Tert (telomerase reverse transcriptase) - Rat Genome Database

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Gene: Tert (telomerase reverse transcriptase) Rattus norvegicus
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Symbol: Tert
Name: telomerase reverse transcriptase
RGD ID: 70494
Description: Predicted to enable several functions, including chaperone binding activity; nucleic acid binding activity; and nucleotidyltransferase activity. Involved in several processes, including negative regulation of apoptotic process; positive regulation of transdifferentiation; and positive regulation of vascular associated smooth muscle cell migration. Located in mitochondrion and nucleus. Used to study chronic kidney disease and transient cerebral ischemia. Biomarker of hepatocellular carcinoma and pulmonary hypertension. Human ortholog(s) of this gene implicated in several diseases, including autosomal dominant dyskeratosis congenita 2; familial melanoma; hepatocellular carcinoma; idiopathic pulmonary fibrosis; and leukemia (multiple). Orthologous to human TERT (telomerase reverse transcriptase); PARTICIPATES IN hypoxia inducible factor pathway; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: telomerase catalytic subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Tertem2Mcwi  
Genetic Models: WKY-Tertem2Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2129,637,213 - 29,659,509 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl129,637,506 - 29,659,561 (-)Ensembl
Rnor_6.0132,250,876 - 32,275,330 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl132,251,714 - 32,272,476 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0133,675,744 - 33,697,542 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4130,445,180 - 30,465,942 (-)NCBIRGSC3.4rn4RGSC3.4
Celera128,286,050 - 28,306,805 (-)NCBICelera
Cytogenetic Map1p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute lymphoblastic leukemia  (ISO)
acute myeloid leukemia  (ISO)
adrenocortical carcinoma  (ISO)
Alcoholic Liver Diseases  (ISO)
aplastic anemia  (ISO)
Autosomal Dominant Dyskeratosis Congenita  (ISO)
autosomal dominant dyskeratosis congenita 1  (ISO,ISS)
autosomal dominant dyskeratosis congenita 2  (ISO)
autosomal recessive dyskeratosis congenita 1  (ISO)
autosomal recessive dyskeratosis congenita 4  (ISO)
B-Cell Chronic Lymphocytic Leukemia  (ISO)
basal cell carcinoma  (ISO)
beta thalassemia  (ISO)
breast cancer  (ISO)
breast carcinoma  (ISO)
Breast Neoplasms  (ISO)
cervix uteri carcinoma in situ  (ISO)
Chronic Hepatitis B  (ISO)
chronic kidney disease  (IDA)
chronic myeloid leukemia  (ISO)
chronic recurrent multifocal osteomyelitis  (ISO)
colon adenocarcinoma  (ISO)
coronary artery disease  (ISO)
Coronary Disease  (ISO)
Cri-du-Chat syndrome  (ISO)
Cutaneous Malignant Melanoma, Susceptibility To, 1  (ISO)
Diabetic Cardiomyopathies  (IEP)
disease of cellular proliferation  (ISO)
Disease Progression  (ISO)
ductal carcinoma in situ  (ISO)
dyskeratosis congenita  (ISO)
dysplastic nevus syndrome  (ISO)
Endometrial Neoplasms  (ISO)
esophageal atresia  (ISO)
esophagus squamous cell carcinoma  (ISO)
Experimental Diabetes Mellitus  (IEP)
Experimental Liver Cirrhosis  (IEP)
Experimental Melanoma  (ISO)
familial melanoma  (ISO)
fibrosarcoma  (ISO)
gallbladder carcinoma  (ISO)
gastrointestinal stromal tumor  (ISO)
Genetic Predisposition to Disease  (ISO)
hepatitis C  (ISO)
hepatocellular carcinoma  (IEP,ISO)
hepatocellular clear cell carcinoma  (ISO)
hereditary breast ovarian cancer syndrome  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
high grade glioma  (ISO)
Hoyeraal Hreidarsson Syndrome  (ISO)
Hypoxia-Ischemia, Brain  (IDA)
idiopathic pulmonary fibrosis  (ISO)
interstitial lung disease  (ISO)
kidney disease  (ISO)
leiomyosarcoma  (ISO)
Liver Neoplasms  (ISO)
Liver Reperfusion Injury  (ISO)
lung adenocarcinoma  (ISO)
Lung Neoplasms  (ISO)
lung non-small cell carcinoma  (ISO)
lung squamous cell carcinoma  (ISO)
lymphoid leukemia  (ISO)
macrocytic anemia  (ISO)
melanoma  (ISO)
microcephaly  (ISO)
multiple myeloma  (ISO)
myelodysplastic syndrome  (ISO)
myeloid neoplasm  (ISO)
nasopharynx carcinoma  (ISO)
nephroblastoma  (ISO)
neuroblastoma  (ISO)
Nonimmune Chronic Idiopathic Neutropenia, Adult  (ISO)
oral squamous cell carcinoma  (ISO)
Ovarian Neoplasms  (ISO)
pancreatic cancer  (ISO)
Parkinsonism-Dystonia, Infantile  (ISO)
plasma cell leukemia  (ISO)
primary immunodeficiency disease  (ISO)
prostate adenocarcinoma  (ISO)
prostate cancer  (ISO)
Prostatic Neoplasms  (ISO)
Pulmonary Fibrosis and/or Bone Marrow Failure, Telomere-Related, 1  (ISO)
pulmonary hypertension  (IEP,ISO)
Refractory Anemia  (ISO)
Refractory Anemia with Excess of Blasts  (ISO)
renal cell carcinoma  (ISO)
Reperfusion Injury  (ISO)
skin melanoma  (ISO)
small cell carcinoma  (ISO)
Spinal Cord Injuries  (IEP,ISO)
systemic lupus erythematosus  (ISO)
teratoma  (ISO)
Thyroid Neoplasms  (ISO)
transient cerebral ischemia  (IDA)
transitional cell carcinoma  (ISO)
urinary bladder cancer  (ISO)
Uterine Cervical Neoplasms  (ISO)
Uterine Neoplasms  (ISO)
viral hepatitis  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(R,R,R)-alpha-tocopherol  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-(5-isoquinolinesulfonyl)-2-methylpiperazine  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3',5'-cyclic AMP  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3-aminobenzamide  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-hydroperoxycyclophosphamide  (ISO)
5-(2-methylpiperazine-1-sulfonyl)isoquinoline  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
9-cis-retinoic acid  (ISO)
abacavir  (ISO)
acetamide  (EXP)
acetic acid  (ISO)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
aflatoxin B1  (EXP,ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
anilines  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
azoxystrobin  (ISO)
benzamide  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
berberine  (ISO)
bicalutamide  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
Boldine  (ISO)
bromochloroacetic acid  (ISO)
bucladesine  (ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
camptothecin  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chelidonine  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
cisplatin  (ISO)
citric acid  (ISO)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
deguelin  (ISO)
diarsenic trioxide  (ISO)
dibenziodolium  (ISO)
dibenzoylmethane  (ISO)
dicrotophos  (ISO)
dimethyl sulfoxide  (ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
elemental selenium  (EXP,ISO)
ellagic acid  (EXP,ISO)
endosulfan  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
fumagillin  (EXP)
furan  (EXP)
gefitinib  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
glutathione  (ISO)
Honokiol  (ISO)
hydrogen peroxide  (ISO)
iprodione  (EXP)
iron atom  (EXP)
iron(0)  (EXP)
isothiocyanate  (ISO)
isotretinoin  (ISO)
L-ascorbic acid  (ISO)
letrozole  (ISO)
LY294002  (EXP,ISO)
mangiferin  (ISO)
manumycin A  (ISO)
medroxyprogesterone acetate  (ISO)
methapyrilene  (ISO)
mitomycin C  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
Nandrolone decanoate  (ISO)
nicotinamide  (EXP)
Osajin  (ISO)
ozone  (ISO)
paclitaxel  (ISO)
parathion  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosalone  (EXP)
picoxystrobin  (ISO)
platycodin D  (ISO)
Pomiferin  (ISO)
pterostilbene  (ISO)
puerarin  (ISO)
quercetin  (ISO)
raloxifene  (EXP,ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
Rosavin  (ISO)
SB 203580  (ISO)
selenium atom  (EXP,ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
sphingosine  (ISO)
stanozolol  (EXP)
staurosporine  (ISO)
succimer  (ISO)
sulforaphane  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
Tomentosin  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
wortmannin  (ISO)
zidovudine  (ISO)
zinc dichloride  (ISO)
zinc oxide  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular response to hypoxia  (IEP,ISO)
DNA biosynthetic process  (ISO)
DNA strand elongation  (ISO)
double-stranded RNA biosynthetic process  (ISO)
establishment of protein localization to telomere  (ISO)
mitochondrion organization  (ISO)
negative regulation of apoptotic process  (IMP)
negative regulation of cellular senescence  (ISO)
negative regulation of endothelial cell apoptotic process  (IDA)
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of glial cell proliferation  (IDA)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of production of siRNA involved in RNA interference  (ISO)
positive regulation of angiogenesis  (IDA)
positive regulation of G1/S transition of mitotic cell cycle  (IMP)
positive regulation of glucose import  (ISO)
positive regulation of hair cycle  (ISO)
positive regulation of miRNA transcription  (ISO)
positive regulation of nitric-oxide synthase activity  (ISO)
positive regulation of protein binding  (ISO)
positive regulation of protein localization to nucleolus  (ISO)
positive regulation of stem cell proliferation  (ISO)
positive regulation of transdifferentiation  (IMP)
positive regulation of vascular associated smooth muscle cell migration  (IMP)
positive regulation of vascular associated smooth muscle cell proliferation  (IMP)
positive regulation of Wnt signaling pathway  (ISO)
production of siRNA involved in RNA interference  (ISO)
regulation of protein stability  (ISO)
replicative senescence  (ISO)
response to cadmium ion  (IEP)
RNA-dependent DNA biosynthetic process  (ISO)
telomere maintenance via telomerase  (IBA,ISO,ISS)
