodeling  (ISO,ISS)
positive regulation of apoptotic process  (IMP)
positive regulation of axon regeneration  (IDA)
positive regulation of bone mineralization  (ISO,ISS)
positive regulation of cell differentiation  (ISO)
positive regulation of cell division  (IEA)
positive regulation of cell population proliferation  (ISO)
positive regulation of cell-substrate adhesion  (IDA)
positive regulation of dendrite development  (ISO,ISS)
positive regulation of hepatocyte proliferation  (IDA,ISO)
positive regulation of leukocyte chemotaxis  (ISO,ISS)
positive regulation of neuron projection development  (IDA)
positive regulation of oligodendrocyte differentiation  (ISO,ISS)
positive regulation of ossification  (IMP)
positive regulation of skeletal muscle acetylcholine-gated channel clustering  (IDA)
positive regulation of stem cell differentiation  (ISO,ISS)
receptor clustering  (ISO,ISS)
regulation of cell shape  (IMP)
regulation of endothelial cell migration  (ISS)
regulation of hemopoiesis  (ISO,ISS)
regulation of myelination  (ISO,ISS)
regulation of stem cell population maintenance  (ISO,ISS)
regulation of synaptic plasticity  (ISO,ISS)
response to activity  (IEP)
response to auditory stimulus  (ISO,ISS)
response to ciliary neurotrophic factor  (IEP)
response to estradiol  (IEP)
response to kainic acid  (IEP)
response to nerve growth factor  (IEP)
response to progesterone  (IEP)
response to xenobiotic stimulus  (IEP)
retina development in camera-type eye  (IEP)
retinal rod cell differentiation  (IMP)
rod bipolar cell differentiation  (IEP)
spinal cord development  (IEP)
thalamus development  (IEP)
tissue regeneration  (ISO,ISS)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Antoine M, etal., Biochem Biophys Res Commun. 2005 Dec 2;337(4):1153-64. Epub 2005 Oct 6.
2. Asahina K, etal., Am J Pathol 2002 Jun;160(6):2191-205.
3. Attia M, etal., J Orthop Res. 2012 Jan;30(1):61-71. doi: 10.1002/jor.21479. Epub 2011 Jun 17.
4. Bao X, etal., J Biol Chem. 2005 Mar 11;280(10):9180-91. Epub 2005 Jan 4.
5. Besse S, etal., J Physiol Pharmacol. 2010 Dec;61(6):651-61.
6. Caruelle D, etal., J Muscle Res Cell Motil. 2004;25(1):45-53.
7. Ezquerra L, etal., Growth Factors. 2008 Feb;26(1):44-8. doi: 10.1080/08977190801987711.
8. Fang W, etal., J Biol Chem. 1992 Dec 25;267(36):25889-97.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. Gieffers C, etal., Eur J Cell Biol. 1993 Dec;62(2):352-61.
11. GOA data from the GO Consortium
12. Gramage E and Herradon G, Eur J Pharmacol. 2010 Nov 25;647(1-3):97-102. doi: 10.1016/j.ejphar.2010.08.029. Epub 2010 Sep 6.
