Prkdc (protein kinase, DNA-activated, catalytic subunit) - Rat Genome Database

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Gene: Prkdc (protein kinase, DNA-activated, catalytic subunit) Rattus norvegicus
Analyze
Symbol: Prkdc
Name: protein kinase, DNA-activated, catalytic subunit
RGD ID: 1308982
Description: Predicted to enable several functions, including DNA-dependent protein kinase activity; enzyme binding activity; and nucleic acid binding activity. Involved in several processes, including hematopoietic or lymphoid organ development; negative regulation of cellular senescence; and negative regulation of response to gamma radiation. Predicted to be located in nucleolus and nucleoplasm. Predicted to be part of several cellular components, including DNA-dependent protein kinase-DNA ligase 4 complex; protein-DNA complex; and small-subunit processome. Predicted to be active in nucleus. Used to study severe combined immunodeficiency. Human ortholog(s) of this gene implicated in immunodeficiency 26. Orthologous to human PRKDC (protein kinase, DNA-activated, catalytic subunit); PARTICIPATES IN non-homologous end joining pathway of double-strand break repair; phosphatidylinositol 3-kinase-Akt signaling pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: DNA-dependent protein kinase catalytic subunit; LOC360748; MGC189093
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Prkdcem1Kyo   Prkdcem2Kyo   Prkdcem4Kyo  
Genetic Models: TM-Prkdcem4KyoIl2rgem5Kyo F344-Prkdcem2KyoIl2rgem6Kyo F344-Prkdcem1Kyo
Is Marker For: Strains:   F344-Prkdcem1Kyo   F344-Prkdcem2KyoIl2rgem6Kyo   TM-Prkdcem4KyoIl2rgem5Kyo   SD-Prkdcem1Sage  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21185,040,790 - 85,258,357 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1185,040,792 - 85,257,952 (-)Ensembl
Rnor_6.01189,293,547 - 89,510,948 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1189,293,696 - 89,510,871 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01192,347,175 - 92,565,022 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41186,951,420 - 87,169,229 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11186,992,362 - 87,209,825 (-)NCBI
Celera1183,781,535 - 83,998,574 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-demecolcine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-nitropyrene  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3-aminobenzamide  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-Nitrofluoranthene  (ISO)
4-amino-1,8-naphthalimide  (ISO)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (ISO)
acrolein  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
aphidicolin  (ISO)
arecoline  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
biphenyl-4-amine  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
butanal  (ISO)
caffeine  (ISO)
capsaicin  (ISO)
casticin  (ISO)
chromium atom  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
curcumin  (ISO)
Deguelin  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP,ISO)
dichlorvos  (EXP)
dicrotophos  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
etoposide  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gallic acid  (ISO)
glyphosate  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
indometacin  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
josamycin  (ISO)
lead diacetate  (ISO)
lycopene  (ISO)
methapyrilene  (ISO)
monocrotaline  (ISO)
motexafin gadolinium  (ISO)
myristicin  (ISO)
N-acetyl-L-cysteine  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP,ISO)
ochratoxin A  (EXP)
ouabain  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
phenol  (ISO)
phenytoin  (ISO)
phosphoramide mustard  (EXP)
pirinixic acid  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
resveratrol  (EXP)
rifampicin  (ISO)
serpentine asbestos  (ISO)
sodium arsenite  (ISO)
tamibarotene  (ISO)
tetrachloromethane  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
tungsten  (ISO)
urethane  (ISO)
usnic acid  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)
zinc acetate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of innate immune response  (ISO)
B cell lineage commitment  (ISO)
brain development  (ISO)
cellular response to DNA damage stimulus  (ISO)
cellular response to insulin stimulus  (ISO)
double-strand break repair  (IBA,ISO)
double-strand break repair via nonhomologous end joining  (ISO)
ectopic germ cell programmed cell death  (ISO)
heart development  (ISO)
immunoglobulin production  (IMP)
immunoglobulin V(D)J recombination  (IBA,ISO)
intrinsic apoptotic signaling pathway in response to DNA damage  (IBA,ISO)
lymphocyte differentiation  (ISO)
maturation of 5.8S rRNA  (ISO)
mitotic G1 DNA damage checkpoint signaling  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of cellular senescence  (IMP)
negative regulation of immunoglobulin production  (IMP)
negative regulation of protein phosphorylation  (ISO)
negative regulation of response to gamma radiation  (IMP)
peptidyl-serine phosphorylation  (ISO)
peptidyl-threonine phosphorylation  (ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of developmental growth  (IMP)
positive regulation of double-strand break repair via nonhomologous end joining  (ISO)
positive regulation of erythrocyte differentiation  (ISO)
positive regulation of fibroblast proliferation  (IMP)
positive regulation of immune system process  (IMP)
positive regulation of lymphocyte differentiation  (ISO)
positive regulation of platelet formation  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of translation  (ISO)
pro-B cell differentiation  (ISO)
protein destabilization  (ISO)
protein phosphorylation  (ISO)
regulation of circadian rhythm  (ISO)
regulation of epithelial cell proliferation  (ISO)
regulation of hematopoietic stem cell differentiation  (ISO)
regulation of smooth muscle cell proliferation  (ISO)
response to activity  (IEP)
response to gamma radiation  (ISO)
response to ionizing radiation  (ISO)
small-subunit processome assembly  (ISO)
somitogenesis  (ISO)
spleen development  (IMP)
T cell differentiation in thymus  (ISO)
T cell lineage commitment  (ISO)
T cell receptor V(D)J recombination  (ISO)
telomere capping  (ISO)
telomere maintenance  (IBA,ISO)
thymus development  (IMP)
V(D)J recombination  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:7671312   PMID:8133891   PMID:8788039   PMID:8889548   PMID:9768755   PMID:11751629   PMID:12477932   PMID:12604618   PMID:15010310   PMID:15194694   PMID:16166097   PMID:16687486  
PMID:17145779   PMID:18710952   PMID:19135898   PMID:19303849   PMID:19946888   PMID:20150414   PMID:20383123   PMID:20972425   PMID:21731742   PMID:22139836   PMID:22504299   PMID:22658674  
PMID:22681889   PMID:23836881   PMID:23979707   PMID:24158435   PMID:24485452   PMID:25852083   PMID:25941166   PMID:26237645   PMID:27829214   PMID:28712728   PMID:32103174  


Genomics

Comparative Map Data
Prkdc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21185,040,790 - 85,258,357 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1185,040,792 - 85,257,952 (-)Ensembl
Rnor_6.01189,293,547 - 89,510,948 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1189,293,696 - 89,510,871 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01192,347,175 - 92,565,022 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41186,951,420 - 87,169,229 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11186,992,362 - 87,209,825 (-)NCBI
Celera1183,781,535 - 83,998,574 (-)NCBICelera
Cytogenetic Map11q23NCBI
PRKDC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl847,773,111 - 47,960,178 (-)EnsemblGRCh38hg38GRCh38
GRCh38847,773,111 - 47,960,136 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37848,685,672 - 48,872,696 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36848,848,222 - 49,035,296 (-)NCBINCBI36hg18NCBI36
Build 34848,848,221 - 49,035,296NCBI
Celera844,671,051 - 44,858,151 (-)NCBI
Cytogenetic Map8q11.21NCBI
HuRef844,148,581 - 44,335,706 (-)NCBIHuRef
CHM1_1848,738,053 - 48,925,105 (-)NCBICHM1_1
Prkdc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391615,455,698 - 15,660,103 (+)NCBIGRCm39mm39
GRCm39 Ensembl1615,455,730 - 15,660,099 (+)Ensembl
GRCm381615,637,444 - 15,842,239 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1615,637,866 - 15,842,235 (+)EnsemblGRCm38mm10GRCm38
MGSCv371615,637,959 - 15,842,332 (+)NCBIGRCm37mm9NCBIm37
MGSCv361615,551,467 - 15,755,813 (+)NCBImm8
Celera1616,214,291 - 16,413,213 (+)NCBICelera
Cytogenetic Map16A2NCBI
cM Map1610.09NCBI
Prkdc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554547,733,978 - 7,890,867 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554547,733,697 - 7,890,896 (-)NCBIChiLan1.0ChiLan1.0
PRKDC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1841,593,022 - 41,778,299 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl841,593,029 - 41,778,299 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0844,201,391 - 44,386,803 (-)NCBIMhudiblu_PPA_v0panPan3
PRKDC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12924,904 - 243,926 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2935,007 - 243,895 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha29449,958 - 669,362 (-)NCBI
ROS_Cfam_1.02920,665 - 241,975 (-)NCBI
UMICH_Zoey_3.12920,944 - 240,298 (-)NCBI
UNSW_CanFamBas_1.029218,160 - 435,150 (-)NCBI
UU_Cfam_GSD_1.029285,564 - 503,393 (-)NCBI
Prkdc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530379,533,069 - 79,697,823 (+)NCBI
SpeTri2.0NW_0049365904,722,914 - 4,887,615 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRKDC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl479,687,359 - 79,847,281 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1479,687,375 - 79,850,146 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2487,185,946 - 87,343,690 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRKDC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1843,915,226 - 44,119,547 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl843,914,636 - 44,119,541 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603997,968,963 - 98,158,648 (+)NCBIVero_WHO_p1.0
Prkdc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247357,534,483 - 7,702,079 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH131824  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21185,040,934 - 85,041,118 (+)MAPPERmRatBN7.2
Rnor_6.01189,293,692 - 89,293,875NCBIRnor6.0
Rnor_5.01192,347,320 - 92,347,503UniSTSRnor5.0
RGSC_v3.41186,951,563 - 86,951,746UniSTSRGSC3.4
Celera1183,781,680 - 83,781,863UniSTS
RH 3.4 Map2860.69UniSTS
Cytogenetic Map11q23UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat


Related Rat Strains
The following Strains have been annotated to Prkdc


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

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:33
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000035247, ENSRNOT00000065799
Prediction methods: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 10 32 16 18 16 4 4 49 26 35 8 4
Low 3 33 25 25 1 25 4 7 25 9 6 3 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035247   ⟹   ENSRNOP00000037412
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1185,040,792 - 85,257,952 (-)Ensembl
Rnor_6.0 Ensembl1189,293,696 - 89,510,871 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115346   ⟹   ENSRNOP00000081845
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1185,040,792 - 85,257,952 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115554   ⟹   ENSRNOP00000090424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1185,040,792 - 85,257,952 (-)Ensembl
RefSeq Acc Id: NM_001108327   ⟹   NP_001101797
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21185,040,790 - 85,257,952 (-)NCBI
RefSeq Acc Id: XM_008768933   ⟹   XP_008767155
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21185,040,790 - 85,258,185 (-)NCBI
Rnor_6.01189,293,547 - 89,510,948 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598214   ⟹   XP_017453703
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21185,040,790 - 85,224,080 (-)NCBI
Rnor_6.01189,293,547 - 89,476,765 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088537   ⟹   XP_038944465
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21185,040,790 - 85,258,357 (-)NCBI
RefSeq Acc Id: XM_039088538   ⟹   XP_038944466
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21185,040,790 - 85,159,790 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_008767155   ⟸   XM_008768933
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453703   ⟸   XM_017598214
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000037412   ⟸   ENSRNOT00000035247
RefSeq Acc Id: XP_038944465   ⟸   XM_039088537
- Peptide Label: isoform X2
RefSeq Acc Id: NP_001101797   ⟸   NM_001108327
RefSeq Acc Id: XP_038944466   ⟸   XM_039088538
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000081845   ⟸   ENSRNOT00000115346
RefSeq Acc Id: ENSRNOP00000090424   ⟸   ENSRNOT00000115554
Protein Domains
FAT   FATC   PI3K/PI4K

Transcriptome

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

Promoters
RGD ID:13698355
Promoter ID:EPDNEW_R8875
Type:multiple initiation site
Name:Prkdc_2
Description:protein kinase, DNA activated, catalytic polypeptide
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8876  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01189,510,693 - 89,510,753EPDNEW
RGD ID:13698359
Promoter ID:EPDNEW_R8876
Type:single initiation site
Name:Prkdc_1
Description:protein kinase, DNA activated, catalytic polypeptide
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8875  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01189,510,931 - 89,510,991EPDNEW

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)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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
F344/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
FHH/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
FHH/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)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/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
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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: 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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 85250524 85250525 T C snv ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), HXB2/IpcvMcwi (2019), WKY/N (2020), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WKY/NCrl (2019), HXB31/IpcvMcwi (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308982 AgrOrtholog
Ensembl Genes ENSRNOG00000025028 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000037412 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035247 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1070.11 UniProtKB/TrEMBL
InterPro ARM-type_fold UniProtKB/TrEMBL
  DNA-PK_dom UniProtKB/TrEMBL
  FATC UniProtKB/TrEMBL
  Kinase-like_dom UniProtKB/TrEMBL
  NUC194 UniProtKB/TrEMBL
  PI3/4_kinase_cat_dom UniProtKB/TrEMBL
  PI3/4_kinase_cat_sf UniProtKB/TrEMBL
  PI3/4_kinase_CS UniProtKB/TrEMBL
  PIK-rel_kinase_FAT UniProtKB/TrEMBL
  PIK_FAT UniProtKB/TrEMBL
NCBI Gene 360748 ENTREZGENE
Pfam FAT UniProtKB/TrEMBL
  FATC UniProtKB/TrEMBL
  NUC194 UniProtKB/TrEMBL
  PI3_PI4_kinase UniProtKB/TrEMBL
PhenoGen Prkdc PhenoGen
PROSITE FAT UniProtKB/TrEMBL
  FATC UniProtKB/TrEMBL
  PI3_4_KINASE_1 UniProtKB/TrEMBL
  PI3_4_KINASE_2 UniProtKB/TrEMBL
  PI3_4_KINASE_3 UniProtKB/TrEMBL
SMART FATC UniProtKB/TrEMBL
  NUC194 UniProtKB/TrEMBL
  PI3Kc UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
  Kinase_like UniProtKB/TrEMBL
UniProt D3ZTN0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Prkdc  protein kinase, DNA activated, catalytic polypeptide   Prkdc_predicted  protein kinase, DNA activated, catalytic polypeptide (predicted)  'predicted' is removed 2292626 APPROVED