Sparc (secreted protein acidic and cysteine rich) - Rat Genome Database

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Gene: Sparc (secreted protein acidic and cysteine rich) Rattus norvegicus
Analyze
Symbol: Sparc
Name: secreted protein acidic and cysteine rich
RGD ID: 3742
Description: Enables calcium ion binding activity. Involved in several processes, including animal organ development; response to L-ascorbic acid; and response to lead ion. Located in several cellular components, including extracellular space; nucleus; and vesicle. Is active in glutamatergic synapse. Biomarker of diabetic angiopathy; membranoproliferative glomerulonephritis; membranous glomerulonephritis; myocardial infarction; and stomach carcinoma. Human ortholog(s) of this gene implicated in cervix carcinoma; endometrial carcinoma; and osteogenesis imperfecta type 17. Orthologous to human SPARC (secreted protein acidic and cysteine rich); INTERACTS WITH 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: basement-membrane protein 40; BM-40; ON; osteonectin; Secreted acidic cystein-rich glycoprotein (osteonectin); secreted acidic cysteine rich glycoprotein; secreted protein acidic and rich in cysteine; secreted protein, acidic, cysteine-rich (osteonectin)
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
mRatBN7.21039,516,394 - 39,538,252 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1039,516,406 - 39,538,396 (-)Ensembl
Rnor_6.01040,742,390 - 40,764,232 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1040,742,400 - 40,764,185 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01040,573,510 - 40,595,261 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41040,809,730 - 40,831,481 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11040,823,352 - 40,845,104 (-)NCBI
Celera1038,848,158 - 38,869,906 (-)NCBICelera
RH 3.4 Map10414.6RGD
Cytogenetic Map10q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-camphor  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
acetylsalicylic acid  (ISO)
acrylamide  (EXP)
aldehydo-D-glucose  (ISO)
alendronic acid  (EXP)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arachidonic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
avobenzone  (ISO)
benzene  (EXP,ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
berberine  (ISO)
bexarotene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
boric acid  (ISO)
buspirone  (EXP)
cadmium atom  (EXP,ISO)
cadmium dichloride  (ISO)
calciol  (ISO)
calcitriol  (EXP)
camphor  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
casticin  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-glucose  (ISO)
DDT  (ISO)
dexamethasone  (EXP)
dextran sulfate  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
Ethoxyacetic acid  (ISO)
fenamidone  (ISO)
fipronil  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furan  (EXP)
furosemide  (EXP)
gallocatechin  (EXP)
gamma-aminobutyric acid  (EXP)
gamma-Oryzanol (TN)  (EXP)
genistein  (EXP)
glucose  (ISO)
glycerol 2-phosphate  (ISO)
indometacin  (ISO)
isoflavones  (ISO)
L-ascorbic acid  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
L-methionine  (ISO)
lipopolysaccharide  (ISO)
losartan  (EXP)
magnesium atom  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylmercury(1+)  (EXP)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP)
nimesulide  (EXP)
notoginsenoside R1  (ISO)
oxaliplatin  (EXP)
p-toluidine  (EXP)
paclitaxel  (ISO)
palbociclib  (ISO)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
piroxicam  (ISO)
poly(vinylpyrrolidone)  (EXP)
potassium dichromate  (ISO)
progesterone  (ISO)
raloxifene  (EXP)
resveratrol  (EXP,ISO)
rimonabant  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (EXP)
silver atom  (EXP)
silver(0)  (EXP)
sodium arsenite  (ISO)
sodium fluoride  (EXP)
Soman  (EXP)
streptozocin  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP,ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
Trapidil  (EXP)
triacsin C  (ISO)
trichloroethene  (EXP)
triclosan  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Au E, etal., J Neurosci. 2007 Jul 4;27(27):7208-21.