13. Imai S, etal., J Cell Biol. 1998 Nov 16;143(4):1113-28.
14. Kinnunen A, etal., Eur J Neurosci. 1998 Feb;10(2):635-48.
15. Kinnunen A, etal., Eur J Neurosci. 1999 Feb;11(2):491-502.
16. Kinnunen T, etal., J Biol Chem. 1996 Jan 26;271(4):2243-8.
17. Lauri SE, etal., Eur J Neurosci. 1998 Jan;10(1):188-94.
18. Lauri SE, etal., Neuroreport. 1996 Jul 8;7(10):1670-4.
19. Li J, etal., J Biol Chem. 2007 Nov 30;282(48):34984-93. Epub 2007 Oct 9.
20. Li YS, etal., Science. 1990 Dec 21;250(4988):1690-4.
21. Liu X, etal., Glia. 1998 Dec;24(4):390-7.
22. Maeda N, etal., J Biol Chem. 1996 Aug 30;271(35):21446-52.
23. Mailleux P, etal., Neurosci Lett. 1994 Jul 4;175(1-2):25-7.
24. Matsumoto K, etal., Brain Res Dev Brain Res. 1994 Jun 17;79(2):229-41.
25. Merenmies J and Rauvala H, J Biol Chem 1990 Oct 5;265(28):16721-4.
26. MGD data from the GO Consortium
27. Milhiet PE, etal., J Endocrinol. 1998 Sep;158(3):389-99.
28. Nakanishi K, etal., Neurochem Res. 2010 Aug;35(8):1131-7. doi: 10.1007/s11064-010-0164-9. Epub 2010 Apr 6.
29. NCBI rat LocusLink and RefSeq merged data July 26, 2002
30. Ottis P, etal., PLoS One. 2013 Sep 19;8(9):e75112. doi: 10.1371/journal.pone.0075112. eCollection 2013.
31. Park TJ, etal., Mol Carcinog. 2008 Oct;47(10):784-96. doi: 10.1002/mc.20438.
32. Parthymou A, etal., Eur J Cell Biol. 2008 Jan;87(1):17-29. Epub 2007 Sep 18.
33. Paveliev M, etal., Sci Rep. 2016 Sep 27;6:33916. doi: 10.1038/srep33916.
34. Peng HB, etal., J Neurosci. 1995 Apr;15(4):3027-38.
35. Piltonen M, etal., Exp Neurol. 2009 Oct;219(2):499-506. doi: 10.1016/j.expneurol.2009.07.002. Epub 2009 Jul 15.
36. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
37. Raulo E, etal., J Biol Chem. 1994 Apr 29;269(17):12999-3004.
38. Rauvala H, etal., Brain Res Dev Brain Res. 1994 Jun 17;79(2):157-76.
39. RGD automated data pipeline
40. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
41. RGD automated import pipeline for gene-chemical interactions
42. Roger J, etal., Dev Biol. 2006 Oct 15;298(2):527-39. Epub 2006 Jul 12.
43. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
44. Szabat E and Rauvala H, Dev Biol. 1996 Aug 25;178(1):77-89.
45. Takeda A, etal., Neuroscience. 1995 Sep;68(1):57-64.
46. Tamura M, etal., Endocrine. 1995 Jan;3(1):21-4. doi: 10.1007/BF02917444.
47. Wakisaka S, etal., Arch Histol Cytol. 1998 Dec;61(5):475-80.
48. Wanaka A, etal., Brain Res Dev Brain Res. 1993 Mar 19;72(1):133-44.
49. Wewetzer K, etal., Brain Res. 1995 Sep 25;693(1-2):31-8.
50. Xu J, etal., Stem Cells Dev. 2008 Feb;17(1):143-55.
51. Yeh HJ, etal., J Neurosci. 1998 May 15;18(10):3699-707.
52. Yu Y, etal., Basic Res Cardiol. 2010 Nov;105(6):713-24. doi: 10.1007/s00395-010-0117-0. Epub 2010 Sep 10.
Additional References at PubMed
PMID:1700712   PMID:1733956   PMID:2388713   PMID:11414790   PMID:11999218   PMID:12093164   PMID:12413943   PMID:12786979   PMID:12840014   PMID:14586627   PMID:15121180   PMID:15482347  
PMID:15489334   PMID:15949466   PMID:16155004   PMID:16325783   PMID:16619002   PMID:17121547   PMID:17360581   PMID:17368428   PMID:18599487   PMID:18727926   PMID:19141530   PMID:19384682  
PMID:19442624   PMID:20873783   PMID:21791434   PMID:21928404   PMID:23000062   PMID:25000129   PMID:25108770   PMID:26222257   PMID:26615567   PMID:26896299   PMID:27445335   PMID:28657144  
PMID:30497772   PMID:30667096  


Genomics

Comparative Map Data
Ptn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2465,293,731 - 65,375,572 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl465,293,734 - 65,375,456 (-)Ensembl
Rnor_6.0464,239,156 - 64,330,996 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl464,239,158 - 64,330,996 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0464,063,952 - 64,156,123 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4464,078,755 - 64,160,135 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1464,354,886 - 64,436,265 (-)NCBI
Celera460,333,929 - 60,415,522 (-)NCBICelera
Cytogenetic Map4q22NCBI
PTN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7137,227,341 - 137,343,774 (-)EnsemblGRCh38hg38GRCh38
GRCh387137,227,341 - 137,343,733 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh377136,912,088 - 137,028,479 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367136,562,628 - 136,679,086 (-)NCBINCBI36hg18NCBI36
Build 347136,369,349 - 136,485,801NCBI
Celera7131,651,010 - 131,767,463 (-)NCBI
Cytogenetic Map7q33NCBI
HuRef7131,217,379 - 131,333,760 (-)NCBIHuRef
CHM1_17136,845,103 - 136,961,863 (-)NCBICHM1_1
CRA_TCAGchr7v27136,256,123 - 136,372,579 (-)NCBI
Ptn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39636,691,859 - 36,787,114 (-)NCBIGRCm39mm39
GRCm39 Ensembl636,691,864 - 36,787,155 (-)Ensembl
