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

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Gene: Prkdc (protein kinase, DNA-activated, catalytic subunit) Rattus norvegicus
Analyze
Symbol: Prkdc
Name: protein kinase, DNA-activated, catalytic subunit
RGD ID: 1308982
Description: Predicted to enable several functions, including RNA polymerase II-specific DNA-binding transcription factor binding activity; U3 snoRNA binding activity; and protein serine/threonine kinase activity. Involved in several processes, including hematopoietic or lymphoid organ development; negative regulation of cellular senescence; and negative regulation of response to gamma radiation. Predicted to be located in nucleolus. Predicted to be part of several cellular components, including nucleus; protein-DNA complex; and small-subunit processome. Predicted to be active in chromatin and nucleus. Used to study severe combined immunodeficiency. Human ortholog(s) of this gene implicated in immunodeficiency 26. Orthologous to human PRKDC (protein kinase, DNA-activated, catalytic subunit); PARTICIPATES IN non-homologous end joining pathway of double-strand break repair; phosphatidylinositol 3-kinase-Akt signaling pathway; INTERACTS WITH (+)-schisandrin B; 1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DNA-dependent protein kinase catalytic subunit; LOC360748; MGC189093
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: Prkdcem1Kyo ; Prkdcem2Kyo ; Prkdcem4Kyo ; Prkdcem1Sage
Genetic Models: SD-Prkdcem1Sage ; TM-Prkdcem4KyoIl2rgem5Kyo ; F344-Prkdcem2KyoIl2rgem6Kyo ; F344-Prkdcem1Kyo
Is Marker For: Strains:   F344-Prkdcem1Kyo ; F344-Prkdcem2KyoIl2rgem6Kyo ; TM-Prkdcem4KyoIl2rgem5Kyo
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81198,544,952 - 98,762,499 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1198,544,954 - 98,762,108 (-)EnsemblGRCr8
mRatBN7.21185,040,790 - 85,258,357 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1185,040,792 - 85,257,952 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1193,767,902 - 93,984,974 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01186,429,067 - 86,646,132 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01185,482,663 - 85,699,739 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01189,293,547 - 89,510,948 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1189,293,696 - 89,510,871 (-)Ensemblrn6Rnor6.0
Rnor_5.01192,347,175 - 92,565,022 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41186,951,420 - 87,169,229 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1183,781,535 - 83,998,574 (-)NCBICelera
RGSC_v3.11186,992,362 - 87,209,825 (-)NCBI
Cytogenetic Map11q23NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-alpha-phellandrene  (ISO)
(-)-demecolcine  (ISO)
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (EXP)
1-chloro-2,4-dinitrobenzene  (ISO)
1-nitropyrene  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-tribromophenol  (ISO)
2,6-dimethoxyphenol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-aminobenzamide  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-Nitrofluoranthene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-amino-1,8-naphthalimide  (ISO)
4-hydroxynon-2-enal  (ISO)
4-nitrophenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (ISO)
acrolein  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
alpha-phellandrene  (ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
aphidicolin  (ISO)
arecoline  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-lapachone  (ISO)
biphenyl-4-amine  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (ISO)
bisphenol AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
bromoacetate  (ISO)
butanal  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
capsaicin  (ISO)
casticin  (ISO)
chlorpyrifos  (ISO)
chromium atom  (ISO)
cisplatin  (ISO)
citalopram  (EXP)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
curcumin  (ISO)
deguelin  (ISO)
dexamethasone  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP,ISO)
dichlorvos  (EXP)
dicrotophos  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
etoposide  (ISO)
folic acid  (ISO)
FR900359  (ISO)
fulvestrant  (ISO)
furan  (EXP)
furfural  (ISO)
gallic acid  (ISO)
glyphosate  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
indometacin  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
josamycin  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
lycopene  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methapyrilene  (ISO)
monocrotaline  (ISO)
motexafin gadolinium  (ISO)
myristicin  (ISO)
N-acetyl-L-cysteine  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP,ISO)
ochratoxin A  (EXP)
ouabain  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenol  (ISO)
phenytoin  (ISO)
phosphoramide mustard  (EXP)
pifithrin-alpha hydrobromide  (ISO)
pirinixic acid  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium chloride  (ISO)
tamibarotene  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
trovafloxacin  (ISO)
tungsten  (ISO)
urethane  (ISO)
usnic acid  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)
zinc acetate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component

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

References - curated
# Reference Title Reference Citation
1. Nonsense mutation at Tyr-4046 in the DNA-dependent protein kinase catalytic subunit of severe combined immune deficiency mice. Araki R, etal., Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2438-43.
2. Severe-combined immunodeficient rats can be used to generate a model of perinatal hypoxic-ischemic brain injury to facilitate studies of engrafted human neural stem cells. Beldick SR, etal., PLoS One. 2018 Nov 28;13(11):e0208105. doi: 10.1371/journal.pone.0208105. eCollection 2018.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Lieber MR Annu Rev Biochem. 2010;79:181-211. doi: 10.1146/annurev.biochem.052308.093131.
6. Generation and characterization of severe combined immunodeficiency rats. Mashimo T, etal., Cell Rep. 2012 Sep 27;2(3):685-94. doi: 10.1016/j.celrep.2012.08.009. Epub 2012 Sep 13.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
9. GOA pipeline RGD automated data pipeline
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Comprehensive gene review and curation RGD comprehensive gene curation
13. Habitual exercise increases resistance of lymphocytes to oxidant-induced DNA damage by upregulating expression of antioxidant and DNA repairing enzymes. Siu PM, etal., Exp Physiol. 2011 Sep;96(9):889-906. doi: 10.1113/expphysiol.2011.058396. Epub 2011 May 27.
14. Genotoxic stress response gene expression in the mid-organogenesis rat conceptus. Vinson RK and Hales BF, Toxicol Sci. 2003 Jul;74(1):157-64. Epub 2003 May 2.
Additional References at PubMed
PMID:7671312   PMID:8133891   PMID:8788039   PMID:8889548   PMID:9768755   PMID:11751629   PMID:12477932   PMID:12604618   PMID:15010310   PMID:15194694   PMID:16166097   PMID:16687486  
PMID:17145779   PMID:18710952   PMID:19135898   PMID:19303849   PMID:19946888   PMID:20150414   PMID:20383123   PMID:20972425   PMID:21731742   PMID:22139836   PMID:22504299   PMID:22658674  
PMID:22681889   PMID:23836881   PMID:23979707   PMID:24158435   PMID:24485452   PMID:25852083   PMID:25941166   PMID:26237645   PMID:27829214   PMID:28712728   PMID:32103174   PMID:33450132  
PMID:34797489  


