Ncoa1 (nuclear receptor coactivator 1) - Rat Genome Database

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Gene: Ncoa1 (nuclear receptor coactivator 1) Rattus norvegicus
Analyze
Symbol: Ncoa1
Name: nuclear receptor coactivator 1
RGD ID: 1309046
Description: Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity and nuclear receptor binding activity. Involved in several processes, including animal organ development; estrous cycle; and mating behavior. Located in cytoplasm; neuron projection; and nucleus. Biomarker of hypothyroidism. Orthologous to human NCOA1 (nuclear receptor coactivator 1); PARTICIPATES IN aldosterone signaling pathway; androgen signaling pathway; cortisol signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: SRC-1; steroid receptor coactivator 1
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
mRatBN7.2627,232,609 - 27,507,992 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl627,232,611 - 27,475,664 (-)Ensembl
Rnor_6.0628,677,563 - 28,931,844 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl628,677,540 - 28,931,843 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0638,483,476 - 38,734,322 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4627,224,396 - 27,473,926 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1627,229,075 - 27,336,790 (-)NCBI
Celera626,704,021 - 26,946,167 (-)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
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)
2,3,4,5-Tetrachloro-4'-biphenylol  (ISO)
2,3,4,7,8-Pentachlorodibenzofuran  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4-dinitrotoluene  (EXP)
2,8-bis-Trifluoromethyl-4-quinoline carboxylic acid  (ISO)
2-butan-2-yl-4-[4-[4-[4-[[2-(2,4-dichlorophenyl)-2-(1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy]phenyl]-1-piperazinyl]phenyl]-1,2,4-triazol-3-one  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (ISO)
9-cis-retinoic acid  (ISO)
Acetyl tributyl citrate  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
alfacalcidol  (ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (ISO)
androst-4-ene-3,17-dione  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bezafibrate  (ISO)
bicalutamide  (ISO)
biochanin A  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butamben  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
calcitriol  (ISO)
camptothecin  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (EXP)
ciglitazone  (ISO)
clemizole  (ISO)
clofibrate  (ISO)
clotrimazole  (ISO)
corticosterone  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cyproterone acetate  (ISO)
daidzein  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (ISO)
diethylstilbestrol  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
econazole  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
enzacamene  (EXP)
estrone  (ISO)
ethanol  (ISO)
flavonol  (ISO)
folic acid  (ISO)
fulvestrant  (EXP,ISO)
galangin  (ISO)
genistein  (ISO)
gentamycin  (EXP)
guggulsterone  (ISO)
GW 4064  (ISO)
hexestrol  (ISO)
irinotecan  (ISO)
isopimpinellin  (ISO)
isoxazoles  (ISO)
itraconazole  (ISO)
ketoconazole  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
linoleic acid  (ISO)
lipopolysaccharide  (ISO)
lithocholic acid  (ISO)
Meclizine  (ISO)
medroxyprogesterone acetate  (ISO)
melatonin  (ISO)
methapyrilene  (ISO)
methoxychlor  (EXP,ISO)
methylseleninic acid  (ISO)
methyltestosterone  (ISO)
miconazole  (ISO)
Mitotane  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
naphthalenes  (ISO)
Nonylphenol  (ISO)
omeprazole  (ISO)
ormeloxifene  (EXP)
oxaliplatin  (EXP)
oxiconazole  (ISO)
p-tert-Amylphenol  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
pazopanib  (ISO)
permethrin  (ISO)
Phenoxybenzamine  (ISO)
phenytoin  (ISO)
phthalic acid  (ISO)
pimecrolimus  (ISO)
piperine  (ISO)
pirinixic acid  (ISO)
PK-11195  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
quinolines  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
tamoxifen  (EXP,ISO)
topotecan  (EXP)
trimegestone  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vitamin D  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (ISO)
cytoplasm  (IDA)
cytosol  (IEA,ISO)
neuron projection  (IDA)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IDA)
plasma membrane  (IEA,ISO)
protein-containing complex  (ISO)

References

References - curated
1. Auger AP, etal., Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7551-5.
2. Bian C, etal., Steroids. 2012 Jan;77(1-2):149-56. Epub 2011 Nov 9.
3. Camacho-Arroyo I, etal., J Steroid Biochem Mol Biol. 2005 Feb;94(1-3):267-72. Epub 2005 Feb 17.
4. Chmelar R, etal., Int J Cancer. 2007 Feb 15;120(4):719-33.
5. Daverey A, etal., J Steroid Biochem Mol Biol. 2009 Aug;116(1-2):93-101. Epub 2009 May 19.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Green AR, etal., Breast Cancer Res Treat. 2007 Sep 28;.