GRCm38636,714,924 - 36,810,179 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl636,714,929 - 36,810,220 (-)EnsemblGRCm38mm10GRCm38
MGSCv37636,665,663 - 36,761,361 (-)NCBIGRCm37mm9NCBIm37
MGSCv36636,645,815 - 36,741,513 (-)NCBImm8
Celera636,692,206 - 36,788,072 (-)NCBICelera
Cytogenetic Map6B1NCBI
cM Map615.48NCBI
Ptn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554945,580,422 - 5,684,190 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554945,580,264 - 5,681,848 (+)NCBIChiLan1.0ChiLan1.0
PTN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17141,678,056 - 141,794,565 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7141,701,430 - 141,705,623 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07129,184,786 - 129,300,815 (-)NCBIMhudiblu_PPA_v0panPan3
PTN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11611,283,078 - 11,382,820 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1611,283,077 - 11,382,814 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1612,295,731 - 12,396,391 (+)NCBI
ROS_Cfam_1.01611,248,309 - 11,349,640 (+)NCBI
UMICH_Zoey_3.11611,708,020 - 11,809,056 (+)NCBI
UNSW_CanFamBas_1.01610,807,935 - 10,909,300 (+)NCBI
UU_Cfam_GSD_1.01610,950,643 - 11,051,479 (+)NCBI
Ptn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511817,455,142 - 17,512,824 (+)NCBI
SpeTri2.0NW_0049365921,706,979 - 1,806,345 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1812,219,790 - 12,311,922 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11812,219,708 - 12,309,045 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21812,892,250 - 12,981,603 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PTN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121105,911,171 - 106,027,108 (-)NCBI
ChlSab1.1 Ensembl21105,911,120 - 106,027,215 (-)Ensembl
Vero_WHO_p1.0NW_0236660722,777,500 - 2,887,026 (-)NCBI
Ptn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476517,523,086 - 17,625,264 (-)NCBI

Position Markers
RH131587  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2465,293,810 - 65,293,963 (+)MAPPERmRatBN7.2
Rnor_6.0464,239,235 - 64,239,387NCBIRnor6.0
Rnor_5.0464,064,031 - 64,064,183UniSTSRnor5.0
RGSC_v3.4464,078,834 - 64,078,986UniSTSRGSC3.4
Celera460,334,008 - 60,334,160UniSTS
RH 3.4 Map4412.8UniSTS
Cytogenetic Map4q22UniSTS
BE116184  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2465,293,947 - 65,294,114 (+)MAPPERmRatBN7.2
Rnor_6.0464,239,372 - 64,239,538NCBIRnor6.0
Rnor_5.0464,064,168 - 64,064,334UniSTSRnor5.0
RGSC_v3.4464,078,971 - 64,079,137UniSTSRGSC3.4
Celera460,334,145 - 60,334,311UniSTS
RH 3.4 Map4415.8UniSTS
Cytogenetic Map4q22UniSTS
AA819154  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2465,294,084 - 65,294,233 (+)MAPPERmRatBN7.2
Rnor_6.0464,239,509 - 64,239,657NCBIRnor6.0
Rnor_5.0464,064,305 - 64,064,453UniSTSRnor5.0
RGSC_v3.4464,079,108 - 64,079,256UniSTSRGSC3.4
Celera460,334,282 - 60,334,430UniSTS
RH 3.4 Map4408.1UniSTS
Cytogenetic Map4q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
4889969Bss96Bone structure and strength QTL 964.9tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)45664777678882945Rat
4889972Bss97Bone structure and strength QTL 975.6tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)45664777678882945Rat
5685009Bmd86Bone mineral density QTL 863.7tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)45664777678882945Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)45664777678882945Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711443291360801Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)457114432102114432Rat
61336Bp21Blood pressure QTL 214.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711470578881294Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)457486946102486946Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45843213392991462Rat
631671Iddm11Insulin dependent diabetes mellitus QTL 113.60.0012blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)45863587778886137Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)460220938105220938Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)460220938105220938Rat
2300179Bmd50Bone mineral density QTL 505.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)460928534105928534Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658103194791Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658115089733Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462879517107879517Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46293326987483707Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)46293350882490359Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)462933508114921294Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:63
Interacting mature miRNAs:78
Transcripts:ENSRNOT00000016088
