Cdk6 (cyclin-dependent kinase 6) - Rat Genome Database

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Gene: Cdk6 (cyclin-dependent kinase 6) Rattus norvegicus
Analyze
Symbol: Cdk6
Name: cyclin-dependent kinase 6
RGD ID: 621121
Description: Enables cyclin binding activity. Predicted to be involved in several processes, including negative regulation of cellular senescence; negative regulation of osteoblast differentiation; and regulation of myeloid cell differentiation. Predicted to act upstream of or within several processes, including hemopoiesis; regulation of gene expression; and regulation of hematopoietic stem cell differentiation. Predicted to be located in several cellular components, including centrosome; nucleoplasm; and ruffle. Predicted to be part of cyclin D2-CDK6 complex and mediator complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in high grade glioma; lung non-small cell carcinoma; pancreatic adenocarcinoma; pancreatic ductal carcinoma; and primary autosomal recessive microcephaly 12. Orthologous to human CDK6 (cyclin dependent kinase 6); PARTICIPATES IN G1/S transition pathway; cell cycle pathway, mitotic; ceramide signaling pathway; INTERACTS WITH (Z)-3-butylidenephthalide; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cell division protein kinase 6
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
mRatBN7.2430,637,650 - 30,829,688 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl430,646,460 - 30,829,634 (-)Ensembl
Rnor_6.0427,781,728 - 27,969,653 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl427,785,647 - 27,966,398 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0427,685,042 - 27,872,388 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4427,362,656 - 27,618,006 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1427,471,179 - 27,635,330 (-)NCBI
Celera426,070,823 - 26,248,747 (-)NCBICelera
Cytogenetic Map4q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
(Z)-3-butylidenephthalide  (EXP,ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP,ISO)
2,4-D  (ISO)
2-methylcholine  (ISO)
3,3'-diindolylmethane  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acteoside  (ISO)
adefovir pivoxil  (ISO)
all-trans-retinoic acid  (EXP,ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
aniline  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
berberine  (ISO)
betulinic acid  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
BMS-754807  (ISO)
Butylparaben  (ISO)
butyric acid  (ISO)
cadmium dichloride  (ISO)
cantharidin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chloroacetaldehyde  (ISO)
chloropicrin  (ISO)
choline  (ISO)
chromium(6+)  (EXP,ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
cobalt dichloride  (ISO)
columbamine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
coptisine  (ISO)
CU-O LINKAGE  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cyclosporin A  (ISO)
Deguelin  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
diclofenac  (ISO)
dieldrin  (EXP)
dioscin  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
dronedarone  (ISO)
embelin  (ISO)
endosulfan  (ISO)
enzyme inhibitor  (ISO)
erlotinib hydrochloride  (ISO)
ethyl methanesulfonate  (ISO)
eugenol  (ISO)
fenpyroximate  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furazolidone  (ISO)
galangin  (ISO)
gefitinib  (ISO)
geldanamycin  (ISO)
genistein  (ISO)
glyphosate  (ISO)
hypochlorous acid  (ISO)
ibuprofen  (ISO)
ifosfamide  (ISO)
indole-3-methanol  (EXP,ISO)
indometacin  (ISO)
irinotecan  (ISO)
isoeugenol  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (EXP)
L-methionine  (ISO)
lipopolysaccharide  (EXP,ISO)
mercury dibromide  (ISO)
metformin  (EXP)
methamphetamine  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylmercury(1+)  (EXP)
methylparaben  (ISO)
methylseleninic acid  (ISO)
microcystin-LR  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (EXP)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
nicotine  (ISO)
ouabain  (ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
palbociclib  (ISO)
Panduratin A  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
piperine  (ISO)
pirinixic acid  (ISO)
platycodin D  (ISO)
ponatinib  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
propylparaben  (ISO)
quercetin  (ISO)
quizartinib  (ISO)
ranitidine  (EXP)
resveratrol  (ISO)
ritonavir  (ISO)
rottlerin  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
silibinin  (ISO)
sodium arsenite  (ISO)
sorafenib  (ISO)
sulindac  (ISO)
tamoxifen  (ISO)
tebufenpyrad  (ISO)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thimerosal  (ISO)
torcetrapib  (ISO)
trans-isoeugenol  (ISO)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
Triptolide  (ISO)
troglitazone  (ISO)
Tryptanthrine  (ISO)
tunicamycin  (ISO)
usnic acid  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vismodegib  (ISO)
vorinostat  (ISO)
zidovudine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Boylan JM and Gruppuso PA, Biochem Biophys Res Commun. 2005 May 13;330(3):722-30.
2. Costello JF, etal., Cancer Res. 1997 Apr 1;57(7):1250-4.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Huang M, etal., Cancer Lett. 2014 Oct 10;353(1):32-40. doi: 10.1016/j.canlet.2014.06.021. Epub 2014 Jul 19.
6. Igarashi K, etal., Br J Cancer. 1999 Oct;81(4):705-11. doi: 10.1038/sj.bjc.6690752.
7. Keutgen XM, etal., Cancer. 2018 Feb 1;124(3):636-647. doi: 10.1002/cncr.31057. Epub 2017 Nov 17.
8. Lam PY, etal., Br J Neurosurg. 2000 Feb;14(1):28-32.
9. Li B, etal., Oncol Rep. 2012 Sep;28(3):909-14. doi: 10.3892/or.2012.1884. Epub 2012 Jun 25.
10. Malumbres M and Barbacid M, Trends Biochem Sci. 2005 Nov;30(11):630-41. Epub 2005 Oct 19.
11. Marsh JL, etal., Front Biosci (Landmark Ed). 2014 Jan 1;19:113-25.
12. Mendrzyk F, etal., J Clin Oncol. 2005 Dec 1;23(34):8853-62. doi: 10.1200/JCO.2005.02.8589.
13. MGD data from the GO Consortium
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. Obaya AJ, etal., J Biol Chem 2002 Aug 23;277(34):31263-9.
16. Pipeline to import KEGG annotations from KEGG into RGD
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Sherr CJ Cancer Res. 2000 Jul 15;60(14):3689-95.
21. Walentinsson A, etal., Cancer Res 2001 Nov 15;61(22):8263-73.
22. Walentinsson A, etal., Mamm Genome 2001 Dec;12(12):900-8.
23. Wu Y, etal., Mol Ther Nucleic Acids. 2013 Apr 16;2:e84. doi: 10.1038/mtna.2013.14.
24. Zhang J, etal., Eur Rev Med Pharmacol Sci. 2016 Nov;20(21):4494-4499.
Additional References at PubMed
PMID:7739547   PMID:8114739   PMID:9751050   PMID:10205165   PMID:12833137   PMID:12861051   PMID:14985467   PMID:15254224   PMID:15315761   PMID:16548883   PMID:17420273   PMID:17431401  
PMID:18495667   PMID:18504428   PMID:18700867   PMID:20466002   PMID:20501390   PMID:20668294   PMID:21508411   PMID:22893700   PMID:23918663   PMID:25342715   PMID:26542173   PMID:26699910  
PMID:26707878   PMID:30701428  


Genomics

Comparative Map Data
Cdk6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2430,637,650 - 30,829,688 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl430,646,460 - 30,829,634 (-)Ensembl
Rnor_6.0427,781,728 - 27,969,653 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl427,785,647 - 27,966,398 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0427,685,042 - 27,872,388 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4427,362,656 - 27,618,006 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1427,471,179 - 27,635,330 (-)NCBI
Celera426,070,823 - 26,248,747 (-)NCBICelera
Cytogenetic Map4q13NCBI
CDK6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl792,604,921 - 92,836,573 (-)EnsemblGRCh38hg38GRCh38
GRCh38792,604,921 - 92,836,573 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37792,234,235 - 92,465,887 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36792,072,171 - 92,301,148 (-)NCBINCBI36hg18NCBI36
Build 34791,878,887 - 92,107,863NCBI
Celera786,938,762 - 87,170,471 (-)NCBI
Cytogenetic Map7q21.2NCBI
HuRef786,843,599 - 87,075,188 (-)NCBIHuRef
CHM1_1792,164,273 - 92,395,977 (-)NCBICHM1_1
CRA_TCAGchr7v2791,563,451 - 91,795,159 (-)NCBI
Cdk6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3953,391,004 - 3,581,008 (+)NCBIGRCm39mm39
GRCm39 Ensembl53,391,485 - 3,581,008 (+)Ensembl
GRCm3853,341,004 - 3,531,008 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl53,341,485 - 3,531,008 (+)EnsemblGRCm38mm10GRCm38
MGSCv3753,344,312 - 3,522,225 (+)NCBIGRCm37mm9NCBIm37
MGSCv3653,350,318 - 3,528,231 (+)NCBImm8
Celera53,279,311 - 3,457,786 (+)NCBICelera
Cytogenetic Map5A1NCBI
cM Map52.04NCBI
Cdk6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554329,521,794 - 9,726,417 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554329,521,794 - 9,727,772 (-)NCBIChiLan1.0ChiLan1.0
CDK6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1798,198,740 - 98,430,305 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0784,603,419 - 84,835,082 (-)NCBIMhudiblu_PPA_v0panPan3
CDK6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11418,178,352 - 18,413,869 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1418,188,429 - 18,419,869 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1417,739,051 - 17,984,302 (-)NCBI
ROS_Cfam_1.01417,990,661 - 18,231,585 (-)NCBI
UMICH_Zoey_3.11418,145,467 - 18,391,128 (-)NCBI
UNSW_CanFamBas_1.01417,862,908 - 18,101,297 (-)NCBI
UU_Cfam_GSD_1.01418,137,407 - 18,377,659 (-)NCBI
Cdk6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511831,562,931 - 31,777,533 (-)NCBI
SpeTri2.0NW_0049368031,025,047 - 1,229,396 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDK6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl972,518,101 - 72,764,129 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1972,510,858 - 72,765,631 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2979,239,881 - 79,316,977 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDK6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12156,167,731 - 56,403,976 (+)NCBI
ChlSab1.1 Ensembl2156,170,450 - 56,393,808 (+)Ensembl
Vero_WHO_p1.0NW_02366604247,876,694 - 48,113,340 (-)NCBI
Cdk6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624809349,453 - 588,986 (+)NCBI


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
70222Eae2Experimental allergic encephalomyelitis QTL 24.3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)42133334339505420Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42133334344463908Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
8552803Bw144Body weight QTL 14416body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)42271068534430484Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:56
Count of miRNA genes:49
Interacting mature miRNAs:53
Transcripts:ENSRNOT00000012597
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 1 18 26 16 17 16 31 29 39 11
Low 2 25 31 25 2 25 8 9 43 6 2 8
Below cutoff 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012597   ⟹   ENSRNOP00000012597
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl430,646,460 - 30,828,229 (-)Ensembl
Rnor_6.0 Ensembl427,785,647 - 27,966,398 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104799   ⟹   ENSRNOP00000087481
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl430,648,341 - 30,829,634 (-)Ensembl
RefSeq Acc Id: NM_001191861   ⟹   NP_001178790
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,646,460 - 30,826,780 (-)NCBI
Rnor_6.0427,785,640 - 27,966,398 (-)NCBI
Rnor_5.0427,685,042 - 27,872,388 (-)NCBI
Celera426,070,823 - 26,248,747 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236019   ⟹   XP_006236081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,637,650 - 30,828,148 (-)NCBI
Rnor_6.0427,781,728 - 27,967,870 (-)NCBI
Rnor_5.0427,685,042 - 27,872,388 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236020   ⟹   XP_006236082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,637,650 - 30,828,005 (-)NCBI
Rnor_6.0427,781,728 - 27,967,870 (-)NCBI
Rnor_5.0427,685,042 - 27,872,388 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006236021   ⟹   XP_006236083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,637,650 - 30,829,688 (-)NCBI
Rnor_6.0427,781,728 - 27,969,653 (-)NCBI
Rnor_5.0427,685,042 - 27,872,388 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039106910   ⟹   XP_038962838
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,732,962 - 30,829,688 (-)NCBI
RefSeq Acc Id: XR_005503140
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,647,075 - 30,829,688 (-)NCBI
RefSeq Acc Id: XR_005503141
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2430,697,997 - 30,829,688 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001178790   ⟸   NM_001191861
- UniProtKB: F1MA87 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236083   ⟸   XM_006236021
- Peptide Label: isoform X1
- UniProtKB: F1MA87 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236081   ⟸   XM_006236019
- Peptide Label: isoform X1
- UniProtKB: F1MA87 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006236082   ⟸   XM_006236020
- Peptide Label: isoform X1
- UniProtKB: F1MA87 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012597   ⟸   ENSRNOT00000012597
RefSeq Acc Id: XP_038962838   ⟸   XM_039106910
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000087481   ⟸   ENSRNOT00000104799
Protein Domains
Protein kinase

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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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:621121 AgrOrtholog
Ensembl Genes ENSRNOG00000009258 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012597 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012597 ENTREZGENE, UniProtKB/TrEMBL
InterPro CDK6 UniProtKB/TrEMBL
  Kinase-like_dom UniProtKB/TrEMBL
  Prot_kinase_cat_dom UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/TrEMBL
KEGG Report rno:114483 UniProtKB/TrEMBL
NCBI Gene 114483 ENTREZGENE
Pfam Pkinase UniProtKB/TrEMBL
PhenoGen Cdk6 PhenoGen
PROSITE PROTEIN_KINASE_ATP UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/TrEMBL
SMART S_TKc UniProtKB/TrEMBL
Superfamily-SCOP Kinase_like UniProtKB/TrEMBL
UniProt F1MA87 ENTREZGENE, UniProtKB/TrEMBL
  Q99MD0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Cdk6  cyclin-dependent kinase 6      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Cdk6        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease upregulated in hormone-dependent endometrial cancers 70348
gene_disease upregulated in hormone-dependent endometrial cancers 70557
gene_expression expressed in uterus 70348
gene_expression expressed in uterus 70557