Thra (thyroid hormone receptor alpha) - Rat Genome Database

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Gene: Thra (thyroid hormone receptor alpha) Rattus norvegicus
Analyze
Symbol: Thra
Name: thyroid hormone receptor alpha
RGD ID: 3857
Description: Enables DNA-binding transcription factor activity, RNA polymerase II-specific; nucleic acid binding activity; and protein homodimerization activity. Involved in several processes, including animal organ development; digestive tract development; and regulation of transcription, DNA-templated. Located in cytosol; mitochondrion; and nucleus. Human ortholog(s) of this gene implicated in congenital nongoitrous hypothyroidism 6 and renal cell carcinoma. Orthologous to human THRA (thyroid hormone receptor alpha); INTERACTS WITH 17beta-estradiol; 2,2',4,4',5,5'-hexachlorobiphenyl; 2,4-dibromophenyl 2,4,5-tribromophenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 1; c-erb-A thyroid hormone receptor; c-erbA-1; C-erbA-alpha; c-erbA-alpha2; c-erbAalpha2; ERBA1; nuclear receptor subfamily 1 group A member 1; Thra1; thyroid hormone receptor; Thyroid hormone receptor alpha 1 (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 1 formerly ERBA1); Thyroid hormone receptor, alpha 1 (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 1, formerly ERBA1)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Thra_v2   Thra_v1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21083,701,885 - 83,729,408 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1083,700,755 - 83,729,936 (+)Ensembl
Rnor_6.01086,657,285 - 86,684,935 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1086,657,285 - 86,684,933 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01086,453,436 - 86,480,928 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41087,514,443 - 87,542,306 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11087,540,629 - 87,556,674 (+)NCBI
Celera1082,449,971 - 82,477,615 (+)NCBICelera
RH 3.4 Map10839.79RGD
Cytogenetic Map10q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
(E)-thiamethoxam  (ISO)
(R)-lipoic acid  (ISO)
(S)-colchicine  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-Hydroxypyrene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,5-trichlorophenol  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP)
2-[(2,4-dichlorophenyl)methyl]-4-(2,4,4-trimethylpentan-2-yl)phenol  (EXP)
2-hydroxypropanoic acid  (ISO)
2-methoxyethanol  (EXP)
3,3',5'-triiodo-L-thyronine  (ISO)
3,3',5'-triiodothyronine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP,ISO)
3,3',5,5'-tetraiodothyroacetic acid  (ISO)
3,3',5-triiodo-L-thyronine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-iodoprop-2-yn-1-yl butylcarbamate  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-Methyl-4-(2,6,6-trimethyl-2-cyclohexen-1-yl)-3-buten-2-one  (ISO)
4'-epidoxorubicin  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-hydroxynon-2-enal  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
9-phenanthrol  (ISO)
[4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID  (ISO)
actinomycin D  (ISO)
adefovir pivoxil  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP,ISO)
ammonium chloride  (EXP,ISO)
amsacrine  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
aprepitant  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bexarotene  (ISO)
bezafibrate  (EXP)
bicalutamide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (EXP)
bisphenol F  (EXP,ISO)
bithionol  (EXP)
bortezomib  (ISO)
bromobenzene  (EXP)
buta-1,3-diene  (ISO)
butanal  (ISO)
calciol  (EXP)
camptothecin  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
chlordecone  (ISO)
Chlorobenzilate  (ISO)
chloroprene  (EXP,ISO)
chloroquine  (ISO)
chlorpyrifos-methyl  (ISO)
chromium(6+)  (ISO)
chrysin  (ISO)
ciglitazone  (EXP)
clomiphene  (ISO)
clomipramine  (ISO)
closantel  (EXP)
clozapine  (EXP)
cocaine  (ISO)
copper(II) sulfate  (ISO)
coumarin  (EXP)
crocidolite asbestos  (ISO)
daidzein  (ISO)
DDE  (EXP)
decabromodiphenyl ether  (EXP,ISO)
dexamethasone  (ISO)
diazinon  (EXP)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP)
diethyl hydrogen phosphate  (EXP)
diethylstilbestrol  (ISO)
digitoxin  (ISO)
diiodine  (ISO)
diniconazole  (ISO)
disulfiram  (ISO)
domperidone  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
dronedarone  (EXP,ISO)
elemental selenium  (ISO)
emetine  (ISO)
endosulfan  (EXP)
enilconazole  (ISO)
equilin  (ISO)
estriol  (ISO)
ethanol  (ISO)
fenarimol  (ISO)
fenitrothion  (ISO)
fenpyroximate  (ISO)
fenvalerate  (EXP,ISO)
fipronil  (EXP)
flavonoids  (EXP)
fludioxonil  (ISO)
Flumetralin  (ISO)
flutamide  (ISO)
folic acid  (ISO)
genistein  (ISO)
glyphosate  (EXP)
haloperidol  (EXP)
hydroxyflutamide  (ISO)
indometacin  (ISO)
iprodione  (ISO)
isoprenaline  (EXP)
isotretinoin  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
linuron  (ISO)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
mebendazole  (ISO)
menadione  (ISO)
methylmercury chloride  (ISO)
microcystin-LR  (ISO)
mifepristone  (ISO)
mycophenolic acid  (ISO)
N-benzoyl-L-alanine  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
napropamide  (ISO)
nebivolol  (ISO)
nickel atom  (ISO)
nitrofen  (EXP,ISO)
norethisterone  (ISO)
ozone  (EXP)
p-tert-Amylphenol  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
pazopanib  (ISO)
PCB138  (ISO)
perfluorodecanoic acid  (ISO)
perfluorododecanoic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
perfluoroundecanoic acid  (ISO)
phenobarbital  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
phoxim  (ISO)
pirinixic acid  (EXP,ISO)
propanil  (ISO)
propylparaben  (ISO)
pyridaben  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
staurosporine  (ISO)
sulfasalazine  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tegaserod  (ISO)
telithromycin  (ISO)
Temsirolimus  (ISO)
teniposide  (ISO)
Tetrachlorobisphenol A  (ISO)
tetrachloromethane  (EXP,ISO)
thiamethoxam  (ISO)
thiazolidinediones  (EXP)
thioacetamide  (EXP)
thyroxine  (EXP,ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
trichloroethene  (EXP)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
troglitazone  (EXP,ISO)
tungsten  (ISO)
valinomycin  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP,ISO)
vincristine  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adrenal gland development  (IEP)
animal organ morphogenesis  (ISO)
brain development  (IEP)
cartilage condensation  (IEA,ISO)
cell differentiation  (IBA)
cytoplasmic sequestering of transcription factor  (ISO)
digestive tract development  (IEP)
embryonic organ development  (IEP)
erythrocyte differentiation  (IEA,ISO)
female courtship behavior  (IEA,ISO)
hormone-mediated signaling pathway  (IBA,IEA,ISO)
intracellular receptor signaling pathway  (IEA)
kidney development  (IEP)
learning or memory  (IEA,ISO)
liver development  (IEP)
lung development  (IEP)
mRNA transcription by RNA polymerase II  (ISO)
negative regulation of DNA-binding transcription factor activity  (IDA)
negative regulation of DNA-templated transcription, initiation  (ISO)
negative regulation of RNA polymerase II transcription preinitiation complex assembly  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IBA)
negative regulation of transcription, DNA-templated  (ISO)
ossification  (IEA,ISO)
positive regulation of cold-induced thermogenesis  (ISO,ISS)
positive regulation of female receptivity  (IEA,ISO)
positive regulation of myotube differentiation  (ISO)
positive regulation of thyroid hormone mediated signaling pathway  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,IDA,IEA,ISO)
regulation of heart contraction  (IEA,ISO)
regulation of lipid catabolic process  (IEA,ISO)
regulation of myeloid cell apoptotic process  (IEA,ISO)
regulation of thyroid hormone mediated signaling pathway  (IEA,ISO)
regulation of transcription by RNA polymerase II  (ISO)
response to cold  (IEA,ISO)
response to nutrient levels  (IEP)
response to xenobiotic stimulus  (IEP)
thyroid gland development  (IEA,ISO)
thyroid hormone mediated signaling pathway  (IBA)
transcription by RNA polymerase II  (IEA,ISO)
type I pneumocyte differentiation  (IEA,ISO)

Cellular Component

References

References - curated
1. Dayton AI, etal., Proc Natl Acad Sci U S A. 1984 Jul;81(14):4495-9.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. GOA data from the GO Consortium
4. Guyot R, etal., BMC Mol Biol. 2010 Jan 15;11:3. doi: 10.1186/1471-2199-11-3.
5. Kamiya Y, etal., Carcinogenesis. 2002 Jan;23(1):25-33.
6. Katz D and Lazar MA, J Biol Chem. 1993 Oct 5;268(28):20904-10.
7. Keijzer R, etal., J Mol Endocrinol. 2007 May;38(5):523-35.
8. Kenessey A, etal., Am J Physiol Heart Circ Physiol. 2006 Jan;290(1):H381-9. Epub 2005 Sep 9.
9. Koenig RJ, etal., Nature. 1989 Feb 16;337(6208):659-61.
10. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
11. Lazar MA and Chin WW, Mol Endocrinol 1988 Jun;2(6):479-84.
12. Lazar MA, etal., Mol Endocrinol 1988 Oct;2(10):893-901.
13. Li X, etal., J Biol Chem 2002 Aug 9;277(32):28656-62.
14. McCabe CJ, etal., J Clin Endocrinol Metab. 1999 Feb;84(2):649-53.
15. MGD data from the GO Consortium
16. OMIM Disease Annotation Pipeline
17. Pantos C, etal., Eur J Endocrinol. 2007 Apr;156(4):415-24.
18. Pathak A, etal., Cereb Cortex. 2010 Apr 5.
19. Puzianowska-Kuznicka M, etal., J Clin Endocrinol Metab. 2002 Mar;87(3):1120-8.
20. Ramadan W, etal., Endocrinology. 2011 Aug;152(8):3093-102. doi: 10.1210/en.2011-0139. Epub 2011 Jun 7.
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Sato I, etal., Cells Tissues Organs. 2006;183(4):195-205.
24. Silva JM, etal., Oncogene. 2002 Jun 20;21(27):4307-16.
25. Stein EJ, etal., Psychoneuroendocrinology. 2009 Feb;34(2):281-6. Epub 2008 Oct 17.
26. Sugizaki MM, etal., Can J Physiol Pharmacol. 2009 Sep;87(9):666-73.
27. Thompson CC, etal., Science 1987 Sep 25;237(4822):1610-4.
28. Xu B and Koenig RJ, J Biol Chem. 2004 Aug 6;279(32):33051-6. Epub 2004 Jun 4.
29. Xu B and Koenig RJ, Mol Cell Endocrinol. 2005 Dec 21;245(1-2):147-57. Epub 2005 Dec 13.
Additional References at PubMed
PMID:1371278   PMID:2841611   PMID:2879243   PMID:3387247   PMID:7501015   PMID:8051130   PMID:8524305   PMID:8710870   PMID:8889548   PMID:9250685   PMID:9430637   PMID:9653119  
PMID:9927422   PMID:10769387   PMID:10866662   PMID:11641275   PMID:11773436   PMID:12869545   PMID:14657007   PMID:15062575   PMID:15240882   PMID:15322135   PMID:15340084   PMID:15466465  
PMID:15498821   PMID:15701601   PMID:15831522   PMID:16322094   PMID:16717100   PMID:16730242   PMID:16803873   PMID:17129617   PMID:17952069   PMID:18000305   PMID:18052923   PMID:18203951  
PMID:18299881   PMID:18622044   PMID:19001373   PMID:19158403   PMID:19171649   PMID:19629520   PMID:20414976   PMID:20560106   PMID:20730619   PMID:21442236   PMID:22001906   PMID:22930759  
PMID:22985455   PMID:25156012   PMID:25726374   PMID:26861177   PMID:31534055   PMID:33255695  


Genomics

Comparative Map Data
Thra
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21083,701,885 - 83,729,408 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1083,700,755 - 83,729,936 (+)Ensembl
Rnor_6.01086,657,285 - 86,684,935 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1086,657,285 - 86,684,933 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01086,453,436 - 86,480,928 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41087,514,443 - 87,542,306 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11087,540,629 - 87,556,674 (+)NCBI
Celera1082,449,971 - 82,477,615 (+)NCBICelera
RH 3.4 Map10839.79RGD
Cytogenetic Map10q31NCBI
THRA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1740,058,290 - 40,093,867 (+)EnsemblGRCh38hg38GRCh38
GRCh381740,062,193 - 40,093,867 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371738,218,446 - 38,250,120 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361735,472,589 - 35,503,646 (+)NCBINCBI36hg18NCBI36
Build 341735,472,588 - 35,499,815NCBI
Celera1734,878,512 - 34,910,230 (+)NCBI
Cytogenetic Map17q21.1NCBI
HuRef1734,012,227 - 34,043,856 (+)NCBIHuRef
CHM1_11738,454,163 - 38,485,823 (+)NCBICHM1_1
Thra
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391198,631,539 - 98,659,832 (+)NCBIGRCm39mm39
GRCm39 Ensembl1198,631,464 - 98,659,832 (+)Ensembl
GRCm381198,740,776 - 98,769,006 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1198,740,638 - 98,769,006 (+)EnsemblGRCm38mm10GRCm38
MGSCv371198,603,187 - 98,626,425 (+)NCBIGRCm37mm9NCBIm37
MGSCv361198,557,963 - 98,581,201 (+)NCBImm8
Celera11108,407,991 - 108,419,811 (+)NCBICelera
Cytogenetic Map11DNCBI
cM Map1162.58NCBI
Thra
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545114,731,746 - 14,744,367 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545114,731,746 - 14,743,545 (+)NCBIChiLan1.0ChiLan1.0
THRA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11717,420,186 - 17,448,502 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01717,196,459 - 17,226,263 (-)NCBIMhudiblu_PPA_v0panPan3
THRA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1922,469,466 - 22,493,445 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl922,468,594 - 22,493,445 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha921,941,798 - 21,965,472 (-)NCBI
ROS_Cfam_1.0923,262,655 - 23,286,090 (-)NCBI
UMICH_Zoey_3.1922,036,085 - 22,059,532 (-)NCBI
UNSW_CanFamBas_1.0922,295,080 - 22,318,722 (-)NCBI
UU_Cfam_GSD_1.0922,419,817 - 22,443,287 (-)NCBI
Thra
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560221,869,085 - 21,886,778 (-)NCBI
SpeTri2.0NW_00493649015,188,341 - 15,206,032 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
THRA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1222,270,062 - 22,296,618 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11222,270,506 - 22,296,684 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21222,488,984 - 22,497,735 (+)NCBISscrofa10.2Sscrofa10.2susScr3
THRA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11666,087,071 - 66,118,137 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607736,990,432 - 37,021,543 (-)NCBIVero_WHO_p1.0
Thra
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247953,109,663 - 3,132,494 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D10Got130  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,723,587 - 83,723,721 (+)MAPPERmRatBN7.2
Rnor_6.01086,679,115 - 86,679,248NCBIRnor6.0
Rnor_5.01086,475,135 - 86,475,268UniSTSRnor5.0
RGSC_v3.41087,536,143 - 87,536,275RGDRGSC3.4
RGSC_v3.41087,536,142 - 87,536,275UniSTSRGSC3.4
RGSC_v3.11087,550,513 - 87,550,645RGD
Celera1082,471,824 - 82,471,961UniSTS
RH 3.4 Map10809.69UniSTS
RH 3.4 Map10809.69RGD
RH 2.0 Map10955.4RGD
Cytogenetic Map10q31UniSTS
Thra  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,725,066 - 83,725,146 (+)MAPPERmRatBN7.2
Rnor_6.01086,680,593 - 86,680,672NCBIRnor6.0
Rnor_5.01086,476,613 - 86,476,692UniSTSRnor5.0
RGSC_v3.41087,537,620 - 87,537,699UniSTSRGSC3.4
Celera1082,473,306 - 82,473,385UniSTS
Cytogenetic Map10q31UniSTS
RH133144  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,729,162 - 83,729,353 (+)MAPPERmRatBN7.2
Rnor_6.01086,684,690 - 86,684,880NCBIRnor6.0
Rnor_5.01086,480,683 - 86,480,873UniSTSRnor5.0
RGSC_v3.41087,542,061 - 87,542,251UniSTSRGSC3.4
Celera1082,477,370 - 82,477,560UniSTS
RH 3.4 Map10858.6UniSTS
Cytogenetic Map10q31UniSTS
AW259572  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,729,114 - 83,729,206 (+)MAPPERmRatBN7.2
Rnor_6.01086,684,642 - 86,684,733NCBIRnor6.0
Rnor_5.01086,480,635 - 86,480,726UniSTSRnor5.0
RGSC_v3.41087,542,013 - 87,542,104UniSTSRGSC3.4
Celera1082,477,322 - 82,477,413UniSTS
Cytogenetic Map10q31UniSTS
RH94515  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,725,316 - 83,725,484 (+)MAPPERmRatBN7.2
Rnor_6.01086,680,843 - 86,681,010NCBIRnor6.0
Rnor_5.01086,476,863 - 86,477,030UniSTSRnor5.0
RGSC_v3.41087,537,870 - 87,538,037UniSTSRGSC3.4
Celera1082,473,556 - 82,473,723UniSTS
RH 3.4 Map10839.79UniSTS
Cytogenetic Map10q31UniSTS
D17S1644E  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,729,253 - 83,729,324 (+)MAPPERmRatBN7.2
Rnor_6.01086,684,781 - 86,684,851NCBIRnor6.0
Rnor_5.01086,480,774 - 86,480,844UniSTSRnor5.0
RGSC_v3.41087,542,152 - 87,542,222UniSTSRGSC3.4
Celera1082,477,461 - 82,477,531UniSTS
Cytogenetic Map10q31UniSTS
MARC_26124-26125:1030369359:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,724,189 - 83,724,774 (+)MAPPERmRatBN7.2
Rnor_6.01086,679,717 - 86,680,300NCBIRnor6.0
Rnor_5.01086,475,737 - 86,476,320UniSTSRnor5.0
RGSC_v3.41087,536,744 - 87,537,327UniSTSRGSC3.4
Celera1082,472,430 - 82,473,013UniSTS
Cytogenetic Map10q31UniSTS
MARC_5497-5498:996690469:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,728,799 - 83,729,539 (+)MAPPERmRatBN7.2
Rnor_6.01086,684,327 - 86,685,066NCBIRnor6.0
Rnor_5.01086,480,320 - 86,481,059UniSTSRnor5.0
RGSC_v3.41087,541,698 - 87,542,437UniSTSRGSC3.4
Celera1082,477,007 - 82,477,746UniSTS
Cytogenetic Map10q31UniSTS
RH125185  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,728,377 - 83,728,548 (+)MAPPERmRatBN7.2
Rnor_6.01086,683,905 - 86,684,075NCBIRnor6.0
Rnor_5.01086,479,898 - 86,480,068UniSTSRnor5.0
RGSC_v3.41087,541,276 - 87,541,446UniSTSRGSC3.4
Celera1082,476,585 - 82,476,755UniSTS
Cytogenetic Map10q31UniSTS
PMC64989P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,724,738 - 83,724,993 (+)MAPPERmRatBN7.2
Rnor_6.01086,680,265 - 86,680,519NCBIRnor6.0
Rnor_5.01086,476,285 - 86,476,539UniSTSRnor5.0
RGSC_v3.41087,537,292 - 87,537,546UniSTSRGSC3.4
Celera1082,472,978 - 82,473,232UniSTS
Cytogenetic Map10q31UniSTS
PMC87157P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,723,979 - 83,724,810 (+)MAPPERmRatBN7.2
Rnor_6.01086,679,507 - 86,680,336NCBIRnor6.0
Rnor_5.01086,475,527 - 86,476,356UniSTSRnor5.0
RGSC_v3.41087,536,534 - 87,537,363UniSTSRGSC3.4
Celera1082,472,220 - 82,473,049UniSTS
Cytogenetic Map10q31UniSTS
NR1D1_2626  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,728,163 - 83,728,854 (+)MAPPERmRatBN7.2
Rnor_6.01086,683,691 - 86,684,381NCBIRnor6.0
Rnor_5.01086,479,684 - 86,480,374UniSTSRnor5.0
RGSC_v3.41087,541,062 - 87,541,752UniSTSRGSC3.4
Celera1082,476,371 - 82,477,061UniSTS
Cytogenetic Map10q31UniSTS
THRA_2263  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,728,582 - 83,729,339 (+)MAPPERmRatBN7.2
Rnor_6.01086,684,110 - 86,684,866NCBIRnor6.0
Rnor_5.01086,480,103 - 86,480,859UniSTSRnor5.0
RGSC_v3.41087,541,481 - 87,542,237UniSTSRGSC3.4
Celera1082,476,790 - 82,477,546UniSTS
Cytogenetic Map10q31UniSTS
THRA  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21083,721,509 - 83,722,496 (+)MAPPERmRatBN7.2
Rnor_6.01086,677,037 - 86,678,023NCBIRnor6.0
Rnor_5.01086,473,057 - 86,474,043UniSTSRnor5.0
RGSC_v3.41087,534,064 - 87,535,050UniSTSRGSC3.4
Celera1082,469,746 - 82,470,732UniSTS
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:201
Count of miRNA genes:133
Interacting mature miRNAs:150
Transcripts:ENSRNOT00000012340
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 42 22 12 7 12 8 11 72 35 35 11 8
Low 1 35 29 12 29 2 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012340   ⟹   ENSRNOP00000012340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1083,715,882 - 83,729,406 (+)Ensembl
Rnor_6.0 Ensembl1086,669,233 - 86,684,933 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087346   ⟹   ENSRNOP00000072739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1083,701,885 - 83,725,530 (+)Ensembl
Rnor_6.0 Ensembl1086,657,285 - 86,681,056 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104844   ⟹   ENSRNOP00000093530
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1083,700,755 - 83,729,936 (+)Ensembl
RefSeq Acc Id: NM_001017960   ⟹   NP_001017960
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,701,885 - 83,725,553 (+)NCBI
Rnor_6.01086,657,285 - 86,681,079 (+)NCBI
Rnor_5.01086,453,436 - 86,480,928 (+)NCBI
RGSC_v3.41087,514,443 - 87,542,306 (+)RGD
Celera1082,449,971 - 82,473,792 (+)NCBI
Sequence:
RefSeq Acc Id: NM_031134   ⟹   NP_112396
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21083,713,705 - 83,729,408 (+)NCBI
Rnor_6.01086,669,233 - 86,684,935 (+)NCBI
Rnor_5.01086,453,436 - 86,480,928 (+)NCBI
RGSC_v3.41087,514,443 - 87,542,306 (+)RGD
Celera1082,461,788 - 82,477,615 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001017960   ⟸   NM_001017960
- Peptide Label: isoform TRalpha1
- UniProtKB: P63059 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_112396   ⟸   NM_031134
- Peptide Label: isoform TRalpha2
- UniProtKB: P63059 (UniProtKB/Swiss-Prot),   G3V764 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012340   ⟸   ENSRNOT00000012340
RefSeq Acc Id: ENSRNOP00000072739   ⟸   ENSRNOT00000087346
RefSeq Acc Id: ENSRNOP00000093530   ⟸   ENSRNOT00000104844
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13697669
Promoter ID:EPDNEW_R8194
Type:multiple initiation site
Name:Thra_1
Description:thyroid hormone 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_6.01086,657,289 - 86,657,349EPDNEW

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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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)
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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)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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
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)
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
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)
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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)
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
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 86480422 86480423 G T snv SBH/Ygl (MCW), MR/N (KNAW), BBDP/WorN (KNAW), LEW/Crl (KNAW), IS-Tlk/Kyo (KyushuU), SBH/Ygl (KNAW), IS/Kyo (KyushuU), HTX/Kyo (KyushuU), LEW/NCrl (KNAW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 83728902 83728903 G T snv LEW/Crl (2019)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 86684429 86684430 G T snv SBH/Ygl (MCW), MR/N (MCW), BBDP/Wor (RGD), LEW/Crl (2019), LEW/NCrlBR (RGD), SBH/Ygl (RGD), LEW/Crl (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 87541800 87541801 G T snv MR/N (KNAW), BBDP/WorN (ICL), SBH/Ygl (ICL), LEW/NCrl (ICL), LEW/Crl (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3857 AgrOrtholog
Ensembl Genes ENSRNOG00000009066 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012340 UniProtKB/TrEMBL
  ENSRNOP00000072739 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000012340 UniProtKB/TrEMBL
  ENSRNOT00000087346 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro NHR-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ThyrH_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:81812 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 81812 ENTREZGENE
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Thra PhenoGen
PRINTS STRDHORMONER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  THYROIDHORMR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOLI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V764 ENTREZGENE, UniProtKB/TrEMBL
  P63059 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P10685 UniProtKB/Swiss-Prot
  P15827 UniProtKB/Swiss-Prot
  P16416 UniProtKB/Swiss-Prot
  P37241 UniProtKB/Swiss-Prot
  Q63107 UniProtKB/Swiss-Prot
  Q63195 UniProtKB/Swiss-Prot
  Q63196 UniProtKB/Swiss-Prot
  Q99146 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2003-04-09 Thra  thyroid hormone receptor alpha      Symbol and Name status set to approved 629479 APPROVED
2003-03-04 Thra  thyroid hormone receptor alpha  Thra1  Thyroid hormone receptor, alpha 1 (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 1, formerly ERBA1)  Symbol and Name updated to reflect Human and Mouse nomenclature 61478 PROVISIONAL
2002-06-10 Thra1  Thyroid hormone receptor, alpha 1 (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 1, formerly ERBA1)      Symbol and Name status set to approved 70586 APPROVED