Prediction methods:Miranda, 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 21 2 17
Medium 3 38 43 27 19 27 4 4 53 33 24 9 4
Low 5 14 14 14 4 7 2 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016088   ⟹   ENSRNOP00000016088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl465,293,734 - 65,375,456 (-)Ensembl
Rnor_6.0 Ensembl464,239,158 - 64,330,996 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095619   ⟹   ENSRNOP00000080308
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl465,293,734 - 65,351,785 (-)Ensembl
RefSeq Acc Id: NM_017066   ⟹   NP_058762
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2465,293,732 - 65,375,306 (-)NCBI
Rnor_6.0464,239,156 - 64,330,996 (-)NCBI
Rnor_5.0464,063,952 - 64,156,123 (-)NCBI
RGSC_v3.4464,078,755 - 64,160,135 (-)RGD
Celera460,333,929 - 60,415,522 (-)RGD
Sequence:
RefSeq Acc Id: XM_017592475   ⟹   XP_017447964
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2465,293,731 - 65,351,620 (-)NCBI
Rnor_6.0464,239,156 - 64,307,309 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107076   ⟹   XP_038963004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2465,293,731 - 65,375,572 (-)NCBI
RefSeq Acc Id: XM_039107077   ⟹   XP_038963005
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2465,293,731 - 65,375,572 (-)NCBI
RefSeq Acc Id: XM_039107078   ⟹   XP_038963006
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2465,293,731 - 65,369,407 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_058762   ⟸   NM_017066
- Peptide Label: precursor
- UniProtKB: P63090 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017447964   ⟸   XM_017592475
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000016088   ⟸   ENSRNOT00000016088
RefSeq Acc Id: XP_038963005   ⟸   XM_039107077
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038963004   ⟸   XM_039107076
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038963006   ⟸   XM_039107078
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000080308   ⟸   ENSRNOT00000095619

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)
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)
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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)
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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
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)
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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
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)
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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/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)
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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
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)
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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)
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)
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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)
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)
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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)
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:3444 AgrOrtholog
Ensembl Genes ENSRNOG00000011946 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000016088 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000016088 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.20.60.10 UniProtKB/Swiss-Prot
  2.30.90.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5621277 IMAGE-MGC_LOAD
InterPro Midkine_heparin-bd_GF UniProtKB/Swiss-Prot
  PTN/MK_C_dom UniProtKB/Swiss-Prot
  PTN/MK_C_dom_sf UniProtKB/Swiss-Prot
  PTN/MK_diS_sf UniProtKB/Swiss-Prot
  PTN/MK_N_dom UniProtKB/Swiss-Prot
  PTN/MK_N_dom_sf UniProtKB/Swiss-Prot
  PTN_MK_heparin-bd_GF_CS UniProtKB/Swiss-Prot
KEGG Report rno:24924 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72496 IMAGE-MGC_LOAD
NCBI Gene 24924 ENTREZGENE
PANTHER PTHR13850 UniProtKB/Swiss-Prot
Pfam PTN_MK_C UniProtKB/Swiss-Prot
  PTN_MK_N UniProtKB/Swiss-Prot
PhenoGen Ptn PhenoGen
PRINTS PTNMIDKINE UniProtKB/Swiss-Prot
PROSITE PTN_MK_1 UniProtKB/Swiss-Prot
  PTN_MK_2 UniProtKB/Swiss-Prot
SMART PTN UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57288 UniProtKB/Swiss-Prot
UniProt P63090 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P20935 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ptn  Pleiotrophin (Heparine binding factor, Hbnf, in the mouse)      Symbol and Name status set to approved 70586 APPROVED