transcription, RNA-templated  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:9398860   PMID:9443919   PMID:9454332   PMID:10197982   PMID:10449030   PMID:11313459   PMID:11432839   PMID:11701125   PMID:11927518   PMID:12135483   PMID:12632524   PMID:12729609  
PMID:12729792   PMID:13679242   PMID:14701760   PMID:15057822   PMID:15632080   PMID:15687494   PMID:16037417   PMID:16043710   PMID:16107853   PMID:16205635   PMID:16248892   PMID:16424384  
PMID:16454671   PMID:16507993   PMID:16785237   PMID:17456401   PMID:17940095   PMID:18082603   PMID:18818403   PMID:19567472   PMID:19571879   PMID:19701182   PMID:19751963   PMID:19855065  
PMID:20351177   PMID:20540267   PMID:20564349   PMID:20736004   PMID:20864668   PMID:21141566   PMID:21455098   PMID:21531765   PMID:21829167   PMID:22073357   PMID:22226966   PMID:22446191  
PMID:23193663   PMID:23450462   PMID:23474713   PMID:24415760   PMID:24882549   PMID:24970747   PMID:25156787   PMID:25569094   PMID:25589350   PMID:25662949   PMID:26194824   PMID:26505494  
PMID:27251157   PMID:29017189   PMID:29436610   PMID:29695869   PMID:30338789   PMID:33999989   PMID:34559580  


Genomics

Comparative Map Data
Tert
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2129,637,213 - 29,659,509 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl129,637,506 - 29,659,561 (-)Ensembl
Rnor_6.0132,250,876 - 32,275,330 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl132,251,714 - 32,272,476 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0133,675,744 - 33,697,542 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4130,445,180 - 30,465,942 (-)NCBIRGSC3.4rn4RGSC3.4
Celera128,286,050 - 28,306,805 (-)NCBICelera
Cytogenetic Map1p11NCBI
TERT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl51,253,147 - 1,295,068 (-)EnsemblGRCh38hg38GRCh38
GRCh3851,253,167 - 1,295,068 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3751,253,282 - 1,295,183 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3651,306,282 - 1,348,162 (-)NCBINCBI36hg18NCBI36
Build 3451,306,286 - 1,348,159NCBI
Celera51,290,088 - 1,332,097 (-)NCBI
Cytogenetic Map5p15.33NCBI
HuRef51,234,692 - 1,275,531 (-)NCBIHuRef
CHM1_151,253,108 - 1,294,322 (-)NCBICHM1_1
Tert
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391373,775,030 - 73,797,962 (+)NCBIGRCm39mm39
GRCm39 Ensembl1373,775,030 - 73,797,962 (+)Ensembl
GRCm381373,626,911 - 73,649,843 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1373,626,911 - 73,649,843 (+)EnsemblGRCm38mm10GRCm38
MGSCv371373,764,449 - 73,786,489 (+)NCBIGRCm37mm9NCBIm37
MGSCv361374,093,003 - 74,115,043 (+)NCBImm8
Celera1375,955,877 - 75,977,918 (+)NCBICelera
Cytogenetic Map13C1NCBI
cM Map1340.12NCBI
Tert
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955504651,779 - 670,589 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955504649,248 - 669,796 (-)NCBIChiLan1.0ChiLan1.0
TERT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.151,300,397 - 1,338,241 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl51,300,960 - 1,338,872 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v051,542,217 - 1,586,775 (-)NCBIMhudiblu_PPA_v0panPan3
TERT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13411,288,622 - 11,307,790 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3411,288,622 - 11,307,951 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3415,798,490 - 15,817,661 (+)NCBI
ROS_Cfam_1.03411,189,290 - 11,208,463 (+)NCBI
ROS_Cfam_1.0 Ensembl3411,189,290 - 11,208,512 (+)Ensembl
UMICH_Zoey_3.13411,240,107 - 11,259,262 (+)NCBI
UNSW_CanFamBas_1.03411,219,414 - 11,238,599 (+)NCBI
UU_Cfam_GSD_1.03411,430,438 - 11,449,614 (+)NCBI
Tert
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213244,307,679 - 244,331,058 (+)NCBI
SpeTri2.0NW_004936815468,987 - 492,666 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TERT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1679,258,591 - 79,276,421 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11679,258,591 - 79,276,421 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21685,917,150 - 85,935,085 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TERT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.141,082,894 - 1,119,373 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl41,083,384 - 1,117,468 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605435,649,406 - 35,684,819 (-)NCBIVero_WHO_p1.0
Tert
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624751624,569 - 647,198 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
PMC27918P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,657,353 - 29,657,717 (+)MAPPERmRatBN7.2
Rnor_6.0132,271,017 - 32,271,380NCBIRnor6.0
Rnor_5.0133,695,885 - 33,696,248UniSTSRnor5.0
RGSC_v3.4130,464,483 - 30,464,846UniSTSRGSC3.4
Celera128,305,346 - 28,305,709UniSTS
