Ncor2 (nuclear receptor co-repressor 2) - Rat Genome Database
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Gene: Ncor2 (nuclear receptor co-repressor 2) Rattus norvegicus
Analyze
Symbol: Ncor2
Name: nuclear receptor co-repressor 2
RGD ID: 1310293
Description: Exhibits chromatin binding activity; glucocorticoid receptor binding activity; and retinoid X receptor binding activity. Involved in several processes, including estrous cycle; lactation; and response to estradiol. Localizes to chromatin and nucleus. Human ortholog(s) of this gene implicated in osteoarthritis. Orthologous to human NCOR2 (nuclear receptor corepressor 2); PARTICIPATES IN aldosterone signaling pathway; altered androgen signaling pathway; androgen signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC360801; nuclear receptor corepressor 2
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
mRatBN7.21231,466,418 - 31,628,319 (+)NCBI
Rnor_6.0 Ensembl1236,871,999 - 37,033,701 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01236,871,917 - 37,033,701 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01238,748,528 - 38,909,933 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41232,617,643 - 32,725,753 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11232,481,030 - 32,589,136 (+)NCBI
Celera1233,158,042 - 33,319,623 (+)NCBICelera
Cytogenetic Map12q15NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
3,3',5,5'-tetraiodothyroacetic acid  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-aminopyridine  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bicalutamide  (ISO)
bicuculline  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
butyric acid  (ISO)
cadmium dichloride  (EXP)
calciol  (EXP)
calcitriol  (ISO)
camptothecin  (ISO)
cefaloridine  (EXP)
cisplatin  (ISO)
crotonaldehyde  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fipronil  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
glyphosate  (EXP)
indometacin  (ISO)
ketoconazole  (ISO)
leflunomide  (ISO)
lithocholic acid  (ISO)
menadione  (ISO)
methamphetamine  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
methylphenidate  (ISO)
methylseleninic acid  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-N-nitrosourea  (EXP)
okadaic acid  (EXP)
ozone  (ISO)
paracetamol  (ISO)
parthenolide  (ISO)
phosgene  (ISO)
propiconazole  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
thyroxine  (ISO)
titanium dioxide  (ISO)
trichostatin A  (EXP,ISO)
troglitazone  (ISO)
tungsten  (ISO)
vitamin D  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Barbieri CE, etal., Eur Urol. 2013 Oct;64(4):567-76. doi: 10.1016/j.eururo.2013.05.029. Epub 2013 May 18.
2. Camacho-Arroyo I, etal., J Steroid Biochem Mol Biol. 2005 Feb;94(1-3):267-72. Epub 2005 Feb 17.
3. Chmelar R, etal., Int J Cancer. 2007 Feb 15;120(4):719-33.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Girault I, etal., Maturitas. 2006 Jul 20;54(4):342-51. Epub 2006 Jul 5.
6. GOA data from the GO Consortium
7. Hall JM and McDonnell DP, Mol Interv. 2005 Dec;5(6):343-57.
8. Iannacone EA, etal., Mol Cell Endocrinol. 2002 Jan 15;186(1):49-59.
9. Kershah SM, etal., Gynecol Oncol. 2004 Jan;92(1):304-13.
10. Ki SH, etal., Mol Cell Biol. 2005 May;25(10):4150-65.
11. Korutla L, etal., J Neurochem. 2007 May;101(3):611-8. Epub 2007 Jan 24.
12. Macejova D, etal., Life Sci. 2005 Sep 30;77(20):2584-93.
13. Madauss KP, etal., Mol Endocrinol. 2007 May;21(5):1066-81. Epub 2007 Mar 13.
14. MGD data from the GO Consortium
15. Misiti S, etal., Endocrinology. 1998 May;139(5):2493-500.
16. Pipeline to import KEGG annotations from KEGG into RGD
17. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
18. RGD automated data pipeline
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. RGD comprehensive gene curation
22. Rochette-Egly C and Germain P, Nucl Recept Signal. 2009 May 8;7:e005.
23. Simons SS Jr Curr Opin Pharmacol. 2010 Dec;10(6):613-9. Epub 2010 Aug 26.
24. Valdes AM, etal., Arthritis Rheum. 2004 Aug;50(8):2497-507.
25. van Agthoven T, etal., Br J Cancer. 2009 Dec 1;101(11):1824-32. Epub 2009 Nov 10.
26. van der Laan S, etal., Brain Res. 2005 Oct 19;1059(2):113-21. Epub 2005 Oct 5.
27. Villamar-Cruz O, etal., Brain Res Bull. 2006 Apr 14;69(3):276-81. Epub 2006 Jan 17.
28. Wang D, etal., PLoS One. 2010 Mar 24;5(3):e9853.
29. Wang L, etal., Arch Biochem Biophys. 2004 Aug 1;428(1):92-8.
30. Yan J, etal., Mol Endocrinol. 2007 Jul;21(7):1630-41. Epub 2007 Apr 24.
31. Yan JH, etal., Chin Med J (Engl). 2010 Jan 20;123(2):221-6.
32. Yang J and Fuller PJ, Mol Cell Endocrinol. 2012 Mar 24;350(2):196-205. doi: 10.1016/j.mce.2011.07.001. Epub 2011 Jul 18.
Additional References at PubMed
PMID:10077563   PMID:10097068   PMID:10713164   PMID:11641275   PMID:11804585   PMID:12628926   PMID:15681609   PMID:15832170   PMID:16030140   PMID:16893456   PMID:16924111   PMID:17158926  
PMID:17928865   PMID:18052923   PMID:18347093   PMID:19066220   PMID:19144721   PMID:19299558   PMID:19946888   PMID:19955185   PMID:20388878   PMID:20812024   PMID:21328542   PMID:22001906  
PMID:22082260  


Genomics

Comparative Map Data
Ncor2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21231,466,418 - 31,628,319 (+)NCBI
Rnor_6.0 Ensembl1236,871,999 - 37,033,701 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01236,871,917 - 37,033,701 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01238,748,528 - 38,909,933 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41232,617,643 - 32,725,753 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11232,481,030 - 32,589,136 (+)NCBI
Celera1233,158,042 - 33,319,623 (+)NCBICelera
Cytogenetic Map12q15NCBI
NCOR2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl12124,324,415 - 124,567,589 (-)EnsemblGRCh38hg38GRCh38
GRCh3812124,324,415 - 124,567,612 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3712124,808,961 - 125,052,158 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612123,374,914 - 123,586,102 (-)NCBINCBI36hg18NCBI36
Build 3412123,333,841 - 123,527,720NCBI
Celera12124,408,964 - 124,651,550 (-)NCBI
Cytogenetic Map12q24.31NCBI
HuRef12121,771,692 - 121,986,984 (-)NCBIHuRef
CHM1_112124,630,482 - 124,873,188 (-)NCBICHM1_1
Ncor2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395125,094,217 - 125,256,302 (-)NCBIGRCm39mm39
GRCm39 Ensembl5125,094,217 - 125,256,283 (-)Ensembl
GRCm385125,017,153 - 125,179,238 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5125,017,153 - 125,179,219 (-)EnsemblGRCm38mm10GRCm38
MGSCv375125,497,525 - 125,659,584 (-)NCBIGRCm37mm9NCBIm37
MGSCv365125,306,141 - 125,468,032 (-)NCBImm8
Celera5122,035,046 - 122,198,419 (-)NCBICelera
Cytogenetic Map5G1.1NCBI
Ncor2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554824,942,221 - 5,031,904 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554824,927,482 - 5,031,848 (+)NCBIChiLan1.0ChiLan1.0
NCOR2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112126,200,793 - 126,412,757 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12126,201,779 - 126,372,745 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012121,913,368 - 122,155,031 (-)NCBIMhudiblu_PPA_v0panPan3
NCOR2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl265,331,459 - 5,493,830 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1265,352,670 - 5,493,741 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ncor2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936558658,723 - 775,263 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCOR2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1428,624,702 - 28,819,404 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11428,642,774 - 28,819,404 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21430,287,166 - 30,514,759 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap14q21NCBI
NCOR2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111119,675,363 - 119,917,059 (-)NCBI
ChlSab1.1 Ensembl11119,676,345 - 119,917,000 (-)Ensembl
Ncor2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474723,777,645 - 23,887,804 (-)NCBI

Position Markers
BE098792  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01237,033,433 - 37,033,635NCBIRnor6.0
Rnor_5.01238,909,665 - 38,909,867UniSTSRnor5.0
RGSC_v3.41232,725,485 - 32,725,687UniSTSRGSC3.4
Celera1233,319,355 - 33,319,557UniSTS
RH 3.4 Map12561.8UniSTS
Cytogenetic Map12q15UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)121176499537522089Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721150320041Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121441977552716770Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121502198652716770Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121571460941291738Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121590890052716770Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121590890052716770Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121718558044098244Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121796086538409001Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121834247752716770Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121834247752716770Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121872904352716770Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121875259352716770Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101875259352716770Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)122265070245946937Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265070248598906Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)122265070252716770Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265072141291738Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)122287629743799153Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122490659052716770Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122609884552716770Rat
