Nog (noggin) - Rat Genome Database
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Gene: Nog (noggin) Rattus norvegicus
Analyze
Symbol: Nog
Name: noggin
RGD ID: 3183
Description: Predicted to have cytokine binding activity and protein homodimerization activity. Involved in several processes, including hippocampus development; learning or memory; and regulation of gliogenesis. Localizes to axon; extracellular space; and protein-containing complex. Biomarker of acute kidney tubular necrosis and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in Huntington's disease; cleft lip; dysostosis (multiple); hyperopia; and proximal symphalangism. Orthologous to human NOG (noggin); PARTICIPATES IN Bone morphogenetic proteins signaling pathway; transforming growth factor-beta superfamily mediated signaling pathway; INTERACTS WITH (20S)-ginsenoside Rg3; 17beta-estradiol; amitriptyline.
Type: protein-coding
RefSeq Status: VALIDATED
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21074,128,712 - 74,130,339 (-)NCBI
Rnor_6.0 Ensembl1076,811,759 - 76,813,386 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01076,811,759 - 76,813,386 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01076,677,612 - 76,679,239 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41077,689,244 - 77,690,871 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11077,703,801 - 77,704,728 (-)NCBI
Celera1073,029,127 - 73,030,754 (-)NCBICelera
Cytogenetic Map10q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(20S)-ginsenoside Rg3  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3',5'-cyclic AMP  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
acetic acid  (ISO)
all-trans-retinoic acid  (ISO)
amitriptyline  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bromochloroacetic acid  (ISO)
butanal  (ISO)
chloroprene  (EXP)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
dexamethasone  (EXP)
dibutyl phthalate  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
folic acid  (ISO)
furan  (EXP)
glycerol 2-phosphate  (EXP)
icariin  (ISO)
L-ascorbic acid  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
maneb  (ISO)
manganese(II) chloride  (ISO)
mercury dibromide  (ISO)
mercury dichloride  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (EXP)
neomycin  (ISO)
nickel atom  (ISO)
octreotide  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
pasireotide  (ISO)
pentane-2,3-dione  (EXP)
phenethyl caffeate  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (EXP,ISO)
Salidroside  (ISO)
SB 431542  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sulforaphane  (ISO)
testosterone  (ISO)
thimerosal  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure formation involved in morphogenesis  (ISO)
atrial cardiac muscle tissue morphogenesis  (IEA,ISO)
axial mesoderm development  (IEA,ISO)
axon guidance  (ISO)
BMP signaling pathway involved in heart development  (IEA,ISO)
brain development  (ISO)
cartilage development  (IEA)
cell differentiation in hindbrain  (IEA,ISO)
cellular response to BMP stimulus  (IEP,ISO)
cellular response to hypoxia  (IEP)
central nervous system development  (ISO)
dorsal/ventral pattern formation  (IBA,IEA,ISO)
embryonic digit morphogenesis  (IEA,ISO)
embryonic skeletal joint morphogenesis  (IEA,ISO)
embryonic skeletal system development  (ISO)
endocardial cushion morphogenesis  (IEA,ISO)
endoderm development  (ISO)
endoderm formation  (IEA,ISO)
epithelial to mesenchymal transition  (IEA,ISO,ISS)
face morphogenesis  (IEA,ISO)
fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation  (IEA,ISO)
forebrain development  (IEP)
heart trabecula morphogenesis  (IEA,ISO)
hippocampus development  (IEP)
in utero embryonic development  (IEA,ISO)
limb development  (ISO)
lung morphogenesis  (IEA,ISO)
membranous septum morphogenesis  (IEA,ISO)
memory  (IMP)
mesenchymal cell differentiation  (IMP,ISO)
mesoderm formation  (IEA,ISO)
middle ear morphogenesis  (IEA,ISO)
motor neuron axon guidance  (IEA,ISO)
negative regulation of apoptotic signaling pathway  (IEA,ISO)
negative regulation of astrocyte differentiation  (IEA,IMP,ISO,ISS)
negative regulation of BMP signaling pathway  (IBA,IEA,ISO,ISS)
negative regulation of canonical Wnt signaling pathway  (IEA,ISO)
negative regulation of cardiac muscle cell proliferation  (IEA,ISO,ISS)
negative regulation of cartilage development  (IEA,ISO)
negative regulation of cell migration  (IEA,ISO)
negative regulation of cytokine activity  (IEA,ISO)
negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation  (IEA,ISO)
negative regulation of gene expression  (IEA,ISO)
negative regulation of osteoblast differentiation  (IEA,ISO)
negative regulation of pathway-restricted SMAD protein phosphorylation  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
neural plate morphogenesis  (IEA,ISO)
neural tube closure  (IEA,ISO)
neural tube development  (ISO)
notochord morphogenesis  (IEA,ISO)
ossification  (IEP)
osteoblast differentiation  (IBA,IEA,ISO,ISS)
outflow tract morphogenesis  (IEA,ISO)
pattern specification process  (ISO)
pharyngeal arch artery morphogenesis  (IEA,ISO)
pituitary gland development  (IEA,ISO)
positive regulation of branching involved in ureteric bud morphogenesis  (IEA,ISO,ISS)
positive regulation of cell population proliferation  (IMP)
positive regulation of epithelial cell proliferation  (IEA,ISO)
positive regulation of gene expression  (IEA,ISO)
positive regulation of glomerulus development  (IEA,ISO,ISS)
positive regulation of oligodendrocyte progenitor proliferation  (IMP)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
prostatic bud formation  (IEA,ISO)
regulation of BMP signaling pathway  (ISO)
regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation  (IEA,ISO)
skeletal system development  (ISO)
somatic stem cell population maintenance  (IEA,ISO)
somite development  (IEA,ISO)
spinal cord development  (IEA,ISO)
ureteric bud development  (ISO)
ureteric bud formation  (IEA,ISO)
urogenital system development  (ISO)
ventricular compact myocardium morphogenesis  (IEA,ISO)
ventricular septum morphogenesis  (ISO)
visual learning  (IMP)
wound healing  (IEA,IEP,ISO,ISS)

Cellular Component
axon  (IDA)
extracellular space  (IBA,IDA,IEA,ISO)
protein-containing complex  (IDA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Andersson T, etal., Mol Cell Neurosci. 2011 May;47(1):10-8. doi: 10.1016/j.mcn.2011.01.006. Epub 2011 Jan 14.
2. Bostrom KI, etal., Circ Res. 2011 Feb 18;108(4):446-57. doi: 10.1161/CIRCRESAHA.110.236596. Epub 2010 Dec 30.
3. Cho SR, etal., J Clin Invest. 2007 Oct;117(10):2889-902.
4. Declau F, etal., Otol Neurotol. 2005 Sep;26(5):934-40.
5. Dudaric L, etal., Coll Antropol. 2013 Dec;37(4):1291-8.
6. Fan X, etal., Brain Res Brain Res Protoc. 2004 Jun;13(2):99-105.
7. Fan X, etal., Brain Res Dev Brain Res 2003 Dec 19;146(1-2):51-8.
8. Fan XT, etal., Acta Pharmacol Sin. 2003 May;24(5):394-7.
9. Fan XT, etal., Neurosci Lett. 2004 Aug 5;366(1):107-11.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. GOA data from the GO Consortium
