Prkd1 (protein kinase D1) - Rat Genome Database

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Gene: Prkd1 (protein kinase D1) Rattus norvegicus
Analyze
Symbol: Prkd1
Name: protein kinase D1
RGD ID: 620964
Description: Enables protein serine/threonine kinase activity. Involved in intracellular signal transduction. Predicted to be located in several cellular components, including autophagosome membrane; cell-cell junction; and trans-Golgi network. Orthologous to human PRKD1 (protein kinase D1); PARTICIPATES IN insulin-like growth factor signaling pathway; INTERACTS WITH 2,3',4,4',5-Pentachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: nPKC-D1; nPKC-mu; Pkcm; Prkcm; protein kinase C mu type; protein kinase C, mu; protein kinase D; serine/threonine-protein kinase D1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2667,725,193 - 68,039,002 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl667,725,905 - 68,039,042 (-)Ensembl
Rnor_6.0671,035,017 - 71,349,531 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl671,035,332 - 71,349,249 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0680,600,725 - 80,914,319 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4670,364,135 - 70,682,006 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1670,393,721 - 70,394,895 (-)NCBI
Celera666,643,414 - 66,954,727 (-)NCBICelera
Cytogenetic Map6q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2-methoxyethanol  (EXP)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol F  (ISO)
butanal  (ISO)
calcitriol  (ISO)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
capsaicin  (EXP,ISO)
chlorpyrifos  (EXP)
cisplatin  (ISO)
dapsone  (ISO)
DDT  (EXP)
dibutylstannane  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
fenvalerate  (EXP)
Goe 6976  (ISO)
Ingenol 3,20-dibenzoate  (ISO)
malathion  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methapyrilene  (ISO)
methoxyacetic acid  (EXP)
methylmercury chloride  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenylephrine  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
resveratrol  (EXP,ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
tributylstannane  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
angiogenesis  (IEA)
apoptotic process  (IEA)
cell differentiation  (IEA)
cellular response to amino acid starvation  (ISO)
cellular response to hydroperoxide  (ISO)
cellular response to oxidative stress  (ISO,ISS)
cellular response to vascular endothelial growth factor stimulus  (ISO,ISS)
defense response to Gram-negative bacterium  (ISO)
Golgi organization  (ISO,ISS)
Golgi vesicle transport  (ISO,ISS)
inflammatory response  (IEA)
innate immune response  (IEA)
intracellular signal transduction  (IDA,IEA,ISO)
negative regulation of cell death  (ISO,ISS)
nervous system development  (IEA)
peptidyl-serine phosphorylation  (ISO)
peptidyl-threonine phosphorylation  (ISO)
positive regulation of angiogenesis  (ISO,ISS)
positive regulation of autophagy  (ISO)
positive regulation of blood vessel endothelial cell migration  (ISO)
positive regulation of CREB transcription factor activity  (ISO)
positive regulation of endothelial cell chemotaxis  (ISO)
positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway  (ISO)
positive regulation of endothelial cell migration  (ISO,ISS)
positive regulation of endothelial cell proliferation  (ISO)
positive regulation of histone deacetylase activity  (ISO)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (ISO,ISS)
positive regulation of neuron projection development  (ISO,ISS)
positive regulation of NF-kappaB transcription factor activity  (ISO,ISS)
positive regulation of osteoblast differentiation  (ISO,ISS)
positive regulation of peptidyl-serine phosphorylation  (ISO)
positive regulation of protein import into nucleus  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
protein autophosphorylation  (ISO,ISS)
protein kinase D signaling  (IBA,ISO)
protein phosphorylation  (IEA,ISO)
Ras protein signal transduction  (ISO,ISS)
regulation of keratinocyte proliferation  (ISO,ISS)
regulation of protein stability  (ISO,ISS)
regulation of release of sequestered calcium ion into cytosol  (ISO)
vascular endothelial growth factor receptor signaling pathway  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10831594   PMID:10882525   PMID:11239398   PMID:11884618   PMID:12359306   PMID:12505989   PMID:12637538   PMID:12891705   PMID:13679307   PMID:15096499   PMID:15471852   PMID:15652511  
PMID:17306383   PMID:18059339   PMID:18164589   PMID:18296710   PMID:18332134   PMID:18378685   PMID:18440775   PMID:18784310   PMID:18845574   PMID:19029091   PMID:19059215   PMID:19211839  
PMID:19875622   PMID:20018189   PMID:20177824   PMID:20463010   PMID:20497126   PMID:20725733   PMID:20937274   PMID:21041300   PMID:22076634   PMID:22095288   PMID:22158620   PMID:22593072  
PMID:22636676   PMID:23159540   PMID:23479225   PMID:24219103   PMID:24623306   PMID:24647541   PMID:24740233   PMID:25931508   PMID:26443497   PMID:27184844   PMID:27369082   PMID:27782176  
PMID:28428613   PMID:31759056  


Genomics

Comparative Map Data
Prkd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2667,725,193 - 68,039,002 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl667,725,905 - 68,039,042 (-)Ensembl
Rnor_6.0671,035,017 - 71,349,531 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl671,035,332 - 71,349,249 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0680,600,725 - 80,914,319 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4670,364,135 - 70,682,006 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1670,393,721 - 70,394,895 (-)NCBI
Celera666,643,414 - 66,954,727 (-)NCBICelera
Cytogenetic Map6q22NCBI
PRKD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1429,576,479 - 30,191,898 (-)EnsemblGRCh38hg38GRCh38
GRCh381429,576,479 - 29,927,847 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371430,045,685 - 30,397,053 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361429,115,436 - 29,466,650 (-)NCBINCBI36hg18NCBI36
Build 341429,115,439 - 29,466,652NCBI
Celera149,911,927 - 10,263,081 (-)NCBI
Cytogenetic Map14q12NCBI
HuRef1410,161,470 - 10,512,671 (-)NCBIHuRef
CHM1_11430,044,967 - 30,396,713 (-)NCBICHM1_1
Prkd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391250,388,009 - 50,696,075 (-)NCBIGRCm39mm39
GRCm39 Ensembl1250,388,014 - 50,695,881 (-)Ensembl
GRCm381250,341,226 - 50,649,271 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1250,341,231 - 50,649,098 (-)EnsemblGRCm38mm10GRCm38
MGSCv371251,442,218 - 51,750,210 (-)NCBIGRCm37mm9NCBIm37
MGSCv361251,217,854 - 51,571,105 (-)NCBImm8
Celera1251,654,217 - 51,955,593 (-)NCBICelera
Cytogenetic Map12B3NCBI
Prkd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540930,554,013 - 30,860,649 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540930,554,095 - 30,860,588 (+)NCBIChiLan1.0ChiLan1.0
PRKD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11428,499,753 - 28,650,036 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1428,496,282 - 28,650,030 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01410,353,284 - 10,707,841 (-)NCBIMhudiblu_PPA_v0panPan3
PRKD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.189,004,641 - 9,327,054 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl89,005,115 - 9,328,358 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha88,933,899 - 9,256,073 (-)NCBI
ROS_Cfam_1.089,106,948 - 9,429,506 (-)NCBI
UMICH_Zoey_3.188,787,713 - 9,109,715 (-)NCBI
UNSW_CanFamBas_1.088,868,816 - 9,191,637 (-)NCBI
UU_Cfam_GSD_1.089,140,306 - 9,462,703 (-)NCBI
Prkd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864040,963,196 - 41,207,484 (-)NCBI
SpeTri2.0NW_0049364944,469,092 - 4,601,183 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRKD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl769,527,910 - 69,872,865 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1769,527,743 - 69,872,374 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2774,585,433 - 74,730,165 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Prkd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248202,408,562 - 2,726,199 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D6Got79  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2668,030,865 - 68,031,133 (+)MAPPERmRatBN7.2
mRatBN7.2668,030,865 - 68,031,246 (+)MAPPERmRatBN7.2
Rnor_6.0671,341,109 - 71,341,685NCBIRnor6.0
Rnor_6.0671,341,109 - 71,341,376NCBIRnor6.0
Rnor_5.0680,905,903 - 80,906,479UniSTSRnor5.0
Rnor_5.0680,905,903 - 80,906,170UniSTSRnor5.0
RGSC_v3.4670,674,174 - 70,674,442RGDRGSC3.4
RGSC_v3.4670,674,175 - 70,674,442UniSTSRGSC3.4
RGSC_v3.1670,677,301 - 70,677,568RGD
RH 3.4 Map6491.4RGD
RH 3.4 Map6491.4UniSTS
RH 2.0 Map6664.5RGD
Cytogenetic Map6q22UniSTS
Prkcm  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2667,725,799 - 67,726,005 (+)MAPPERmRatBN7.2
Rnor_6.0671,035,620 - 71,035,825NCBIRnor6.0
Rnor_5.0680,600,837 - 80,601,042UniSTSRnor5.0
RGSC_v3.4670,363,966 - 70,364,171UniSTSRGSC3.4
Celera666,643,245 - 66,643,450UniSTS
Cytogenetic Map6q22UniSTS
BQ209938  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2667,728,118 - 67,728,268 (+)MAPPERmRatBN7.2
Rnor_6.0671,037,939 - 71,038,088NCBIRnor6.0
Rnor_5.0680,603,156 - 80,603,305UniSTSRnor5.0
RGSC_v3.4670,366,285 - 70,366,434UniSTSRGSC3.4
Celera666,645,564 - 66,645,713UniSTS
RH 3.4 Map6489.3UniSTS
Cytogenetic Map6q22UniSTS
UniSTS:224841  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2667,725,747 - 67,725,901 (+)MAPPERmRatBN7.2
Rnor_6.0671,035,568 - 71,035,721NCBIRnor6.0
Rnor_5.0680,600,785 - 80,600,938UniSTSRnor5.0
RGSC_v3.4670,363,914 - 70,364,067UniSTSRGSC3.4
Celera666,643,193 - 66,643,346UniSTS
Cytogenetic Map6q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63207442872227641Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63509870971636405Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
4889848Pur25Proteinuria QTL 25140.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)65672856290198260Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)657730540104085867Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)657730540104085867Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)658632962103632962Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
2293088Iddm28Insulin dependent diabetes mellitus QTL 285.21blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)66304056271636266Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:22
Count of miRNA genes:21
Interacting mature miRNAs:22
Transcripts:ENSRNOT00000068077
Prediction methods: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 4 31 27 34 3
Low 3 39 40 24 19 24 8 11 43 8 7 8 8
Below cutoff 17 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001276715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039113014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039113015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039113017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039113018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039113019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039113020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039113021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039113022 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039113023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039113024 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005505595 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB020616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000068077   ⟹   ENSRNOP00000063159
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl667,725,905 - 68,039,042 (-)Ensembl
Rnor_6.0 Ensembl671,035,789 - 71,349,249 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081883   ⟹   ENSRNOP00000074836
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl667,725,905 - 67,889,169 (-)Ensembl
Rnor_6.0 Ensembl671,035,332 - 71,199,110 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100654   ⟹   ENSRNOP00000089750
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl667,725,905 - 68,039,042 (-)Ensembl
RefSeq Acc Id: NM_001276715   ⟹   NP_001263644
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,969 - 68,038,697 (-)NCBI
Rnor_6.0671,035,789 - 71,349,249 (-)NCBI
Rnor_5.0680,600,725 - 80,914,319 (-)NCBI
Celera666,643,414 - 66,954,727 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240074   ⟹   XP_006240136
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 68,038,999 (-)NCBI
Rnor_6.0671,035,017 - 71,349,529 (-)NCBI
Rnor_5.0680,600,725 - 80,914,319 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039113014   ⟹   XP_038968942
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 68,039,000 (-)NCBI
RefSeq Acc Id: XM_039113015   ⟹   XP_038968943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 68,039,000 (-)NCBI
RefSeq Acc Id: XM_039113017   ⟹   XP_038968945
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 67,893,935 (-)NCBI
RefSeq Acc Id: XM_039113018   ⟹   XP_038968946
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 67,893,977 (-)NCBI
RefSeq Acc Id: XM_039113019   ⟹   XP_038968947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 67,907,036 (-)NCBI
RefSeq Acc Id: XM_039113020   ⟹   XP_038968948
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 67,797,125 (-)NCBI
RefSeq Acc Id: XM_039113021   ⟹   XP_038968949
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 67,797,124 (-)NCBI
RefSeq Acc Id: XM_039113022   ⟹   XP_038968950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 67,794,811 (-)NCBI
RefSeq Acc Id: XM_039113023   ⟹   XP_038968951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 67,794,204 (-)NCBI
RefSeq Acc Id: XM_039113024   ⟹   XP_038968952
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,725,193 - 67,763,995 (-)NCBI
RefSeq Acc Id: XR_005505595
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2667,751,895 - 68,039,002 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001263644   ⟸   NM_001276715
- UniProtKB: Q9WTQ1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240136   ⟸   XM_006240074
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000074836   ⟸   ENSRNOT00000081883
RefSeq Acc Id: ENSRNOP00000063159   ⟸   ENSRNOT00000068077
RefSeq Acc Id: XP_038968943   ⟸   XM_039113015
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968942   ⟸   XM_039113014
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968947   ⟸   XM_039113019
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038968946   ⟸   XM_039113018
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038968945   ⟸   XM_039113017
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038968948   ⟸   XM_039113020
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038968949   ⟸   XM_039113021
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038968950   ⟸   XM_039113022
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038968951   ⟸   XM_039113023
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038968952   ⟸   XM_039113024
- Peptide Label: isoform X7
RefSeq Acc Id: ENSRNOP00000089750   ⟸   ENSRNOT00000100654
Protein Domains
PH   Phorbol-ester/DAG-type   Protein kinase

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)
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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
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)
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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
BBDP/Wor (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
BN-Lx/CubMcwi (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 (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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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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)
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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/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)
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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)
SS/JrHsdMcwi (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/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)
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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
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)
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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
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)
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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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620964 AgrOrtholog
Ensembl Genes ENSRNOG00000004165 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063159 UniProtKB/Swiss-Prot
  ENSRNOP00000074836 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068077 UniProtKB/Swiss-Prot
  ENSRNOT00000081883 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro DAG/PE-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PE/DAG-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_Kinase_C_mu-related UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:85421 UniProtKB/Swiss-Prot
NCBI Gene 85421 ENTREZGENE
PANTHER PTHR22968 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam C1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00169 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Prkd1 PhenoGen
PIRSF PKC_mu_nu_D2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS DAGPEDOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PH_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_DAG_PE_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_DAG_PE_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00109 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00233 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K928_RAT UniProtKB/TrEMBL
  KPCD1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-17 Prkd1  protein kinase D1  Prkcm  protein kinase C, mu  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Prkcm  protein kinase C, mu  Pkcm    Symbol updated 1299863 APPROVED
2002-08-07 Pkcm  protein kinase C, mu      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to Golgi apparatus and cytosol 724658
gene_regulation activation mediated by P2X7 receptors 724658