Ripk3 (receptor-interacting serine-threonine kinase 3) - Rat Genome Database

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Gene: Ripk3 (receptor-interacting serine-threonine kinase 3) Rattus norvegicus
Analyze
Symbol: Ripk3
Name: receptor-interacting serine-threonine kinase 3
RGD ID: 628899
Description: Predicted to enable NF-kappaB-inducing kinase activity; identical protein binding activity; and protein serine/threonine kinase activity. Predicted to be involved in several processes, including hematopoietic or lymphoid organ development; necroptotic process; and positive regulation of phosphate metabolic process. Predicted to act upstream of or within several processes, including I-kappaB kinase/NF-kappaB signaling; positive regulation of intrinsic apoptotic signaling pathway; and positive regulation of protein deacetylation. Predicted to be located in cytosol and nucleus. Predicted to be part of protein-containing complex. Predicted to be active in cytoplasm. Orthologous to human RIPK3 (receptor interacting serine/threonine kinase 3); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Hcyp2; homocysteine respondent protein HCYP2; receptor-interacting protein 3; receptor-interacting serine/threonine-protein kinase 3; RIP-3; RIP-like protein kinase 3; Rip3
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
mRatBN7.21529,283,153 - 29,292,107 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1529,283,145 - 29,292,121 (-)Ensembl
Rnor_6.01534,470,796 - 34,479,741 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,470,796 - 34,479,741 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01538,359,304 - 38,368,247 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41533,947,406 - 33,956,351 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11533,963,105 - 33,972,051 (-)NCBI
Celera1528,858,091 - 28,867,036 (-)NCBICelera
Cytogenetic Map15p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-acetamidofluorene  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrolein  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
butanal  (ISO)
C.I. Natural Red 20  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
cisplatin  (ISO)
Cuprizon  (EXP)
dextran sulfate  (ISO)
Dihydrotanshinone I  (ISO)
dioxygen  (EXP,ISO)
doxorubicin  (EXP)
endosulfan  (EXP)
ethanol  (ISO)
ferric oxide  (EXP)
fingolimod hydrochloride  (ISO)
folic acid  (EXP,ISO)
gallic acid  (ISO)
genistein  (EXP)
gentamycin  (EXP)
glycerol  (EXP)
glycidol  (EXP)
hydrogen peroxide  (ISO)
lipopolysaccharide  (ISO)
melatonin  (EXP,ISO)
metformin  (ISO)
methapyrilene  (EXP)
methoxyacetic acid  (EXP)
methylmercury chloride  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-phosphocreatine  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP)
p-menthan-3-ol  (ISO)
paclitaxel  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
phenacetin  (EXP)
phenylephrine  (ISO)
phenylhydrazine  (EXP)
phenylpropanolamine  (ISO)
pirinixic acid  (ISO)
Pranoprofen  (ISO)
pterostilbene  (ISO)
quetiapine fumarate  (ISO)
resveratrol  (ISO)
rimonabant  (ISO)
rotenone  (EXP)
Shikonin  (ISO)
simvastatin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP,ISO)
tamoxifen  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
theophylline  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
Tributyltin oxide  (EXP)
Triptolide  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of protein kinase activity  (ISO,ISS)
amyloid fibril formation  (ISO,ISS)
apoptotic process  (IEA)
cellular response to hydrogen peroxide  (ISO)
defense response to virus  (ISO,ISS)
execution phase of necroptosis  (ISO,ISS)
I-kappaB kinase/NF-kappaB signaling  (ISO)
lymph node development  (ISO,ISS)
necroptotic process  (ISO,ISS)
necroptotic signaling pathway  (ISO)
NIK/NF-kappaB signaling  (IEA)
positive regulation of intrinsic apoptotic signaling pathway  (ISO)
positive regulation of ligase activity  (ISO)
positive regulation of necroptotic process  (ISO,ISS)
positive regulation of necrotic cell death  (ISO)
positive regulation of NF-kappaB transcription factor activity  (ISO)
positive regulation of oxidoreductase activity  (ISO)
positive regulation of phosphatase activity  (ISO)
positive regulation of protein deacetylation  (ISO)
positive regulation of reactive oxygen species metabolic process  (ISO)
programmed necrotic cell death  (ISO)
protein autophosphorylation  (ISO,ISS)
regulation of activated T cell proliferation  (ISO,ISS)
regulation of activation-induced cell death of T cells  (ISO,ISS)
regulation of adaptive immune response  (ISO,ISS)
regulation of apoptotic process  (ISO,ISS)
regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation  (ISO,ISS)
regulation of interferon-gamma production  (ISO,ISS)
regulation of reactive oxygen species metabolic process  (ISO)
regulation of T cell mediated cytotoxicity  (ISO,ISS)
signal transduction  (IBA)
spleen development  (ISO,ISS)
T cell differentiation in thymus  (ISO,ISS)
T cell homeostasis  (ISO,ISS)
thymus development  (ISO,ISS)