70169Eae13Experimental allergic encephalomyelitis QTL 130.032nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)122719024042196641Rat
8693658Alc33Alcohol consumption QTL 332.10.68drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122911360949560679Rat
8693635Alc28Alcohol consumption QTL 282.70.439drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122911360950757185Rat
1556747Calcic1Intracellular calcium level QTL 13.6platelet calcium amount (VT:0010500)platelet intracellular calcium level (CMO:0000922)123172356547433663Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)123172356551955754Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)123172356552716770Rat
1331787Rf41Renal function QTL 412.998kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)123172368845946802Rat
631829Alc6Alcohol consumption QTL 64.7consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)123228978243305579Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:137
Count of miRNA genes:91
Interacting mature miRNAs:116
Transcripts:ENSRNOT00000001334
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 33 25 17 7 17 3 66 29 38 8
Low 10 32 24 12 24 8 8 8 6 3 3 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001108334 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598393 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598394 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598398 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089589 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089590 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089591 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089593 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089594 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000001334   ⟹   ENSRNOP00000001334
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1236,871,999 - 37,033,701 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084236   ⟹   ENSRNOP00000069011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1236,872,020 - 37,032,904 (+)Ensembl
RefSeq Acc Id: NM_001108334   ⟹   NP_001101804
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,466,588 - 31,628,319 (+)NCBI
Rnor_6.01236,871,999 - 37,033,701 (+)NCBI
Rnor_5.01238,748,528 - 38,909,933 (+)NCBI
RGSC_v3.41232,617,643 - 32,725,753 (+)RGD
Celera1233,158,042 - 33,319,623 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249305   ⟹   XP_006249367
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,466,418 - 31,628,316 (+)NCBI
Rnor_6.01236,871,917 - 37,033,698 (+)NCBI
Rnor_5.01238,748,528 - 38,909,933 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249320   ⟹   XP_006249382
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,466,418 - 31,628,316 (+)NCBI
Rnor_6.01236,871,918 - 37,033,698 (+)NCBI
Rnor_5.01238,748,528 - 38,909,933 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249323   ⟹   XP_006249385
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01236,871,918 - 37,033,698 (+)NCBI
Rnor_5.01238,748,528 - 38,909,933 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598390   ⟹   XP_017453879
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01236,897,827 - 37,033,698 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598391   ⟹   XP_017453880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,525,360 - 31,628,316 (+)NCBI
Rnor_6.01236,897,827 - 37,033,698 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598392   ⟹   XP_017453881
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,525,360 - 31,628,316 (+)NCBI
Rnor_6.01236,897,827 - 37,033,698 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598393   ⟹   XP_017453882
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,466,710 - 31,628,316 (+)NCBI
Rnor_6.01236,872,088 - 37,033,698 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598394   ⟹   XP_017453883
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,503,721 - 31,628,316 (+)NCBI
Rnor_6.01236,908,231 - 37,033,698 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598395   ⟹   XP_017453884
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01236,897,827 - 37,033,698 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598396   ⟹   XP_017453885
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,525,360 - 31,627,325 (+)NCBI
Rnor_6.01236,897,827 - 37,033,698 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598397   ⟹   XP_017453886
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,466,419 - 31,628,316 (+)NCBI
Rnor_6.01236,871,918 - 37,033,698 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598398   ⟹   XP_017453887
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,466,419 - 31,628,316 (+)NCBI
Rnor_6.01236,871,918 - 37,033,698 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039089589   ⟹   XP_038945517
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,525,360 - 31,628,316 (+)NCBI
RefSeq Acc Id: XM_039089590   ⟹   XP_038945518
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,525,360 - 31,628,316 (+)NCBI
RefSeq Acc Id: XM_039089591   ⟹   XP_038945519
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,502,809 - 31,628,316 (+)NCBI
RefSeq Acc Id: XM_039089592   ⟹   XP_038945520
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,585,110 - 31,628,316 (+)NCBI
RefSeq Acc Id: XM_039089593   ⟹   XP_038945521
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,466,418 - 31,628,316 (+)NCBI
RefSeq Acc Id: XM_039089594   ⟹   XP_038945522
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21231,466,419 - 31,628,316 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101804   ⟸   NM_001108334
- UniProtKB: D3ZXN9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006249367   ⟸   XM_006249305
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006249382   ⟸   XM_006249320
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006249385   ⟸   XM_006249323
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017453886   ⟸   XM_017598397
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017453887   ⟸   XM_017598398
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017453882   ⟸   XM_017598393
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017453879   ⟸   XM_017598390
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453881   ⟸   XM_017598392
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017453884   ⟸   XM_017598395
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017453885   ⟸   XM_017598396
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017453880   ⟸   XM_017598391
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453883   ⟸   XM_017598394
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000001334   ⟸   ENSRNOT00000001334
RefSeq Acc Id: ENSRNOP00000069011   ⟸   ENSRNOT00000084236
RefSeq Acc Id: XP_038945521   ⟸   XM_039089593
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038945522   ⟸   XM_039089594
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038945519   ⟸   XM_039089591
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038945517   ⟸   XM_039089589
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038945518   ⟸   XM_039089590
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038945520   ⟸   XM_039089592
- Peptide Label: isoform X7
Protein Domains
SANT

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)
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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
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)
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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)
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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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 38877542 38877543 G A snv KFRS3B/Kyo (KyushuU), ACI/EurMcwi (KNAW), GH/OmrMcwi (MCW), RCS/Kyo (KyushuU), SS/JrHsdMcwi (KNAW), SR/JrHsd (MCW), HTX/Kyo (KyushuU), SS/Jr (KNAW), NIG-III/Hok (KyushuU), FHL/EurMcwi (MCW), WN/N (KNAW), M520/N (KNAW), SR/JrHsd (KNAW), ACI/EurMcwi (MCW), GK/Ox (KNAW), COP/CrCrl (MCW & UW), FHL/EurMcwi (KNAW), FHH/EurMcwi (KNAW), SS/JrHsdMcwi (MCW), BUF/N (KNAW), FHH/EurMcwi (MCW), ACI/N (KNAW)
12 38900399 38900400 C T snv BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), BDIX/NemOda (KyushuU), RCS/Kyo (KyushuU), HTX/Kyo (KyushuU), NIG-III/Hok (KyushuU), WN/N (KNAW), M520/N (KNAW), GK/Ox (KNAW), FHL/EurMcwi (KNAW), FHH/EurMcwi (KNAW), BUF/N (KNAW), ACI/N (KNAW), SS/JrHsdMcwi (KNAW), SS/Jr (KNAW), SR/JrHsd (KNAW), MHS/Gib (KNAW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), ACI/EurMcwi (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 37001310 37001311 G A snv ACI/N (MCW), SR/JrHsd (RGD), FHH/EurMcwi (MCW), SS/JrHsdMcwi (MCW), GK/Ox (RGD), GH/OmrMcwi (MCW), ACI/EurMcwi (MCW), FHH/EurMcwi (RGD), SR/JrHsd (MCW), ACI/EurMcwi (RGD), COP/CrCrl (MCW & UW), FHL/EurMcwi (RGD), FHL/EurMcwi (MCW), SS/JrHsdMcwi (RGD)
12 37024167 37024168 C T snv SR/JrHsd (RGD), SS/JrHsdMcwi (RGD), MHS/Gib (RGD), GK/Ox (RGD), FHH/EurMcwi (RGD), ACI/EurMcwi (RGD), FHL/EurMcwi (RGD), WN/N (MCW), M520/N (MCW), ACI/N (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 32693362 32693363 G A snv FHH/EurMcwi (MDC), LCR/2Mco (UMich), ACI/N (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), GK/Ox (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), SS/JrHsdMcwi (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310293 AgrOrtholog
Ensembl Genes ENSRNOG00000001004 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001334 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069011 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001334 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000084236 UniProtKB/TrEMBL
InterPro Homeodomain-like UniProtKB/TrEMBL
  N-CoR_GPS2_interact UniProtKB/TrEMBL
  SANT_DNA-bd UniProtKB/TrEMBL
  SANT_eukarya UniProtKB/TrEMBL
KEGG Report rno:360801 UniProtKB/TrEMBL
NCBI Gene 360801 ENTREZGENE
Pfam GPS2_interact UniProtKB/TrEMBL
  Myb_DNA-binding UniProtKB/TrEMBL
PhenoGen Ncor2 PhenoGen
PROSITE SANT UniProtKB/TrEMBL
SMART SANT UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A0A0G2JU91_RAT UniProtKB/TrEMBL
  D3ZXN9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ncor2  nuclear receptor co-repressor 2   Ncor2_predicted  nuclear receptor co-repressor 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ncor2_predicted  nuclear receptor co-repressor 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED