Apex1 (apurinic/apyrimidinic endodeoxyribonuclease 1) - Rat Genome Database

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Gene: Apex1 (apurinic/apyrimidinic endodeoxyribonuclease 1) Rattus norvegicus
Analyze
Symbol: Apex1
Name: apurinic/apyrimidinic endodeoxyribonuclease 1
RGD ID: 2126
Description: Enables NF-kappaB binding activity and endoribonuclease activity. Involved in several processes, including cellular response to organonitrogen compound; negative regulation of smooth muscle cell migration; and positive regulation of G1/S transition of mitotic cell cycle. Located in mitochondrion and nucleus. Part of transcription regulator complex. Biomarker of brain ischemia; lung disease; status epilepticus; and visual epilepsy. Human ortholog(s) of this gene implicated in breast cancer; female reproductive organ cancer (multiple); spina bifida; and urinary bladder cancer. Orthologous to human APEX1 (apurinic/apyrimidinic endodeoxyribonuclease 1); PARTICIPATES IN base excision repair pathway; hypoxia inducible factor pathway; INTERACTS WITH (+)-pilocarpine; (+)-schisandrin B; 1,2,4-trimethylbenzene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: AP endonuclease 1; APE; APEN; Apex; APEX nuclease (multifunctional DNA repair enzyme) 1; APEX nuclease 1; apurinic-apyrimidinic endonuclease 1; apurinic/apyrimidinic endonuclease; Apurinic/apyrimidinic endonuclease 1; DNA-(apurinic or apyrimidinic site) endonuclease; DNA-(apurinic or apyrimidinic site) lyase; redox factor-1; REF-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21524,144,595 - 24,146,785 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1524,144,362 - 24,146,785 (+)Ensembl
Rnor_6.01527,849,943 - 27,852,083 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1527,849,979 - 27,852,082 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01531,682,368 - 31,684,508 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41526,904,124 - 26,906,224 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11526,919,823 - 26,921,924 (+)NCBI
Celera1524,464,809 - 24,466,909 (+)NCBICelera
Cytogenetic Map15p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(+)-schisandrin B  (EXP)
(S)-nicotine  (ISO)
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
1,4-dithiothreitol  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP)
1H-pyrazole  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrotoluene  (EXP)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
2-nitrofluorene  (EXP)
2-nitropropane  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-hydroperoxycyclophosphamide  (EXP)
4-hydroxynon-2-enal  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (ISO)
8-hydroxy-2'-deoxyguanosine  (ISO)
acrylamide  (ISO)
aflatoxin B1  (EXP)
ammonium chloride  (EXP)
amphibole asbestos  (ISO)
aniline  (EXP)
arecoline  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzoquinones  (ISO)
beryllium dichloride  (ISO)
bezafibrate  (ISO)
bisphenol A  (EXP,ISO)
busulfan  (ISO)
cadmium atom  (ISO)
caffeine  (ISO)
carbon atom  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chloroform  (EXP)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (EXP)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclophosphamide  (EXP)
cyproconazole  (EXP)
dacarbazine  (ISO)
daunorubicin  (ISO)
diamminedichloroplatinum  (ISO)
dibenziodolium  (ISO)
dibutyl phthalate  (ISO)
dichlorine  (EXP)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
elemental carbon  (ISO)
enzyme inhibitor  (ISO)
epoxiconazole  (EXP)
erythromycin estolate  (EXP)
ethanol  (EXP)
ethene  (EXP)
etoposide  (ISO)
fenofibrate  (EXP)
fenpyroximate  (ISO)
floxuridine  (ISO)
flutamide  (EXP)
folic acid  (ISO)
furan  (EXP)
gentamycin  (EXP)
glafenine  (EXP)
glycine betaine  (EXP)
hydrogen peroxide  (EXP,ISO)
hypochlorous acid  (ISO)
imiquimod  (ISO)
iron trichloride  (ISO)
isoprenaline  (ISO)
ivermectin  (ISO)
kainic acid  (EXP)
L-1,4-dithiothreitol  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
menadione  (ISO)
metformin  (ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
miconazole  (EXP)
microcystin-LR  (ISO)
mitomycin C  (ISO)
monocrotophos  (ISO)
N-acetyl-L-cysteine  (ISO)
N-ethylmaleimide  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
naloxone  (EXP)
nefazodone  (EXP)
nicotine  (ISO)
nimesulide  (EXP)
nitroglycerin  (EXP)
O-acetyl-L-carnitine  (EXP)
ochratoxin A  (EXP)
oxirane  (EXP)
ozone  (EXP)
paracetamol  (EXP)
paraquat  (EXP,ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
potassium bromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (ISO)
propiconazole  (ISO)
rac-lactic acid  (ISO)
raloxifene  (EXP)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP,ISO)
streptozocin  (ISO)
sunitinib  (ISO)
tamoxifen  (EXP,ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
theophylline  (EXP)
thioacetamide  (EXP)
Thiotepa  (ISO)
transplatin  (ISO)
Tributyltin oxide  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
trovafloxacin  (ISO)
troxacitabine  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vitamin E  (ISO)
zalcitabine  (ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Barnes T, etal., Nucleic Acids Res. 2009 Jul;37(12):3946-58. Epub 2009 Apr 28.
2. Chen L, etal., J Urol. 2006 Jan;175(1):108-12; discussion 112.
3. Cho CG, etal., Exp Gerontol. 2003 May;38(5):539-48.
4. DAGCI T, etal., Physiol Res. 2009;58(3):427-34. Epub 2008 Jul 18.
5. Fishel ML, etal., DNA Repair (Amst). 2008 Feb 1;7(2):177-86. Epub 2007 Oct 31.
6. Frossi B, etal., Eur J Immunol. 2003 Aug;33(8):2168-77.
7. Gangwar R, etal., Urology. 2009 Mar;73(3):675-80. Epub 2008 Nov 28.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Gorbunov NV, etal., Antioxid Redox Signal. 2007 Apr;9(4):483-95.
10. Gurusamy N, etal., Free Radic Biol Med. 2007 Aug 1;43(3):397-407. Epub 2007 Apr 29.
11. He T, etal., Am J Physiol Heart Circ Physiol. 2003 Aug;285(2):H804-12. Epub 2003 May 1.
12. Hung RJ, etal., Am J Epidemiol. 2005 Nov 15;162(10):925-42. Epub 2005 Oct 12.
13. Kelley MR, etal., Clin Cancer Res. 2001 Apr;7(4):824-30.
14. Korashy HM, etal., Anticancer Res. 2017 Sep;37(9):4899-4909. doi: 10.21873/anticanres.11899.
15. Lee HM, etal., Circ Res. 2009 Jan 30;104(2):219-27, 5p following 227. Epub 2008 Nov 26.
16. Mantha AK, etal., J Neurosci Res. 2012 Jun;90(6):1230-9. doi: 10.1002/jnr.23018. Epub 2012 Feb 20.
17. MGD data from the GO Consortium
18. Nagai R, etal., J Pineal Res. 2008 Oct;45(3):271-6. Epub 2008 Mar 26.
19. Nakamura T, etal., Neurosurg Focus. 2003 Oct 15;15(4):ECP4.
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Nishimura J, etal., Toxicol Sci. 2007 May;97(1):44-54. Epub 2007 Jan 29.
22. Olshan AF, etal., Am J Med Genet A. 2005 Jun 15;135(3):268-73.
23. Pieretti M, etal., Mutat Res. 2001 Jan;432(3-4):53-9.
24. Pipeline to import KEGG annotations from KEGG into RGD
25. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
26. Puglisi F, etal., Oncol Rep. 2002 Jan-Feb;9(1):11-7.
27. Qing Y, etal., Sichuan Da Xue Xue Bao Yi Xue Ban. 2009 Jan;40(1):125-8.
28. Quach N, etal., Brain Res. 2005 May 3;1042(2):236-40.
29. Reactome
30. RGD automated data pipeline
31. RGD automated import pipeline for gene-chemical interactions
32. Shekari M, etal., Cancer Biomark. 2008;4(2):63-71.
33. Smith TR, etal., Carcinogenesis. 2008 Nov;29(11):2132-8. Epub 2008 Aug 13.
34. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
35. Tan Z, etal., Brain Res. 2002 Mar 1;929(1):129-38.
36. Tell G, etal., Horm Metab Res 2002 Jun;34(6):303-10.
37. Tell G, etal., Mutat Res. 2001 Mar 7;485(2):143-52.
38. Walton M, etal., Brain Res Mol Brain Res. 1997 Feb;44(1):167-70.
39. Zhang Y, etal., Int J Oncol. 2009 Nov;35(5):1069-79.
40. Ziel KA, etal., FASEB J. 2004 Jun;18(9):986-8. Epub 2004 Apr 14.
Additional References at PubMed
PMID:7510394   PMID:8086453   PMID:8701782   PMID:8932386   PMID:9119221   PMID:9560228   PMID:10631378   PMID:11286553   PMID:11478795   PMID:11809897   PMID:11832948   PMID:12524539  
PMID:13679060   PMID:14594818   PMID:14706345   PMID:15489334   PMID:15661660   PMID:15707971   PMID:15942031   PMID:17148573   PMID:18973764   PMID:19084962   PMID:19188445   PMID:19351502  
PMID:19728933   PMID:19934257   PMID:20231292   PMID:20573957   PMID:20808729   PMID:21496894   PMID:21570442   PMID:21741887   PMID:21911894   PMID:22076170   PMID:22172708   PMID:22681889  
PMID:23148211   PMID:23352893   PMID:24114393   PMID:24337968   PMID:24703901   PMID:26164266   PMID:26608791   PMID:26639148   PMID:27698937   PMID:27893608   PMID:27986089   PMID:28404743  
PMID:28946662   PMID:28965839   PMID:29772245   PMID:31432320  


Genomics

Comparative Map Data
Apex1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21524,144,595 - 24,146,785 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1524,144,362 - 24,146,785 (+)Ensembl
Rnor_6.01527,849,943 - 27,852,083 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1527,849,979 - 27,852,082 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01531,682,368 - 31,684,508 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41526,904,124 - 26,906,224 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11526,919,823 - 26,921,924 (+)NCBI
Celera1524,464,809 - 24,466,909 (+)NCBICelera
Cytogenetic Map15p14NCBI
APEX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1420,455,191 - 20,457,772 (+)EnsemblGRCh38hg38GRCh38
GRCh381420,455,226 - 20,457,767 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371420,923,385 - 20,925,926 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361419,993,130 - 19,995,766 (+)NCBINCBI36hg18NCBI36
Celera14784,440 - 787,076 (+)NCBI
Cytogenetic Map14q11.2NCBI
HuRef141,044,909 - 1,047,550 (+)NCBIHuRef
CHM1_11420,924,670 - 20,927,311 (+)NCBICHM1_1
Apex1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391451,162,406 - 51,164,645 (+)NCBIGRCm39mm39
GRCm39 Ensembl1451,162,425 - 51,164,596 (+)Ensembl
GRCm381450,924,949 - 50,927,188 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1450,924,968 - 50,927,139 (+)EnsemblGRCm38mm10GRCm38
MGSCv371451,544,696 - 51,546,813 (+)NCBIGRCm37mm9NCBIm37
MGSCv361449,846,972 - 49,849,089 (+)NCBImm8
Celera1447,224,610 - 47,226,746 (+)NCBICelera
Cytogenetic Map14C1NCBI
cM Map1426.3NCBI
Apex1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555501,273,284 - 1,279,743 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555501,273,170 - 1,275,843 (+)NCBIChiLan1.0ChiLan1.0
APEX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11419,381,911 - 19,384,542 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1419,381,911 - 19,384,542 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0141,329,745 - 1,332,315 (+)NCBIMhudiblu_PPA_v0panPan3
APEX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11517,786,808 - 17,789,422 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1517,786,357 - 17,789,422 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1518,269,795 - 18,272,409 (+)NCBI
ROS_Cfam_1.01518,043,890 - 18,046,511 (+)NCBI
ROS_Cfam_1.0 Ensembl1518,042,845 - 18,046,514 (+)Ensembl
UMICH_Zoey_3.11517,726,748 - 17,729,354 (+)NCBI
UNSW_CanFamBas_1.01517,781,386 - 17,784,004 (+)NCBI
UU_Cfam_GSD_1.01517,910,565 - 17,913,179 (+)NCBI
Apex1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864077,685,350 - 77,688,067 (+)NCBI
SpeTri2.0NW_004936877666,545 - 669,351 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APEX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl778,451,851 - 78,454,938 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1778,451,845 - 78,454,938 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2783,479,687 - 83,481,839 (-)NCBISscrofa10.2Sscrofa10.2susScr3
APEX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12920,978,878 - 20,981,393 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605925,448,880 - 25,451,389 (-)NCBIVero_WHO_p1.0
Apex1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248254,711,921 - 4,714,926 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH140031  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21524,146,908 - 24,147,119 (+)MAPPERmRatBN7.2
Rnor_6.01527,852,207 - 27,852,417NCBIRnor6.0
Rnor_5.01531,684,632 - 31,684,842UniSTSRnor5.0
RGSC_v3.41526,906,352 - 26,906,562UniSTSRGSC3.4
Celera1524,467,037 - 24,467,247UniSTS
Cytogenetic Map15p14UniSTS
RH94450  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01531,684,377 - 31,684,477NCBIRnor5.0
Rnor_5.0413,025,353 - 13,025,466NCBIRnor5.0
Rnor_5.0416,724,065 - 16,724,178NCBIRnor5.0
RGSC_v3.4412,044,171 - 12,044,283UniSTSRGSC3.4
RGSC_v3.41526,906,098 - 26,906,197UniSTSRGSC3.4
Celera411,977,447 - 11,977,559UniSTS
Celera1524,466,783 - 24,466,882UniSTS
Cytogenetic Map15p14UniSTS
Cytogenetic Map4q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151448116528469888Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:117
Count of miRNA genes:89
Interacting mature miRNAs:94
Transcripts:ENSRNOT00000013176
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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013176   ⟹   ENSRNOP00000013176
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1524,144,362 - 24,146,785 (+)Ensembl
Rnor_6.0 Ensembl1527,849,979 - 27,852,079 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087958   ⟹   ENSRNOP00000068673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1524,144,508 - 24,146,785 (+)Ensembl
Rnor_6.0 Ensembl1527,850,151 - 27,852,082 (+)Ensembl
RefSeq Acc Id: NM_024148   ⟹   NP_077062
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21524,144,681 - 24,146,781 (+)NCBI
Rnor_6.01527,849,979 - 27,852,079 (+)NCBI
Rnor_5.01531,682,368 - 31,684,508 (+)NCBI
RGSC_v3.41526,904,124 - 26,906,224 (+)RGD
Celera1524,464,809 - 24,466,909 (+)RGD
Sequence:
RefSeq Acc Id: XM_006251913   ⟹   XP_006251975
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21524,144,595 - 24,146,785 (+)NCBI
Rnor_6.01527,849,943 - 27,852,083 (+)NCBI
Rnor_5.01531,682,368 - 31,684,508 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599805   ⟹   XP_017455294
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21524,144,931 - 24,146,785 (+)NCBI
Rnor_6.01527,850,293 - 27,852,083 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_077062   ⟸   NM_024148
- UniProtKB: P43138 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006251975   ⟸   XM_006251913
- Peptide Label: isoform X1
- UniProtKB: P43138 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017455294   ⟸   XM_017599805
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000068673   ⟸   ENSRNOT00000087958
RefSeq Acc Id: ENSRNOP00000013176   ⟸   ENSRNOT00000013176
Protein Domains
Endo/exonuclease/phosphatase

Transcriptome

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

Promoters
RGD ID:13699625
Promoter ID:EPDNEW_R10147
Type:initiation region
Name:Apex1_1
Description:apurinic/apyrimidinic endodeoxyribonuclease 1
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_6.01527,849,979 - 27,850,039EPDNEW

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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2126 AgrOrtholog
Ensembl Genes ENSRNOG00000009663 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000013176 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000068673 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000013176 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000087958 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.60.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7127205 IMAGE-MGC_LOAD
InterPro AP_endonuc_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AP_endonuclease_F1_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AP_endonuclease_F1_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Endo/exonu/phosph_ase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Endo/exonuclease/phosphatase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:79116 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93413 IMAGE-MGC_LOAD
NCBI Gene 79116 ENTREZGENE
PANTHER PTHR22748 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Exo_endo_phos UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB APEX1 RGD
PhenoGen Apex1 PhenoGen
PROSITE AP_NUCLEASE_F1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AP_NUCLEASE_F1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AP_NUCLEASE_F1_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AP_NUCLEASE_F1_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56219 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs xth UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt APEX1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q99PF3_RAT UniProtKB/TrEMBL
UniProt Secondary Q548N9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-15 Apex1  apurinic/apyrimidinic endodeoxyribonuclease 1  Apex1  APEX nuclease (multifunctional DNA repair enzyme) 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Apex1  APEX nuclease (multifunctional DNA repair enzyme) 1  Apex1  apurinic/apyrimidinic endonuclease 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Apex1  apurinic/apyrimidinic endonuclease 1      Symbol and Name updated 629477 APPROVED
2003-03-07 Apex1  apurinic/apyrimidinic endonuclease 1  Apex    Data Merged 628472 PROVISIONAL
2002-08-07 Apex        Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Apex1  Apurinic/apyrimidinic endonuclease 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to nucleus and cytoplasm 634652
gene_process regulates the transcriptional activity of Pax8 634652
gene_process may have roles in DNA repair and in redox homeostasis 634652
gene_regulation cell localization is regulated by thyroid hormone 634652