8. Hall JM and McDonnell DP, Mol Interv. 2005 Dec;5(6):343-57.
9. Iannacone EA, etal., Mol Cell Endocrinol. 2002 Jan 15;186(1):49-59.
10. Igarashi-Migitaka J, etal., Eur J Endocrinol. 2005 Oct;153(4):595-604.
11. Jenkins BD, etal., Trends Endocrinol Metab. 2001 Apr;12(3):122-6.
12. Kershah SM, etal., Gynecol Oncol. 2004 Jan;92(1):304-13.
13. Linja MJ, etal., Clin Cancer Res. 2004 Feb 1;10(3):1032-40.
14. Macejova D, etal., Life Sci. 2005 Sep 30;77(20):2584-93.
15. Martinez de Arrieta C, etal., Endocrinology. 2000 May;141(5):1693-8.
16. McInerney EM, etal., Genes Dev. 1998 Nov 1;12(21):3357-68.
17. MGD data from the GO Consortium
18. Miard S, etal., Aging Cell. 2009 Aug;8(4):449-59. Epub 2009 May 22.
19. Misiti S, etal., Endocrinology. 1998 May;139(5):2493-500.
20. Mitev YA, etal., FASEB J. 2003 Mar;17(3):518-9. Epub 2003 Jan 22.
21. Molenda-Figueira HA, etal., Endocrinology. 2008 Oct;149(10):5272-9. Epub 2008 Jun 19.
22. Molenda-Figueira HA, etal., Horm Behav. 2006 Sep;50(3):383-92.
23. Nicolaides NC, etal., Steroids. 2010 Jan;75(1):1-12. Epub 2009 Oct 7.
24. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
25. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
26. RGD automated import pipeline for gene-chemical interactions
27. RGD comprehensive gene curation
28. Rochette-Egly C and Germain P, Nucl Recept Signal. 2009 May 8;7:e005.
29. Trousson A, etal., J Steroid Biochem Mol Biol. 2007 May;104(3-5):305-11. Epub 2007 Mar 23.
30. Wang L, etal., Arch Biochem Biophys. 2004 Aug 1;428(1):92-8.
31. Wang XL, etal., J Biol Chem. 2004 Aug 13;279(33):34191-200. Epub 2004 May 27.
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.
33. Yousefi B, etal., Thyroid. 2005 Apr;15(4):314-9.
34. Zhang D, etal., Brain Res. 2011 Mar 25;1382:88-97. Epub 2011 Jan 15.
35. Zhang D, etal., Dev Neurosci. 2011;33(1):57-63. Epub 2011 Jan 11.
Additional References at PubMed
PMID:9223431   PMID:10207113   PMID:10934189   PMID:11891224   PMID:12039952   PMID:12089347   PMID:12446761   PMID:12917342   PMID:14534427   PMID:15155786   PMID:15219413   PMID:15367689  
PMID:15456935   PMID:15564339   PMID:15641800   PMID:15681609   PMID:15831516   PMID:15919756   PMID:16109736   PMID:16148126   PMID:16723356   PMID:17218095   PMID:17363140   PMID:17786964  
PMID:18063853   PMID:18563714   PMID:18798693   PMID:19423554   PMID:20685850   PMID:24550004   PMID:26223010   PMID:26482332   PMID:29263093  


Genomics

Comparative Map Data
Ncoa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2627,232,609 - 27,507,992 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl627,232,611 - 27,475,664 (-)Ensembl
Rnor_6.0628,677,563 - 28,931,844 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl628,677,540 - 28,931,843 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0638,483,476 - 38,734,322 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4627,224,396 - 27,473,926 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1627,229,075 - 27,336,790 (-)NCBI
Celera626,704,021 - 26,946,167 (-)NCBICelera
Cytogenetic Map6q14NCBI
NCOA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl224,491,254 - 24,770,702 (+)EnsemblGRCh38hg38GRCh38
GRCh38224,491,254 - 24,770,702 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37224,714,123 - 24,993,571 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36224,660,850 - 24,847,075 (+)NCBINCBI36hg18NCBI36
Build 34224,718,996 - 24,905,219NCBI
Celera224,648,250 - 24,833,882 (+)NCBI
Cytogenetic Map2p23.3NCBI
HuRef224,545,896 - 24,731,418 (+)NCBIHuRef
CHM1_1224,736,919 - 24,923,129 (+)NCBICHM1_1
Ncoa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39124,297,362 - 4,569,452 (-)NCBIGRCm39mm39
GRCm39 Ensembl124,297,362 - 4,527,182 (-)Ensembl
GRCm38124,247,362 - 4,477,206 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl124,247,362 - 4,477,182 (-)EnsemblGRCm38mm10GRCm38
