Cdk5 (cyclin-dependent kinase 5) - Rat Genome Database

Send us a Message



 Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper VCMap
Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Cdk5 (cyclin-dependent kinase 5) Rattus norvegicus
Analyze
Symbol: Cdk5
Name: cyclin-dependent kinase 5
RGD ID: 70514
Description: Enables several functions, including ephrin receptor binding activity; protein kinase activity; and voltage-gated calcium channel activity involved in positive regulation of presynaptic cytosolic calcium levels. Involved in several processes, including cellular response to amyloid-beta; positive regulation of apoptotic process; and protein phosphorylation. Acts upstream of or within protein phosphorylation. Located in several cellular components, including Schaffer collateral - CA1 synapse; glutamatergic synapse; and postsynaptic density. Part of protein kinase 5 complex. Colocalizes with microtubule. Used to study brain ischemia; mental depression; and trigeminal neuralgia. Biomarker of Alzheimer's disease; transient cerebral ischemia; and vascular dementia. Human ortholog(s) of this gene implicated in Alzheimer's disease and lissencephaly 7 with cerebellar hypoplasia. Orthologous to human CDK5 (cyclin dependent kinase 5); PARTICIPATES IN dopamine signaling pathway; ephrin - ephrin receptor bidirectional signaling axis; Reelin signaling pathway; INTERACTS WITH (+)-schisandrin B; (S)-amphetamine; (S)-colchicine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cell division protein kinase 5; cyclin-dependent-like kinase 5; serine/threonine-protein kinase PSSALRE; tau protein kinase II catalytic subunit; TPKII catalytic subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   BB/OK  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2410,754,682 - 10,760,110 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl410,754,687 - 10,760,112 (+)Ensembl
Rnor_6.047,282,945 - 7,287,427 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl47,282,948 - 7,288,383 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.047,294,309 - 7,298,791 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.446,119,704 - 6,124,186 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.146,119,703 - 6,124,185 (+)NCBI
Celera46,369,255 - 6,373,737 (+)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(S)-amphetamine  (EXP)
(S)-colchicine  (EXP)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
acrylamide  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alvocidib  (EXP)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
antimycin A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP)
atrazine  (ISO)
azoxystrobin  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
cadmium dichloride  (EXP)
Calpeptin  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chlorpromazine  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
clozapine  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper(II) sulfate  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
deguelin  (ISO)
diarsenic trioxide  (EXP)
diazinon  (EXP)
diclofenac  (ISO)
diethylstilbestrol  (ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
fluoxetine  (ISO)
flutamide  (EXP)
folic acid  (ISO)
genistein  (ISO)
haloperidol  (EXP)
hydrogen peroxide  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
lead diacetate  (EXP,ISO)
lovastatin  (EXP)
lycopene  (ISO)
methamphetamine  (EXP,ISO)
methoxyacetic acid  (EXP)
methylseleninic acid  (ISO)
monosodium L-glutamate  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
nickel dichloride  (EXP)
oxidopamine  (EXP)
paracetamol  (ISO)
resveratrol  (EXP,ISO)
rimonabant  (ISO)
ritonavir  (ISO)
rotenone  (ISO)
sarin  (ISO)
simvastatin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sunitinib  (ISO)
tetrachloromethane  (EXP)
thifluzamide  (ISO)