Cellular Component
cytoplasm  (IBA,ISO,ISS)
cytosol  (ISO,ISS)
nucleus  (ISO,ISS)
protein-containing complex  (ISO)

References

References - curated
1. Bian P, etal., Front Microbiol. 2020 Mar 24;11:368. doi: 10.3389/fmicb.2020.00368. eCollection 2020.
2. Bonnet MC, etal., Immunity. 2011 Oct 28;35(4):572-82. doi: 10.1016/j.immuni.2011.08.014. Epub 2011 Oct 13.
3. Cao M, etal., Cell Death Differ. 2019 Dec;26(12):2622-2636. doi: 10.1038/s41418-019-0323-8. Epub 2019 Apr 3.
4. Chen H, etal., Cell Death Differ. 2020 Sep;27(9):2568-2585. doi: 10.1038/s41418-020-0524-1. Epub 2020 Mar 9.
5. Cho YS, etal., Cell. 2009 Jun 12;137(6):1112-23. doi: 10.1016/j.cell.2009.05.037.
6. Csak T, etal., Hepatology. 2011 Jun;53(6):1917-31. doi: 10.1002/hep.24301. Epub 2011 May 2.
7. Downey J, etal., PLoS Pathog. 2017 Apr 14;13(4):e1006326. doi: 10.1371/journal.ppat.1006326. eCollection 2017 Apr.
8. Duprez L, etal., Immunity. 2011 Dec 23;35(6):908-18. doi: 10.1016/j.immuni.2011.09.020.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. González-Juarbe N, etal., Cell Death Differ. 2017 May;24(5):917-928. doi: 10.1038/cdd.2017.49. Epub 2017 Apr 7.
11. Guo H, etal., Cell Death Dis. 2018 Jul 26;9(8):816. doi: 10.1038/s41419-018-0868-3.
12. Han L, etal., Tohoku J Exp Med. 2019 Apr;247(4):237-245. doi: 10.1620/tjem.247.237.
13. Huang HR, etal., Am J Respir Cell Mol Biol. 2021 May;64(5):579-591. doi: 10.1165/rcmb.2020-0312OC.
14. Kitur K, etal., Cell Rep. 2016 Aug 23;16(8):2219-2230. doi: 10.1016/j.celrep.2016.07.039. Epub 2016 Aug 11.
15. Li J, etal., Sci Rep. 2019 Nov 22;9(1):17369. doi: 10.1038/s41598-019-53910-y.
16. Lu Y, etal., Sci Rep. 2017 Feb 16;7:42736. doi: 10.1038/srep42736.
17. MGD data from the GO Consortium
18. Murakami Y, etal., Cell Death Differ. 2013 Aug 16. doi: 10.1038/cdd.2013.109.
19. Murakami Y, etal., Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14598-603. doi: 10.1073/pnas.1206937109. Epub 2012 Aug 20.
20. Newton K, etal., Mol Cell Biol 2004 Feb;24(4):1464-9.
21. Nogusa S, etal., Cell Host Microbe. 2016 Jul 13;20(1):13-24. doi: 10.1016/j.chom.2016.05.011. Epub 2016 Jun 16.
22. Qin C, etal., Biomed Res Int. 2019 Apr 7;2019:2121357. doi: 10.1155/2019/2121357. eCollection 2019.
23. RGD automated data pipeline
24. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
25. RGD automated import pipeline for gene-chemical interactions
26. RGD, Sept. 2003
27. Sai K, etal., J Cell Biol. 2019 Jun 3;218(6):1994-2005. doi: 10.1083/jcb.201810014. Epub 2019 Apr 11.
28. Santos LD, etal., Eur Respir J. 2020 Dec 10. pii: 13993003.03764-2020. doi: 10.1183/13993003.03764-2020.
29. Shi J, etal., Sci Rep. 2019 Feb 27;9(1):2902. doi: 10.1038/s41598-019-39721-1.
30. Stutz MD, etal., Front Immunol. 2018 May 28;9:1178. doi: 10.3389/fimmu.2018.01178. eCollection 2018.
31. Wang X, etal., Nat Immunol. 2014 Dec;15(12):1126-33. doi: 10.1038/ni.3015. Epub 2014 Oct 19.
32. Wang X, etal., Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15438-43. doi: 10.1073/pnas.1412767111. Epub 2014 Oct 14.
33. Webster JD, etal., J Leukoc Biol. 2020 Jun;107(6):941-952. doi: 10.1002/JLB.3MA1219-398R. Epub 2020 Jan 27.
34. Wen SH, etal., Int Immunopharmacol. 2014 Dec;23(2):709-18. doi: 10.1016/j.intimp.2014.10.027.
35. Wu J, etal., Cell Res. 2013 Aug;23(8):994-1006. doi: 10.1038/cr.2013.91. Epub 2013 Jul 9.
36. Xu J, etal., Invest Ophthalmol Vis Sci. 2018 May 1;59(6):2445-2458. doi: 10.1167/iovs.18-24086.
37. Xu J, etal., Mol Vis. 2018 May 18;24:379-394. eCollection 2018.
38. Xu YL, etal., Oncotarget. 2017 Apr 25;8(17):27715-27724. doi: 10.18632/oncotarget.16016.
39. Zhang T, etal., Cell. 2020 Mar 19;180(6):1115-1129.e13. doi: 10.1016/j.cell.2020.02.050.
40. Zhao X, etal., Mucosal Immunol. 2017 Nov;10(6):1553-1568. doi: 10.1038/mi.2017.12. Epub 2017 Apr 12.
Additional References at PubMed
PMID:10490590   PMID:12477932   PMID:14743216   PMID:19498109   PMID:20042608   PMID:21052097   PMID:21368763   PMID:21402742   PMID:21737330   PMID:21876153   PMID:21931591   PMID:22037414  
PMID:22265413   PMID:22265414   PMID:22675671   PMID:22817896   PMID:24012422   PMID:24095729   PMID:24920296   PMID:25352744   PMID:25907058   PMID:26559832   PMID:26726877   PMID:26985994  
PMID:27258785   PMID:27281190   PMID:27377128   PMID:27514644   PMID:27622324   PMID:28289909   PMID:28501693   PMID:28579326   PMID:28816233   PMID:29883609   PMID:30215665   PMID:31082470  
PMID:31658855   PMID:32471717   PMID:32580628   PMID:33130681   PMID:33359086   PMID:34056794   PMID:34360749   PMID:34384567  


Genomics

Comparative Map Data
Ripk3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21529,283,153 - 29,292,107 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1529,283,145 - 29,292,121 (-)Ensembl
Rnor_6.01534,470,796 - 34,479,741 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,470,796 - 34,479,741 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01538,359,304 - 38,368,247 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41533,947,406 - 33,956,351 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11533,963,105 - 33,972,051 (-)NCBI
Celera1528,858,091 - 28,867,036 (-)NCBICelera
Cytogenetic Map15p13NCBI
RIPK3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1424,336,025 - 24,340,022 (-)EnsemblGRCh38hg38GRCh38
GRCh381424,336,025 - 24,339,991 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371424,805,231 - 24,809,197 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361423,875,067 - 23,879,082 (-)NCBINCBI36hg18NCBI36
Build 341423,875,071 - 23,879,013NCBI
Celera144,669,852 - 4,673,867 (-)NCBI
Cytogenetic Map14q12NCBI
HuRef144,920,121 - 4,924,136 (-)NCBIHuRef
CHM1_11424,803,822 - 24,807,837 (-)NCBICHM1_1
Ripk3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391456,022,452 - 56,026,314 (-)NCBIGRCm39mm39
GRCm39 Ensembl1456,022,452 - 56,026,322 (-)Ensembl
GRCm381455,784,995 - 55,788,857 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1455,784,995 - 55,788,865 (-)EnsemblGRCm38mm10GRCm38
MGSCv371456,403,832 - 56,407,694 (-)NCBIGRCm37mm9NCBIm37
MGSCv361454,739,068 - 54,742,857 (-)NCBImm8
Celera1453,590,028 - 53,593,890 (-)NCBICelera
Cytogenetic Map14C3NCBI
Ripk3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540935,937,880 - 35,965,712 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540935,961,604 - 35,965,477 (+)NCBIChiLan1.0ChiLan1.0
RIPK3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11423,235,796 - 23,239,821 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1423,235,796 - 23,239,821 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0145,112,512 - 5,116,486 (-)NCBIMhudiblu_PPA_v0panPan3
RIPK3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.184,304,167 - 4,309,514 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl84,305,250 - 4,309,325 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha84,227,031 - 4,231,283 (-)NCBI
ROS_Cfam_1.084,416,047 - 4,420,326 (-)NCBI
UMICH_Zoey_3.184,106,383 - 4,110,679 (-)NCBI
UNSW_CanFamBas_1.084,168,389 - 4,172,700 (-)NCBI
UU_Cfam_GSD_1.084,430,799 - 4,435,106 (-)NCBI
Ripk3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864036,176,140 - 36,180,016 (-)NCBI
SpeTri2.0NW_004936722209,019 - 212,817 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RIPK3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl774,951,060 - 74,955,192 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1774,951,145 - 74,955,255 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2780,222,514 - 80,226,187 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RIPK3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1241,318,265 - 1,322,610 (-)NCBIChlSab1.1chlSab2
ChlSab1.1241,318,265 - 1,322,610 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl241,318,216 - 1,322,462 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603613,002,814 - 13,006,980 (-)NCBIVero_WHO_p1.0
Ripk3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248208,165,546 - 8,169,172 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH129786  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21529,283,184 - 29,283,381 (+)MAPPERmRatBN7.2
Rnor_6.01534,470,819 - 34,471,015NCBIRnor6.0
Rnor_5.01538,359,330 - 38,359,526UniSTSRnor5.0
RGSC_v3.41533,947,429 - 33,947,625UniSTSRGSC3.4
Celera1528,858,114 - 28,858,310UniSTS
RH 3.4 Map15260.81UniSTS
