Spp1 (secreted phosphoprotein 1) - Rat Genome Database

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Gene: Spp1 (secreted phosphoprotein 1) Rattus norvegicus
Analyze
Symbol: Spp1
Name: secreted phosphoprotein 1
RGD ID: 3752
Description: Predicted to enable extracellular matrix binding activity and integrin binding activity. Involved in several processes, including negative regulation of collateral sprouting of intact axon in response to injury; osteoblast differentiation; and positive regulation of bone resorption. Located in several cellular components, including extracellular space; perinuclear region of cytoplasm; and vesicle. Used to study several diseases, including encephalomyelitis; myocarditis; radiculopathy; renovascular hypertension; and visual epilepsy. Biomarker of autosomal dominant polycystic kidney disease; calcinosis; and glomerulosclerosis. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); biliary atresia; coronary artery disease (multiple); disease of cellular proliferation (multiple); and hepatitis. Orthologous to human SPP1 (secreted phosphoprotein 1); PARTICIPATES IN diabetic nephropathy pathway; c-Jun N-terminal kinases MAPK signaling pathway; fibroblast growth factor signaling pathway; INTERACTS WITH (R,R)-tramadol; (S)-naringenin; 1,3,5-trinitro-1,3,5-triazinane.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: bone sialoprotein 1; LOC100359743; OSP; osteopontin; osteopontin-like; Sialoprotein (osteopontin); SPP-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Spp1em1Mcwi   spp1em3Mcwi   Spp1em4Mcwi   Spp1em2Mcwi  
Genetic Models: SS-Spp1em3Mcwi SHRSP-Spp1em2Mcwi SHRSP-Spp1em1Mcwi SS-Spp1em4Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2145,308,885 - 5,315,120 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl145,308,885 - 5,315,162 (-)Ensembl
Rnor_6.0146,673,686 - 6,679,965 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl146,673,686 - 6,679,901 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0146,653,086 - 6,658,937 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.1146,422,741 - 6,426,400 (-)NCBI
Celera145,447,814 - 5,453,553 (-)NCBICelera
RH 3.4 Map1484.5RGD
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute kidney failure  (ISO)
adenocarcinoma  (ISO)
Albuminuria  (IEP)
Alcoholic Liver Diseases  (ISO)
allergic contact dermatitis  (ISO)
allergic disease  (ISO)
Aneurysm  (ISO)
Angina Pectoris  (ISO)
anti-basement membrane glomerulonephritis  (ISO)
asbestosis  (ISO)
autosomal dominant polycystic kidney disease  (IEP,ISO)
biliary atresia  (ISO)
Brain Neoplasms  (ISO)
Breast Neoplasms  (ISO)
calcinosis  (IEP,ISO)
Cardiomegaly  (ISO)
carotid stenosis  (ISO)
Cerebral Hemorrhage  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
Chronic Hepatitis C  (ISO)
coronary artery disease  (ISO)
coronary restenosis  (ISO)
Cystic, Mucinous, and Serous Neoplasms  (ISO)
Diabetic Cardiomyopathies  (ISO)
Diabetic Nephropathies  (IDA)
disease of cellular proliferation  (ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
encephalomyelitis  (IDA)
Endometrioid Carcinomas  (ISO)
Experimental Autoimmune Neuritis  (IDA)
Experimental Diabetes Mellitus  (IDA)
Experimental Liver Cirrhosis  (IDA)
Experimental Liver Neoplasms  (ISO)
Experimental Neoplasms  (ISO)
Fibrosis  (ISO)
focal segmental glomerulosclerosis  (ISO)
Foreign-Body Reaction  (ISO)
glomerulonephritis  (IMP)
glomerulosclerosis  (IEP)
heart disease  (ISO)
heart valve disease  (ISO)
hepatitis  (ISO)
hepatocellular carcinoma  (ISO)
high grade glioma  (IDA,ISO)
Inflammation  (ISO)
Kidney Calculi  (IEP,ISO)
kidney disease  (ISO)
kidney failure  (ISO)
Laryngeal Neoplasms  (ISO)
Leukoencephalopathies  (ISO)
liver cirrhosis  (ISO)
Lung Neoplasms  (ISO)
lung non-small cell carcinoma  (ISO)
malaria  (ISO)
Mammary Neoplasms, Experimental  (ISO)