troglitazone  (EXP)
tunicamycin  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
apoptotic process  (ISO)
associative learning  (ISO)
axon extension  (TAS)
axonogenesis  (IBA,ISO)
behavioral response to cocaine  (ISO)
calcium ion import  (ISO)
cell division  (IEA)
cell migration  (ISO)
cell-matrix adhesion  (ISO)
cellular response to amyloid-beta  (IDA)
central nervous system development  (TAS)
central nervous system neuron development  (ISO)
cerebellar cortex development  (ISO)
cerebellar cortex formation  (ISO)
cerebellum development  (ISO)
cerebral cortex development  (ISO)
corpus callosum development  (ISO)
cortical actin cytoskeleton organization  (IMP)
dendrite morphogenesis  (ISO)
excitatory postsynaptic potential  (ISO)
exocytosis  (IMP)
forebrain development  (ISO)
hippocampus development  (ISO)
histone phosphorylation  (IMP)
induction of synaptic vesicle exocytosis by positive regulation of presynaptic cytosolic calcium ion concentration  (IEA)
intracellular protein transport  (ISO)
layer formation in cerebral cortex  (ISO)
mitochondrion organization  (IMP)
motor neuron axon guidance  (ISO)
negative regulation of axon extension  (ISO)
negative regulation of cell cycle  (ISO)
negative regulation of neuron death  (ISO)
negative regulation of protein export from nucleus  (ISO)
negative regulation of protein ubiquitination  (ISO)
negative regulation of proteolysis  (ISO)
negative regulation of synaptic plasticity  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
neuron apoptotic process  (IBA,IMP,ISO)
neuron differentiation  (IDA,ISO)
neuron migration  (ISO)
neuron projection development  (IMP)
neuron projection morphogenesis  (IMP)
nucleocytoplasmic transport  (IMP)
oligodendrocyte differentiation  (ISO)
peptidyl-serine phosphorylation  (IDA,ISO)
peptidyl-threonine phosphorylation  (ISO)
phosphorylation  (ISO)
positive regulation of calcium ion-dependent exocytosis  (ISO)
positive regulation of glial cell apoptotic process  (IMP)
positive regulation of neuron apoptotic process  (IDA)
positive regulation of neuron death  (IMP)
positive regulation of presynaptic cytosolic calcium concentration  (IMP)
positive regulation of protein binding  (ISO)
positive regulation of protein kinase activity  (ISO)
positive regulation of protein phosphorylation  (IMP)
positive regulation of protein targeting to membrane  (ISO)
positive regulation of voltage-gated calcium channel activity  (IMP)
protein autophosphorylation  (IDA)
protein localization to synapse  (ISO)
protein phosphorylation  (IBA,IDA,ISO)
receptor catabolic process  (ISO)
receptor clustering  (ISO)
regulated exocytosis  (IMP)
regulation of cell migration  (ISO)
regulation of dendritic spine morphogenesis  (ISO,ISS)
regulation of postsynaptic membrane potential  (ISO)
regulation of protein localization to plasma membrane  (ISO)
regulation of synaptic plasticity  (IMP)
regulation of synaptic transmission, glutamatergic  (ISO)
regulation of transcription involved in G1/S transition of mitotic cell cycle  (IBA)
response to cocaine  (ISO)
response to wounding  (IMP)
rhythmic process  (IEA)
Schwann cell development  (ISO)
sensory perception of pain  (ISO)
serine phosphorylation of STAT protein  (ISO)
skeletal muscle tissue development  (IEP,ISO,TAS)
synapse assembly  (ISO)
synapse pruning  (EXP,IDA,IMP)
synaptic transmission, dopaminergic  (ISO)
synaptic transmission, glutamatergic  (ISO)
synaptic vesicle endocytosis  (IMP)
synaptic vesicle transport  (IBA)
telencephalon development  (ISO)
visual learning  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bhaskar K, etal., Neurochem Int. 2004 Jan;44(1):35-44.
2. Bibb JA, etal., Nature 2001 Mar 15;410(6826):376-80.
3. Cancino GI, etal., Neurobiol Aging. 2011 Jul;32(7):1249-61. doi: 10.1016/j.neurobiolaging.2009.07.007. Epub 2009 Aug 22.
