Rara (retinoic acid receptor, alpha) - Rat Genome Database

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Gene: Rara (retinoic acid receptor, alpha) Rattus norvegicus
Analyze
Symbol: Rara
Name: retinoic acid receptor, alpha
RGD ID: 3534
Description: Enables histone deacetylase binding activity; nucleic acid binding activity; and phosphatidylinositol 3-kinase regulator activity. Involved in several processes, including animal organ development; positive regulation of intracellular signal transduction; and response to vitamin A. Located in dendrite; nucleus; and perinuclear region of cytoplasm. Biomarker of amyotrophic lateral sclerosis. Human ortholog(s) of this gene implicated in acute promyelocytic leukemia. Orthologous to human RARA (retinoic acid receptor alpha); PARTICIPATES IN retinoic acid signaling pathway; acute myeloid leukemia pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,2',5,5'-tetrachlorobiphenyl; 3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: retinoic acid receptor alpha
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
mRatBN7.21083,883,490 - 83,928,932 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1083,893,384 - 83,928,142 (+)Ensembl
Rnor_6.01086,838,819 - 86,884,224 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1086,860,685 - 86,884,210 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01086,663,856 - 86,681,847 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41087,740,479 - 87,753,265 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11087,754,841 - 87,767,635 (+)NCBI
Celera1082,656,708 - 82,669,574 (+)NCBICelera
Cytogenetic Map10q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1-(5-isoquinolinesulfonyl)-2-methylpiperazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-(tert-butylimino)-5-phenyl-3-(propan-2-yl)-1,3,5-thiadiazinan-4-one  (ISO)
2-bromohexadecanoic acid  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (ISO)
4'-epidoxorubicin  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-diisothiocyano-trans-stilbene-2,2'-disulfonic acid  (ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-aminopyridine  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-(2-methylpiperazine-1-sulfonyl)isoquinoline  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
8'-apo-beta,psi-caroten-8'-al  (ISO)
9-cis-retinoic acid  (EXP,ISO)
adefovir pivoxil  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
alendronic acid  (EXP)
all-trans-4-hydroxyretinoic acid  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-4-oxoretinol  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP,ISO)
all-trans-retinyl palmitate  (EXP)
allethrin  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
androgen antagonist  (EXP)
Antimony trioxide  (ISO)
antirheumatic drug  (ISO)
arotinoid acid  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
beta-carotene  (ISO)
bicuculline  (EXP)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
buprofezin  (ISO)
cadmium atom  (ISO)
calciol  (EXP,ISO)
camptothecin  (ISO)
carnosic acid  (ISO)
chenodeoxycholic acid  (ISO)
chloroacetaldehyde  (ISO)
chlorogenic acid  (ISO)
chlorpromazine  (EXP)
choline  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (EXP,ISO)
clodronic acid  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumaphos  (ISO)
curcumin  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (EXP,ISO)
D-gluconic acid  (EXP)
DAPT  (ISO)
deguelin  (ISO)
deoxycholic acid  (EXP,ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dieldrin  (EXP)
dioxygen  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
dizocilpine maleate  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
enilconazole  (ISO)
ethanol  (ISO)
fenofibrate  (EXP,ISO)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (ISO)
gentamycin  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
griseofulvin  (ISO)
hydroxyurea  (ISO)
ibuprofen  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
indometacin  (ISO)
isotretinoin  (EXP,ISO)
kojic acid  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
limonene  (EXP)
lipopolysaccharide  (ISO)
melatonin  (ISO)
mercury atom  (EXP)
mercury(0)  (EXP)
methoxychlor  (ISO)
mitoxantrone  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N-nitrosourea  (EXP,ISO)
N-nitrosodiethylamine  (EXP,ISO)
nickel dichloride  (EXP)
nitrofen  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
ochratoxin A  (EXP)
okadaic acid  (EXP)
Osajin  (ISO)
parathion  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
phenethyl caffeate  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosalone  (ISO)
picene  (ISO)
Pomiferin  (ISO)
prochloraz  (ISO)
propiconazole  (ISO)
puerarin  (ISO)
quinoxyfen  (ISO)
raloxifene  (EXP)
resveratrol  (ISO)
Ro 41-5253  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium cholate  (ISO)
sodium dodecyl sulfate  (EXP)
sunitinib  (ISO)
Sunset Yellow FCF  (ISO)
tamibarotene  (EXP,ISO)
tamoxifen  (ISO)
tartrazine  (ISO)
terbufos  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
tetraphene  (ISO)
thiophenes  (ISO)
toluene  (ISO)
trichostatin A  (EXP)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
valproic acid  (EXP,ISO)
vanadyl sulfate  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
apoptotic cell clearance  (ISO)
bone development  (ISO)
cell differentiation  (IBA)
cellular response to estrogen stimulus  (ISO)
cellular response to lipopolysaccharide  (ISO)
cellular response to retinoic acid  (ISO)
chondroblast differentiation  (ISO)
embryonic camera-type eye development  (ISO)
face development  (ISO)
female pregnancy  (IEP)
germ cell development  (ISO)
glandular epithelial cell development  (ISO)
growth plate cartilage development  (ISO)
hippocampus development  (IEP)
hormone-mediated signaling pathway  (IBA)
limb development  (ISO)
liver development  (IEP)
male gonad development  (IDA)
mRNA transcription by RNA polymerase II  (IEA,ISO)
multicellular organism growth  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of cartilage development  (ISO)
negative regulation of cell differentiation  (ISO)
negative regulation of cell population proliferation  (IDA)
negative regulation of gene expression  (ISO)
negative regulation of granulocyte differentiation  (ISO)
negative regulation of interferon-gamma production  (ISO)
negative regulation of pri-miRNA transcription by RNA polymerase II  (ISO)
negative regulation of transcription by RNA polymerase II  (IBA,ISO)
negative regulation of transcription, DNA-templated  (ISO)
negative regulation of translation  (IDA)
negative regulation of translational initiation  (ISO)
negative regulation of tumor necrosis factor production  (ISO)
neural tube closure  (ISO)
outflow tract septum morphogenesis  (ISO)
positive regulation of binding  (ISO)
positive regulation of cell cycle  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of ERK1 and ERK2 cascade  (IMP)
positive regulation of gene expression  (ISO)
positive regulation of interleukin-13 production  (ISO)
positive regulation of interleukin-4 production  (ISO)
positive regulation of interleukin-5 production  (ISO)
positive regulation of neuron differentiation  (IDA)
positive regulation of phosphatidylinositol 3-kinase signaling  (IMP)
positive regulation of protein kinase B signaling  (IMP)
positive regulation of T-helper 2 cell differentiation  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,ISO)
positive regulation of transcription, DNA-templated  (ISO)
prostate gland development  (IEP)
protein phosphorylation  (ISO)
regulation of apoptotic process  (IDA)
regulation of granulocyte differentiation  (ISO)
regulation of myelination  (IDA)
regulation of phosphatidylinositol 3-kinase activity  (IEA)
regulation of synaptic plasticity  (IDA)
regulation of transcription, DNA-templated  (ISO)
response to cytokine  (IEP)
response to estradiol  (IEP)
response to ethanol  (IDA)
response to retinoic acid  (ISO)
response to vitamin A  (IEP)
retinoic acid receptor signaling pathway  (IBA,ISO)
Sertoli cell fate commitment  (ISO)
signal transduction  (ISO)
spermatogenesis  (ISO)
trachea cartilage development  (ISO)
ureteric bud development  (ISO)
ventricular cardiac muscle cell differentiation  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Akmal KM, etal., Biol Reprod 1996 May;54(5):1111-9.
2. Akmal KM, etal., Biol Reprod 1997 Feb;56(2):549-56.
3. Akmal KM, etal., Endocrinology 1998 Mar;139(3):1239-48.
4. Aoto J, etal., Neuron. 2008 Oct 23;60(2):308-20.
5. Balasubramaniyan N, etal., Am J Physiol Gastrointest Liver Physiol. 2005 Feb;288(2):G251-60. Epub 2004 Sep 23.
6. Boulogne B, etal., Mol Reprod Dev. 2003 Jun;65(2):194-203.
7. Braun KW, etal., Biol Reprod 2002 Jul;67(1):29-37.
8. Chen XN, etal., Biol Psychiatry. 2009 Nov 1;66(9):832-9. Epub 2009 Jul 12.
9. Dickmann LJ, etal., Biochem Pharmacol. 2008 Apr 15;75(8):1677-87. Epub 2008 Feb 7.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Germain P, etal., Pharmacol Rev. 2006 Dec;58(4):712-25.