melanoma  (ISO)
Mesothelioma  (ISO)
multiple myeloma  (ISO)
multiple sclerosis  (ISO)
myocardial infarction  (ISO)
Myocardial Reperfusion Injury  (ISO)
myocarditis  (IDA)
Neoplasm Metastasis  (ISO)
Neovascularization, Pathologic  (ISO)
Nervous System Trauma  (IDA)
Osteolysis  (ISO)
Ovarian Neoplasms  (ISO)
pancreas disease  (ISO)
pancreatic cancer  (ISO)
Pleural Neoplasms  (ISO)
pneumonia  (ISO)
progressive osseous heteroplasia  (ISO)
prostate carcinoma  (ISO)
Prostatic Neoplasms  (ISO)
proteinuria  (ISO)
pulmonary fibrosis  (ISO)
radiculopathy  (IDA)
renovascular hypertension  (IDA)
Reperfusion Injury  (ISO)
rheumatoid arthritis  (ISO)
scrapie  (ISO)
Spinal Cord Injuries  (ISO)
Stomach Neoplasms  (ISO)
Thyroid Neoplasms  (ISO)
tuberculosis  (ISO)
uremia  (ISO)
urinary bladder cancer  (ISO)
Urinary Calculi  (ISO)
Vascular System Injuries  (ISO)
visual epilepsy  (IDA)
Wounds and Injuries  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R,R)-tramadol  (EXP)
(S)-naringenin  (EXP)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3,5-trinitro-1,3,5-triazinane  (EXP)
1,4-dichlorobenzene  (ISO)
1-chloro-2,4-dinitrobenzene  (EXP)
1-fluoro-2,4-dinitrobenzene  (ISO)
1-methylphenanthrene  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
1-nitropyrene  (ISO)
11-deoxycorticosterone  (EXP)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
2-amino-2-deoxy-D-galactopyranose  (ISO)
2-Hydroxy-6-(8,11,14-pentadecatrienyl)benzoic acid  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-aminobenzamide  (ISO)
3-chloropropane-1,2-diol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-aminophenol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP,ISO)
8-Br-cAMP  (EXP,ISO)
8-bromo-3',5'-cyclic GMP  (EXP)
9-cis-retinoic acid  (ISO)
acetaldehyde  (ISO)
acetylsalicylic acid  (EXP)
acrylic acid  (EXP)
adefovir  (EXP)
adenine  (EXP)
aflatoxin B1  (EXP,ISO)
agomelatine  (EXP)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
allyl alcohol  (EXP)
aluminium oxide  (ISO)
aminoglutethimide  (EXP)
ammonium chloride  (EXP)
amphotericin B  (EXP)
amphotericin B methyl ester  (ISO)
andrographolide  (ISO)
aniline  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
anthracen-2-amine  (EXP)
aristolochic acid  (EXP,ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
asperentin  (ISO)
astaxanthin  (ISO)
aucubin  (ISO)
bacitracin  (EXP)
benazepril  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (EXP,ISO)
berberine  (ISO)
beta-naphthoflavone  (ISO)
bexarotene  (EXP)
bezafibrate  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
bortezomib  (ISO)
budesonide  (ISO)
Butylparaben  (ISO)
butyric acid  (EXP)
C60 fullerene  (EXP)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP)
calciol  (ISO)
calcitriol  (EXP,ISO)
calcium atom  (EXP,ISO)
calcium carbonate  (ISO)
calcium(0)  (EXP,ISO)
cannabidiol  (ISO)
capsaicin  (EXP)
carbamazepine  (ISO)
carbofuran  (EXP)
carbon nanotube  (EXP,ISO)
celecoxib  (EXP)
ceric oxide  (EXP)
chitosan  (ISO)
chloroprene  (ISO)
chlorpromazine  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (EXP,ISO)
Clofop  (ISO)
clozapine  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
curcumin  (EXP)
cyanuric acid  (EXP)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (EXP,ISO)
cypermethrin  (ISO)
D-glucose  (EXP,ISO)
DDT  (EXP,ISO)
decabromodiphenyl ether  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diamminedichloroplatinum  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (EXP,ISO)
dibenzo[a,l]pyrene  (EXP)
dibutyl phthalate  (EXP)
diethylstilbestrol  (ISO)
dioxygen  (EXP,ISO)
dipyridamole  (EXP)
disodium selenite  (ISO)
divanadium pentaoxide  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (ISO)
enalapril  (EXP,ISO)
endosulfan  (EXP)
entinostat  (ISO)
Erionite  (ISO)
ethanol  (EXP,ISO)
ethylene glycol  (EXP)