12. Gong Y, etal., Nat Genet. 1999 Mar;21(3):302-4.
13. Gutiérrez SJ, etal., Acta Odontol Latinoam. 2010;23(1):13-9.
14. Hampton DW, etal., Exp Neurol. 2007 Mar;204(1):366-79. Epub 2006 Dec 22.
15. Hwang CH and Wu DK, Hum Mol Genet. 2008 Mar 15;17(6):844-53. Epub 2007 Dec 20.
16. Ishino T, etal., Eur J Med Genet. 2015 Sep;58(9):427-32. doi: 10.1016/j.ejmg.2015.06.005. Epub 2015 Jul 26.
17. Kondo T and Raff MC, Dev Biol 2004 Mar 1;267(1):242-51.
18. Lehmann K, etal., Am J Hum Genet. 2007 Aug;81(2):388-96. Epub 2007 Jun 8.
19. Leslie EJ, etal., Am J Hum Genet. 2015 Mar 5;96(3):397-411. doi: 10.1016/j.ajhg.2015.01.004. Epub 2015 Feb 19.
20. Li Y, etal., Dev Dyn. 2007 Mar;236(3):746-54.
21. Liu F, etal., Clin Chim Acta. 2014 Feb 15;429:129-33. doi: 10.1016/j.cca.2013.12.004. Epub 2013 Dec 8.
22. Matsuura I, etal., J Neurochem. 2008 May;105(4):1471-9. doi: 10.1111/j.1471-4159.2008.05251.x. Epub 2008 Jan 24.
23. MGD data from the GO Consortium
24. Mikawa S and Sato K, Neuroscience. 2011 Jun 16;184:38-53. doi: 10.1016/j.neuroscience.2011.03.036. Epub 2011 Apr 9.
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. OMIM Disease Annotation Pipeline
27. Paez-Pereda M, etal., Proc Natl Acad Sci U S A 2003 Feb 4;100(3):1034-9.
28. Pipeline to import KEGG annotations from KEGG into RGD
29. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
30. Qureshi AT, etal., Clin Orthop Relat Res. 2015 Sep;473(9):2831-9. doi: 10.1007/s11999-015-4240-y.
31. RGD automated data pipeline
32. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
33. RGD automated import pipeline for gene-chemical interactions
34. RGD comprehensive gene curation
35. Shen K, etal., Orthod Craniofac Res. 2009 Aug;12(3):254-62. doi: 10.1111/j.1601-6343.2009.01460.x.
36. Song T, etal., Am J Med Genet A. 2015 Jan;167A(1):137-41. doi: 10.1002/ajmg.a.36802. Epub 2014 Oct 22.
37. Takahashi T, etal., Clin Genet. 2001 Dec;60(6):447-51.
38. Tang J, etal., Biochem Biophys Res Commun. 2009 Jul 31;385(3):341-5. doi: 10.1016/j.bbrc.2009.05.067. Epub 2009 May 20.
39. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
40. Urshansky N, etal., J Neuroimmunol. 2011 Mar;232(1-2):171-8. doi: 10.1016/j.jneuroim.2010.10.007. Epub 2010 Nov 26.
41. Valenzuela DM, etal., J Neurosci 1995 Sep;15(9):6077-84.
42. Villanueva S, etal., Am J Physiol Regul Integr Comp Physiol. 2006 Apr;290(4):R861-70. Epub 2005 Nov 10.
43. Winkler DG, etal., J Biol Chem. 2004 Aug 27;279(35):36293-8. Epub 2004 Jun 14.
44. Wu XB, etal., J Clin Invest. 2003 Sep;112(6):924-34.
45. Yang K, etal., Am J Physiol Cell Physiol. 2015 Jun 1;308(11):C869-78. doi: 10.1152/ajpcell.00349.2014. Epub 2015 Mar 4.