2. Bagavandoss P, etal., J Histochem Cytochem. 1998 Sep;46(9):1043-49.
3. Brown TJ, etal., Gynecol Oncol. 1999 Oct;75(1):25-33.
4. Camino AM, etal., J Gene Med. 2008 Sep;10(9):993-1004.
5. Chang W, etal., Endocrinology. 2002 Apr;143(4):1467-74.
6. Cheng CY Biochem Biophys Res Commun. 1990 Mar 30;167(3):1393-9.
7. Cheng D, etal., Mol Cell Proteomics. 2006 Jun;5(6):1158-70. doi: 10.1074/mcp.D500009-MCP200. Epub 2006 Feb 28.
8. Engelmann GL Cardiovasc Res. 1993 Sep;27(9):1598-605.
9. Fujii M, etal., Kobe J Med Sci. 1997 Feb;43(1):13-23.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Gilbert RE, etal., Kidney Int. 1995 Oct;48(4):1216-25.
12. GOA data from the GO Consortium
13. Hinojos CA, etal., Hypertension 2005 Apr;45(4):698-704. Epub 2005 Feb 14.
14. Inagaki H, etal., Life Sci. 1996;58(11):927-34.
15. Ishigaki R, etal., Histochem J. 2002 Jan-Feb;34(1-2):57-66.
16. Jandeleit-Dahm K, etal., Microvasc Res. 2000 Jan;59(1):61-71.
17. Kim J, etal., J Microbiol Biotechnol. 2020 Mar 28;30(3):427-438. doi: 10.4014/jmb.1910.10055.
18. Kim SY, etal., J Cutan Pathol. 2008 Sep;35(9):826-31. doi: 10.1111/j.1600-0560.2007.00904.x. Epub 2008 Apr 18.
19. Komatsubara I, etal., Cardiovasc Pathol. 2003 Jul-Aug;12(4):186-94.
20. Kucukdereli H, etal., Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):E440-9. doi: 10.1073/pnas.1104977108. Epub 2011 Jul 25.