Cytogenetic Map15p13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:32
Count of miRNA genes:32
Interacting mature miRNAs:32
Transcripts:ENSRNOT00000027759
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 3 4 14 6 19 6 5 6
Low 39 43 35 35 8 11 74 35 34 5 8
Below cutoff 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027759   ⟹   ENSRNOP00000027759
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1529,283,160 - 29,292,101 (-)Ensembl
Rnor_6.0 Ensembl1534,470,796 - 34,479,741 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097021   ⟹   ENSRNOP00000078176
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1529,283,145 - 29,292,110 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117419   ⟹   ENSRNOP00000087719
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1529,283,159 - 29,292,121 (-)Ensembl
RefSeq Acc Id: NM_139342   ⟹   NP_647558
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21529,283,162 - 29,292,107 (-)NCBI
Rnor_6.01534,470,796 - 34,479,741 (-)NCBI
Rnor_5.01538,359,304 - 38,368,247 (-)NCBI
RGSC_v3.41533,947,406 - 33,956,351 (-)RGD
Celera1528,858,091 - 28,867,036 (-)RGD
Sequence:
RefSeq Acc Id: XM_039092983   ⟹   XP_038948911
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21529,283,153 - 29,286,823 (-)NCBI
RefSeq Acc Id: XM_039092984   ⟹   XP_038948912
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21529,283,153 - 29,286,114 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_647558   ⟸   NM_139342
- Sequence:
RefSeq Acc Id: ENSRNOP00000027759   ⟸   ENSRNOT00000027759
RefSeq Acc Id: XP_038948911   ⟸   XM_039092983
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948912   ⟸   XM_039092984
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000087719   ⟸   ENSRNOT00000117419
RefSeq Acc Id: ENSRNOP00000078176   ⟸   ENSRNOT00000097021
Protein Domains
Protein kinase

Transcriptome

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

Promoters
RGD ID:13699691
Promoter ID:EPDNEW_R10214
Type:multiple initiation site
Name:Ripk3_1
Description:receptor-interacting serine-threonine kinase 3
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_6.01534,479,752 - 34,479,812EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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)
Visual CSV TAB Printer
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)
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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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628899 AgrOrtholog
Ensembl Genes ENSRNOG00000020465 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000027759 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027759 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7378607 IMAGE-MGC_LOAD
InterPro Kinase-like_dom_sf UniProtKB/Swiss-Prot
  Prot_kinase_dom UniProtKB/Swiss-Prot
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot
  RHIM_dom UniProtKB/Swiss-Prot
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot
KEGG Report rno:246240 UniProtKB/Swiss-Prot
MGC_CLONE MGC:187331 IMAGE-MGC_LOAD
NCBI Gene 246240 ENTREZGENE
Pfam Pkinase UniProtKB/Swiss-Prot
  RHIM UniProtKB/Swiss-Prot
PhenoGen Ripk3 PhenoGen
PROSITE PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot
SMART S_TKc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56112 UniProtKB/Swiss-Prot
UniProt Q9Z2P5 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary B0BMV6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-04-22 Ripk3  receptor-interacting serine-threonine kinase 3  Hcyp2  homocysteine respondent protein HCYP2  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 APPROVED
2003-02-27 Hcyp2  homocysteine respondent protein HCYP2      Symbol and Name status set to provisional 70820 PROVISIONAL