etoposide  (ISO)
Falecalcitriol  (ISO)
flavonoids  (EXP)
flunisolide  (ISO)
fluoranthene  (ISO)
fluvastatin  (EXP)
folic acid  (ISO)
fulvestrant  (EXP,ISO)
furan  (EXP)
gadodiamide hydrate  (EXP)
gallocatechin  (EXP)
gemcitabine  (ISO)
genistein  (EXP,ISO)
gentamycin  (EXP)
Ginkgoic acid  (ISO)
glucose  (EXP,ISO)
glycerol 2-phosphate  (ISO)
glycidol  (ISO)
glyoxylic acid  (EXP)
graphite  (EXP,ISO)
griseofulvin  (ISO)
Hexachloro-1,3-butadiene  (EXP)
hydrogen peroxide  (EXP,ISO)
icariin  (EXP,ISO)
imperatorin  (EXP)
indole-3-methanol  (EXP)
iron(2+) sulfate (anhydrous)  (ISO)
isocyanuric acid  (EXP)
isoniazide  (EXP,ISO)
isonicotinamide  (ISO)
isoprenaline  (EXP,ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
jaspamide  (ISO)
kaempferol  (ISO)
kojic acid  (ISO)
KT 5823  (EXP)
L-ascorbic acid  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
linalool  (EXP)
lipopolysaccharide  (ISO)
LY294002  (EXP)
magnesium atom  (ISO)
medroxyprogesterone acetate  (ISO)
melamine  (EXP)
mercury atom  (ISO)
mercury dibromide  (ISO)
mercury dichloride  (EXP,ISO)
mercury(0)  (ISO)
mesalamine  (EXP)
metaproterenol  (EXP)
methapyrilene  (EXP)
methotrexate  (EXP)
methylmercury chloride  (EXP,ISO)
methylparaben  (ISO)
milrinone  (EXP)
mitoxantrone  (EXP)
mometasone furoate  (ISO)
mycophenolic acid  (ISO)
mycotoxin  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-acetyl-L-cysteine  (EXP)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (ISO)
naproxen  (EXP)
naringin  (EXP,ISO)
Natamycin  (ISO)
neoechinulin A  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
nifedipine  (ISO)
nitric oxide  (ISO)
nitroprusside  (ISO)
nystatin  (ISO)
O-methyleugenol  (ISO)
ochratoxin A  (EXP,ISO)
okadaic acid  (ISO)
orciprenaline  (EXP)
oxalic acid  (ISO)
oxaliplatin  (EXP)
oxidopamine  (EXP)
ozone  (EXP,ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
paricalcitol  (ISO)
PD 0325901  (ISO)
PD123319  (EXP)
pentane-2,3-dione  (EXP)
Pentoxifylline  (EXP)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
phenobarbital  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosphonoformic acid  (ISO)
phosphorus atom  (ISO)
phosphorus(.)  (ISO)
phylloquinone  (ISO)
pioglitazone  (EXP)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium bromate  (EXP,ISO)
progesterone  (ISO)
protein kinase inhibitor  (ISO)
Ptaquiloside  (ISO)
pyrrolidine dithiocarbamate  (EXP)
quartz  (EXP)
quercetin  (EXP,ISO)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
rolipram  (EXP)
rotenone  (EXP,ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
Salidroside  (ISO)
Salinomycin  (ISO)
SB 203580  (EXP)
SB 431542  (ISO)
sclareol  (ISO)
Se-methyl-L-selenocysteine  (ISO)
Se-methylselenocysteine  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP,ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sodium fluoride  (EXP,ISO)
sterigmatocystin  (ISO)
streptozocin  (EXP)
strontium atom  (ISO)
succimer  (ISO)
sulfasalazine  (ISO)
sulforaphane  (ISO)
sumatriptan  (EXP)
SWINHOLIDE A  (ISO)
tacrolimus hydrate  (EXP)
tamibarotene  (ISO)
tamoxifen  (ISO)
Tanshinone I  (EXP)
temozolomide  (ISO)
Tesaglitazar  (EXP)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
thioacetamide  (EXP)
thiourea  (ISO)
titanium atom  (EXP)
titanium dioxide  (EXP,ISO)
topotecan  (EXP,ISO)
tramadol  (EXP)
transplatin  (ISO)
tremolite asbestos  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
trimethyltin  (ISO)
troglitazone  (EXP,ISO)
tubocurarine  (ISO)
Tungsten carbide  (ISO)
uranium atom  (ISO)
urethane  (ISO)
valproic acid  (ISO)
valsartan  (EXP)
vanadyl sulfate  (EXP)
vancomycin  (EXP,ISO)
vitamin D  (ISO)
vitamin K  (EXP)
vorinostat  (ISO)
warfarin  (EXP,ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
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16. GOA data from the GO Consortium
17. Guarino V, etal., J Clin Endocrinol Metab. 2005 Sep;90(9):5270-8. Epub 2005 Jul 5.
18. Guo H, etal., Dig Dis Sci. 2005 Jul;50(7):1288-98.
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47. MGD data from the GO Consortium
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52. NCBI rat LocusLink and RefSeq merged data July 26, 2002
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55. Pipeline to import KEGG annotations from KEGG into RGD
56. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
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58. Razzouk S, etal., Bone. 2002 Jan;30(1):40-7.
59. RGD automated data pipeline
60. RGD automated import pipeline for gene-chemical interactions
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64. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
65. Suzuki K, etal., J Bone Miner Res 2002 Aug;17(8):1486-97.
66. Tajiri T, etal., Dig Dis Sci. 2005 Jan;50(1):188-95.
67. Takahashi F, etal., Int J Cancer. 2002 Apr 10;98(5):707-12.
68. Tamura A, etal., Circ J. 2003 Sep;67(9):742-4.
69. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
70. Tsai AT, etal., Biomaterials. 2005 Oct;26(29):5835-43. Epub 2005 Apr 21.
71. Vernon HJ, etal., Kidney Int. 2005 Sep;68(3):938-47.
72. Wejheden C, etal., Biochem Biophys Res Commun. 2006 Mar 3;341(1):116-20. Epub 2006 Jan 6.
73. Whitington PF, etal., Pediatr Res. 2005 Jun;57(6):837-44. Epub 2005 Apr 21.
74. Xie Z, etal., Hypertension. 2004 Dec;44(6):826-31. Epub 2004 Nov 8.
75. Xie Z, etal., J Biol Chem. 2003 Dec 5;278(49):48546-52. Epub 2003 Sep 18.
76. Xu G, etal., J Clin Invest. 2005 Apr;115(4):1060-7. Epub 2005 Mar 3.
77. Yan X, etal., Cardiovasc Diabetol. 2010 Oct 29;9:70.
78. Ye B, etal., Clin Cancer Res. 2006 Jan 15;12(2):432-41.
79. Yu DW, etal., J Invest Dermatol 2001 Dec;117(6):1554-8.
80. Zaravinos A, etal., PLoS One. 2011 Apr 5;6(4):e18255.
81. Zhang ZX, etal., J Immunol. 2010 Jul 15;185(2):967-73. Epub 2010 Jun 14.
82. Zhou C, etal., Am J Nephrol. 2010;32(4):324-31. Epub 2010 Aug 19.
83. Zhu XL, etal., Biochem Cell Biol 2001;79(6):737-46.
84. Zohar R, etal., Am J Physiol Heart Circ Physiol. 2004 Oct;287(4):H1730-9. Epub 2004 May 27.
85. Zuo J, etal., Nephrol Dial Transplant. 2011 Jun;26(6):1785-96. Epub 2011 Mar 4.
Additional References at PubMed
PMID:2736258   PMID:3167835   PMID:3469201   PMID:8408622   PMID:8889548   PMID:11967208   PMID:12505755   PMID:15121739   PMID:15153550   PMID:15482851   PMID:15489334   PMID:15516325  
PMID:15548430   PMID:15557322   PMID:15865444   PMID:16187297   PMID:16253490   PMID:16502470   PMID:16518820   PMID:16720713   PMID:16753026   PMID:16807234   PMID:16883060   PMID:17546625  
PMID:17643430   PMID:17868879   PMID:17898038   PMID:17973907   PMID:18036861   PMID:18041732   PMID:18158341   PMID:18180311   PMID:18235026   PMID:18378437   PMID:18415800   PMID:18471361  
PMID:18638458   PMID:18703563   PMID:18703867   PMID:18712054   PMID:18728346   PMID:18757743   PMID:19032867   PMID:19076167   PMID:19124839   PMID:19686792   PMID:19723557   PMID:19901966  
PMID:20211246   PMID:20392802   PMID:20396353   PMID:20407481   PMID:20417179   PMID:20439489   PMID:20450731   PMID:20596651   PMID:20626561   PMID:20714131   PMID:20838370   PMID:21264948  
PMID:21283687   PMID:21321126   PMID:21806466   PMID:21940634   PMID:21949681   PMID:22036853   PMID:22049796   PMID:22087764   PMID:22496158   PMID:22552891   PMID:22692550   PMID:22779921  
PMID:22814749   PMID:22847642   PMID:23161527   PMID:23241663   PMID:23376485   PMID:23457612   PMID:23466073   PMID:23467880   PMID:23498805   PMID:23533145   PMID:23788374   PMID:24247243  
PMID:24449951   PMID:24687376   PMID:24841674   PMID:25146847   PMID:25467747   PMID:25839998   PMID:26099282   PMID:26216642   PMID:26482249   PMID:26581507   PMID:27026710   PMID:27089830  
PMID:27262843   PMID:27486809   PMID:27585571   PMID:27659347   PMID:27717860   PMID:27743892   PMID:28270094   PMID:28302392   PMID:28442375   PMID:28978514   PMID:29337251   PMID:29602294  
PMID:30758811   PMID:30893567   PMID:31544532   PMID:31914633   PMID:32061643   PMID:32271401   PMID:32423114   PMID:33645892   PMID:33883409  


Genomics

Comparative Map Data
Spp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2145,308,885 - 5,315,120 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl145,308,885 - 5,315,162 (-)Ensembl
Rnor_6.0146,673,686 - 6,679,965 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl146,673,686 - 6,679,901 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0146,653,086 - 6,658,937 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.1146,422,741 - 6,426,400 (-)NCBI
Celera145,447,814 - 5,453,553 (-)NCBICelera
RH 3.4 Map1484.5RGD
Cytogenetic Map14p22NCBI
SPP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl487,975,667 - 87,983,532 (+)EnsemblGRCh38hg38GRCh38
GRCh38487,975,714 - 87,983,411 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37488,896,866 - 88,904,563 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36489,115,826 - 89,123,587 (+)NCBINCBI36hg18NCBI36
Build 34489,253,980 - 89,261,741NCBI
Celera486,188,727 - 86,196,490 (+)NCBI
Cytogenetic Map4q22.1NCBI
HuRef484,643,231 - 84,650,994 (+)NCBIHuRef
CHM1_1488,873,591 - 88,881,352 (+)NCBICHM1_1
Spp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395104,582,977 - 104,588,919 (+)NCBIGRCm39mm39
GRCm39 Ensembl5104,582,984 - 104,588,916 (+)Ensembl
GRCm385104,435,111 - 104,441,053 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5104,435,118 - 104,441,050 (+)EnsemblGRCm38mm10GRCm38
MGSCv375104,864,137 - 104,870,069 (+)NCBIGRCm37mm9NCBIm37
MGSCv365104,657,300 - 104,681,345 (+)NCBImm8
Celera5101,744,286 - 101,750,760 (+)NCBICelera
Cytogenetic Map5E5NCBI
cM Map550.68NCBI
Spp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554741,913,829 - 1,922,016 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554741,914,477 - 1,922,025 (-)NCBIChiLan1.0ChiLan1.0
SPP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1490,988,200 - 90,995,935 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl490,988,200 - 90,995,935 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0480,263,711 - 80,271,466 (+)NCBIMhudiblu_PPA_v0panPan3
SPP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13211,354,070 - 11,362,325 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3211,353,953 - 11,362,069 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3230,592,131 - 30,600,371 (-)NCBI
ROS_Cfam_1.03211,406,381 - 11,414,630 (+)NCBI
UMICH_Zoey_3.13211,490,535 - 11,498,773 (+)NCBI
UNSW_CanFamBas_1.03211,316,506 - 11,324,744 (+)NCBI
UU_Cfam_GSD_1.03228,630,350 - 28,638,599 (-)NCBI
Spp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244052851,729,610 - 1,736,282 (-)NCBI
SpeTri2.0NW_004936905148,956 - 156,023 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8131,077,786 - 131,085,340 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18131,077,786 - 131,085,334 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28140,307,933 - 140,315,453 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap8qNCBI
SPP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1736,337,165 - 36,344,927 (+)NCBI
ChlSab1.1 Ensembl736,338,386 - 36,344,407 (+)Ensembl
Vero_WHO_p1.0NW_02366603715,089,529 - 15,097,556 (+)NCBI
Spp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248724,505,796 - 4,513,247 (+)NCBI

Position Markers
RH94678  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2145,309,008 - 5,309,173 (+)MAPPERmRatBN7.2
Rnor_6.0146,673,810 - 6,673,974NCBIRnor6.0
Rnor_5.0146,653,210 - 6,653,374UniSTSRnor5.0
Celera145,447,938 - 5,448,102UniSTS
RH 3.4 Map1484.5UniSTS
Cytogenetic Map14p22UniSTS
RH129494  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2145,309,016 - 5,309,234 (+)MAPPERmRatBN7.2
Rnor_6.0146,673,818 - 6,674,035NCBIRnor6.0
Rnor_5.0146,653,218 - 6,653,435UniSTSRnor5.0
Celera145,447,946 - 5,448,163UniSTS
Cytogenetic Map14p22UniSTS
RH136964  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2145,308,890 - 5,309,100 (+)MAPPERmRatBN7.2
Rnor_6.0146,673,692 - 6,673,901NCBIRnor6.0
Rnor_5.0146,653,092 - 6,653,301UniSTSRnor5.0
Celera145,447,820 - 5,448,029UniSTS
RH 3.4 Map1488.1UniSTS