4. Cao Y, etal., Acta Biochim Biophys Sin (Shanghai). 2016 May;48(5):437-46. doi: 10.1093/abbs/gmw024.
5. Cheng K, etal., J Biol Chem 2002 Aug 30;277(35):31988-93.
6. Cheung ZH, etal., PLoS Biol. 2007 Apr;5(4):e63.
7. Cho YE, etal., PLoS One. 2017 Jan 20;12(1):e0169945. doi: 10.1371/journal.pone.0169945. eCollection 2017.
8. Dhavan R, etal., J Neurosci. 2002 Sep 15;22(18):7879-91.
9. Fu AK, etal., Nat Neurosci. 2001 Apr;4(4):374-81.
10. Fu WY, etal., Nat Neurosci. 2007 Jan;10(1):67-76. Epub 2006 Dec 3.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. GOA data from the GO Consortium
13. Gong X, etal., Neuron. 2003 Apr 10;38(1):33-46.
14. Hellmich MR, etal., Proc Natl Acad Sci U S A 1992 Nov 15;89(22):10867-71.
15. Hou Z, etal., J Biol Chem. 2007 Jun 29;282(26):18666-70. Epub 2007 May 9.
16. Humbert S, etal., J Cell Sci. 2000 Mar;113 ( Pt 6):975-83.
17. Hyun HW, etal., Neurosci Res. 2017 Jun;119:24-37. doi: 10.1016/j.neures.2017.01.006. Epub 2017 Jan 30.
18. Kim SH and Ryan TA, J Neurosci. 2013 May 22;33(21):8937-50. doi: 10.1523/JNEUROSCI.4288-12.2013.
19. Li BS, etal., Proc Natl Acad Sci U S A 2001 Oct 23;98(22):12742-7.
20. Li T, etal., J Biol Chem. 2007 Mar 2;282(9):6619-28. Epub 2007 Jan 3.
21. Li W, etal., Shanghai Kou Qiang Yi Xue. 2010 Oct;19(5):545-8.
22. Meyer DA, etal., J Neurosci. 2014 Jun 11;34(24):8259-67. doi: 10.1523/JNEUROSCI.4368-13.2014.
23. Meyerson M, etal., EMBO J 1992 Aug;11(8):2909-17.
24. MGD data from the GO Consortium
25. Moy LY and Tsai LH, J Biol Chem. 2004 Dec 24;279(52):54487-93. Epub 2004 Oct 7.
26. NCBI rat LocusLink and RefSeq merged data July 26, 2002
27. Nguyen MD, etal., Neuron 2001 Apr;30(1):135-47.
28. Nikolic M, etal., Genes Dev. 1996 Apr 1;10(7):816-25.
29. Norrholm SD, etal., Neuroscience. 2003;116(1):19-22.
30. O'Hare MJ, etal., J Neurosci. 2005 Sep 28;25(39):8954-66.
31. Ohnishi T, etal., Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):E4465-74. doi: 10.1073/pnas.1421182112. Epub 2015 Jul 29.
32. Pant AC, etal., Brain Res. 1997 Aug 15;765(2):259-66.
33. Pareek TK, etal., Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):791-6. doi: 10.1073/pnas.0510405103. Epub 2006 Jan 9.
34. Pipeline to import KEGG annotations from KEGG into RGD
35. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
36. Prema A, etal., J Alzheimers Dis. 2017;60(s1):S209-S220. doi: 10.3233/JAD-161103.
37. Rademakers R, etal., Neurobiol Aging. 2005 Aug-Sep;26(8):1145-51. doi: 10.1016/j.neurobiolaging.2004.10.003. Epub 2004 Dec 22.
