Ripk2 (receptor-interacting serine-threonine kinase 2) - Rat Genome Database

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Gene: Ripk2 (receptor-interacting serine-threonine kinase 2) Rattus norvegicus
Analyze
Symbol: Ripk2
Name: receptor-interacting serine-threonine kinase 2
RGD ID: 1309167
Description: Predicted to enable several functions, including JUN kinase kinase kinase activity; caspase binding activity; and protein domain specific binding activity. Predicted to be involved in several processes, including cellular response to muramyl dipeptide; positive regulation of cellular protein metabolic process; and regulation of gene expression. Predicted to act upstream of or within several processes, including immune response-regulating signaling pathway; positive regulation of cytokine production; and response to bacterium. Predicted to be located in cytoskeleton; cytosol; and vesicle. Predicted to be part of protein-containing complex. Orthologous to human RIPK2 (receptor interacting serine/threonine kinase 2); PARTICIPATES IN interleukin-12 signaling pathway; nuclear factor kappa B signaling pathway; neurotrophic factor signaling pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 2,3,7,8-tetrachlorodibenzodioxine; aconitine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC362491; receptor (TNFRSF)-interacting serine-threonine kinase 2; receptor-interacting serine/threonine-protein kinase 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2529,630,806 - 29,662,804 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl529,631,570 - 29,662,657 (-)Ensembl
Rnor_6.0529,838,713 - 29,870,390 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl529,838,747 - 29,870,735 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0534,512,111 - 34,543,807 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4530,714,817 - 30,745,941 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1530,715,463 - 30,738,284 (-)NCBI
Celera528,836,598 - 28,867,674 (-)NCBICelera
Cytogenetic Map5q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-methylcholine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6alpha-methylprednisolone  (ISO)
aconitine  (EXP,ISO)
all-trans-retinoic acid  (ISO)
aristolochic acid  (ISO)
azathioprine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
capsaicin  (ISO)
cholesterol  (EXP)
cisplatin  (ISO)
cobalt atom  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
DDE  (EXP)
deoxynivalenol  (ISO)
dicrotophos  (ISO)
dieldrin  (EXP)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
etoposide  (ISO)
fipronil  (EXP)
fluoranthene  (ISO)
flutamide  (EXP)
folic acid  (ISO)
furan  (EXP)
gentamycin  (EXP)
lamivudine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
metam  (ISO)
metformin  (ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
Mitotane  (EXP)
N-acetyl-L-cysteine  (EXP)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
ochratoxin A  (ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
paraquat  (ISO)
perfluorononanoic acid  (ISO)
phenethyl isothiocyanate  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
prednisolone  (ISO)
propylparaben  (ISO)
quercetin  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium aurothiomalate  (ISO)
Soman  (EXP)
sulfasalazine  (ISO)
tert-butyl hydroperoxide  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (ISO)
Triptolide  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
Tungsten carbide  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
zidovudine  (ISO)
zinc oxide  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity  (ISO)
adaptive immune response  (IBA,ISO)
cellular response to lipopolysaccharide  (ISO)
cellular response to lipoteichoic acid  (ISO)
cellular response to muramyl dipeptide  (ISO)
cellular response to peptidoglycan  (ISO)
defense response to Gram-positive bacterium  (ISO)
I-kappaB kinase/NF-kappaB signaling  (ISO)
innate immune response  (IBA,ISO)
lipopolysaccharide-mediated signaling pathway  (ISO)
nucleotide-binding oligomerization domain containing 1 signaling pathway  (ISO)
nucleotide-binding oligomerization domain containing 2 signaling pathway  (ISO)
positive regulation of alpha-beta T cell proliferation  (ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of cell death  (ISO)
positive regulation of chemokine production  (ISO)
positive regulation of cytokine-mediated signaling pathway  (ISO)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (ISO)
positive regulation of immature T cell proliferation  (ISO)
positive regulation of interferon-gamma production  (ISO)
positive regulation of interleukin-1 beta production  (ISO)
positive regulation of interleukin-2 production  (ISO)
positive regulation of interleukin-6 production  (ISO)
positive regulation of JNK cascade  (ISO)
positive regulation of NF-kappaB transcription factor activity  (IBA,ISO)
positive regulation of peptidyl-serine phosphorylation  (ISO)
positive regulation of peptidyl-threonine phosphorylation  (ISO)
positive regulation of peptidyl-tyrosine phosphorylation  (ISO)
positive regulation of protein binding  (ISO)
positive regulation of protein ubiquitination  (ISO)
positive regulation of stress-activated MAPK cascade  (ISO)
positive regulation of T-helper 1 cell differentiation  (ISO)
positive regulation of T-helper 1 type immune response  (ISO)
positive regulation of tumor necrosis factor production  (ISO)
positive regulation of xenophagy  (ISO)
protein phosphorylation  (IEA)
regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
response to exogenous dsRNA  (ISO)
response to interleukin-1  (ISO)
response to interleukin-12  (ISO)
response to interleukin-18  (ISO)
T cell proliferation  (ISO)
T cell receptor signaling pathway  (ISO)
toll-like receptor 2 signaling pathway  (ISO)
toll-like receptor 4 signaling pathway  (ISO)