12. GOA data from the GO Consortium
13. Goncalves MB, etal., Dev Biol. 2009 Feb 15;326(2):305-13. Epub 2008 Dec 7.
14. Grisendi S and Pandolfi PP, N Engl J Med. 2005 Jan 20;352(3):291-2.
15. Huang H, et al., Brain Res. 2008 Aug 28;1227:26-33. doi: 10.1016/j.brainres.2008.06.073. Epub 2008 Jun 27.
16. Jokic N, etal., J Neurochem. 2007 Dec;103(5):1821-33. Epub 2007 Sep 13.
17. Latasa MJ, etal., Glia. 2010 Sep;58(12):1451-64.
18. Li H and Kim KH, Biol Reprod. 2004 Mar;70(3):687-93. Epub 2003 Nov 12.
19. Li H and Kim KH, J Androl. 2003 Sep-Oct;24(5):653-60.
20. McGrane MM J Nutr Biochem. 2007 Aug;18(8):497-508. Epub 2007 Feb 22.
21. Mey J, etal., Glia. 2007 Jan 15;55(2):152-64.
22. Mezaki Y, etal., J Histochem Cytochem. 2009 Jul;57(7):687-99. Epub 2009 Mar 30.
23. MGD data from the GO Consortium
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. OMIM Disease Annotation Pipeline