MGSCv37124,247,362 - 4,484,060 (-)NCBIGRCm37mm9NCBIm37
MGSCv36124,257,424 - 4,491,127 (-)NCBImm8
Celera124,179,857 - 4,348,692 (-)NCBICelera
Cytogenetic Map12A1.1NCBI
Ncoa1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554696,794,821 - 6,892,566 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554696,676,780 - 6,892,587 (+)NCBIChiLan1.0ChiLan1.0
NCOA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A24,581,645 - 24,859,488 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A24,733,117 - 24,859,488 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A24,485,068 - 24,764,135 (+)NCBIMhudiblu_PPA_v0panPan3
NCOA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11718,880,676 - 19,124,300 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1718,880,383 - 19,122,258 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1718,777,980 - 19,021,230 (+)NCBI
ROS_Cfam_1.01719,302,445 - 19,397,682 (+)NCBI
UMICH_Zoey_3.11718,890,805 - 19,134,195 (+)NCBI
UNSW_CanFamBas_1.01718,899,937 - 19,143,634 (+)NCBI
UU_Cfam_GSD_1.01718,940,197 - 19,183,703 (+)NCBI
Ncoa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629263,234,427 - 63,471,108 (+)NCBI
SpeTri2.0NW_0049364937,368,393 - 7,605,754 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCOA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3113,997,236 - 114,251,078 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13113,997,214 - 114,251,080 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23121,230,135 - 121,286,004 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.23121,349,942 - 121,379,022 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NCOA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11482,898,368 - 83,028,137 (-)NCBI
ChlSab1.1 Ensembl1482,897,348 - 83,013,589 (-)Ensembl
Vero_WHO_p1.0NW_02366604528,994,261 - 29,270,072 (+)NCBI
Ncoa1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247386,770,745 - 7,054,616 (+)NCBI

Position Markers
D6Rat89  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2627,392,666 - 27,392,902 (+)MAPPERmRatBN7.2
Rnor_6.0628,841,077 - 28,841,312NCBIRnor6.0
Rnor_5.0638,646,507 - 38,646,742UniSTSRnor5.0
RGSC_v3.4627,388,747 - 27,388,983RGDRGSC3.4
RGSC_v3.4627,388,748 - 27,388,983UniSTSRGSC3.4
RGSC_v3.1627,391,700 - 27,391,936RGD
Celera626,863,437 - 26,863,672UniSTS
FHH x ACI Map625.9999RGD
FHH x ACI Map625.9999UniSTS
Cytogenetic Map6q14UniSTS
D6Rat171  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2627,261,609 - 27,261,739 (+)MAPPERmRatBN7.2
Rnor_6.0628,706,592 - 28,706,721NCBIRnor6.0
Rnor_5.0638,512,104 - 38,512,233UniSTSRnor5.0
RGSC_v3.4627,253,868 - 27,253,998RGDRGSC3.4
RGSC_v3.4627,253,869 - 27,253,998UniSTSRGSC3.4
RGSC_v3.1627,256,821 - 27,256,951RGD
Celera626,732,958 - 26,733,087UniSTS
SHRSP x BN Map625.1499RGD
SHRSP x BN Map625.1499UniSTS
Cytogenetic Map6q14UniSTS
D6Got21  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2627,375,920 - 27,376,215 (+)MAPPERmRatBN7.2
Rnor_6.0628,823,943 - 28,824,237NCBIRnor6.0
Rnor_5.0638,629,373 - 38,629,667UniSTSRnor5.0
RGSC_v3.4627,371,915 - 27,372,210RGDRGSC3.4
RGSC_v3.4627,371,916 - 27,372,210UniSTSRGSC3.4
RGSC_v3.1627,374,869 - 27,375,163RGD
Celera626,846,830 - 26,847,124UniSTS
RH 3.4 Map6107.5UniSTS
RH 3.4 Map6107.5RGD
RH 2.0 Map6222.5RGD
Cytogenetic Map6q14UniSTS
D6Got22  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2627,306,935 - 27,307,104 (+)MAPPERmRatBN7.2
Rnor_6.0628,751,750 - 28,751,922NCBIRnor6.0
Rnor_5.0638,557,127 - 38,557,299UniSTSRnor5.0
RGSC_v3.4627,299,768 - 27,299,941RGDRGSC3.4
RGSC_v3.4627,299,769 - 27,299,941UniSTSRGSC3.4
RGSC_v3.1627,302,722 - 27,302,894RGD
Celera626,778,484 - 26,778,656UniSTS
RH 3.4 Map6116.9UniSTS
RH 3.4 Map6116.9RGD
RH 2.0 Map6223.6RGD
Cytogenetic Map6q14UniSTS
D6Got18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2627,471,732 - 27,471,889 (-)MAPPERmRatBN7.2
mRatBN7.2627,471,732 - 27,471,889 (+)MAPPERmRatBN7.2
Rnor_6.0628,927,909 - 28,928,065NCBIRnor6.0
Rnor_6.0630,363,565 - 30,363,721NCBIRnor6.0
Rnor_5.0638,730,388 - 38,730,544UniSTSRnor5.0
Rnor_5.0639,528,946 - 39,529,102UniSTSRnor5.0
RGSC_v3.4627,469,991 - 27,470,147UniSTSRGSC3.4
RGSC_v3.4627,469,990 - 27,470,147RGDRGSC3.4
RGSC_v3.1627,472,944 - 27,473,100RGD
Celera626,942,236 - 26,942,392UniSTS
RH 3.4 Map6102.5UniSTS
RH 3.4 Map6102.5RGD
RH 2.0 Map6224.2RGD
Cytogenetic Map6q14UniSTS
AU046409  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2627,261,597 - 27,261,766 (+)MAPPERmRatBN7.2
Rnor_6.0628,706,580 - 28,706,748NCBIRnor6.0
Rnor_5.0638,512,092 - 38,512,260UniSTSRnor5.0
RGSC_v3.4627,253,857 - 27,254,025UniSTSRGSC3.4
Celera626,732,946 - 26,733,114UniSTS
Cytogenetic Map6q14UniSTS
RH137721  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2627,355,388 - 27,355,637 (+)MAPPERmRatBN7.2
Rnor_6.0628,802,879 - 28,803,127NCBIRnor6.0
Rnor_5.0638,608,309 - 38,608,557UniSTSRnor5.0
RGSC_v3.4627,350,973 - 27,351,221UniSTSRGSC3.4
Celera626,826,766 - 26,827,014UniSTS
RH 3.4 Map6114.0UniSTS
Cytogenetic Map6q14UniSTS
RH80592  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2627,234,627 - 27,234,858 (+)MAPPERmRatBN7.2
Rnor_6.0628,679,581 - 28,679,811NCBIRnor6.0
Rnor_5.0638,485,494 - 38,485,724UniSTSRnor5.0
RGSC_v3.4627,226,412 - 27,226,642UniSTSRGSC3.4
Celera626,706,037 - 26,706,267UniSTS
Cytogenetic Map6q14UniSTS
Ncoa1Cpn_6027473879  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.4627,473,879 - 27,473,879 (-)RGDRGSC3.4


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)61653614027261739Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:281
Count of miRNA genes:195
Interacting mature miRNAs:213
Transcripts:ENSRNOT00000068531
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 3 37 20 4 19 4 8 10 74 35 34 11 8
Low 6 37 37 37 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068531   ⟹   ENSRNOP00000061906
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl627,232,611 - 27,475,664 (-)Ensembl
Rnor_6.0 Ensembl628,677,565 - 28,931,843 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091659   ⟹   ENSRNOP00000071037
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl627,233,124 - 27,475,664 (-)Ensembl
Rnor_6.0 Ensembl628,677,540 - 28,862,159 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105343   ⟹   ENSRNOP00000095601
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl627,237,445 - 27,475,664 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110405   ⟹   ENSRNOP00000095436
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl627,233,873 - 27,475,664 (-)Ensembl
RefSeq Acc Id: NM_001108012   ⟹   NP_001101482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,232,611 - 27,475,664 (-)NCBI
Rnor_6.0628,677,565 - 28,931,843 (-)NCBI
Rnor_5.0638,483,476 - 38,734,322 (-)NCBI
RGSC_v3.4627,224,396 - 27,473,926 (-)RGD
Celera626,704,021 - 26,946,167 (-)RGD
Sequence:
RefSeq Acc Id: XM_017594128   ⟹   XP_017449617
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,234,747 - 27,475,786 (-)NCBI
Rnor_6.0628,677,563 - 28,931,844 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039112177   ⟹   XP_038968105
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,234,747 - 27,507,992 (-)NCBI
RefSeq Acc Id: XM_039112178   ⟹   XP_038968106
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,234,747 - 27,460,314 (-)NCBI
RefSeq Acc Id: XM_039112179   ⟹   XP_038968107
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,232,609 - 27,476,260 (-)NCBI
RefSeq Acc Id: XM_039112180   ⟹   XP_038968108
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,234,747 - 27,476,260 (-)NCBI
RefSeq Acc Id: XM_039112182   ⟹   XP_038968110
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,234,747 - 27,476,260 (-)NCBI
RefSeq Acc Id: XM_039112183   ⟹   XP_038968111
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,234,604 - 27,476,260 (-)NCBI
RefSeq Acc Id: XM_039112184   ⟹   XP_038968112
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,234,604 - 27,476,260 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101482   ⟸   NM_001108012
- Sequence:
RefSeq Acc Id: XP_017449617   ⟸   XM_017594128
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000061906   ⟸   ENSRNOT00000068531
RefSeq Acc Id: ENSRNOP00000071037   ⟸   ENSRNOT00000091659
RefSeq Acc Id: XP_038968107   ⟸   XM_039112179
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968112   ⟸   XM_039112184
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968111   ⟸   XM_039112183
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968105   ⟸   XM_039112177
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968110   ⟸   XM_039112182
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968108   ⟸   XM_039112180
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968106   ⟸   XM_039112178
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000095436   ⟸   ENSRNOT00000110405
RefSeq Acc Id: ENSRNOP00000095601   ⟸   ENSRNOT00000105343
Protein Domains
bHLH   PAS

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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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
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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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
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)
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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
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)
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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
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309046 AgrOrtholog
Ensembl Genes ENSRNOG00000004068 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061906 UniProtKB/TrEMBL
  ENSRNOP00000071037 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068531 UniProtKB/TrEMBL
  ENSRNOT00000091659 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.1070 UniProtKB/TrEMBL
  4.10.280.10 UniProtKB/TrEMBL
InterPro DUF1518 UniProtKB/TrEMBL
  HLH_DNA-bd UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
  NCOA1 UniProtKB/TrEMBL
  Nuc_rcpt_coact UniProtKB/TrEMBL
  Nuc_rcpt_coact_Ncoa-typ UniProtKB/TrEMBL
  Nuc_rcpt_coact_Ncoa_int_sf UniProtKB/TrEMBL
  Nuclear_rcpt_coactivator UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
  PAS-like_dom_sf UniProtKB/TrEMBL
  PAS_fold UniProtKB/TrEMBL
  SRC-1 UniProtKB/TrEMBL
KEGG Report rno:313929 UniProtKB/TrEMBL
NCBI Gene 313929 ENTREZGENE
PANTHER PTHR10684 UniProtKB/TrEMBL
  PTHR10684:SF1 UniProtKB/TrEMBL
Pfam DUF1518 UniProtKB/TrEMBL
  HLH UniProtKB/TrEMBL
  Nuc_rec_co-act UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
  SRC-1 UniProtKB/TrEMBL
PhenoGen Ncoa1 PhenoGen
PIRSF Nuclear_receptor_coactivator UniProtKB/TrEMBL
PROSITE HLH UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
SMART DUF1518 UniProtKB/TrEMBL
  HLH UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
  Nuc_recept_coact UniProtKB/TrEMBL
  SSF55785 UniProtKB/TrEMBL
UniProt A0A0G2JZG4_RAT UniProtKB/TrEMBL
  D4A3Q3_RAT UniProtKB/TrEMBL
UniProt Secondary D4AB68 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ncoa1  nuclear receptor coactivator 1   Ncoa1_predicted  nuclear receptor coactivator 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ncoa1_predicted  nuclear receptor coactivator 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED