Pde4dip (phosphodiesterase 4D interacting protein) - Rat Genome Database

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Gene: Pde4dip (phosphodiesterase 4D interacting protein) Rattus norvegicus
Analyze
Symbol: Pde4dip
Name: phosphodiesterase 4D interacting protein
RGD ID: 708410
Description: Enables enzyme binding activity. Involved in cellular protein-containing complex assembly. Located in Golgi apparatus; centrosome; and myofibril. Orthologous to human PDE4DIP (phosphodiesterase 4D interacting protein); INTERACTS WITH 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC64183; myomegalin; phosphodiesterase 4D interacting protein (myomegalin); phosphodiesterase 4D-interacting protein; phosphodiesterase-binding protein clone 46
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22185,293,236 - 185,490,100 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2185,293,214 - 185,468,379 (-)Ensembl
Rnor_6.02199,867,965 - 200,066,034 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2199,867,972 - 200,003,443 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02219,345,687 - 219,479,200 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42192,534,747 - 192,671,053 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12192,497,500 - 192,633,807 (-)NCBI
Celera2177,786,301 - 177,918,988 (-)NCBICelera
Cytogenetic Map2q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
7,12-dimethyltetraphene  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arachidonic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
choline  (ISO)
clofibrate  (ISO)
clothianidin  (ISO)
cobalt dichloride  (EXP)
cocaine  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
folic acid  (ISO)
geldanamycin  (ISO)
genistein  (ISO)
gentamycin  (EXP)
heroin  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methamphetamine  (ISO)
methyl methanesulfonate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
ochratoxin A  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
pentanal  (ISO)
permethrin  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
progesterone  (EXP)
propanal  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
triacsin C  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc protoporphyrin  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:11374908   PMID:21399614   PMID:21569246   PMID:24625528   PMID:27666745   PMID:29162697  


Genomics

Comparative Map Data
Pde4dip
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22185,293,236 - 185,490,100 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2185,293,214 - 185,468,379 (-)Ensembl
Rnor_6.02199,867,965 - 200,066,034 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2199,867,972 - 200,003,443 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02219,345,687 - 219,479,200 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42192,534,747 - 192,671,053 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12192,497,500 - 192,633,807 (-)NCBI
Celera2177,786,301 - 177,918,988 (-)NCBICelera
Cytogenetic Map2q34NCBI
PDE4DIP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1148,808,181 - 149,048,286 (+)EnsemblGRCh38hg38GRCh38
GRCh381148,808,198 - 149,051,277 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371144,851,424 - 145,076,025 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361143,562,784 - 143,787,436 (-)NCBINCBI36hg18NCBI36
Build 341142,440,804 - 142,565,067NCBI
Celera1121,506,245 - 121,526,690 (+)NCBI
Cytogenetic Map1q21.2NCBI
HuRef1119,165,611 - 119,191,824 (-)ENTREZGENEHuRef
HuRef1119,290,177 - 119,290,733 (-)NCBIHuRef
HuRef1119,142,103 - 119,150,668 (-)NCBIHuRef
HuRef1119,153,319 - 119,162,328 (-)NCBIHuRef
HuRef1119,196,278 - 119,206,613 (-)NCBIHuRef
HuRef1119,235,190 - 119,235,681 (-)NCBIHuRef
HuRef1119,268,039 - 119,268,444 (-)NCBIHuRef
CHM1_11150,176,307 - 150,401,145 (+)NCBICHM1_1
Pde4dip
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39397,597,144 - 97,796,023 (-)NCBIGRCm39mm39
GRCm39 Ensembl397,597,140 - 97,796,023 (-)Ensembl
GRCm38397,689,828 - 97,888,707 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl397,689,824 - 97,888,707 (-)EnsemblGRCm38mm10GRCm38
MGSCv37397,493,751 - 97,692,630 (-)NCBIGRCm37mm9NCBIm37
MGSCv36397,775,233 - 97,974,112 (-)NCBImm8
Celera399,089,670 - 99,287,699 (-)NCBICelera
Cytogenetic Map3F2.2NCBI
cM Map342.28NCBI
Pde4dip
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555681,322,470 - 1,546,256 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555681,321,053 - 1,546,351 (-)NCBIChiLan1.0ChiLan1.0
LOC100977296
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11113,064,912 - 113,084,501 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01122,445,609 - 122,452,842 (-)NCBIMhudiblu_PPA_v0panPan3
PDE4DIPP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11757,135,716 - 57,359,348 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1757,135,308 - 57,358,978 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1756,773,133 - 56,996,596 (+)NCBI