21. Kumei Y, etal., Ann N Y Acad Sci. 2006 Dec;1090:311-7.
22. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
23. Lee MJ, etal., Arch Toxicol 1995;69(9):590-5.
24. Li J, etal., Am J Physiol Endocrinol Metab 2002 Jun;282(6):E1334-41.
25. Liao H, etal., Eur J Oral Sci 1998 Jan;106 Suppl 1:418-23.
26. Maeng HY, etal., Jpn J Cancer Res. 2002 Sep;93(9):960-7.
27. Mendis DB, etal., Neurochem Res. 1998 Aug;23(8):1117-23.
28. MGD data from the GO Consortium
29. Mothe AJ and Brown IR, Hear Res. 2001 May;155(1-2):161-74.
30. Nahar NN, etal., J Bone Miner Metab. 2008;26(5):514-9. Epub 2008 Aug 30.
31. NCBI rat LocusLink and RefSeq merged data July 26, 2002
32. Nimphius W, etal., Virchows Arch. 2007 Feb;450(2):179-85.
33. Onyia JE, etal., J Cell Biochem. 2005 May 15;95(2):403-18.
34. Pichler RH, etal., Am J Pathol. 1996 Apr;148(4):1153-67.
35. Pichler RH, etal., Kidney Int. 1996 Dec;50(6):1978-89.
36. Puolakkainen P, etal., Dig Dis Sci. 1999 Aug;44(8):1554-64.
37. Reed MJ, etal., J Histochem Cytochem. 1993 Oct;41(10):1467-77.
38. RGD automated data pipeline
39. RGD automated import pipeline for gene-chemical interactions
40. Rodriguez-Jimenez FJ, etal., Oncol Rep. 2007 Jun;17(6):1301-7.
41. Said N, etal., Mol Cancer Res. 2007 Oct;5(10):1015-30.
42. Sakai N, etal., Hum Pathol. 2001 Oct;32(10):1064-70.
43. Sauk JJ, etal., Toxicol Appl Pharmacol. 1992 Oct;116(2):240-7.
44. Socha MJ, etal., Am J Pathol. 2007 Oct;171(4):1104-12. Epub 2007 Aug 23.
45. Sova P, etal., Cancer Epidemiol Biomarkers Prev. 2006 Jan;15(1):114-23.
46. Strandjord TP, etal., Am J Respir Cell Mol Biol. 1995 Sep;13(3):279-87.
47. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
48. Sugimoto M, etal., J Bone Miner Res. 1998 Feb;13(2):271-8.
49. Tartare-Deckert S, etal., J Biol Chem. 2001 Jun 22;276(25):22231-7. Epub 2001 Apr 9.
50. Turner RT, etal., Alcohol Clin Exp Res. 2001 May;25(5):667-71.
51. Walpen S, etal., J Am Soc Nephrol. 2000 Mar;11(3):468-76.
52. Yamanaka M, etal., J Urol. 2001 Dec;166(6):2495-9.
Additional References at PubMed
PMID:1737102   PMID:3400777   PMID:3427055   PMID:7034958   PMID:7848824   PMID:8906420   PMID:9501084   PMID:10559001   PMID:11856645   PMID:12867428   PMID:14505356   PMID:15389586  
PMID:16093428   PMID:16443258   PMID:17299058   PMID:18757743   PMID:19285050   PMID:19837135   PMID:22289652   PMID:22306863   PMID:22876197   PMID:22880013   PMID:23910024   PMID:24006456  
PMID:24245505   PMID:25340873   PMID:26110898   PMID:26420865   PMID:27068509   PMID:27339669   PMID:28499910   PMID:30424792   PMID:30560317  


Genomics

Candidate Gene Status
Sparc is a candidate Gene for QTL Vetf2
Sparc is a candidate Gene for QTL Vetf10
Comparative Map Data
Sparc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21039,516,394 - 39,538,252 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1039,516,406 - 39,538,396 (-)Ensembl
Rnor_6.01040,742,390 - 40,764,232 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1040,742,400 - 40,764,185 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01040,573,510 - 40,595,261 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41040,809,730 - 40,831,481 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11040,823,352 - 40,845,104 (-)NCBI
Celera1038,848,158 - 38,869,906 (-)NCBICelera
RH 3.4 Map10414.6RGD
Cytogenetic Map10q22NCBI
SPARC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5151,661,096 - 151,686,975 (-)EnsemblGRCh38hg38GRCh38
GRCh385151,661,096 - 151,686,915 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375151,040,657 - 151,066,476 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365151,021,201 - 151,046,710 (-)NCBINCBI36hg18NCBI36
Build 345151,021,203 - 151,046,710NCBI
Celera5147,122,406 - 147,147,929 (-)NCBI
Cytogenetic Map5q33.1NCBI
HuRef5146,186,043 - 146,212,010 (-)NCBIHuRef
CHM1_15150,473,070 - 150,499,042 (-)NCBICHM1_1
Sparc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391155,284,985 - 55,310,906 (-)NCBIGRCm39mm39
GRCm39 Ensembl1155,285,326 - 55,314,009 (-)Ensembl
GRCm381155,394,159 - 55,420,080 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1155,394,500 - 55,423,183 (-)EnsemblGRCm38mm10GRCm38
MGSCv371155,208,003 - 55,233,582 (-)NCBIGRCm37mm9NCBIm37
MGSCv361155,237,924 - 55,263,289 (-)NCBImm8
Celera1159,982,920 - 59,995,424 (-)NCBICelera
Cytogenetic Map11B1.3NCBI
cM Map1133.04NCBI
Sparc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554086,099,003 - 6,122,459 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554086,100,123 - 6,122,460 (-)NCBIChiLan1.0ChiLan1.0
SPARC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15153,091,160 - 153,115,745 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5153,090,181 - 153,115,750 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05147,087,903 - 147,112,466 (-)NCBIMhudiblu_PPA_v0panPan3
SPARC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1457,659,541 - 57,682,147 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl457,659,650 - 57,681,711 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha457,479,010 - 57,501,597 (+)NCBI
ROS_Cfam_1.0458,102,077 - 58,124,747 (+)NCBI
UMICH_Zoey_3.1457,918,069 - 57,940,655 (+)NCBI
UNSW_CanFamBas_1.0458,016,600 - 58,039,187 (+)NCBI
UU_Cfam_GSD_1.0458,519,992 - 58,542,658 (+)NCBI
Sparc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213112,576,762 - 112,597,465 (+)NCBI
SpeTri2.0NW_00493651511,026,156 - 11,046,812 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPARC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1671,357,703 - 71,381,160 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11671,368,164 - 71,380,972 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21677,576,864 - 77,584,734 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SPARC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12354,224,003 - 54,248,869 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2354,222,838 - 54,238,006 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603423,456,066 - 23,481,034 (+)NCBIVero_WHO_p1.0
Sparc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473337,348,993 - 37,369,804 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH128632  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21039,516,544 - 39,516,733 (+)MAPPERmRatBN7.2
Rnor_6.01040,742,541 - 40,742,729NCBIRnor6.0
Rnor_5.01040,573,661 - 40,573,849UniSTSRnor5.0
RGSC_v3.41040,809,881 - 40,810,069UniSTSRGSC3.4
Celera1038,848,309 - 38,848,497UniSTS
RH 3.4 Map10408.7UniSTS
Cytogenetic Map10q22UniSTS
RH94599  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21039,516,435 - 39,516,593 (+)MAPPERmRatBN7.2
Rnor_6.01040,742,432 - 40,742,589NCBIRnor6.0
Rnor_5.01040,573,552 - 40,573,709UniSTSRnor5.0
RGSC_v3.41040,809,772 - 40,809,929UniSTSRGSC3.4
Celera1038,848,200 - 38,848,357UniSTS
RH 3.4 Map10414.6UniSTS
Cytogenetic Map10q22UniSTS
RH140308  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21039,516,913 - 39,517,093 (+)MAPPERmRatBN7.2
Rnor_6.01040,742,910 - 40,743,089NCBIRnor6.0
Rnor_5.01040,574,030 - 40,574,209UniSTSRnor5.0
RGSC_v3.41040,810,250 - 40,810,429UniSTSRGSC3.4
Celera1038,848,678 - 38,848,857UniSTS
RH 3.4 Map10408.0UniSTS
Cytogenetic Map10q22UniSTS
PMC151926P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21039,517,071 - 39,518,238 (+)MAPPERmRatBN7.2
Rnor_6.01040,743,068 - 40,744,234NCBIRnor6.0
Rnor_5.01040,574,188 - 40,575,354UniSTSRnor5.0
RGSC_v3.41040,810,408 - 40,811,574UniSTSRGSC3.4
Celera1038,848,836 - 38,850,002UniSTS
Cytogenetic Map10q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103449055945579777Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103539226751793994Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:303
Count of miRNA genes:175
Interacting mature miRNAs:209
Transcripts:ENSRNOT00000017486
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 24 2 3 4 8 14 26 9 3
Medium 3 19 57 41 17 41 5 7 66 21 15 2 5
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012656 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC127919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC061777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D28875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212746 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214649 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214673 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220287 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220507 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220572 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220686 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220827 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222224 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224996 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225609 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225688 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225694 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226299 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226584 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226599 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226651 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226673 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226731 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226746 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227708 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227749 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228032 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229230 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229299 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229785 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230381 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230595 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230864 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231632 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232862 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233178 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233203 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234589 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234657 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234685 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235038 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U75928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y13714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000017486   ⟹   ENSRNOP00000017486
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1039,516,416 - 39,538,242 (-)Ensembl
Rnor_6.0 Ensembl1040,742,400 - 40,764,185 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098312   ⟹   ENSRNOP00000094410
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1039,516,406 - 39,538,396 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099801   ⟹   ENSRNOP00000083269
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1039,516,406 - 39,526,241 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115607   ⟹   ENSRNOP00000093140
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1039,517,585 - 39,538,180 (-)Ensembl
RefSeq Acc Id: NM_012656   ⟹   NP_036788
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21039,516,394 - 39,538,149 (-)NCBI
Rnor_6.01040,742,390 - 40,764,141 (-)NCBI
Rnor_5.01040,573,510 - 40,595,261 (-)NCBI
RGSC_v3.41040,809,730 - 40,831,481 (-)RGD
Celera1038,848,158 - 38,869,906 (-)RGD
Sequence:
RefSeq Acc Id: XM_008767663   ⟹   XP_008765885
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21039,516,395 - 39,538,252 (-)NCBI
Rnor_6.01040,742,391 - 40,764,232 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036788   ⟸   NM_012656
- Peptide Label: precursor
- UniProtKB: P16975 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008765885   ⟸   XM_008767663
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000017486   ⟸   ENSRNOT00000017486
RefSeq Acc Id: ENSRNOP00000094410   ⟸   ENSRNOT00000098312
RefSeq Acc Id: ENSRNOP00000083269   ⟸   ENSRNOT00000099801
RefSeq Acc Id: ENSRNOP00000093140   ⟸   ENSRNOT00000115607
Protein Domains
EF-hand   Follistatin-like   Kazal-like

Transcriptome

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

Promoters
RGD ID:13697202
Promoter ID:EPDNEW_R7726
Type:initiation region
Name:Sparc_1
Description:secreted protein acidic and cysteine rich
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_6.01040,764,175 - 40,764,235EPDNEW

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)
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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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/CubMcwi (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
BXH3/CubMcwi (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/DuCrl (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/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
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)
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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)
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)
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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)
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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
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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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)
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)
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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)
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)
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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)
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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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)
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/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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3742 AgrOrtholog
Ensembl Genes ENSRNOG00000012840 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000017486 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000017486 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5621666 IMAGE-MGC_LOAD
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot
  Fol_N UniProtKB/Swiss-Prot
  Follistatin/Osteonectin_EGF UniProtKB/Swiss-Prot
  Kazal_dom UniProtKB/Swiss-Prot
  Kazal_dom_sf UniProtKB/Swiss-Prot
  Osteonectin_CS UniProtKB/Swiss-Prot
  SPARC UniProtKB/Swiss-Prot
  SPARC/Testican_Ca-bd-dom UniProtKB/Swiss-Prot
KEGG Report rno:24791 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72514 IMAGE-MGC_LOAD
NCBI Gene 24791 ENTREZGENE
PANTHER PTHR13866:SF6 UniProtKB/Swiss-Prot
Pfam FOLN UniProtKB/Swiss-Prot
  Kazal_1 UniProtKB/Swiss-Prot
  SPARC_Ca_bdg UniProtKB/Swiss-Prot
PhenoGen Sparc PhenoGen
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot
  KAZAL_2 UniProtKB/Swiss-Prot
  OSTEONECTIN_1 UniProtKB/Swiss-Prot
  OSTEONECTIN_2 UniProtKB/Swiss-Prot
SMART FOLN UniProtKB/Swiss-Prot
  KAZAL UniProtKB/Swiss-Prot
Superfamily-SCOP SSF100895 UniProtKB/Swiss-Prot
  SSF47473 UniProtKB/Swiss-Prot
UniProt P16975 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O08953 UniProtKB/Swiss-Prot
  Q6GSZ4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-03 Sparc  secreted protein acidic and cysteine rich  Sparc  secreted protein, acidic, cysteine-rich (osteonectin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Sparc  secreted protein, acidic, cysteine-rich (osteonectin)  Sparc  secreted acidic cysteine rich glycoprotein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Sparc  Secreted acidic cystein-rich glycoprotein (osteonectin)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expression is increased 2.2 fold in SHR compared with WKY rats 1357414
gene_expression mRNA expressed in osteoblasts, odontoblasts, and fibroblasts during development 730043
gene_regulation expression increases at the onset of high-fat-diet obesity 625747