Genomics

Comparative Map Data
Prkdc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81198,544,952 - 98,762,499 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1198,544,954 - 98,762,108 (-)EnsemblGRCr8
mRatBN7.21185,040,790 - 85,258,357 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1185,040,792 - 85,257,952 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1193,767,902 - 93,984,974 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01186,429,067 - 86,646,132 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01185,482,663 - 85,699,739 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01189,293,547 - 89,510,948 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1189,293,696 - 89,510,871 (-)Ensemblrn6Rnor6.0
Rnor_5.01192,347,175 - 92,565,022 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41186,951,420 - 87,169,229 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1183,781,535 - 83,998,574 (-)NCBICelera
RGSC_v3.11186,992,362 - 87,209,825 (-)NCBI
Cytogenetic Map11q23NCBI
PRKDC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38847,773,111 - 47,960,136 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl847,773,108 - 47,960,182 (-)Ensemblhg38GRCh38
GRCh37848,685,672 - 48,872,696 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36848,848,222 - 49,035,296 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34848,848,221 - 49,035,296NCBI
Celera844,671,051 - 44,858,151 (-)NCBICelera
Cytogenetic Map8q11.21NCBI
HuRef844,148,581 - 44,335,706 (-)NCBIHuRef
CHM1_1848,738,053 - 48,925,105 (-)NCBICHM1_1
T2T-CHM13v2.0848,149,356 - 48,336,384 (-)NCBIT2T-CHM13v2.0
Prkdc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391615,455,698 - 15,660,103 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1615,455,730 - 15,660,099 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381615,637,444 - 15,842,239 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1615,637,866 - 15,842,235 (+)Ensemblmm10GRCm38
MGSCv371615,637,959 - 15,842,332 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361615,551,467 - 15,755,813 (+)NCBIMGSCv36mm8
Celera1616,214,291 - 16,413,213 (+)NCBICelera
Cytogenetic Map16A2NCBI
cM Map1610.09NCBI
Prkdc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554547,733,978 - 7,890,867 (-)Ensembl
ChiLan1.0NW_0049554547,733,697 - 7,890,896 (-)NCBIChiLan1.0ChiLan1.0
PRKDC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2763,407,112 - 63,593,508 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1839,100,871 - 39,287,251 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0844,201,391 - 44,386,803 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1841,593,022 - 41,778,299 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl841,593,029 - 41,778,299 (-)EnsemblpanPan2panpan1.1
PRKDC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12924,904 - 243,926 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2935,007 - 243,895 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha29449,958 - 669,362 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02920,665 - 241,975 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2922,025 - 241,944 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12920,944 - 240,298 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.029218,160 - 435,150 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.029285,564 - 503,393 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Prkdc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530379,533,069 - 79,697,823 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365904,722,873 - 4,890,156 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365904,722,914 - 4,887,615 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRKDC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl479,687,375 - 79,846,656 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1479,687,375 - 79,850,146 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2487,185,946 - 87,343,690 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRKDC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1843,915,226 - 44,119,547 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl843,914,636 - 44,119,541 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603997,968,963 - 98,158,648 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prkdc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247357,534,506 - 7,700,305 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247357,534,483 - 7,702,079 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Prkdc
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14986,537 - 1,186,900 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:33
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000035247, ENSRNOT00000065799
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)117385089499753367Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)115892833699753367Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)116796218499753367Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)116985594399753367Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)117330831599753367Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)117961851999753367Rat

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


Related Rat Strains
The following Strains have been annotated to Prkdc
F344-Prkdcem1Kyo     F344-Prkdcem2KyoIl2rgem6Kyo     TM-Prkdcem4KyoIl2rgem5Kyo    


Genetic Models
This gene Prkdc is modified in the following models/strains:
SD-Prkdcem1Sage     TM-Prkdcem4KyoIl2rgem5Kyo     F344-Prkdcem2KyoIl2rgem6Kyo     F344-Prkdcem1Kyo    


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000035247   ⟹   ENSRNOP00000037412
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1198,544,954 - 98,762,108 (-)Ensembl
mRatBN7.2 Ensembl1185,040,792 - 85,257,952 (-)Ensembl
Rnor_6.0 Ensembl1189,293,696 - 89,510,871 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000115346   ⟹   ENSRNOP00000081845
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1198,544,954 - 98,762,108 (-)Ensembl
mRatBN7.2 Ensembl1185,040,792 - 85,257,952 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000115554   ⟹   ENSRNOP00000090424
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1198,544,954 - 98,762,108 (-)Ensembl
mRatBN7.2 Ensembl1185,040,792 - 85,257,952 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000144394   ⟹   ENSRNOP00000103526
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1198,544,954 - 98,762,108 (-)Ensembl
RefSeq Acc Id: NM_001108327   ⟹   NP_001101797
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81198,544,952 - 98,762,108 (-)NCBI
mRatBN7.21185,040,790 - 85,257,952 (-)NCBI
RefSeq Acc Id: XM_008768933   ⟹   XP_008767155
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81198,544,956 - 98,762,322 (-)NCBI
mRatBN7.21185,040,790 - 85,258,185 (-)NCBI
Rnor_6.01189,293,547 - 89,510,948 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598214   ⟹   XP_017453703
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81198,544,956 - 98,728,238 (-)NCBI
mRatBN7.21185,040,790 - 85,224,080 (-)NCBI
Rnor_6.01189,293,547 - 89,476,765 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088537   ⟹   XP_038944465
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81198,544,956 - 98,762,499 (-)NCBI
mRatBN7.21185,040,790 - 85,258,357 (-)NCBI
RefSeq Acc Id: XP_008767155   ⟸   XM_008768933
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ADM3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017453703   ⟸   XM_017598214
- Peptide Label: isoform X3
- UniProtKB: A0A8I5ZT26 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000037412   ⟸   ENSRNOT00000035247
RefSeq Acc Id: XP_038944465   ⟸   XM_039088537
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZT26 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001101797   ⟸   NM_001108327
- UniProtKB: D3ZTN0 (UniProtKB/TrEMBL),   A0A8I6ADM3 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000081845   ⟸   ENSRNOT00000115346
Ensembl Acc Id: ENSRNOP00000090424   ⟸   ENSRNOT00000115554
Ensembl Acc Id: ENSRNOP00000103526   ⟸   ENSRNOT00000144394
Protein Domains
FAT   FATC   PI3K/PI4K catalytic

Transcriptome

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

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308982 AgrOrtholog
BioCyc Gene G2FUF-20542 BioCyc
Ensembl Genes ENSRNOG00000025028 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035247 ENTREZGENE
  ENSRNOT00000035247.9 UniProtKB/TrEMBL
  ENSRNOT00000115346.2 UniProtKB/TrEMBL
  ENSRNOT00000115554.2 UniProtKB/TrEMBL
  ENSRNOT00000144394.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1070.11 UniProtKB/TrEMBL
  1.25.10.10 UniProtKB/TrEMBL
  Phosphatidylinositol 3-kinase Catalytic Subunit, Chain A, domain 4 UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  DDR_Repair_Kinase UniProtKB/TrEMBL
  DNA-PK_dom UniProtKB/TrEMBL
  DNA-PKcs_N UniProtKB/TrEMBL
  DNAPKcs_CC1-2 UniProtKB/TrEMBL
  DNAPKcs_CC5 UniProtKB/TrEMBL
  FATC UniProtKB/TrEMBL
  Kinase-like_dom UniProtKB/TrEMBL
  NUC194 UniProtKB/TrEMBL
  PI3/4_kinase_cat_dom UniProtKB/TrEMBL
  PI3/4_kinase_cat_sf UniProtKB/TrEMBL
  PI3/4_kinase_CS UniProtKB/TrEMBL
  PIK-rel_kinase_FAT UniProtKB/TrEMBL
  PIK_FAT UniProtKB/TrEMBL
NCBI Gene 360748 ENTREZGENE
PANTHER ATAXIA TELANGIECTASIA MUTATED ATM -RELATED UniProtKB/TrEMBL
  DNA-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT UniProtKB/TrEMBL
Pfam DNA-PKcs_N UniProtKB/TrEMBL
  DNAPKcs_CC1-2 UniProtKB/TrEMBL
  DNAPKcs_CC5 UniProtKB/TrEMBL
  FAT UniProtKB/TrEMBL
  FATC UniProtKB/TrEMBL
  NUC194 UniProtKB/TrEMBL
  PI3_PI4_kinase UniProtKB/TrEMBL
PhenoGen Prkdc PhenoGen
PROSITE FAT UniProtKB/TrEMBL
  FATC UniProtKB/TrEMBL
  PI3_4_KINASE_1 UniProtKB/TrEMBL
  PI3_4_KINASE_2 UniProtKB/TrEMBL
  PI3_4_KINASE_3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025028 RatGTEx
SMART FATC UniProtKB/TrEMBL
  NUC194 UniProtKB/TrEMBL
  PI3Kc UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
  Kinase_like UniProtKB/TrEMBL
UniProt A0A8I5ZT26 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6ADM3 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LP43_RAT UniProtKB/TrEMBL
  D3ZTN0 ENTREZGENE, UniProtKB/TrEMBL


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