Smad4 (SMAD family member 4) - Rat Genome Database

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Gene: Smad4 (SMAD family member 4) Rattus norvegicus
Analyze
Symbol: Smad4
Name: SMAD family member 4
RGD ID: 3033
Description: Enables DNA binding activity; SMAD binding activity; and filamin binding activity. Involved in several processes, including ERK1 and ERK2 cascade; cellular response to glucose stimulus; and positive regulation of cardiac muscle cell apoptotic process. Located in cytoplasm and nucleus. Part of protein-containing complex. Used to study pulmonary fibrosis. Biomarker of several diseases, including artery disease (multiple); gastrointestinal system cancer (multiple); lung disease (multiple); prostatitis; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in several diseases, including female reproductive organ cancer (multiple); hereditary hemorrhagic telangiectasia; juvenile polyposis syndrome; juvenile polyposis-hereditary hemorrhagic telangiectasia syndrome; and seminoma. Orthologous to human SMAD4 (SMAD family member 4); PARTICIPATES IN transforming growth factor-beta Smad dependent signaling pathway; altered transforming growth factor-beta Smad dependent signaling pathway; Bone morphogenetic proteins signaling pathway; INTERACTS WITH 1,2-dimethylhydrazine; 2,2,2-tetramine; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: MAD (mothers against decapentaplegic Drosophila) homolog 4; MAD (mothers against decapentaplegic, Drosophila) homolog 4; MAD homolog 4; MAD homolog 4 (Drosophila); Madh4; mothers against decapentaplegic homolog 4; mothers against DPP homolog 4; SMAD 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21867,243,742 - 67,274,438 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1867,243,742 - 67,274,438 (-)Ensembl
Rnor_6.01869,626,682 - 69,657,373 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1869,627,757 - 69,671,199 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01868,773,326 - 68,802,354 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41870,432,705 - 70,461,541 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11870,504,785 - 70,534,814 (-)NCBI
Celera1865,246,042 - 65,276,480 (-)NCBICelera
Cytogenetic Map18q12.2NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
17-beta hydroxysteroid dehydrogenase 3 deficiency  (ISO)
Acro-Osteolysis  (ISO)
aortic disease  (ISO)
brachydactyly  (ISO)
breast cancer  (ISO)
Breast Neoplasms  (ISO)
cervical cancer  (ISO)
cholangiocarcinoma  (ISO)
Chronic Hepatitis C  (ISO)
chronic myeloid leukemia  (ISO)
chronic obstructive pulmonary disease  (IEP)
Cicatrix  (IMP)
cognitive disorder  (ISO)
colon cancer  (IEP,ISO)
colon carcinoma  (ISO)
colorectal adenoma  (ISO)
colorectal cancer  (ISO)
colorectal carcinoma  (ISO)
Colorectal Neoplasms  (ISO)
Craniofacial Abnormalities  (ISO)
Cronkhite-Canada syndrome  (ISO)
Deafness  (ISO)
endometrial carcinoma  (ISO)
esophageal carcinoma  (ISO)
esophagus adenocarcinoma  (ISO)
Experimental Colitis  (ISO)
Experimental Liver Cirrhosis  (IEP,ISO)
gallbladder cancer  (ISO)
Gallstones  (ISO)
gastric adenocarcinoma  (ISO)
gastrointestinal system cancer  (ISO)
genetic disease  (ISO)
Growth Mental Deficiency Syndrome of Myhre  (ISO)
head and neck squamous cell carcinoma  (ISO)
hemorrhagic disease  (ISO)
hepatocellular carcinoma  (IEP,ISO)
hereditary hemorrhagic telangiectasia  (ISO)
Hereditary Hemorrhagic Telangiectasia, Type 1  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
Heterotopic Ossification  (IMP)
Human Viral Hepatitis  (ISO)
Hypoglossal Nerve Injuries  (IEP)
intellectual disability  (ISO)
intrahepatic cholangiocarcinoma  (ISO)
invasive ductal carcinoma  (ISO)
juvenile polyposis syndrome  (ISO)
juvenile polyposis-hereditary hemorrhagic telangiectasia syndrome  (ISO)
Laryngotracheal Stenosis, Progressive, with Short Stature and Arthropathy  (ISO)
Liver Metastasis  (ISO)
lung adenocarcinoma  (ISO)
lung cancer  (ISO)
Lymphatic Metastasis  (ISO)
Lynch syndrome  (ISO)
Microphthalmia, Cataracts, and Iris Abnormalities  (ISO)
muscular disease  (ISO)
myocardial infarction  (IEP)
Myocardial Reperfusion Injury  (IEP)
Neoplasm Metastasis  (ISO)
nephroblastoma  (ISO)
non-alcoholic steatohepatitis  (ISO)
Odontogenic Cysts  (ISO)
osteogenesis imperfecta  (ISS)
ovarian cancer  (ISO)
pancreatic adenocarcinoma  (ISO)
pancreatic cancer  (ISO)
pancreatic carcinoma  (ISO,ISS)
pancreatic ductal carcinoma  (ISO)
Parasitic Liver Diseases  (ISO)
pre-malignant neoplasm  (IEP)
Primary Pulmonary Hypertension, 1  (ISO)
prostate adenocarcinoma  (ISO)
prostate carcinoma in situ  (ISO)
Prostatic Neoplasms  (ISO)
prostatitis  (IEP)
pulmonary fibrosis  (IDA,IEP)
pulmonary hypertension  (IEP)
renal cell carcinoma  (ISO)
seminoma  (ISO)
Stomach Neoplasms  (ISO)
thoracic aortic aneurysm  (ISO)
thrombocytopenia  (ISO)
transitional cell carcinoma  (ISO)
type 2 diabetes mellitus  (IEP)
urinary bladder cancer  (ISO)
Uterine Cervical Neoplasms  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(R,R,R)-alpha-tocopherol  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
17alpha-ethynylestradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2,2-tetramine  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
2-methoxyethanol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-fluorouracil  (ISO)
acetaldehyde  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
amlodipine  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
Candesartan cilexetil  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chromium atom  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
curcumin  (EXP,ISO)
cyclosporin A  (ISO)
D-glucose  (EXP,ISO)
deguelin  (ISO)
dexamethasone  (ISO)
dibenziodolium  (EXP)
diclofenac  (ISO)
dorsomorphin  (ISO)
doxazosin  (ISO)
doxorubicin  (EXP,ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
farrerol  (EXP)
fenofibrate  (ISO)
folic acid  (ISO)
galangin  (ISO)
gallic acid  (ISO)
gentamycin  (EXP)
glucose  (EXP,ISO)
glycerol 2-phosphate  (ISO)
glycyrrhizinic acid  (ISO)
glyphosate  (ISO)
icariin  (ISO)
Isoangustone A  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
leptomycin B  (ISO)
Methylazoxymethanol acetate  (EXP)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
monosodium L-glutamate  (EXP)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
nitric oxide  (EXP)
nitrofen  (ISO)
osthole  (ISO)
ouabain  (ISO)
paracetamol  (ISO)
pentacarbonyliron  (ISO)
phenylmercury acetate  (ISO)
picoxystrobin  (ISO)
platycodin D  (ISO)
progesterone  (ISO)
quercetin  (ISO)
resveratrol  (EXP,ISO)
rutin  (EXP)
SB 431542  (ISO)
sodium arsenite  (EXP,ISO)
streptozocin  (EXP,ISO)
tamibarotene  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP)
theobromine  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vincristine  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adrenal gland development  (IEP)
aging  (IEP)
anatomical structure morphogenesis  (IBA,ISO)
anterior/posterior pattern specification  (ISO)
atrioventricular canal development  (IEA,ISO)
atrioventricular valve formation  (IEA,ISO)
axon guidance  (IEA,ISO)
BMP signaling pathway  (IBA,IEA,ISO)
brainstem development  (IEA,ISO)
branching involved in ureteric bud morphogenesis  (IEA,ISO)
cardiac septum development  (ISO)
cell differentiation  (IBA,ISO)
cell population proliferation  (IEA,ISO)
cellular iron ion homeostasis  (IEA,ISO)
cellular response to glucose stimulus  (IDA)
developmental growth  (IEA,ISO)
embryonic digit morphogenesis  (IEA,ISO)
endocardial cell differentiation  (IEA,ISO)
endoderm development  (ISO)
endothelial cell activation  (IEA,ISO)
epithelial to mesenchymal transition involved in endocardial cushion formation  (IEA,ISO)
ERK1 and ERK2 cascade  (IMP)
female gonad development  (ISO)
female gonad morphogenesis  (IEA,ISO)
formation of anatomical boundary  (IEA,ISO)
gastrulation  (ISO)
gastrulation with mouth forming second  (IEA,ISO)
in utero embryonic development  (IEA,ISO)
interleukin-6-mediated signaling pathway  (IEA,ISO)
intracellular signal transduction  (IEA,ISO)
kidney development  (ISO)
left ventricular cardiac muscle tissue morphogenesis  (IEA,ISO)
male gonad development  (ISO)
mesendoderm development  (IEA,ISO)
mesoderm development  (ISO)
metanephric mesenchyme morphogenesis  (IEA,ISO)
negative regulation of cardiac muscle hypertrophy  (IEA,ISO)
negative regulation of cardiac myofibril assembly  (IEA,ISO)
negative regulation of cell death  (IEA,ISO)
negative regulation of cell growth  (IEA,ISO)
negative regulation of cell population proliferation  (IEA,ISO)
negative regulation of ERK1 and ERK2 cascade  (IEA,ISO)
negative regulation of protein catabolic process  (IMP)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of transcription, DNA-templated  (ISO)
nephrogenic mesenchyme morphogenesis  (IEA,ISO)
neural crest cell differentiation  (IEA,ISO)
neuron fate commitment  (IEA,ISO)
osteoblast differentiation  (IMP)
outflow tract septum morphogenesis  (IEA,ISO)
ovarian follicle development  (IEA,IEP,ISO)
positive regulation of BMP signaling pathway  (IEA,ISO)
positive regulation of cardiac muscle cell apoptotic process  (IMP)
positive regulation of cell proliferation involved in heart valve morphogenesis  (IEA,ISO)
positive regulation of epithelial to mesenchymal transition  (IEA,ISO)
positive regulation of follicle-stimulating hormone secretion  (IEA,ISO)
positive regulation of histone H3-K4 methylation  (IEA,ISO)
positive regulation of histone H3-K9 acetylation  (IEA,ISO)
positive regulation of luteinizing hormone secretion  (IEA,ISO)
positive regulation of pathway-restricted SMAD protein phosphorylation  (IEA,ISO)
positive regulation of pri-miRNA transcription by RNA polymerase II  (IEA,ISO)
positive regulation of SMAD protein signal transduction  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of transforming growth factor beta receptor signaling pathway  (IEA,ISO)
regulation of binding  (IEA,ISO)
regulation of cell population proliferation  (ISO)
regulation of hair follicle development  (IEA,ISO)
regulation of transcription by RNA polymerase II  (ISO)
regulation of transcription, DNA-templated  (IEA)
regulation of transforming growth factor beta receptor signaling pathway  (ISO)
regulation of transforming growth factor beta2 production  (IEA,ISO)
response to hypoxia  (IEA,ISO)
response to transforming growth factor beta  (ISO)
sebaceous gland development  (IEA,ISO)
secondary palate development  (IEA,ISO)
seminiferous tubule development  (IEA,ISO)
single fertilization  (IEA,ISO)
SMAD protein complex assembly  (IEA,ISO)
SMAD protein signal transduction  (IBA,IEA,ISO)
somite rostral/caudal axis specification  (IEA,ISO)
spermatogenesis  (IEA,ISO)
tissue morphogenesis  (ISO)
transcription, DNA-templated  (IEA,ISO)
transforming growth factor beta receptor signaling pathway  (IBA,IEA,ISO)
uterus development  (IEA,ISO)
ventricular septum morphogenesis  (IEA,ISO)
wound healing  (IEP,IMP)

Cellular Component

References

References - curated
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Additional References at PubMed
PMID:8774881   PMID:9111321   PMID:9256479   PMID:9288972   PMID:9311995   PMID:9389648   PMID:9420335   PMID:9506519   PMID:9702197   PMID:9707553   PMID:9732876   PMID:10626800  
PMID:10647180   PMID:10670756   PMID:10708962   PMID:10823886   PMID:11197776   PMID:11809702   PMID:12161428   PMID:12270938   PMID:12374795   PMID:12411310   PMID:12943993   PMID:14559231  
PMID:14633973   PMID:14691138   PMID:14764653   PMID:15215210   PMID:15282343   PMID:15342483   PMID:15344310   PMID:15459107   PMID:15657445   PMID:15925496   PMID:16007207   PMID:16151019  
PMID:16330325   PMID:16556916   PMID:16777850   PMID:17159989   PMID:17438144   PMID:17568773   PMID:17628518   PMID:17698011   PMID:18212064   PMID:18539898   PMID:18692037   PMID:18832382  
PMID:18986983   PMID:19251704   PMID:19328798   PMID:19366691   PMID:19366699   PMID:19415695   PMID:19793887   PMID:19796622   PMID:20926379   PMID:21300867   PMID:21330551   PMID:21724602  
PMID:21828274   PMID:21988832   PMID:22316667   PMID:22506032   PMID:22507670   PMID:22735812   PMID:23034633   PMID:23426367   PMID:24739304   PMID:24866243   PMID:24971350   PMID:25178280  
PMID:25514493   PMID:25609649   PMID:26494787   PMID:26699655   PMID:28791348   PMID:29183317   PMID:29199336   PMID:31346987   PMID:31582430  


Genomics

Comparative Map Data
Smad4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21867,243,742 - 67,274,438 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1867,243,742 - 67,274,438 (-)Ensembl
Rnor_6.01869,626,682 - 69,657,373 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1869,627,757 - 69,671,199 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01868,773,326 - 68,802,354 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41870,432,705 - 70,461,541 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11870,504,785 - 70,534,814 (-)NCBI