38. RGD automated data pipeline
39. RGD automated import pipeline for gene-chemical interactions
40. Sahlgren CM, etal., EMBO J. 2006 Oct 18;25(20):4808-19. Epub 2006 Oct 12.
41. Sahlgren CM, etal., Mol Cell Biol 2003 Jul;23(14):5090-106.
42. Sakaue F, etal., J Biol Chem. 2005 Sep 9;280(36):31522-9. Epub 2005 Jul 1.
43. Sandal T, etal., J Biol Chem 2002 Jun 7;277(23):20783-93.
44. Sarker KP and Lee KY, Oncogene. 2004 Aug 12;23(36):6064-70.
45. Sato K, etal., J Neurosci Res. 2007 Nov 1;85(14):3071-8. doi: 10.1002/jnr.21438.
46. Seeburg DP, etal., Neuron. 2008 May 22;58(4):571-83. doi: 10.1016/j.neuron.2008.03.021.
47. Shukla V, etal., J Alzheimers Dis. 2017;56(1):335-349. doi: 10.3233/JAD-160916.
48. Sun D, etal., J Biol Chem 1996 Jun 14;271(24):14245-51.
49. Tan TC, etal., Nat Cell Biol 2003 Aug;5(8):701-10.
50. Tian B, etal., Nat Cell Biol. 2009 Feb;11(2):211-8. doi: 10.1038/ncb1829. Epub 2009 Jan 18.
51. Tian F, etal., Neurosci Lett. 2015 Jan 1;584:50-5. doi: 10.1016/j.neulet.2014.09.049. Epub 2014 Oct 7.
52. Ubeda M, etal., J Biol Chem. 2006 Sep 29;281(39):28858-64. Epub 2006 Aug 3.
53. Walentinsson A, etal., Cancer Res 2001 Nov 15;61(22):8263-73.
54. Walentinsson A, etal., Mamm Genome 2001 Dec;12(12):900-8.
55. Wang J, etal., Nat Neurosci 2003 Oct;6(10):1039-47. Epub 2003 Sep 21.
56. Xin X, etal., J Cell Sci. 2004 Sep 15;117(Pt 20):4739-48. Epub 2004 Aug 25.
57. Xiong Y, etal., Cell 1992 Oct 30;71(3):505-14.
58. Yger M and Girault JA, Front Behav Neurosci. 2011 Sep 8;5:56. doi: 10.3389/fnbeh.2011.00056. eCollection 2011.
59. Zhao W, etal., Biochem Biophys Res Commun. 2017 Apr 15;485(4):775-781. doi: 10.1016/j.bbrc.2017.02.130. Epub 2017 Feb 27.
60. Zhen X, etal., Mol Pharmacol. 2004 Dec;66(6):1500-7. Epub 2004 Jul 30.
61. Zheng YL, etal., EMBO J. 2005 Jan 12;24(1):209-20. Epub 2004 Dec 9.
62. Zhu WL, etal., Int J Neuropsychopharmacol. 2012 Jul;15(6):795-809. doi: 10.1017/S1461145711000915. Epub 2011 Jun 20.
63. Zhu YS, etal., J Neurochem. 2005 Sep;94(6):1535-45. Epub 2005 Jun 30.
Additional References at PubMed
PMID:3627430   PMID:8855328   PMID:8891282   PMID:9126296   PMID:9191048   PMID:9202329   PMID:9698328   PMID:10407039   PMID:11163260   PMID:11226314   PMID:11517264   PMID:11978846  
PMID:12056836   PMID:12077184   PMID:12372285   PMID:12393264   PMID:12496365   PMID:12941275   PMID:14521924   PMID:14704270   PMID:14769920   PMID:15067135   PMID:15096606   PMID:15123626  
PMID:15342635   PMID:15489224   PMID:16203963   PMID:16237170   PMID:16996690   PMID:17060449   PMID:17108320   PMID:17113760   PMID:17121855   PMID:17150266   PMID:17194758   PMID:17327227  
PMID:17360491   PMID:17400554   PMID:17401652   PMID:17498664   PMID:17517623   PMID:17529984   PMID:17591690   PMID:17694053   PMID:17699587   PMID:17728463   PMID:17965932   PMID:18032654  
PMID:18032670   PMID:18042622   PMID:18054859   PMID:18351461   PMID:18385322   PMID:18460467   PMID:18480410   PMID:18616564   PMID:18625302   PMID:18628310   PMID:18662245   PMID:18701695  
PMID:18771616   PMID:18818692   PMID:18991853   PMID:19049962   PMID:19141975   PMID:19158499   PMID:19295160   PMID:19304511   PMID:19514269   PMID:19522735   PMID:19531642   PMID:19776350  
PMID:19782753   PMID:20213743   PMID:20357208   PMID:20684275   PMID:20720012   PMID:20826311   PMID:20886068   PMID:21145489   PMID:21187058   PMID:21378178   PMID:21389115   PMID:21457712  
PMID:21554958   PMID:21712386   PMID:21756775   PMID:21978141   PMID:22451679   PMID:22573681   PMID:22778260   PMID:22801079   PMID:22833568   PMID:22870316   PMID:22871113   PMID:22874667  
PMID:22899714   PMID:23000950   PMID:23022559   PMID:23056393   PMID:23077056   PMID:23123677   PMID:23164613   PMID:23415811   PMID:23786497   PMID:23816988   PMID:23954626   PMID:24189275  
PMID:24465591   PMID:24498195   PMID:24548080   PMID:24607229   PMID:24662752   PMID:24766160   PMID:24880860   PMID:25012575   PMID:25055140   PMID:25093719   PMID:25234403   PMID:25533468  
PMID:25598508   PMID:25819553   PMID:25831123   PMID:25843720   PMID:25864429   PMID:25903132   PMID:25931508   PMID:26088971   PMID:26104286   PMID:26179626   PMID:26503494   PMID:26658992  
PMID:26806339   PMID:26902776   PMID:27145370   PMID:27316643   PMID:27461471   PMID:27549397   PMID:28445771   PMID:28559121   PMID:28595035   PMID:28760951   PMID:28941293   PMID:29476059  
PMID:29564811   PMID:29705343   PMID:30537069   PMID:30562750   PMID:30875016   PMID:31156174   PMID:31163256   PMID:31186372   PMID:31403945   PMID:31744861   PMID:31786229   PMID:31983427  
PMID:32310180   PMID:32571373   PMID:32666227   PMID:32883957   PMID:33423166  


Genomics

Comparative Map Data
Cdk5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2410,754,682 - 10,760,110 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl410,754,687 - 10,760,112 (+)Ensembl
Rnor_6.047,282,945 - 7,287,427 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl47,282,948 - 7,288,383 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.047,294,309 - 7,298,791 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.446,119,704 - 6,124,186 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.146,119,703 - 6,124,185 (+)NCBI
Celera46,369,255 - 6,373,737 (+)NCBICelera
Cytogenetic Map4q11NCBI
CDK5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7151,053,815 - 151,057,897 (-)EnsemblGRCh38hg38GRCh38
GRCh387151,053,815 - 151,057,897 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh377150,750,902 - 150,754,984 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367150,381,832 - 150,385,929 (-)NCBINCBI36hg18NCBI36
Build 347150,188,546 - 150,192,644NCBI
Celera7145,308,208 - 145,312,361 (-)NCBI
Cytogenetic Map7q36.1NCBI
HuRef7144,563,235 - 144,567,388 (-)NCBIHuRef
CHM1_17150,759,247 - 150,763,400 (-)NCBICHM1_1
CRA_TCAGchr7v27150,080,438 - 150,084,591 (-)NCBI
Cdk5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39524,612,595 - 24,628,737 (-)NCBIGRCm39mm39
GRCm39 Ensembl524,623,239 - 24,628,528 (-)Ensembl
GRCm38524,407,597 - 24,423,587 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl524,418,241 - 24,423,530 (-)EnsemblGRCm38mm10GRCm38
MGSCv37523,924,060 - 23,929,348 (-)NCBIGRCm37mm9NCBIm37
MGSCv36523,928,307 - 23,933,595 (-)NCBImm8
Celera521,368,049 - 21,373,342 (-)NCBICelera
Cytogenetic Map5A3NCBI
cM Map511.73NCBI
Cdk5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554915,491,744 - 5,497,280 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554915,491,744 - 5,497,280 (-)NCBIChiLan1.0ChiLan1.0
CDK5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17154,793,344 - 154,797,499 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7154,793,344 - 154,797,499 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07142,640,630 - 142,644,785 (-)NCBIMhudiblu_PPA_v0panPan3
CDK5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11615,105,177 - 15,113,085 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1615,101,230 - 15,109,269 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1615,713,427 - 15,717,637 (-)NCBI
ROS_Cfam_1.01616,827,407 - 16,831,617 (-)NCBI
UMICH_Zoey_3.11615,199,846 - 15,204,056 (-)NCBI
UNSW_CanFamBas_1.01615,781,300 - 15,785,509 (-)NCBI
UU_Cfam_GSD_1.01615,832,007 - 15,836,217 (-)NCBI
Cdk5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244051186,419,559 - 6,424,495 (+)NCBI
SpeTri2.0NW_0049365276,478,934 - 6,483,848 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDK5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1186,166,914 - 6,171,157 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2186,536,973 - 6,541,192 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap18q12-q13NCBI
CDK5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121119,235,687 - 119,240,163 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607215,206,191 - 15,211,917 (-)NCBIVero_WHO_p1.0
Cdk5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248005,562,468 - 5,566,458 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
PMC30213P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2410,755,427 - 10,755,743 (+)MAPPERmRatBN7.2
Rnor_6.047,283,686 - 7,284,001NCBIRnor6.0
Rnor_5.047,295,050 - 7,295,365UniSTSRnor5.0
RGSC_v3.446,120,445 - 6,120,760UniSTSRGSC3.4
Celera46,369,996 - 6,370,311UniSTS
Cytogenetic Map4q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
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
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
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


Related Rat Strains
The following Strains have been annotated to Cdk5

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:164
Count of miRNA genes:120
Interacting mature miRNAs:131
Transcripts:ENSRNOT00000011052
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 29 22 6 18 6 74 29 35 11
Low 14 35 35 1 35 8 11 6 6 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011052   ⟹   ENSRNOP00000011052
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl410,754,690 - 10,760,112 (+)Ensembl
Rnor_6.0 Ensembl47,282,948 - 7,288,383 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095452   ⟹   ENSRNOP00000078022
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl410,754,687 - 10,759,166 (+)Ensembl
RefSeq Acc Id: NM_080885   ⟹   NP_543161
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2410,754,687 - 10,759,169 (+)NCBI
Rnor_6.047,282,945 - 7,287,427 (+)NCBI
Rnor_5.047,294,309 - 7,298,791 (+)NCBI
RGSC_v3.446,119,704 - 6,124,186 (+)RGD
Celera46,369,255 - 6,373,737 (+)RGD
Sequence:
RefSeq Acc Id: XR_005503144
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2410,754,682 - 10,760,110 (+)NCBI
Protein Sequences
Protein RefSeqs NP_543161 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40902 (Get FASTA)   NCBI Sequence Viewer  
  EDL99365 (Get FASTA)   NCBI Sequence Viewer  
  EDL99366 (Get FASTA)   NCBI Sequence Viewer  
  EDL99367 (Get FASTA)   NCBI Sequence Viewer  
  Q03114 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_543161   ⟸   NM_080885
- UniProtKB: Q03114 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011052   ⟸   ENSRNOT00000011052
RefSeq Acc Id: ENSRNOP00000078022   ⟸   ENSRNOT00000095452
Protein Domains
Protein kinase

Transcriptome

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

Promoters
RGD ID:13692790
Promoter ID:EPDNEW_R3315
Type:initiation region
Name:Cdk5_1
Description:cyclin-dependent kinase 5
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_6.047,282,962 - 7,283,022EPDNEW

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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 7283668 7283669 A C snv MWF/Hsd (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70514 AgrOrtholog
Ensembl Genes ENSRNOG00000008017 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000011052 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000011052 UniProtKB/Swiss-Prot
InterPro Kinase-like_dom_sf UniProtKB/Swiss-Prot
  Prot_kinase_dom UniProtKB/Swiss-Prot
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot
KEGG Report rno:140908 UniProtKB/Swiss-Prot
NCBI Gene 140908 ENTREZGENE
Pfam Pkinase UniProtKB/Swiss-Prot
PhenoGen Cdk5 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 CDK5_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Cdk5  cyclin-dependent kinase 5      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 Cdk5  cyclin-dependent kinase 5      Symbol and Name status set to provisional 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease upregulated in uterine tumors 70557
gene_expression expressed in uterus 70557
gene_expression prominently expressed in the central nervous system 632377
gene_function phosphorylates serine/threonine sites in (K/RT/SPXK)-type motifs, including synaptic proteins; associates with and phosphorylates NMDA receptor modulatory subunits (Grin2a) 70569
gene_physical_interaction interacts with Pctaire1 at the neuromuscular junction in cultured myotubes and skeletal muscle 632377
gene_process necessary for cAMP-induced apoptosis and inhibition of activity can prevent the cleavage of pro-caspase-3 in cAMP-treated cells 625522
gene_process plays an essential role in neuronal migration, neurite outgrowth, and laminar configuration of the cerebral cortex 69667
gene_process may play a key role in synaptic transmission and plasticity through its up-regulation of N-methyl-D-aspartate (NMDA) class of glutamate receptors (NMDARs) 70569