Cytogenetic Map1p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)11148148232355910Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11543162149361612Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11543162149361612Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11620621049268520Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)12076315844095856Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12234064749361612Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)12234064749361612Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat


Genetic Models
This gene Tert is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:168
Count of miRNA genes:132
Interacting mature miRNAs:144
Transcripts:ENSRNOT00000022683, ENSRNOT00000034937
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 3 3 3 1
Low 3 32 54 38 19 38 74 35 35 11
Below cutoff 11 8 9 5 8

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758684 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017589078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109998 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005504447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005504448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005504449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_589899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC142421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ440965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ440966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ488949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY539717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY539718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY539719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY539720 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BK000660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474002 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ021473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000022683   ⟹   ENSRNOP00000022683
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,638,051 - 29,659,561 (-)Ensembl
Rnor_6.0 Ensembl132,251,714 - 32,272,476 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100559   ⟹   ENSRNOP00000076971
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,637,506 - 29,659,561 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110776   ⟹   ENSRNOP00000086875
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,637,506 - 29,659,561 (-)Ensembl
RefSeq Acc Id: NM_053423   ⟹   NP_445875
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,638,051 - 29,658,813 (-)NCBI
Rnor_6.0132,251,714 - 32,272,476 (-)NCBI
Rnor_5.0133,675,744 - 33,697,542 (-)NCBI
RGSC_v3.4130,445,180 - 30,465,942 (-)RGD
Celera128,286,050 - 28,306,805 (-)RGD
Sequence:
RefSeq Acc Id: XM_008758683   ⟹   XP_008756905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,637,213 - 29,659,060 (-)NCBI
Rnor_6.0132,250,876 - 32,275,330 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589078   ⟹   XP_017444567
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,637,213 - 29,659,499 (-)NCBI
Rnor_6.0132,250,876 - 32,275,330 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109992   ⟹   XP_038965920
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,637,213 - 29,658,161 (-)NCBI
RefSeq Acc Id: XM_039109994   ⟹   XP_038965922
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,649,048 - 29,659,503 (-)NCBI
RefSeq Acc Id: XM_039109998   ⟹   XP_038965926
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,650,718 - 29,659,509 (-)NCBI
RefSeq Acc Id: XM_039110003   ⟹   XP_038965931
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,637,213 - 29,652,970 (-)NCBI
RefSeq Acc Id: XR_005504447
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,638,978 - 29,659,503 (-)NCBI
RefSeq Acc Id: XR_005504448
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,638,051 - 29,659,501 (-)NCBI
RefSeq Acc Id: XR_005504449
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,638,051 - 29,659,501 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_445875   ⟸   NM_053423
- UniProtKB: Q673L6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008756905   ⟸   XM_008758683
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017444567   ⟸   XM_017589078
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000022683   ⟸   ENSRNOT00000022683
RefSeq Acc Id: XP_038965920   ⟸   XM_039109992
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038965931   ⟸   XM_039110003
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038965922   ⟸   XM_039109994
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038965926   ⟸   XM_039109998
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000086875   ⟸   ENSRNOT00000110776
RefSeq Acc Id: ENSRNOP00000076971   ⟸   ENSRNOT00000100559
Protein Domains
Reverse transcriptase

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: