Chek2 (checkpoint kinase 2) - Rat Genome Database

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Gene: Chek2 (checkpoint kinase 2) Rattus norvegicus
Analyze
Symbol: Chek2
Name: checkpoint kinase 2
RGD ID: 621543
Description: Exhibits protein serine/threonine kinase activity. Involved in several processes, including cellular response to bisphenol A; positive regulation of anoikis; and positive regulation of cell cycle. Localizes to nucleus. Predicted to colocalize with chromosome, telomeric region. Biomarker of urinary bladder cancer. Human ortholog(s) of this gene implicated in several diseases, including Li-Fraumeni syndrome 2; breast cancer (multiple); colorectal cancer; osteosarcoma; and prostate cancer. Orthologous to human CHEK2 (checkpoint kinase 2); PARTICIPATES IN p53 signaling pathway; cell cycle pathway, mitotic; INTERACTS WITH 17beta-estradiol; 2,6-dinitrotoluene; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Chk2; CHK2 checkpoint homolog; CHK2 checkpoint homolog (S. pombe); protein kinase Chk2; Rad53; serine/threonine-protein kinase Chk2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21245,788,823 - 45,821,382 (-)NCBI
Rnor_6.0 Ensembl1251,845,796 - 51,877,624 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01251,845,574 - 51,878,098 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01253,583,932 - 53,616,450 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41245,933,900 - 45,965,427 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11245,797,764 - 45,829,292 (-)NCBI
Celera1247,348,969 - 47,380,486 (-)NCBICelera
Cytogenetic Map12q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
B-lymphoblastic leukemia/lymphoma  (ISO)
bone osteosarcoma  (ISO)
breast cancer  (ISO)
Breast Cancer, Familial  (ISO)
Breast Neoplasms  (ISO)
colitis  (ISO)
colon cancer  (ISO)
colon carcinoma  (ISO)
colorectal cancer  (ISO)
Colorectal Neoplasms  (ISO)
Congenital Heart Defects, Multiple Types, 3  (ISO)
congestive heart failure  (ISO)
diffuse midline glioma, H3 K27M-mutant  (ISO)
disease of cellular proliferation  (ISO)
Disease Progression  (ISO)
embryonal carcinoma  (ISO)
endometrial carcinoma  (ISO)
Endometrioid Carcinomas  (ISO)
Familial Prostate Cancer  (ISO)
gastrointestinal carcinoma  (ISO)
Gastrointestinal Hemorrhage  (ISO)
genetic disease  (ISO)
hereditary breast ovarian cancer syndrome  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
high grade glioma  (ISO)
Kidney Neoplasms  (IEP)
leiomyosarcoma  (ISO)
Li-Fraumeni syndrome  (ISO)
Li-Fraumeni syndrome 1  (ISO)
Li-Fraumeni syndrome 2  (ISO)
Lung Neoplasms  (ISO)
male breast cancer  (ISO)
Male Breast Neoplasms  (ISO)
Metabolic Syndrome  (IEP)
NATURAL KILLER CELL ENTEROPATHY  (ISO)
nephroblastoma  (ISO)
neuroblastoma  (ISO)
neurofibromatosis 2  (ISO)
non-Hodgkin lymphoma  (ISO)
osteosarcoma  (ISO)
ovarian cancer  (ISO)
Ovarian Neoplasms  (ISO)
pancreatic cancer  (ISO)
pancreatic carcinoma  (ISO)
primary ovarian insufficiency  (ISO)
prostate cancer  (ISO)
Prostate Cancer, Somatic  (ISO)
Prostatic Neoplasms  (ISO)
sarcoma  (ISO)
seminoma  (ISO)
squamous cell neoplasm  (ISO)
Stargardt disease  (ISO)
Stargardt Disease 1  (ISO)
Stomach Neoplasms  (ISO)
thrombocytopenia  (ISO)
Triple Negative Breast Neoplasms  (ISO)
urinary bladder cancer  (IEP,ISO)
Uterine Cervical Neoplasms  (ISO)
Vulvar Neoplasms  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1S)-bornane-2,3-dione  (ISO)
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-amino-1,8-naphthalimide  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-(cyclohexylmethoxy)-5-nitrosopyrimidine-2,4-diamine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrylamide  (EXP)
aflatoxin B2  (ISO)
Aflatoxin G1  (ISO)
ammonium chloride  (EXP)
amphibole asbestos  (ISO)
anthocyanin  (ISO)
antirheumatic drug  (ISO)
aphidicolin  (ISO)
aristolochic acid  (ISO)
arsenous acid  (EXP,ISO)
artesunate  (ISO)
atrazine  (ISO)
auraptene  (ISO)
benzo[a]pyrene  (ISO)
berberine  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
bleomycin A2  (ISO)
Brevetoxin B  (ISO)
busulfan  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
camptothecin  (ISO)
capsaicin  (ISO)
casticin  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP,ISO)
clofarabine  (ISO)
cobalt atom  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
curcumin  (ISO)
decabromodiphenyl ether  (ISO)
diarsenic trioxide  (EXP,ISO)
dibutyl phthalate  (ISO)
dichlorvos  (EXP)
dieldrin  (EXP)
diethyl sulfate  (ISO)
digitoxin  (ISO)
dihydroxyacetone  (ISO)
dimethyl sulfoxide  (ISO)
dimethylarsinic acid  (EXP)
dioscin  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (ISO)
Enterolactone  (ISO)
etoposide  (ISO)
fenofibrate  (EXP)
fenvalerate  (EXP)
fisetin  (ISO)
flavanones  (ISO)
floxuridine  (ISO)
fluoranthene  (ISO)
flutamide  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (EXP)
furan  (EXP,ISO)
furosemide  (EXP)
genistein  (ISO)
Goe 6976  (ISO)
GW 4064  (ISO)
hellebrigenin  (ISO)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
indole-3-methanol  (EXP)
irinotecan  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
isoflavones  (ISO)
isoflurane  (EXP)
kaempferol  (ISO)
kojic acid  (EXP)
L-ascorbic acid  (EXP,ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leptomycin B  (ISO)
levonorgestrel  (ISO)
lovastatin  (EXP)
melphalan  (ISO)
metformin  (ISO)
methoxsalen  (ISO)
methyl isocyanate  (ISO)
methylmercury chloride  (EXP)
methylseleninic acid  (ISO)
mitomycin C  (ISO)
monocrotaline  (ISO)
morin  (ISO)
myristicin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (EXP)
nicotine  (ISO)
Nonidet P-40  (ISO)
O-methyleugenol  (EXP)
octamethylcyclotetrasiloxane  (ISO)
oroxylin A  (ISO)
oxaliplatin  (EXP,ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
pentobarbital  (EXP)
phenytoin  (ISO)
platinum  (ISO)
platinum(0)  (ISO)
potassium chromate  (ISO)
promethazine  (EXP)
quercetin  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
silibinin  (ISO)
silicon dioxide  (ISO)
silver(1+) nitrate  (ISO)
sodium arsenite  (ISO)
sterigmatocystin  (ISO)
sunitinib  (ISO)
T-2 toxin  (ISO)
temozolomide  (ISO)
testosterone  (ISO)
testosterone undecanoate  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
tungsten  (EXP)
urethane  (ISO)
usnic acid  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
wortmannin  (ISO)
zidovudine  (ISO)
zinc pyrithione  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bartkova J, etal., Oncogene. 2001 Sep 13;20(41):5897-902.
2. Chaturvedi P, etal., Oncogene 1999 Jul 15;18(28):4047-54.
3. Cybulski C, etal., J Med Genet. 2006 Nov;43(11):863-6.
4. Dong X, etal., Am J Hum Genet 2003 Feb;72(2):270-80. Epub 2003 Jan 17.
5. Einarsdottir K, etal., Hum Mol Genet. 2007 Jan 15;16(2):154-64. Epub 2006 Dec 12.
6. Falchetti M, etal., Breast Cancer Res Treat. 2007 Jul 28;.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Hu B, etal., J Biol Chem. 2001 May 25;276(21):17693-8. Epub 2001 Mar 7.
10. Krueger SA, etal., Int J Radiat Oncol Biol Phys. 2010 Aug 1;77(5):1509-17. doi: 10.1016/j.ijrobp.2010.01.028.
11. Kruse JP and Gu W, Cell. 2009 May 15;137(4):609-22. doi: 10.1016/j.cell.2009.04.050.
12. Laitman Y, etal., Isr Med Assoc J. 2007 Nov;9(11):791-6.
13. Lavin MF and Gueven N, Cell Death Differ. 2006 Jun;13(6):941-50.
14. Liu L, etal., Mol Biol Cell. 2009 Dec;20(23):4885-98. doi: 10.1091/mbc.E09-07-0550. Epub 2009 Oct 7.
15. Meijers-Heijboer H, etal., Nat Genet. 2002 May;31(1):55-9. Epub 2002 Apr 22.
16. MGD data from the GO Consortium
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Oh H, etal., Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5378-83. Epub 2003 Apr 17.
19. OMIM Disease Annotation Pipeline
20. Ou TT, etal., J Ethnopharmacol. 2011 Apr 26;135(1):162-72. doi: 10.1016/j.jep.2011.03.011. Epub 2011 Mar 17.
21. Pabla N, etal., J Biol Chem. 2008 Mar 7;283(10):6572-83. Epub 2007 Dec 27.
22. Pipeline to import KEGG annotations from KEGG into RGD
23. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
24. Reddy A, etal., Br J Cancer. 2002 Mar 4;86(5):756-60.
25. RGD automated data pipeline
26. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
27. RGD automated import pipeline for gene-chemical interactions
28. RGD comprehensive gene curation
29. Spallarossa P, etal., Am J Physiol Heart Circ Physiol. 2009 Dec;297(6):H2169-81. Epub 2009 Oct 2.
30. Szymanska-Pasternak J, etal., Gynecol Oncol. 2006 Sep;102(3):429-31. Epub 2006 Jul 10.
31. Takahashi K, etal., Nagoya J Med Sci. 2014 Feb;76(1-2):35-49.
32. Taniai E, etal., Arch Toxicol. 2012 Sep;86(9):1453-64. doi: 10.1007/s00204-012-0829-z. Epub 2012 Mar 13.
33. Williams LH, etal., Clin Cancer Res. 2006 Dec 1;12(23):6967-72.
34. Xin F, etal., Mutat Res Genet Toxicol Environ Mutagen. 2014 Jul 15;769:29-33. doi: 10.1016/j.mrgentox.2014.04.019. Epub 2014 May 21.
35. Yoo BH, etal., Int J Cancer. 2012 Jul 15;131(2):357-66. doi: 10.1002/ijc.26368. Epub 2011 Nov 2.
36. Yu TX, etal., Nucleic Acids Res. 2011 Oct;39(19):8472-87. doi: 10.1093/nar/gkr567. Epub 2011 Jul 10.
37. Zempolich K, etal., Gynecol Oncol. 2008 May;109(2):275-9. Epub 2008 Mar 4.
38. Zlowocka E, etal., Int J Cancer. 2008 Feb 1;122(3):583-6.
Additional References at PubMed
PMID:10710310   PMID:11298456   PMID:12402044   PMID:12717439   PMID:14744935   PMID:15149599   PMID:16481012   PMID:16794575   PMID:17101782   PMID:18239682   PMID:18317453   PMID:18614044  
PMID:18644861   PMID:20364141   PMID:22266820   PMID:22851694   PMID:24550317  


Genomics

Comparative Map Data
Chek2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21245,788,823 - 45,821,382 (-)NCBI
Rnor_6.0 Ensembl1251,845,796 - 51,877,624 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01251,845,574 - 51,878,098 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01253,583,932 - 53,616,450 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41245,933,900 - 45,965,427 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11245,797,764 - 45,829,292 (-)NCBI
Celera1247,348,969 - 47,380,486 (-)NCBICelera
Cytogenetic Map12q16NCBI
CHEK2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2228,687,743 - 28,742,422 (-)EnsemblGRCh38hg38GRCh38
GRCh382228,687,743 - 28,741,866 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372229,083,731 - 29,137,822 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362227,413,731 - 27,467,822 (-)NCBINCBI36hg18NCBI36
Build 342227,408,284 - 27,462,376NCBI
Celera2212,883,692 - 12,937,801 (-)NCBI
Cytogenetic Map22q12.1ENTREZGENE
HuRef2212,048,435 - 12,103,008 (-)NCBIHuRef
CHM1_12229,042,794 - 29,096,883 (-)NCBICHM1_1
Chek2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395110,987,668 - 111,022,006 (+)NCBIGRCm39mm39
GRCm39 Ensembl5110,987,845 - 111,022,011 (+)Ensembl
GRCm385110,839,800 - 110,874,140 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5110,839,979 - 110,874,145 (+)EnsemblGRCm38mm10GRCm38
MGSCv375111,269,036 - 111,303,152 (+)NCBIGRCm37mm9NCBIm37
MGSCv365111,080,319 - 111,114,435 (+)NCBImm8
Celera5107,972,108 - 108,006,794 (+)NCBICelera
Cytogenetic Map5FNCBI
Chek2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554552,969,270 - 3,003,173 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554552,969,113 - 3,008,004 (-)NCBIChiLan1.0ChiLan1.0
CHEK2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12227,455,226 - 27,512,555 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0229,757,038 - 9,811,171 (-)NCBIMhudiblu_PPA_v0panPan3
CHEK2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12622,052,256 - 22,145,675 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2621,427,961 - 22,240,624 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2621,923,947 - 22,017,275 (-)NCBI
ROS_Cfam_1.02622,425,372 - 22,519,047 (-)NCBI
UMICH_Zoey_3.12622,135,806 - 22,229,383 (-)NCBI
UNSW_CanFamBas_1.02622,399,429 - 22,492,792 (-)NCBI
UU_Cfam_GSD_1.02622,461,722 - 22,555,609 (-)NCBI
Chek2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118113,022,347 - 113,064,864 (+)NCBI
SpeTri2.0NW_0049366572,805,947 - 2,848,180 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHEK2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1445,926,613 - 45,967,296 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11445,699,833 - 45,967,350 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CHEK2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11911,567,529 - 11,621,180 (-)NCBI
ChlSab1.1 Ensembl1911,567,528 - 11,604,792 (-)Ensembl
Vero_WHO_p1.0NW_023666045114,532,627 - 114,585,653 (+)NCBI
Chek2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247475,035,045 - 5,072,555 (-)NCBI

Position Markers
RH130548  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21245,812,979 - 45,813,268 (+)MAPPER
Rnor_6.01251,869,727 - 51,870,015NCBIRnor6.0
Rnor_5.01253,608,086 - 53,608,374UniSTSRnor5.0
RGSC_v3.41245,957,530 - 45,957,818UniSTSRGSC3.4
Celera1247,372,589 - 47,372,877UniSTS
RH 3.4 Map12779.63UniSTS
Cytogenetic Map12q16UniSTS
RH141098  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21245,790,817 - 45,791,035 (+)MAPPER
Rnor_6.01251,847,569 - 51,847,786NCBIRnor6.0
Rnor_5.01253,585,927 - 53,586,144UniSTSRnor5.0
RGSC_v3.41245,935,372 - 45,935,589UniSTSRGSC3.4
Celera1247,350,441 - 47,350,658UniSTS
RH 3.4 Map12782.91UniSTS
Cytogenetic Map12q16UniSTS
AU049427  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21245,798,756 - 45,799,048 (+)MAPPER
Rnor_6.01251,855,507 - 51,855,798NCBIRnor6.0
Rnor_5.01253,593,865 - 53,594,156UniSTSRnor5.0
RGSC_v3.41245,943,310 - 45,943,601UniSTSRGSC3.4
Celera1247,358,377 - 47,358,668UniSTS
Cytogenetic Map12q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121441977552716770Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121502198652716770Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121590890052716770Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121590890052716770Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121834247752716770Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121834247752716770Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121872904352716770Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121875259352716770Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101875259352716770Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)122265070252716770Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122490659052716770Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122609884552716770Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)123172356551955754Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)123172356552716770Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123752188451955754Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:23
Count of miRNA genes:20
Interacting mature miRNAs:23
Transcripts:ENSRNOT00000056800
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 18 25 18 18 18 21 18 32 2
Low 25 32 23 1 23 8 10 53 17 9 9 8
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000056800   ⟹   ENSRNOP00000053643
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1251,846,097 - 51,877,624 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085591   ⟹   ENSRNOP00000074651
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1251,845,796 - 51,876,876 (-)Ensembl
RefSeq Acc Id: NM_053677   ⟹   NP_446129
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21245,789,346 - 45,820,879 (-)NCBI
Rnor_6.01251,846,097 - 51,877,624 (-)NCBI
Rnor_5.01253,583,932 - 53,616,450 (-)NCBI
RGSC_v3.41245,933,900 - 45,965,427 (-)RGD
Celera1247,348,969 - 47,380,486 (-)RGD
Sequence:
RefSeq Acc Id: XM_006249518   ⟹   XP_006249580
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21245,788,823 - 45,821,353 (-)NCBI
Rnor_6.01251,845,574 - 51,878,094 (-)NCBI
Rnor_5.01253,583,932 - 53,616,450 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249519   ⟹   XP_006249581
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21245,788,823 - 45,821,382 (-)NCBI
Rnor_6.01251,845,574 - 51,878,090 (-)NCBI
Rnor_5.01253,583,932 - 53,616,450 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249520   ⟹   XP_006249582
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21245,788,823 - 45,821,349 (-)NCBI
Rnor_6.01251,845,574 - 51,878,091 (-)NCBI
Rnor_5.01253,583,932 - 53,616,450 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249521   ⟹   XP_006249583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21245,788,823 - 45,821,358 (-)NCBI
Rnor_6.01251,845,574 - 51,878,098 (-)NCBI
Rnor_5.01253,583,932 - 53,616,450 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008769308   ⟹   XP_008767530
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01251,851,374 - 51,878,090 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039089014   ⟹   XP_038944942
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21245,788,823 - 45,821,382 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446129   ⟸   NM_053677
- UniProtKB: Q9R019 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006249582   ⟸   XM_006249520
- Peptide Label: isoform X1
- UniProtKB: Q9R019 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006249583   ⟸   XM_006249521
- Peptide Label: isoform X1
- UniProtKB: Q9R019 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006249581   ⟸   XM_006249519
- Peptide Label: isoform X1
- UniProtKB: Q9R019 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006249580   ⟸   XM_006249518
- Peptide Label: isoform X1
- UniProtKB: Q9R019 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008767530   ⟸   XM_008769308
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000074651   ⟸   ENSRNOT00000085591
RefSeq Acc Id: ENSRNOP00000053643   ⟸   ENSRNOT00000056800
RefSeq Acc Id: XP_038944942   ⟸   XM_039089014
- Peptide Label: isoform X2
Protein Domains
FHA   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 (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 (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/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 (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
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
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
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/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
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 (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
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
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
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
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
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 (MCW)