46. Zimmer J, etal., PLoS One. 2012;7(4):e35062. doi: 10.1371/journal.pone.0035062. Epub 2012 Apr 18.
Additional References at PubMed
PMID:8582276   PMID:8752214   PMID:8889548   PMID:9585504   PMID:10684250   PMID:10688202   PMID:10780858   PMID:11562478   PMID:11784076   PMID:12141440   PMID:12397106   PMID:12435358  
PMID:15110716   PMID:15252029   PMID:15539560   PMID:15975920   PMID:16712836   PMID:16828469   PMID:16916379   PMID:17218603   PMID:17359964   PMID:17360443   PMID:17400546   PMID:17522159  
PMID:17889703   PMID:18028109   PMID:18028901   PMID:18462699   PMID:19850029   PMID:19852960   PMID:20501701   PMID:20675382   PMID:21624478   PMID:24835669   PMID:27546891  


Genomics

Comparative Map Data
Nog
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21074,128,712 - 74,130,339 (-)NCBI
Rnor_6.0 Ensembl1076,811,759 - 76,813,386 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01076,811,759 - 76,813,386 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01076,677,612 - 76,679,239 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41077,689,244 - 77,690,871 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11077,703,801 - 77,704,728 (-)NCBI
Celera1073,029,127 - 73,030,754 (-)NCBICelera
Cytogenetic Map10q26NCBI
NOG
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1756,593,699 - 56,595,598 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1756,593,699 - 56,595,611 (+)EnsemblGRCh38hg38GRCh38
GRCh381756,593,699 - 56,595,611 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371754,671,060 - 54,672,951 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh371754,671,060 - 54,672,972 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361752,026,274 - 52,027,546 (+)NCBINCBI36hg18NCBI36
Build 341752,026,273 - 52,027,542NCBI
Celera1751,132,757 - 51,134,648 (+)NCBI
Cytogenetic Map17q22NCBI
HuRef1750,031,838 - 50,033,727 (+)NCBIHuRef
CHM1_11754,735,932 - 54,737,820 (+)NCBICHM1_1
Nog
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391189,191,464 - 89,193,385 (-)NCBIGRCm39mm39
GRCm381189,300,638 - 89,302,559 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1189,300,638 - 89,302,332 (-)EnsemblGRCm38mm10GRCm38
MGSCv371189,161,952 - 89,163,873 (-)NCBIGRCm37mm9NCBIm37
MGSCv361189,117,412 - 89,118,110 (-)NCBImm8
Celera1198,919,523 - 98,921,373 (-)NCBICelera
Cytogenetic Map11CNCBI
cM Map1154.34NCBI
Nog
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554516,193,042 - 6,193,740 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554516,192,368 - 6,193,766 (-)NCBIChiLan1.0ChiLan1.0
NOG
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11755,532,208 - 55,533,782 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1755,532,394 - 55,533,092 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01750,669,186 - 50,671,081 (+)NCBIMhudiblu_PPA_v0panPan3
NOG
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1931,453,604 - 31,456,060 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Nog
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364906,262,651 - 6,264,069 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NOG
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1232,891,321 - 32,892,206 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11232,891,321 - 32,892,206 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
NOG
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11636,816,783 - 36,818,693 (-)NCBI
ChlSab1.1 Ensembl1636,817,476 - 36,818,174 (-)Ensembl
Nog
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479511,696,102 - 11,697,367 (+)NCBI

Position Markers
RH66786  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01076,812,454 - 76,812,611NCBIRnor6.0
Rnor_5.01076,678,307 - 76,678,464UniSTSRnor5.0
RGSC_v3.41077,689,939 - 77,690,096UniSTSRGSC3.4
Celera1073,029,822 - 73,029,979UniSTS
Cytogenetic Map10q26UniSTS
Nog  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01076,812,699 - 76,813,059NCBIRnor6.0
Rnor_5.01076,678,552 - 76,678,912UniSTSRnor5.0
RGSC_v3.41077,690,184 - 77,690,544UniSTSRGSC3.4
Celera1073,030,067 - 73,030,427UniSTS
Cytogenetic Map10q26UniSTS
PMC316831P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01076,812,928 - 76,813,139NCBIRnor6.0
Rnor_5.01076,678,781 - 76,678,992UniSTSRnor5.0
RGSC_v3.41077,690,413 - 77,690,624UniSTSRGSC3.4
Celera1073,030,296 - 73,030,507UniSTS
Cytogenetic Map10q26UniSTS
UniSTS:265422  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01076,812,442 - 76,812,963NCBIRnor6.0
Rnor_5.01076,678,295 - 76,678,816UniSTSRnor5.0
RGSC_v3.41077,689,927 - 77,690,448UniSTSRGSC3.4
Celera1073,029,810 - 73,030,331UniSTS
Cytogenetic Map10q26UniSTS
UniSTS:489090  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01076,812,439 - 76,813,137NCBIRnor6.0
Rnor_5.01076,678,292 - 76,678,990UniSTSRnor5.0
RGSC_v3.41077,689,924 - 77,690,622UniSTSRGSC3.4
Celera1073,029,807 - 73,030,505UniSTS
Cytogenetic Map10q26UniSTS
UniSTS:495034  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01076,812,391 - 76,813,202NCBIRnor6.0
Rnor_5.01076,678,244 - 76,679,055UniSTSRnor5.0
RGSC_v3.41077,689,876 - 77,690,687UniSTSRGSC3.4
Celera1073,029,759 - 73,030,570UniSTS
Cytogenetic Map10q26UniSTS
NOG_2549  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01076,812,092 - 76,812,782NCBIRnor6.0
Rnor_5.01076,677,945 - 76,678,635UniSTSRnor5.0
RGSC_v3.41077,689,577 - 77,690,267UniSTSRGSC3.4
Celera1073,029,460 - 73,030,150UniSTS
Cytogenetic Map10q26UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102152390683549467Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103191939778343192Rat
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)103317903078179030Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103334319278343192Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103513942480139424Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103618592982675365Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103618592995845311Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)104051404485514044Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)104051404485514044Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1041260363106105607Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104318865981042642Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1043289657108540162Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104370495588704955Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104659302198939209Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104684834691848346Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104684834691848346Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104684834691848346Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)105063833795638337Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)105128920384596393Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)105128920384596393Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)105128920384596393Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)105128920384596393Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)105128920384596393Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105310471898104718Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105362581598939209Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105363748594807701Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)1055224855100224855Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)1055679084102427604Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1056698730101698730Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1060450007105450007Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1060875260105875260Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1060875260105875260Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1060875260105875260Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1062096293107096293Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106464817584601269Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)1064648175101691360Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1064648175102149713Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1064648175102149713Rat
61402Niddm3Non-insulin dependent diabetes mellitus QTL 34.58blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)106464831185513822Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1065590122110590122Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1065992275110992275Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1065992275110992275Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1067880046112626471Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1067988218110992091Rat
2298481Eau9Experimental allergic uveoretinitis QTL 90.0169uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)106830503785514044Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1069123603101482600Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1069385595112626471Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1069385595112626471Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1070166960112626471Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1070800069112626471Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1071692298112626471Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1073008136112626471Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1073008136112626471Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1073008136112626471Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1073467158112626471Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107504539197308358Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1075544754112626471Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1075544754112626471Rat
2289982Bp303Blood pressure QTL 303arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)107598366278343192Rat
724555Bp150Blood pressure QTL 1500.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107598366280946110Rat
12880053Cm104Cardiac mass QTL 1040.009heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)107598366286419171Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:62
Interacting mature miRNAs:67
Transcripts:ENSRNOT00000032388
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 20 2
Low 3 12 6 6 1 6 8 11 54 19 27 11 8
Below cutoff 15 30 19 13 19 15 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000032388   ⟹   ENSRNOP00000030212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1076,811,759 - 76,813,386 (-)Ensembl
RefSeq Acc Id: NM_012990   ⟹   NP_037122
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21074,128,712 - 74,130,339 (-)NCBI
Rnor_6.01076,811,759 - 76,813,386 (-)NCBI
Rnor_5.01076,677,612 - 76,679,239 (-)NCBI
RGSC_v3.41077,689,244 - 77,690,871 (-)RGD
Celera1073,029,127 - 73,030,754 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_037122 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA83260 (Get FASTA)   NCBI Sequence Viewer  
  EDM05657 (Get FASTA)   NCBI Sequence Viewer  
  Q62809 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037122   ⟸   NM_012990
- Peptide Label: precursor
- UniProtKB: G3V8X8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030212   ⟸   ENSRNOT00000032388

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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)
ACI/EurMcwi (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
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/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 (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)
F344/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
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
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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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
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/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
LE/Stm (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
LEW/Crl (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
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
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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
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
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 (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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 (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
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (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 (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:3183 AgrOrtholog
Ensembl Genes ENSRNOG00000023683 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000030212 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000032388 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.10.90.10 UniProtKB/TrEMBL
InterPro Cystine-knot_cytokine UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Noggin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25495 UniProtKB/TrEMBL
NCBI Gene 25495 ENTREZGENE
PANTHER PTHR10494 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nog PhenoGen
PIRSF Noggin UniProtKB/TrEMBL
Superfamily-SCOP SSF57501 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC206935
UniProt G3V8X8 ENTREZGENE, UniProtKB/TrEMBL
  NOGG_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Nog  Noggin      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the tufted cells of the olfactory bulb, the piriform cortex of the brain, and the Purkinje cells of the cerebellum 729002