Cytogenetic Map14p22UniSTS
PMC316977P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2145,309,424 - 5,309,769 (+)MAPPERmRatBN7.2
Rnor_6.0146,674,226 - 6,674,570NCBIRnor6.0
Rnor_5.0146,653,626 - 6,653,970UniSTSRnor5.0
Celera145,448,354 - 5,448,698UniSTS
Cytogenetic Map14p22UniSTS
UniSTS:280407  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2145,310,624 - 5,312,028 (+)MAPPERmRatBN7.2
Rnor_6.0146,675,426 - 6,676,829NCBIRnor6.0
Rnor_5.0146,654,826 - 6,656,229UniSTSRnor5.0
RGSC_v3.4146,423,677 - 6,425,080UniSTSRGSC3.4
Celera145,449,554 - 5,450,957UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14121760616960180Rat
71115Niddm15Non-insulin dependent diabetes mellitus QTL 154.8blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14121760611030812Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
724541Niddm53Non-insulin dependent diabetes mellitus QTL 530.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1438130749088978Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14381307418274691Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14381307418274691Rat


Genetic Models
This gene Spp1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:400
Count of miRNA genes:226
Interacting mature miRNAs:264
Transcripts:ENSRNOT00000067875
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 1
Medium 20 8 26 34 21 2
Low 2 21 41 33 16 33 8 10 48 20 9 8
Below cutoff 1 2 8 8 2 8 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067875   ⟹   ENSRNOP00000062358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl145,308,885 - 5,315,162 (-)Ensembl
Rnor_6.0 Ensembl146,673,686 - 6,679,901 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075989   ⟹   ENSRNOP00000068511
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl145,308,890 - 5,315,139 (-)Ensembl
Rnor_6.0 Ensembl146,673,746 - 6,679,878 (-)Ensembl
RefSeq Acc Id: NM_012881   ⟹   NP_037013
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2145,308,885 - 5,315,120 (-)NCBI
Rnor_6.0146,673,686 - 6,679,921 (-)NCBI
Rnor_5.0146,653,086 - 6,658,937 (-)NCBI
Celera145,447,814 - 5,453,553 (-)RGD
Sequence:
RefSeq Acc Id: XM_008769996   ⟹   XP_008768218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2145,308,885 - 5,315,117 (-)NCBI
Rnor_6.0146,673,686 - 6,679,965 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037013   ⟸   NM_012881
- Peptide Label: precursor
- UniProtKB: P08721 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008768218   ⟸   XM_008769996
- Peptide Label: isoform X1
- UniProtKB: P08721 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000062358   ⟸   ENSRNOT00000067875
RefSeq Acc Id: ENSRNOP00000068511   ⟸   ENSRNOT00000075989

Transcriptome

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

Promoters
RGD ID:13699171
Promoter ID:EPDNEW_R9696
Type:multiple initiation site
Name:Spp1_1
Description:secreted phosphoprotein 1
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_6.0146,679,910 - 6,679,970EPDNEW

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)
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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
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)
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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
F344/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
FHH/EurMcwi (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
FHH/EurMcwi (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)
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)
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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)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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)
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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)
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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (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
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Br