26. Pipeline to import KEGG annotations from KEGG into RGD
27. Poon MM and Chen L, Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20303-8. Epub 2008 Dec 10.
28. Prins GS, etal., Endocrinology 2002 Sep;143(9):3628-40.
29. Reboul P, etal., Biochem Mol Biol Int. 1995 Aug;36(5):1097-105.
30. Redonnet A, etal., Br J Nutr. 2008 Oct;100(4):722-30. Epub 2008 Apr 3.
31. RGD automated data pipeline
32. RGD automated import pipeline for gene-chemical interactions
33. Rochette-Egly C and Germain P, Nucl Recept Signal. 2009 May 8;7:e005.
34. Schrage K, etal., Eur J Neurosci. 2006 Jan;23(2):285-95.
35. Xu Q, etal., J Biol Chem 2002 Nov 1;277(44):41693-700.
36. Zhang XH, etal., FEBS Lett. 2009 Apr 17;583(8):1231-6. Epub 2009 Mar 16.
37. Zheng B, etal., Cell Res. 2011 Oct;21(10):1487-508. doi: 10.1038/cr.2011.34. Epub 2011 Mar 8.
38. Zheng B, etal., J Biol Chem. 2009 Aug 21;284(34):22773-85. doi: 10.1074/jbc.M109.026989. Epub 2009 Jun 16.
39. Zhu L, etal., Endocrinology. 2009 Dec;150(12):5586-95. doi: 10.1210/en.2009-0868. Epub 2009 Oct 22.
Additional References at PubMed
PMID:1655807   PMID:2825025   PMID:7566114   PMID:7607067   PMID:7823919   PMID:8152920   PMID:8394014   PMID:9376317   PMID:9428411   PMID:9628876   PMID:9659935   PMID:10684250  
PMID:11222375   PMID:11641275   PMID:12039952   PMID:12101409   PMID:12195422   PMID:12477932   PMID:14980219   PMID:15322135   PMID:15528198   PMID:15766748   PMID:15901285   PMID:16417524  
PMID:16456540   PMID:17195188   PMID:17363140   PMID:17538076   PMID:17641689   PMID:17905941   PMID:17928865   PMID:18026104   PMID:18254374   PMID:18416830   PMID:18495661   PMID:18845237  
PMID:18922886   PMID:19389355   PMID:19628791   PMID:19752193   PMID:19917671   PMID:20080953   PMID:20130111   PMID:20201933   PMID:20215566   PMID:20413580   PMID:20649843   PMID:20945395  
PMID:21131358   PMID:21882190   PMID:22337869   PMID:22351778   PMID:23327965   PMID:23613978   PMID:24859384   PMID:25127741   PMID:25209250   PMID:25359573   PMID:27073891   PMID:28570942  
PMID:28645189   PMID:32205185   PMID:33411644  


Genomics

Comparative Map Data
Rara
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21083,883,490 - 83,928,932 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1083,893,384 - 83,928,142 (+)Ensembl
Rnor_6.01086,838,819 - 86,884,224 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1086,860,685 - 86,884,210 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01086,663,856 - 86,681,847 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41087,740,479 - 87,753,265 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11087,754,841 - 87,767,635 (+)NCBI
Celera1082,656,708 - 82,669,574 (+)NCBICelera
Cytogenetic Map10q31NCBI
RARA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1740,309,180 - 40,357,643 (+)EnsemblGRCh38hg38GRCh38
GRCh381740,309,180 - 40,357,643 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371738,465,432 - 38,513,895 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361735,718,972 - 35,767,420 (+)NCBINCBI36hg18NCBI36
Build 341735,740,895 - 35,767,420NCBI
Celera1735,125,565 - 35,174,038 (+)NCBI
Cytogenetic Map17q21.2NCBI
HuRef1734,258,584 - 34,307,018 (+)NCBIHuRef
CHM1_11738,700,731 - 38,749,203 (+)NCBICHM1_1
Rara
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391198,818,626 - 98,865,768 (+)NCBIGRCm39mm39
GRCm39 Ensembl1198,818,644 - 98,865,768 (+)Ensembl
GRCm381198,927,800 - 98,974,942 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1198,927,818 - 98,974,942 (+)EnsemblGRCm38mm10GRCm38
MGSCv371198,799,010 - 98,836,256 (+)NCBIGRCm37mm9NCBIm37
MGSCv361198,753,943 - 98,788,760 (+)NCBImm8
Celera11108,602,792 - 108,640,796 (+)NCBICelera
Cytogenetic Map11DNCBI
cM Map1162.76NCBI
Rara
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545114,897,726 - 14,917,134 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545114,876,663 - 14,917,134 (+)NCBIChiLan1.0ChiLan1.0
RARA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11717,156,923 - 17,205,451 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01716,932,485 - 16,980,958 (-)NCBIMhudiblu_PPA_v0panPan3
RARA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1922,254,803 - 22,298,614 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl922,254,806 - 22,289,459 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha921,727,250 - 21,761,701 (-)NCBI
ROS_Cfam_1.0923,046,731 - 23,091,126 (-)NCBI
UMICH_Zoey_3.1921,821,642 - 21,856,078 (-)NCBI
UNSW_CanFamBas_1.0922,080,340 - 22,114,785 (-)NCBI
UU_Cfam_GSD_1.0922,205,221 - 22,239,665 (-)NCBI
Rara
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560221,654,499 - 21,698,923 (-)NCBI
SpeTri2.0NW_00493649015,376,217 - 15,420,638 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RARA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1222,047,442 - 22,085,674 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11222,047,449 - 22,085,759 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21222,356,038 - 22,403,796 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RARA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11665,817,849 - 65,866,862 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1665,817,757 - 65,866,878 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607736,718,924 - 36,759,030 (-)NCBIVero_WHO_p1.0
Rara
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247952,935,432 - 2,975,226 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH141071  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,927,801 - 83,928,007 (+)MAPPERmRatBN7.2
Rnor_6.01086,883,094 - 86,883,299NCBIRnor6.0
Rnor_5.01086,681,507 - 86,681,712UniSTSRnor5.0
RGSC_v3.41087,752,925 - 87,753,130UniSTSRGSC3.4
Celera1082,669,234 - 82,669,439UniSTS
RH 3.4 Map10860.1UniSTS
Cytogenetic Map10q31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107255241693995749Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)107437208484007272Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107437208494965338Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)107563188787055282Rat