ROS_Cfam_1.01758,127,352 - 58,351,715 (+)NCBI
UMICH_Zoey_3.11757,038,235 - 57,262,228 (+)NCBI
UNSW_CanFamBas_1.01757,074,929 - 57,298,766 (+)NCBI
UU_Cfam_GSD_1.01757,722,757 - 57,947,007 (+)NCBI
LOC100624559
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4100,646,938 - 100,863,250 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14100,646,939 - 100,863,353 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LOC103247253
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366603814,282,358 - 14,312,135 (-)NCBIVero_WHO_p1.0

Position Markers
D13Rat53  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22185,302,209 - 185,302,393 (+)MAPPERmRatBN7.2
Rnor_6.02199,876,939 - 199,877,122NCBIRnor6.0
Rnor_5.02219,353,683 - 219,353,866UniSTSRnor5.0
RGSC_v3.42192,542,742 - 192,542,925RGDRGSC3.4
RGSC_v3.42192,542,743 - 192,542,926UniSTSRGSC3.4
RGSC_v3.12192,505,496 - 192,505,679RGD
Celera2177,794,297 - 177,794,480UniSTS
RH 3.4 Map21255.3UniSTS
RH 3.4 Map21255.3RGD
RH 2.0 Map2947.4RGD
SHRSP x BN Map132.2799RGD
FHH x ACI Map134.92RGD
Cytogenetic Map2q34UniSTS
BE112181  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22185,332,836 - 185,333,008 (+)MAPPERmRatBN7.2
Rnor_6.02199,907,821 - 199,907,992NCBIRnor6.0
Rnor_5.02219,384,031 - 219,384,202UniSTSRnor5.0
RGSC_v3.42192,573,845 - 192,574,016UniSTSRGSC3.4
Celera2177,824,215 - 177,824,386UniSTS
RH 3.4 Map21255.3UniSTS
Cytogenetic Map2q34UniSTS
RH138621  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22185,343,133 - 185,343,287 (+)MAPPERmRatBN7.2
Rnor_6.02199,918,118 - 199,918,271NCBIRnor6.0
Rnor_5.02219,394,328 - 219,394,481UniSTSRnor5.0
RGSC_v3.42192,584,142 - 192,584,295UniSTSRGSC3.4
Celera2177,834,511 - 177,834,664UniSTS
RH 3.4 Map21255.3UniSTS
Cytogenetic Map2q34UniSTS
RH127540  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22185,293,277 - 185,293,470 (+)MAPPERmRatBN7.2
Rnor_6.02199,868,007 - 199,868,199NCBIRnor6.0
Rnor_5.02219,344,751 - 219,344,943UniSTSRnor5.0
RGSC_v3.42192,533,811 - 192,534,003UniSTSRGSC3.4
Celera2177,785,365 - 177,785,557UniSTS
RH 3.4 Map21255.4UniSTS
Cytogenetic Map2q34UniSTS
RH129474  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22185,341,949 - 185,342,129 (+)MAPPERmRatBN7.2
Rnor_6.02199,916,934 - 199,917,113NCBIRnor6.0
Rnor_5.02219,393,144 - 219,393,323UniSTSRnor5.0
RGSC_v3.42192,582,958 - 192,583,137UniSTSRGSC3.4
Celera2177,833,328 - 177,833,507UniSTS
RH 3.4 Map21255.3UniSTS
Cytogenetic Map2q34UniSTS
RH135416  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22185,349,723 - 185,350,818 (+)MAPPERmRatBN7.2
Rnor_6.02199,924,708 - 199,925,802NCBIRnor6.0
Rnor_5.02219,400,918 - 219,402,012UniSTSRnor5.0
RGSC_v3.42192,590,732 - 192,591,826UniSTSRGSC3.4
Celera2177,841,101 - 177,842,195UniSTS
RH 3.4 Map21255.3UniSTS
Cytogenetic Map2q34UniSTS
RH141783  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22185,368,647 - 185,368,852 (+)MAPPERmRatBN7.2
Rnor_6.02199,943,555 - 199,943,759NCBIRnor6.0
Rnor_5.02219,419,765 - 219,419,969UniSTSRnor5.0
RGSC_v3.42192,611,268 - 192,611,472UniSTSRGSC3.4
Celera2177,859,877 - 177,860,081UniSTS
RH 3.4 Map21254.2UniSTS
Cytogenetic Map2q34UniSTS
BF420231  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22185,317,848 - 185,317,945 (+)MAPPERmRatBN7.2
Rnor_6.02199,892,578 - 199,892,674NCBIRnor6.0
Rnor_5.02219,369,322 - 219,369,418UniSTSRnor5.0
RGSC_v3.42192,558,382 - 192,558,478UniSTSRGSC3.4
Celera2177,809,942 - 177,810,038UniSTS
RH 3.4 Map21254.0UniSTS
Cytogenetic Map2q34UniSTS
MARC_23709-23710:1030738086:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22185,354,838 - 185,356,037 (+)MAPPERmRatBN7.2
Rnor_6.02199,929,821 - 199,931,019NCBIRnor6.0
Rnor_5.02219,406,031 - 219,407,229UniSTSRnor5.0
RGSC_v3.42192,595,845 - 192,597,043UniSTSRGSC3.4
Celera2177,846,216 - 177,847,414UniSTS
Cytogenetic Map2q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150341585189039377Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2136916935189599348Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2184165752229165752Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2157142209202446871Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147798556192798556Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2157142078192625452Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2174930955213594495Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2144599348189599348Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
4889834Pur24Proteinuria QTL 245.80.014total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2184114274202447032Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
7488929Bp366Blood pressure QTL 3660.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2184974550193094998Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2143657411190602963Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2143657411190602963Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:83
Count of miRNA genes:78
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000024900
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 43 20 12 18 12 8 11 64 27 17 9 8
Low 3 37 29 1 29 10 8 24 2
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001389233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001389234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001389235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_022382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591070 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591080 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591082 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591084 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103041 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103044 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103047 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001836491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001836492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC121381 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF139185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000024900   ⟹   ENSRNOP00000024900
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2185,295,721 - 185,428,064 (-)Ensembl
Rnor_6.0 Ensembl2199,868,943 - 200,003,443 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087026   ⟹   ENSRNOP00000072921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2185,294,113 - 185,396,912 (-)Ensembl
Rnor_6.0 Ensembl2199,867,972 - 199,971,965 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088041   ⟹   ENSRNOP00000069762
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2185,293,237 - 185,468,379 (-)Ensembl
Rnor_6.0 Ensembl2199,868,943 - 200,003,443 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100009   ⟹   ENSRNOP00000078787
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2185,293,214 - 185,370,905 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118806   ⟹   ENSRNOP00000095141
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2185,293,214 - 185,370,905 (-)Ensembl
RefSeq Acc Id: NM_001389233   ⟹   NP_001376162
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,489,729 (-)NCBI
RefSeq Acc Id: NM_001389234   ⟹   NP_001376163
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,489,729 (-)NCBI
RefSeq Acc Id: NM_001389235   ⟹   NP_001376164
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,243 - 185,489,729 (-)NCBI
RefSeq Acc Id: NM_022382   ⟹   NP_071777
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,428,072 (-)NCBI
Rnor_6.02199,868,943 - 200,003,443 (-)NCBI
Rnor_5.02219,345,687 - 219,479,200 (-)NCBI
RGSC_v3.42192,534,747 - 192,671,053 (-)RGD
Celera2177,786,301 - 177,918,988 (-)RGD
Sequence:
RefSeq Acc Id: XM_017591069   ⟹   XP_017446558
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,083 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591070   ⟹   XP_017446559
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,084 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591071   ⟹   XP_017446560
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,082 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591072   ⟹   XP_017446561
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,083 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591073   ⟹   XP_017446562
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,371,182 (-)NCBI
Rnor_6.02199,867,965 - 199,946,053 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591074   ⟹   XP_017446563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,083 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591075   ⟹   XP_017446564
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,083 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591077   ⟹   XP_017446566
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,085 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591078   ⟹   XP_017446567
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,084 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591079   ⟹   XP_017446568
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,083 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591080   ⟹   XP_017446569
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,085 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591081   ⟹   XP_017446570
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,468,666 (-)NCBI
Rnor_6.02199,867,965 - 200,044,185 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039103040   ⟹   XP_038958968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,084 (-)NCBI
RefSeq Acc Id: XM_039103041   ⟹   XP_038958969
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,294,214 - 185,370,777 (-)NCBI
RefSeq Acc Id: XM_039103042   ⟹   XP_038958970
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,085 (-)NCBI
RefSeq Acc Id: XM_039103043   ⟹   XP_038958971
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,426,308 (-)NCBI
RefSeq Acc Id: XM_039103044   ⟹   XP_038958972
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,468,389 (-)NCBI
RefSeq Acc Id: XM_039103045   ⟹   XP_038958973
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,428,073 (-)NCBI
RefSeq Acc Id: XM_039103046   ⟹   XP_038958974
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,332,515 - 185,490,100 (-)NCBI
RefSeq Acc Id: XM_039103047   ⟹   XP_038958975
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,344,326 - 185,370,777 (-)NCBI
RefSeq Acc Id: XR_001836491
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,083 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001836492
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22185,293,236 - 185,490,082 (-)NCBI
Rnor_6.02199,867,965 - 200,066,034 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001376162 (Get FASTA)   NCBI Sequence Viewer  
  NP_001376163 (Get FASTA)   NCBI Sequence Viewer  
  NP_001376164 (Get FASTA)   NCBI Sequence Viewer  
  NP_071777 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446558 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446559 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446560 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446561 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446562 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446563 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446564 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446566 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446567 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446568 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446569 (Get FASTA)   NCBI Sequence Viewer  
  XP_017446570 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958968 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958969 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958970 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958971 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958972 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958973 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958974 (Get FASTA)   NCBI Sequence Viewer  
  XP_038958975 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD29427 (Get FASTA)   NCBI Sequence Viewer  
  Q9WUJ3 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_071777   ⟸   NM_022382
- Peptide Label: isoform 1
- Sequence:
RefSeq Acc Id: XP_017446568   ⟸   XM_017591079
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_017446564   ⟸   XM_017591075
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017446567   ⟸   XM_017591078
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017446561   ⟸   XM_017591072
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017446560   ⟸   XM_017591071
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017446569   ⟸   XM_017591080
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017446566   ⟸   XM_017591077
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017446563   ⟸   XM_017591074
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017446559   ⟸   XM_017591070
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017446558   ⟸   XM_017591069
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446570   ⟸   XM_017591081
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_017446562   ⟸   XM_017591073
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000072921   ⟸   ENSRNOT00000087026
RefSeq Acc Id: ENSRNOP00000024900   ⟸   ENSRNOT00000024900
RefSeq Acc Id: ENSRNOP00000069762   ⟸   ENSRNOT00000088041
RefSeq Acc Id: XP_038958970   ⟸   XM_039103042
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038958968   ⟸   XM_039103040
- Peptide Label: isoform X9
RefSeq Acc Id: NP_001376162   ⟸   NM_001389233
- Peptide Label: isoform 2
RefSeq Acc Id: NP_001376163   ⟸   NM_001389234
- Peptide Label: isoform 3
RefSeq Acc Id: XP_038958972   ⟸   XM_039103044
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038958973   ⟸   XM_039103045
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038958971   ⟸   XM_039103043
- Peptide Label: isoform X16
RefSeq Acc Id: NP_001376164   ⟸   NM_001389235
- Peptide Label: isoform 4
RefSeq Acc Id: XP_038958969   ⟸   XM_039103041
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038958974   ⟸   XM_039103046
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038958975   ⟸   XM_039103047
- Peptide Label: isoform X19
RefSeq Acc Id: ENSRNOP00000078787   ⟸   ENSRNOT00000100009
RefSeq Acc Id: ENSRNOP00000095141   ⟸   ENSRNOT00000118806
Protein Domains
Olduvai

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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 185298095 185298096 C T snv F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), M520/N (2020), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), M520/NRrrcMcwi (2019), LEXF1C/Stm (2019)
2 185299123 185299124 C T snv F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), M520/NRrrcMcwi (2019), M520/N (2020)
2 185300839 185300840 A C snv GK/FarMcwi (2019), LL/MavRrrcAek (2020), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), BXH2/CubMcwi (2020), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LEXF1C/Stm (2019), FXLE16/Stm (2020), WKY/N (2020), M520/NRrrcMcwi (2019), M520/N (2020), SHRSP/A3NCrl (2019), HXB4/IpcvMcwi (2020), HXB20/IpcvMcwi (2020), HXB10/IpcvMcwi (2019), WKY/NCrl (2019), SR/JrHsd (2020), SHR/OlalpcvMcwi (2019)
2 185307959 185307960 T G snv SR/JrHsd (2020), LL/MavRrrcAek (2020)
2 185316943 185316944 C T snv WKY/N (2020), WKY/NCrl (2019), GK/FarMcwi (2019)
2 185346738 185346739 A C snv M520/N (2020), M520/NRrrcMcwi (2019), LEXF4/Stm (2020), LEXF3/Stm (2020), LEXF1C/Stm (2019), FXLE16/Stm (2020), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), LEXF2B/Stm (2019)
2 185370521 185370522 T C snv F344/DuCrl (2019)
2 185393230 185393231 T C snv SR/JrHsd (2020), LL/MavRrrcAek (2020)
2 185393500 185393501 G A snv LEXF3/Stm (2020), LEXF1C/Stm (2019), FXLE16/Stm (2020), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), LEXF4/Stm (2020), M520/NRrrcMcwi (2019), M520/N (2020), LEXF2B/Stm (2019)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 199870878 199870879 G T snv BBDP/Wor (RGD)
2 199872824 199872825 C T snv F344/NCrl (RGD), MHS/Gib (RGD), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), M520/NRrrcMcwi (2019), M520/N (2020), F344/NRrrc (MCW), M520/N (MCW)
2 199873852 199873853 C T snv F344/NRrrc (MCW), M520/N (2020), F344/NCrl (RGD), MHS/Gib (RGD), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), M520/NRrrcMcwi (2019), M520/N (MCW)
2 199875568 199875569 A C snv LL/MavRrrcAek (2020), M520/NRrrcMcwi (2019), M520/N (2020), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), SR/JrHsd (2020), WKY/NCrl (2019), WKY/N (2020), CDR, CDS, SBH/Ygl (MCW), SR/JrHsd (MCW), F344/NRrrc (MCW), M520/N (MCW), WKY/N (MCW), BBDP/Wor (RGD), F344/NCrl (RGD), GK/Ox (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), SBH/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), BXH2/CubMcwi (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB4/IpcvMcwi (2020), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020)
2 199882688 199882689 T G snv SR/JrHsd (MCW), LL/MavRrrc (RGD), SR/JrHsd (2020), LL/MavRrrcAek (2020), SR/JrHsd (RGD)
2 199891672 199891673 C T snv CDR, CDS, SBH/Ygl (MCW), WKY/N (MCW), GK/Ox (RGD), SBH/Ygl (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), GK/FarMcwi (2019), WKY/NCrl (2019), WKY/N (2020)
2 199921722 199921723 A C snv M520/NRrrcMcwi (2019), LEXF1C/Stm (2019), LEXF3/Stm (2020), LEXF2B/Stm (2019), M520/N (2020), LEXF4/Stm (2020), GH/OmrMcwi (MCW), F344/NRrrc (MCW), F344/NCrl (RGD), MHS/Gib (RGD), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020)
2 199945427 199945428 T C snv F344/DuCrl (2019)
2 199968088 199968089 T C snv SR/JrHsd (2020), LL/MavRrrcAek (2020), SR/JrHsd (RGD), SR/JrHsd (MCW), LL/MavRrrc (RGD)
2 199968358 199968359 G A snv GH/OmrMcwi (MCW), M520/N (2020), M520/N (MCW), F344/NCrl (RGD), MHS/Gib (RGD), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), M520/NRrrcMcwi (2019), F344/NRrrc (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:708410 AgrOrtholog
Ensembl Genes ENSRNOG00000018220 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024900 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069762 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072921 UniProtKB/TrEMBL
  ENSRNOP00000095141 ENTREZGENE
Ensembl Transcript ENSRNOT00000024900 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000087026 UniProtKB/TrEMBL
  ENSRNOT00000088041 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000118806 ENTREZGENE
InterPro Cnn_1N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Olduvai_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64183 UniProtKB/Swiss-Prot
NCBI Gene 64183 ENTREZGENE
Pfam Cnn_1N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Olduvai UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pde4dip PhenoGen
PROSITE NBPF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DUF1220 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JW66_RAT UniProtKB/TrEMBL
  A0A0G2K463_RAT UniProtKB/TrEMBL
  F1M7R5_RAT UniProtKB/TrEMBL
  MYOME_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-08-29 Pde4dip  phosphodiesterase 4D interacting protein  Pde4dip  phosphodiesterase 4D interacting protein (myomegalin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Pde4dip  phosphodiesterase 4D interacting protein (myomegalin)  LOC64183  myomegalin  Symbol and Name updated 1299863 APPROVED