Celera1865,246,042 - 65,276,480 (-)NCBICelera
Cytogenetic Map18q12.2NCBI
SMAD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1851,028,394 - 51,085,045 (+)EnsemblGRCh38hg38GRCh38
GRCh381851,030,213 - 51,085,042 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371848,556,583 - 48,611,412 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361846,810,611 - 46,860,145 (+)NCBINCBI36hg18NCBI36
Build 341846,810,610 - 46,860,144NCBI
Celera1845,413,367 - 45,468,195 (+)NCBI
Cytogenetic Map18q21.2NCBI
HuRef1845,411,927 - 45,466,923 (+)NCBIHuRef
CHM1_11848,551,997 - 48,606,836 (+)NCBICHM1_1
Smad4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391873,767,861 - 73,836,862 (-)NCBIGRCm39mm39
GRCm39 Ensembl1873,772,080 - 73,836,851 (-)Ensembl
GRCm381873,634,790 - 73,703,791 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1873,639,009 - 73,703,780 (-)EnsemblGRCm38mm10GRCm38
MGSCv371873,798,667 - 73,863,395 (-)NCBIGRCm37mm9NCBIm37
MGSCv361873,764,382 - 73,829,110 (-)NCBImm8
Celera1874,884,056 - 74,923,073 (-)NCBICelera
Cytogenetic Map18E2NCBI
cM Map1849.51NCBI
Smad4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540235,961,165 - 35,994,538 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540235,956,080 - 36,001,746 (+)NCBIChiLan1.0ChiLan1.0
SMAD4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11847,692,311 - 47,802,530 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1847,764,568 - 47,797,359 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01844,402,112 - 44,456,779 (+)NCBIMhudiblu_PPA_v0panPan3
SMAD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1123,875,989 - 23,930,027 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl123,882,139 - 23,969,405 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha124,868,005 - 24,956,178 (-)NCBI
ROS_Cfam_1.0123,767,402 - 23,821,366 (-)NCBI
UMICH_Zoey_3.1123,833,038 - 23,921,205 (-)NCBI
UNSW_CanFamBas_1.0123,719,264 - 23,807,404 (-)NCBI
UU_Cfam_GSD_1.0123,987,158 - 24,041,139 (-)NCBI
Smad4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494437,008,523 - 37,038,961 (-)NCBI
SpeTri2.0NW_00493649712,242,869 - 12,278,012 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMAD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1100,514,791 - 100,628,029 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11100,521,843 - 100,633,501 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21110,456,997 - 110,568,659 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMAD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11829,894,157 - 29,951,445 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1829,897,621 - 29,934,478 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660504,018,900 - 4,079,370 (-)NCBIVero_WHO_p1.0
Smad4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477814,570,025 - 14,629,950 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
PMC86557P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21867,260,537 - 67,260,816 (+)MAPPERmRatBN7.2
Rnor_6.01869,643,478 - 69,643,756NCBIRnor6.0
Rnor_5.01868,788,748 - 68,789,026UniSTSRnor5.0
RGSC_v3.41870,448,115 - 70,448,393UniSTSRGSC3.4
Celera1865,262,730 - 65,263,008UniSTS
Cytogenetic Map18q12.3UniSTS
D18Wsu70e  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21867,243,804 - 67,244,056 (+)MAPPERmRatBN7.2
Rnor_6.01869,626,745 - 69,626,996NCBIRnor6.0
Rnor_5.01868,772,247 - 68,772,498UniSTSRnor5.0
RGSC_v3.41870,431,626 - 70,431,877UniSTSRGSC3.4
Celera1865,246,105 - 65,246,356UniSTS
Cytogenetic Map18q12.3UniSTS
RH129873  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21867,243,837 - 67,244,052 (+)MAPPERmRatBN7.2
Rnor_6.01869,626,778 - 69,626,992NCBIRnor6.0
Rnor_5.01868,772,280 - 68,772,494UniSTSRnor5.0
RGSC_v3.41870,431,659 - 70,431,873UniSTSRGSC3.4
Celera1865,246,138 - 65,246,352UniSTS
Cytogenetic Map18q12.3UniSTS
RH143443  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X24,734,938 - 24,735,040 (+)MAPPERmRatBN7.2
mRatBN7.21867,244,710 - 67,244,812 (+)MAPPERmRatBN7.2
Rnor_6.01869,627,651 - 69,627,752NCBIRnor6.0
Rnor_6.0X26,090,613 - 26,090,714NCBIRnor6.0
Rnor_5.01868,773,153 - 68,773,254UniSTSRnor5.0
Rnor_5.0X26,494,877 - 26,494,978UniSTSRnor5.0
RGSC_v3.4X45,395,750 - 45,395,851UniSTSRGSC3.4
RGSC_v3.41870,432,532 - 70,432,633UniSTSRGSC3.4
Celera1865,247,011 - 65,247,112UniSTS
CeleraX25,153,772 - 25,153,873UniSTS
Cytogenetic Map18q12.3UniSTS
PMC324399P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21867,244,543 - 67,245,043 (+)MAPPERmRatBN7.2
Rnor_6.01869,627,484 - 69,627,983NCBIRnor6.0
Rnor_5.01868,772,986 - 68,773,485UniSTSRnor5.0
RGSC_v3.41870,432,365 - 70,432,864UniSTSRGSC3.4
Celera1865,246,844 - 65,247,343UniSTS
Cytogenetic Map18q12.3UniSTS
AF010230  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21867,251,904 - 67,252,073 (+)MAPPERmRatBN7.2
Rnor_6.01869,634,845 - 69,635,013NCBIRnor6.0
Rnor_5.01868,780,115 - 68,780,283UniSTSRnor5.0
RGSC_v3.41870,439,482 - 70,439,650UniSTSRGSC3.4
Celera1865,254,097 - 65,254,265UniSTS
Cytogenetic Map18q12.3UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181179151883218561Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181179151883218561Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181927890183218561Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182479697779788953Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182557098570570985Rat
2293704Bss35Bone structure and strength QTL 354.590.0002femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)182896485373964853Rat
2300157Bmd66Bone mineral density QTL 6613.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)182896485373964853Rat
2300177Bmd65Bone mineral density QTL 6519.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)182896485373964853Rat
9589816Gluco68Glucose level QTL 687.250.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)182979296574792965Rat
8694378Bw157Body weight QTL 1573.590.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)182979296574792965Rat
9590318Scort22Serum corticosterone level QTL 227.640.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)182979296574792965Rat
1331754Bp230Blood pressure QTL 2304.61609arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182979296574792965Rat
738005Anxrr11Anxiety related response QTL 113.4exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)183003981375039813Rat
61429Cia17Collagen induced arthritis QTL 174.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)183135940870263868Rat
2303120Mamtr8Mammary tumor resistance QTL 80.001mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)183135940883218561Rat
631274Sprol1Serum protein level QTL 15.3blood total protein amount (VT:0005567)serum total protein level (CMO:0000661)183139332077209694Rat
631518Bw11Body weight QTL 112.8body mass (VT:0001259)body weight (CMO:0000012)183587072380870723Rat
61367Iddm4Insulin dependent diabetes mellitus QTL 42.330.0074blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)183819245583192455Rat
1598826Anxrr20Anxiety related response QTL 203.04body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)184143297183828827Rat
6893683Bw110Body weight QTL 1102.70.002body mass (VT:0001259)body weight (CMO:0000012)184334502283828827Rat
8694366Abfw8Abdominal fat weight QTL 86.380.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)184664067583828827Rat
8694432Bw165Body weight QTL 1653.810.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)184664067583828827Rat
9589041Epfw12Epididymal fat weight QTL 1217.080.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)184664067583828827Rat
2303571Bw92Body weight QTL 923body mass (VT:0001259)body weight (CMO:0000012)184852004483828827Rat
2303584Gluco55Glucose level QTL 552blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)184852004483828827Rat
738008Hcar14Hepatocarcinoma resistance QTL 144.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion number (CMO:0001462)185146473383218561Rat
1359020Ppulsi2Prepulse inhibition QTL 22.71prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)185229287573997283Rat
631509Sald2Serum aldosterone level QTL 22.9blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)185253976369140759Rat
12880368Bw187Body weight QTL 1870.045body mass (VT:0001259)body weight (CMO:0000012)185253976376104388Rat
12904067Cm122Cardiac mass QTL 1220.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)185253976376104388Rat
12904069Cm123Cardiac mass QTL 1230.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)185253976376104388Rat
12904070Cm124Cardiac mass QTL 1240.01heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)185253976376104388Rat
12904071Am18Aortic mass QTL 180.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)185253976376104388Rat
12904073Kidm71Kidney mass QTL 710.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)185253976376104388Rat
2301417Bp319Blood pressure QTL 3190.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)185253976376104388Rat
1298072Cia26Collagen induced arthritis QTL 263.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)185470976983828827Rat
724542Kidm2Kidney mass QTL 22.6kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)185917211583828827Rat
2312600Bp341Blood pressure QTL 3410.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185933040970263868Rat
2301969Bp324Blood pressure QTL 3244.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185971241776477814Rat
70185BpQTLcluster15Blood pressure QTL cluster 154.61arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185971241776477814Rat
70185BpQTLcluster15Blood pressure QTL cluster 154.61arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)185971241776477814Rat
70185BpQTLcluster15Blood pressure QTL cluster 154.61arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)185971241776477814Rat
70185BpQTLcluster15Blood pressure QTL cluster 154.61arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)185971241776477814Rat
1331770Bp234Blood pressure QTL 2343.807arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)185979647871893566Rat
6903353Bp353Blood pressure QTL 3532.8arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)185979647883828827Rat
6903356Bp354Blood pressure QTL 3544.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)185979647883828827Rat
61384Bp48Blood pressure QTL 4819.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)186062231177209844Rat
631675Iddm15Insulin dependent diabetes mellitus QTL 15urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)186062231177209844Rat

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir146arno-miR-146a-5pMirtarbaseexternal_infoqRT-PCR//Western blotFunctional MTI22735812
Mir29arno-miR-29a-3pMirtarbaseexternal_infoLuciferase reporter assay//Microarray//Northern blFunctional MTI22506032

Predicted Target Of
Summary Value
Count of predictions:120
Count of miRNA genes:104
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000021113
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 57 41 19 41 8 11 74 35 39 11 8
Low 1 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000082484   ⟹   ENSRNOP00000074882
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1867,243,742 - 67,274,438 (-)Ensembl
Rnor_6.0 Ensembl1869,627,757 - 69,671,199 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090198   ⟹   ENSRNOP00000070425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1867,245,016 - 67,274,438 (-)Ensembl
Rnor_6.0 Ensembl1869,627,824 - 69,657,301 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103096   ⟹   ENSRNOP00000079042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1867,243,742 - 67,274,438 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000116718   ⟹   ENSRNOP00000091850
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1867,244,625 - 67,274,438 (-)Ensembl
RefSeq Acc Id: NM_019275   ⟹   NP_062148
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21867,243,742 - 67,274,438 (-)NCBI
Rnor_6.01869,626,682 - 69,657,373 (-)NCBI
Rnor_5.01868,773,326 - 68,802,354 (-)NCBI
RGSC_v3.41870,432,705 - 70,461,541 (-)RGD
Celera1865,246,042 - 65,276,480 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062148   ⟸   NM_019275
- UniProtKB: O70437 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070425   ⟸   ENSRNOT00000090198
RefSeq Acc Id: ENSRNOP00000074882   ⟸   ENSRNOT00000082484
RefSeq Acc Id: ENSRNOP00000079042   ⟸   ENSRNOT00000103096
RefSeq Acc Id: ENSRNOP00000091850   ⟸   ENSRNOT00000116718
Protein Domains
MH1   MH2

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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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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