2325836Bp346Blood pressure QTL 3460.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608584007272Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608594965338Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
724516Uae17Urinary albumin excretion QTL 173.6urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)107821062285220348Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)107889965587307728Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)107981378985160854Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108051528791230079Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108256485692369470Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:313
Count of miRNA genes:174
Interacting mature miRNAs:199
Transcripts:ENSRNOT00000008659
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 28 19 17 11 17 62 30 40 11
Low 1 15 38 24 8 24 8 11 12 5 1 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008767945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085218 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039085219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC141969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC099830 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U15211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000008659   ⟹   ENSRNOP00000008659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1083,914,976 - 83,928,103 (+)Ensembl
Rnor_6.0 Ensembl1086,870,523 - 86,883,434 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084644   ⟹   ENSRNOP00000069776
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1083,893,384 - 83,928,142 (+)Ensembl
Rnor_6.0 Ensembl1086,860,685 - 86,884,210 (+)Ensembl
RefSeq Acc Id: NM_031528   ⟹   NP_113716
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,915,238 - 83,928,142 (+)NCBI
Rnor_6.01086,870,530 - 86,883,434 (+)NCBI
Rnor_5.01086,663,856 - 86,681,847 (+)NCBI
RGSC_v3.41087,740,479 - 87,753,265 (+)RGD
Celera1082,656,708 - 82,669,574 (+)RGD
Sequence:
RefSeq Acc Id: XM_017597010   ⟹   XP_017452499
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,883,490 - 83,928,932 (+)NCBI
Rnor_6.01086,838,819 - 86,884,224 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017597011   ⟹   XP_017452500
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,893,380 - 83,928,932 (+)NCBI
Rnor_6.01086,848,661 - 86,884,224 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039085214   ⟹   XP_038941142
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,902,720 - 83,928,932 (+)NCBI
RefSeq Acc Id: XM_039085216   ⟹   XP_038941144
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,893,456 - 83,928,932 (+)NCBI
RefSeq Acc Id: XM_039085217   ⟹   XP_038941145
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,905,133 - 83,928,932 (+)NCBI
RefSeq Acc Id: XM_039085218   ⟹   XP_038941146
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,895,572 - 83,928,932 (+)NCBI
RefSeq Acc Id: XM_039085219   ⟹   XP_038941147
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,904,427 - 83,928,932 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113716   ⟸   NM_031528
- UniProtKB: Q499N1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017452499   ⟸   XM_017597010
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JW78 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017452500   ⟸   XM_017597011
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JW78 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069776   ⟸   ENSRNOT00000084644
RefSeq Acc Id: ENSRNOP00000008659   ⟸   ENSRNOT00000008659
RefSeq Acc Id: XP_038941144   ⟸   XM_039085216
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038941146   ⟸   XM_039085218
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038941142   ⟸   XM_039085214
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038941147   ⟸   XM_039085219
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038941145   ⟸   XM_039085217
- Peptide Label: isoform X1
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13697674
Promoter ID:EPDNEW_R8198
Type:initiation region
Name:Rara_1
Description:retinoic acid receptor, alpha
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01086,870,468 - 86,870,528EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
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:3534 AgrOrtholog
Ensembl Genes ENSRNOG00000009972 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008659 UniProtKB/TrEMBL
  ENSRNOP00000069776 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008659 UniProtKB/TrEMBL
  ENSRNOT00000084644 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7933868 IMAGE-MGC_LOAD
InterPro NHR_like_domain UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd_core UniProtKB/TrEMBL
  Retinoic_acid_rcpt UniProtKB/TrEMBL
  Str_hrmn_rcpt UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/TrEMBL
KEGG Report rno:24705 UniProtKB/TrEMBL
MGC_CLONE MGC:124599 IMAGE-MGC_LOAD
NCBI Gene 24705 ENTREZGENE
Pfam Hormone_recep UniProtKB/TrEMBL
  zf-C4 UniProtKB/TrEMBL
PhenoGen Rara PhenoGen
PRINTS RETNOICACIDR UniProtKB/TrEMBL
  STRDHORMONER UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/TrEMBL
SMART HOLI UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/TrEMBL
Superfamily-SCOP Str_ncl_receptor UniProtKB/TrEMBL
UniProt A0A0G2JW78 ENTREZGENE, UniProtKB/TrEMBL
  Q499N1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Rara  Retinoic acid receptor, alpha      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the perinuclear region of prostatic cells 625676
gene_expression expressed in the periductal stromal cells of 6 day old pups 625676
gene_expression expressed in the perinuclear region of prostatic cells also expressed in the periductal stromal cells of 6 day old pups 625676
gene_pathway required in the RA pathway in developing and adult prostates 625676
gene_regulation exposure to estrogen upregulates expression in prostatic cells 625676