Cellular Component

References

Additional References at PubMed
PMID:10329646   PMID:11087742   PMID:11432859   PMID:11536016   PMID:11821383   PMID:11894097   PMID:11894098   PMID:12477932   PMID:14638696   PMID:14663141   PMID:14743216   PMID:15190255  
PMID:15383541   PMID:15620648   PMID:15657077   PMID:16920334   PMID:18261938   PMID:19337385   PMID:21469090   PMID:21887730   PMID:21931591   PMID:22033934   PMID:23806334   PMID:24790089  
PMID:25416956   PMID:26138652   PMID:27169686   PMID:30352081  


Genomics

Comparative Map Data
Ripk2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2529,630,806 - 29,662,804 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl529,631,570 - 29,662,657 (-)Ensembl
Rnor_6.0529,838,713 - 29,870,390 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl529,838,747 - 29,870,735 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0534,512,111 - 34,543,807 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4530,714,817 - 30,745,941 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1530,715,463 - 30,738,284 (-)NCBI
Celera528,836,598 - 28,867,674 (-)NCBICelera
Cytogenetic Map5q13NCBI
RIPK2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl889,757,806 - 89,791,064 (+)EnsemblGRCh38hg38GRCh38
GRCh38889,757,816 - 89,791,064 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37890,770,044 - 90,803,292 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36890,839,110 - 90,872,433 (+)NCBINCBI36hg18NCBI36
Build 34890,839,172 - 90,872,432NCBI
Celera886,964,831 - 86,998,139 (+)NCBI
Cytogenetic Map8q21.3NCBI
HuRef885,980,380 - 86,013,697 (+)NCBIHuRef
CHM1_1890,811,006 - 90,844,310 (+)NCBICHM1_1
Ripk2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39416,122,740 - 16,163,674 (-)NCBIGRCm39mm39
GRCm39 Ensembl416,122,733 - 16,163,647 (-)Ensembl
GRCm38416,122,732 - 16,163,678 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl416,122,733 - 16,163,647 (-)EnsemblGRCm38mm10GRCm38
MGSCv37416,050,522 - 16,090,645 (-)NCBIGRCm37mm9NCBIm37
MGSCv36416,050,522 - 16,090,647 (-)NCBImm8
Celera415,919,468 - 15,959,561 (-)NCBICelera
Cytogenetic Map4A2NCBI
cM Map46.7NCBI
Ripk2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554176,669,675 - 6,702,228 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554176,669,675 - 6,698,142 (+)NCBIChiLan1.0ChiLan1.0
RIPK2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1888,397,768 - 88,431,690 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl888,398,468 - 88,456,268 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0886,447,216 - 86,480,511 (+)NCBIMhudiblu_PPA_v0panPan3
RIPK2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12935,283,209 - 35,311,608 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2935,282,072 - 35,311,333 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2935,435,813 - 35,464,812 (+)NCBI
ROS_Cfam_1.02935,480,726 - 35,509,728 (+)NCBI
UMICH_Zoey_3.12935,472,061 - 35,501,046 (+)NCBI
UNSW_CanFamBas_1.02935,492,803 - 35,521,758 (+)NCBI
UU_Cfam_GSD_1.02935,926,135 - 35,955,236 (+)NCBI
Ripk2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530344,137,166 - 44,185,801 (-)NCBI
SpeTri2.0NW_0049365443,606,925 - 3,653,248 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RIPK2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl447,027,092 - 47,074,725 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1447,026,558 - 47,075,133 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2451,491,234 - 51,539,306 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RIPK2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1884,843,391 - 84,881,087 (+)NCBI
ChlSab1.1 Ensembl884,843,471 - 84,881,303 (+)Ensembl
Vero_WHO_p1.0NW_02366603955,998,663 - 56,036,344 (-)NCBI
Ripk2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247442,194,339 - 2,227,498 (-)NCBI

Position Markers
RH144493  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2529,631,649 - 29,631,831 (+)MAPPERmRatBN7.2
Rnor_6.0529,839,557 - 29,839,738NCBIRnor6.0
Rnor_5.0534,512,955 - 34,513,136UniSTSRnor5.0
RGSC_v3.4530,714,897 - 30,715,078UniSTSRGSC3.4
Celera528,836,678 - 28,836,859UniSTS
RH 3.4 Map5161.12UniSTS
Cytogenetic Map5q13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)52483871044045280Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:127
Count of miRNA genes:97
Interacting mature miRNAs:117
Transcripts:ENSRNOT00000012963
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 1 6 17 8 11 10
Low 2 43 51 41 2 41 8 11 66 35 30 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012963   ⟹   ENSRNOP00000012963
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl529,631,570 - 29,662,657 (-)Ensembl
Rnor_6.0 Ensembl529,838,747 - 29,870,735 (-)Ensembl
RefSeq Acc Id: NM_001191865   ⟹   NP_001178794
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2529,631,570 - 29,662,657 (-)NCBI
Rnor_6.0529,839,477 - 29,870,390 (-)NCBI
Rnor_5.0534,512,111 - 34,543,807 (-)NCBI
Celera528,836,598 - 28,867,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593470   ⟹   XP_017448959
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2529,630,806 - 29,662,339 (-)NCBI
Rnor_6.0529,838,713 - 29,870,077 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039110221   ⟹   XP_038966149
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2529,630,806 - 29,657,581 (-)NCBI
RefSeq Acc Id: XR_005504472
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2529,635,658 - 29,662,804 (-)NCBI
RefSeq Acc Id: XR_005504473
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2529,635,582 - 29,662,803 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001178794 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448959 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966149 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI07469 (Get FASTA)   NCBI Sequence Viewer  
  EDL98485 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001178794   ⟸   NM_001191865
- UniProtKB: G3V783 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448959   ⟸   XM_017593470
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000012963   ⟸   ENSRNOT00000012963
RefSeq Acc Id: XP_038966149   ⟸   XM_039110221
- Peptide Label: isoform X2
Protein Domains
CARD   Protein kinase

Transcriptome

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

Promoters
RGD ID:13693582
Promoter ID:EPDNEW_R4107
Type:initiation region
Name:Ripk2_1
Description:receptor-interacting serine-threonine kinase 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0529,870,383 - 29,870,443EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309167 AgrOrtholog
Ensembl Genes ENSRNOG00000009389 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012963 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012963 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7458993 IMAGE-MGC_LOAD
InterPro CARD UniProtKB/TrEMBL
  CARD_RIP2 UniProtKB/TrEMBL
  DEATH-like UniProtKB/TrEMBL
  Kinase-like_dom UniProtKB/TrEMBL
  Prot_kinase_cat_dom UniProtKB/TrEMBL
  Rcpt-int_Ser/Thr_kinase-2 UniProtKB/TrEMBL
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/TrEMBL
  Tyr_kinase_cat_dom UniProtKB/TrEMBL
KEGG Report rno:362491 UniProtKB/TrEMBL
MGC_CLONE MGC:125253 IMAGE-MGC_LOAD
NCBI Gene 362491 ENTREZGENE
Pfam CARD UniProtKB/TrEMBL
  Pkinase_Tyr UniProtKB/TrEMBL
PhenoGen Ripk2 PhenoGen
PIRSF STPK_RIP2 UniProtKB/TrEMBL
PROSITE CARD UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/TrEMBL
SMART S_TKc UniProtKB/TrEMBL
  TyrKc UniProtKB/TrEMBL
Superfamily-SCOP DEATH_like UniProtKB/TrEMBL
  Kinase_like UniProtKB/TrEMBL
UniProt G3V783 ENTREZGENE, UniProtKB/TrEMBL
  Q3B7U0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Ripk2  receptor-interacting serine-threonine kinase 2  Ripk2  receptor (TNFRSF)-interacting serine-threonine kinase 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Ripk2  receptor (TNFRSF)-interacting serine-threonine kinase 2  Ripk2_predicted  receptor (TNFRSF)-interacting serine-threonine kinase 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Ripk2_predicted  receptor (TNFRSF)-interacting serine-threonine kinase 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED