Dnmt3a (DNA methyltransferase 3 alpha) - Rat Genome Database

Send us a Message



 Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper VCMap
Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Dnmt3a (DNA methyltransferase 3 alpha) Rattus norvegicus
Analyze
Symbol: Dnmt3a
Name: DNA methyltransferase 3 alpha
RGD ID: 1303336
Description: Enables chromatin binding activity. Involved in several processes, including cellular response to ethanol; hepatocyte apoptotic process; and response to vitamin A. Located in cytoplasm and nucleus. Used to study lung carcinoma and middle cerebral artery infarction. Biomarker of congenital heart disease; hepatocellular carcinoma; and prostatitis. Human ortholog(s) of this gene implicated in T-cell acute lymphoblastic leukemia; acute lymphoblastic leukemia; acute myeloid leukemia; myelodysplastic syndrome; and stomach cancer. Orthologous to human DNMT3A (DNA methyltransferase 3 alpha); PARTICIPATES IN DNA modification pathway; methionine cycle/metabolic pathway; cysteine and methionine metabolic pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cysteine methyltransferase DNMT3A; DNA (cytosine-5)-methyltransferase 3A; DNA (cytosine-5-)-methyltransferase 3 alpha; DNA methyltransferase 3A; MGC109195
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: LOC289651   LOC308670  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2626,791,517 - 26,902,161 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl626,822,609 - 26,896,687 (+)Ensembl
Rnor_6.0628,205,375 - 28,346,052 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl628,235,695 - 28,340,577 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0638,044,960 - 38,082,583 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0638,132,683 - 38,149,613 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4626,802,612 - 26,878,878 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1626,805,564 - 26,881,831 (+)NCBI
Celera626,297,300 - 26,371,904 (+)NCBICelera
Cytogenetic Map6q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (EXP)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nonylphenol  (ISO)
4-tert-Octylphenol  (ISO)
5-(hydroxymethyl)cytosine  (ISO)
5-aza-2'-deoxycytidine  (EXP,ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
amphetamine  (EXP)
androgen antagonist  (EXP)
aripiprazole  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bexarotene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (ISO)
buta-1,3-diene  (ISO)
Butylparaben  (EXP)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP)
chloroprene  (EXP)
chlorpyrifos  (EXP)
choline  (ISO)
citalopram  (EXP)
clofibrate  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
Cuprizon  (EXP)
curcumin  (ISO)
cycloheximide  (EXP)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
D-penicillamine  (ISO)
daidzein  (EXP)
daidzein 7-O-beta-D-glucoside  (EXP)
DDE  (EXP)
DDT  (EXP)
deoxynivalenol  (EXP)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (EXP,ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (ISO)
Difenacoum  (ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
enzacamene  (EXP)
ethanol  (ISO)
fenvalerate  (EXP)
Flocoumafen  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
genistein  (EXP,ISO)
genistein 7-O-beta-D-glucoside  (EXP)
gibberellin A3  (EXP)
glycitein  (EXP)
glycitin  (EXP)
glyphosate  (EXP,ISO)
guggulsterone  (ISO)
hexane  (EXP)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
ibuprofen  (ISO)
isoprenaline  (EXP,ISO)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
lead nitrate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methotrexate  (ISO)
methoxychlor  (EXP)
microcystin-LR  (ISO)
mitomycin C  (ISO)
Monobutylphthalate  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methylformamide  (ISO)
N-nitrosodiethylamine  (EXP)
ozone  (EXP)
p-tert-Amylphenol  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
procyanidin B2  (ISO)
pterostilbene  (ISO)
quartz  (ISO)
quinoline  (ISO)
resveratrol  (ISO)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
Salinomycin  (ISO)
sinefungin  (ISO)
sodium arsenite  (ISO)
streptozocin  (ISO)
sulforaphane  (ISO)
T-2 toxin  (EXP)
tamoxifen  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
thimerosal  (ISO)
trichloroethene  (EXP,ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
tyrphostin AG 1478  (ISO)
uranium atom  (EXP)
urethane  (ISO)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
vinyl carbamate  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
withaferin A  (ISO)
wortmannin  (ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
catalytic complex  (IEA,ISO)
chromosome, centromeric region  (ISO)
cytoplasm  (IDA,ISO,ISS)
euchromatin  (ISO,ISS)
heterochromatin  (ISO)
nuclear matrix  (ISO,ISS)
nucleoplasm  (IEA,ISO)
nucleus  (IDA,ISO,ISS)
XY body  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Blaze J and Roth TL, Int J Dev Neurosci. 2013 Dec;31(8):804-10. doi: 10.1016/j.ijdevneu.2013.10.001. Epub 2013 Oct 10.
2. Cavuoto P and Fenech MF, Cancer Treat Rev. 2012 Oct;38(6):726-36. doi: 10.1016/j.ctrv.2012.01.004. Epub 2012 Feb 17.
3. Chen T, etal., J Biol Chem. 2002 Oct 11;277(41):38746-54. Epub 2002 Jul 22.
4. Cowin PA, etal., Endocrinology. 2010 Feb;151(2):783-92. doi: 10.1210/en.2009-0982. Epub 2010 Jan 7.
5. Dawson MA and Kouzarides T, Cell. 2012 Jul 6;150(1):12-27. doi: 10.1016/j.cell.2012.06.013.
6. Delatte B, etal., EMBO J. 2014 Jun 2;33(11):1198-211. doi: 10.15252/embj.201488290. Epub 2014 May 13.
7. El Ghannam D, etal., Blood Cells Mol Dis. 2014 Jun-Aug;53(1-2):61-6. doi: 10.1016/j.bcmd.2014.01.004. Epub 2014 Feb 8.
8. Fan H, etal., BMC Med. 2010 Feb 3;8:12. doi: 10.1186/1741-7015-8-12.
9. Feng Y, etal., J Nutr Biochem. 2013 Jul;24(7):1373-80. doi: 10.1016/j.jnutbio.2012.11.005. Epub 2013 Jan 17.
10. Feng YJ, etal., Zhonghua Yi Xue Za Zhi. 2013 Dec 24;93(48):3822-5.
11. Ghoshal K, etal., J Nutr. 2006 Jun;136(6):1522-7.
12. Grossmann V, etal., Genes Chromosomes Cancer. 2013 Apr;52(4):410-22. doi: 10.1002/gcc.22039. Epub 2013 Jan 23.
13. Imai S, etal., J Neurosci. 2011 Oct 26;31(43):15294-9. doi: 10.1523/JNEUROSCI.0921-11.2011.
14. Jiang JX, etal., PLoS One. 2013 Aug 7;8(8):e69089. doi: 10.1371/journal.pone.0069089. eCollection 2013.
15. Kim KH, etal., Ther Apher Dial. 2014 Sep 26. doi: 10.1111/1744-9987.12186.
16. LaPlant Q, etal., Nat Neurosci. 2010 Sep;13(9):1137-43. doi: 10.1038/nn.2619. Epub 2010 Aug 22.
17. Lees-Murdock DJ, etal., Genomics 2004 Jul;84(1):193-204.
18. Li W, etal., Leuk Lymphoma. 2015 Apr;56(4):1066-71. doi: 10.3109/10428194.2014.947607. Epub 2014 Nov 10.
19. Lin J, etal., PLoS One. 2011;6(10):e26906. doi: 10.1371/journal.pone.0026906. Epub 2011 Oct 31.
20. Liu WB, etal., Toxicol Appl Pharmacol. 2011 Feb 15;251(1):70-8. doi: 10.1016/j.taap.2010.12.002. Epub 2010 Dec 14.
21. Liu X and Guo SW, Gynecol Obstet Invest. 2012;74(2):100-8. Epub 2012 May 4.
22. Liu YN, etal., J Huazhong Univ Sci Technolog Med Sci. 2015 Jun;35(3):337-42. doi: 10.1007/s11596-015-1434-1. Epub 2015 Jun 14.
23. Loree J, etal., Int J Radiat Biol. 2006 Nov;82(11):805-15.
24. Majumder S, etal., J Biol Chem. 2002 May 3;277(18):16048-58. Epub 2002 Feb 13.
25. Marcucci G, etal., J Clin Oncol. 2012 Mar 1;30(7):742-50. doi: 10.1200/JCO.2011.39.2092. Epub 2012 Jan 30.
26. Mayle A, etal., Blood. 2015 Jan 22;125(4):629-38.
27. Melas PA, etal., Int J Neuropsychopharmacol. 2012 Jun;15(5):669-79. doi: 10.1017/S1461145711000940. Epub 2011 Jun 20.
28. Meunier L, etal., Endocrinology. 2012 Apr;153(4):1936-47. doi: 10.1210/en.2011-1109. Epub 2012 Feb 14.
29. Mizuno S, etal., Blood. 2001 Mar 1;97(5):1172-9.
30. Morey SR, etal., Cancer Res. 2006 Dec 15;66(24):11659-67.
31. Pandi G, etal., PLoS One. 2013;8(3):e58039. doi: 10.1371/journal.pone.0058039. Epub 2013 Mar 13.
32. Park HJ, etal., Cancer Lett. 2006 Feb 28;233(2):271-8.
33. Pipeline to import KEGG annotations from KEGG into RGD
34. Pol Bodetto S, etal., Neuropharmacology. 2013 Oct;73:31-40. doi: 10.1016/j.neuropharm.2013.05.005. Epub 2013 May 18.
35. RGD automated data pipeline
36. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
37. RGD automated import pipeline for gene-chemical interactions
38. Sakharkar AJ, etal., Int J Neuropsychopharmacol. 2014 Dec;17(12):2057-67. doi: 10.1017/S1461145714001047. Epub 2014 Jun 26.
39. Schneider JS, etal., Toxicol Lett. 2013 Feb 13;217(1):75-81. doi: 10.1016/j.toxlet.2012.12.004. Epub 2012 Dec 15.
40. Sehgal AR, etal., Clin Cancer Res. 2015 Apr 1;21(7):1614-20. doi: 10.1158/1078-0432.CCR-14-0327. Epub 2015 Jan 21.
41. Sharma D, etal., Mol Endocrinol. 2013 Jul;27(7):1142-52. doi: 10.1210/me.2013-1079. Epub 2013 May 13.
42. Singh RP, etal., Cell Transplant. 2009;18(10):1197-211. doi: 10.3727/096368909X12483162197204. Epub 2009 Aug 5.
43. Tao J, etal., J Clin Immunol. 2008 Sep;28(5):432-9. doi: 10.1007/s10875-008-9223-2. Epub 2008 Aug 6.
44. Tryndyak VP, etal., Carcinogenesis. 2006 Aug;27(8):1713-20. Epub 2006 Apr 22.
45. Vinken M, etal., Toxicol In Vitro. 2010 Mar;24(2):445-51. doi: 10.1016/j.tiv.2009.10.003. Epub 2009 Oct 13.
46. Walter MJ, etal., Leukemia. 2011 Jul;25(7):1153-8. doi: 10.1038/leu.2011.44. Epub 2011 Mar 18.
47. Wong M, etal., Front Cell Neurosci. 2013 Dec 25;7:279. doi: 10.3389/fncel.2013.00279. eCollection 2013.
48. Wu X, etal., Neurosci Bull. 2013 Dec;29(6):685-92. doi: 10.1007/s12264-013-1345-8. Epub 2013 May 28.
49. Wu Y, etal., Fertil Steril. 2007 Jan;87(1):24-32. Epub 2006 Nov 1.
50. Zhang Q, etal., Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2013 Feb;31(2):92-5.
51. Zhang X, etal., J Neurochem. 2014 Feb;128(3):344-9. doi: 10.1111/jnc.12465. Epub 2013 Oct 28.
52. Zhang YY, etal., Leuk Res. 2015 Oct;39(10):1041-7. doi: 10.1016/j.leukres.2015.06.015. Epub 2015 Jul 6.
53. Zimmermann N, etal., Biochem J. 2012 Nov 15;448(1):93-102. doi: 10.1042/BJ20120674.
Additional References at PubMed
PMID:9662389   PMID:10555141   PMID:11399089   PMID:11934864   PMID:12477932   PMID:14752048   PMID:15215868   PMID:15456878   PMID:15616584   PMID:15739230   PMID:16322236   PMID:17938196  
PMID:18042343   PMID:19786833   PMID:20385583   PMID:20548288   PMID:20577743   PMID:21047779   PMID:21518035   PMID:21873635   PMID:23042785   PMID:24527678   PMID:24656771   PMID:24945829  
PMID:25190601   PMID:25416223   PMID:25476906   PMID:25743254   PMID:28267064   PMID:28270689   PMID:29056068   PMID:29786779   PMID:30114436   PMID:30478443   PMID:30950138   PMID:31576007  


Genomics

Comparative Map Data
Dnmt3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2626,791,517 - 26,902,161 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl626,822,609 - 26,896,687 (+)Ensembl
Rnor_6.0628,205,375 - 28,346,052 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl628,235,695 - 28,340,577 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0638,044,960 - 38,082,583 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0638,132,683 - 38,149,613 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4626,802,612 - 26,878,878 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1626,805,564 - 26,881,831 (+)NCBI
Celera626,297,300 - 26,371,904 (+)NCBICelera
Cytogenetic Map6q14NCBI
DNMT3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl225,227,855 - 25,342,590 (-)EnsemblGRCh38hg38GRCh38
GRCh38225,227,874 - 25,342,590 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37225,450,743 - 25,565,459 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36225,309,349 - 25,418,963 (-)NCBINCBI36hg18NCBI36
Celera225,296,144 - 25,405,816 (-)NCBI
Cytogenetic Map2p23.3NCBI
HuRef225,193,733 - 25,302,862 (-)NCBIHuRef
CHM1_1225,385,740 - 25,495,369 (-)NCBICHM1_1
Dnmt3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39123,851,559 - 3,964,443 (+)NCBIGRCm39mm39
GRCm39 Ensembl123,856,007 - 3,964,443 (+)Ensembl
GRCm38123,801,559 - 3,914,443 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl123,806,007 - 3,914,443 (+)EnsemblGRCm38mm10GRCm38
MGSCv37123,806,980 - 3,914,443 (+)NCBIGRCm37mm9NCBIm37
MGSCv36123,835,027 - 3,914,455 (+)NCBImm8
Celera123,763,156 - 3,842,112 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
Dnmt3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554697,269,952 - 7,367,059 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554697,264,431 - 7,367,059 (-)NCBIChiLan1.0ChiLan1.0
DNMT3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A25,331,095 - 25,441,785 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A25,331,095 - 25,412,605 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A25,229,593 - 25,344,733 (-)NCBIMhudiblu_PPA_v0panPan3
DNMT3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11719,489,524 - 19,563,074 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1719,492,193 - 19,563,902 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1719,382,990 - 19,486,679 (-)NCBI
ROS_Cfam_1.01719,761,597 - 19,865,311 (-)NCBI
UMICH_Zoey_3.11719,495,608 - 19,599,241 (-)NCBI
UNSW_CanFamBas_1.01719,505,342 - 19,609,205 (-)NCBI
UU_Cfam_GSD_1.01719,551,811 - 19,655,519 (-)NCBI
Dnmt3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629263,826,309 - 63,930,744 (-)NCBI
SpeTri2.0NW_0049364936,963,406 - 7,013,256 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DNMT3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3113,528,926 - 113,609,139 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13113,501,972 - 113,609,148 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23120,579,692 - 120,663,698 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DNMT3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11482,313,414 - 82,427,170 (+)NCBIChlSab1.1chlSab2
ChlSab1.11482,313,414 - 82,427,170 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1482,402,826 - 82,420,819 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604529,732,050 - 29,846,532 (-)NCBIVero_WHO_p1.0
Dnmt3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247387,481,084 - 7,581,332 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH130466  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map6q14UniSTS
BE113641  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2626,870,598 - 26,870,759 (+)MAPPERmRatBN7.2
Rnor_6.0628,314,514 - 28,314,674NCBIRnor6.0
Rnor_5.0638,123,550 - 38,123,710UniSTSRnor5.0
RGSC_v3.4626,851,172 - 26,851,332UniSTSRGSC3.4
Celera626,345,870 - 26,346,030UniSTS
RH 3.4 Map6118.19UniSTS
Cytogenetic Map6q14UniSTS
BF398717  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2626,880,909 - 26,881,078 (+)MAPPERmRatBN7.2
Rnor_6.0628,325,476 - 28,325,644NCBIRnor6.0
Rnor_5.0638,134,512 - 38,134,680UniSTSRnor5.0
RGSC_v3.4626,861,704 - 26,861,872UniSTSRGSC3.4
Celera626,356,203 - 26,356,371UniSTS
RH 3.4 Map6116.5UniSTS
Cytogenetic Map6q14UniSTS
RH135183  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2815,316,303 - 15,316,508 (+)MAPPERmRatBN7.2
mRatBN7.2626,896,118 - 26,896,328 (+)MAPPERmRatBN7.2
Rnor_6.0628,340,009 - 28,340,218NCBIRnor6.0
Rnor_6.0817,367,986 - 17,368,190NCBIRnor6.0
Rnor_5.0817,441,518 - 17,441,722UniSTSRnor5.0
Rnor_5.0638,149,045 - 38,149,254UniSTSRnor5.0
RGSC_v3.4626,878,310 - 26,878,519UniSTSRGSC3.4
RGSC_v3.4815,674,220 - 15,674,424UniSTSRGSC3.4
Celera816,746,468 - 16,746,672UniSTS
Celera626,371,336 - 26,371,545UniSTS
Cytogenetic Map6q14UniSTS
RH139204  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map6q14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)61653614027261739Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:252
Count of miRNA genes:163
Interacting mature miRNAs:183
Transcripts:ENSRNOT00000047210
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 30 21 8 19 8 5 8 74 29 34 11 5
Low 1 13 36 33 33 3 3 6 7 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001003957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001003958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594266 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039112668 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC089916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BN000395 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BN000396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000047210   ⟹   ENSRNOP00000046524
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl626,822,609 - 26,896,687 (+)Ensembl
Rnor_6.0 Ensembl628,235,695 - 28,340,577 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089093   ⟹   ENSRNOP00000069441
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl628,323,647 - 28,340,577 (+)Ensembl
RefSeq Acc Id: NM_001003957   ⟹   NP_001003957
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,879,081 - 26,896,687 (+)NCBI
Rnor_6.0628,323,647 - 28,340,577 (+)NCBI
Rnor_5.0638,132,683 - 38,149,613 (+)NCBI
RGSC_v3.4626,802,612 - 26,878,878 (+)RGD
Celera626,354,374 - 26,371,904 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001003958   ⟹   NP_001003958
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,822,609 - 26,896,687 (+)NCBI
Rnor_6.0628,235,695 - 28,340,577 (+)NCBI
Rnor_5.0638,044,960 - 38,082,583 (+)NCBI
Rnor_5.0638,132,683 - 38,149,613 (+)NCBI
RGSC_v3.4626,802,612 - 26,878,878 (+)RGD
Celera626,297,300 - 26,371,904 (+)RGD
Sequence:
RefSeq Acc Id: XM_017594266   ⟹   XP_017449755
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,796,662 - 26,902,161 (+)NCBI
Rnor_6.0628,209,821 - 28,346,052 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594267   ⟹   XP_017449756
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,791,871 - 26,902,161 (+)NCBI
Rnor_6.0628,205,766 - 28,346,052 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594268   ⟹   XP_017449757
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,791,556 - 26,902,161 (+)NCBI
Rnor_6.0628,205,375 - 28,346,052 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039112661   ⟹   XP_038968589
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,792,467 - 26,902,161 (+)NCBI
RefSeq Acc Id: XM_039112662   ⟹   XP_038968590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,796,662 - 26,902,161 (+)NCBI
RefSeq Acc Id: XM_039112663   ⟹   XP_038968591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,800,586 - 26,902,161 (+)NCBI
RefSeq Acc Id: XM_039112664   ⟹   XP_038968592
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,792,460 - 26,902,161 (+)NCBI
RefSeq Acc Id: XM_039112665   ⟹   XP_038968593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,791,517 - 26,902,161 (+)NCBI
RefSeq Acc Id: XM_039112666   ⟹   XP_038968594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,792,467 - 26,894,469 (+)NCBI
RefSeq Acc Id: XM_039112667   ⟹   XP_038968595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,822,831 - 26,902,161 (+)NCBI
RefSeq Acc Id: XM_039112668   ⟹   XP_038968596
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2626,879,284 - 26,902,161 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001003958   ⟸   NM_001003958
- Peptide Label: isoform 1
- UniProtKB: Q1LZ53 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001003957   ⟸   NM_001003957
- Peptide Label: isoform 2
- UniProtKB: Q1LZ53 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017449757   ⟸   XM_017594268
- Peptide Label: isoform X1
- UniProtKB: Q1LZ53 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017449756   ⟸   XM_017594267
- Peptide Label: isoform X1
- UniProtKB: Q1LZ53 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017449755   ⟸   XM_017594266
- Peptide Label: isoform X1
- UniProtKB: Q1LZ53 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069441   ⟸   ENSRNOT00000089093
RefSeq Acc Id: ENSRNOP00000046524   ⟸   ENSRNOT00000047210
RefSeq Acc Id: XP_038968593   ⟸   XM_039112665
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968592   ⟸   XM_039112664
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968589   ⟸   XM_039112661
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968594   ⟸   XM_039112666
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968590   ⟸   XM_039112662
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968591   ⟸   XM_039112663
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038968595   ⟸   XM_039112667
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038968596   ⟸   XM_039112668
- Peptide Label: isoform X4
Protein Domains
ADD   PWWP   SAM-dependent MTase C5-type

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303336 AgrOrtholog
Ensembl Genes ENSRNOG00000026649 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000046524 UniProtKB/Swiss-Prot
  ENSRNOP00000069441 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000047210 UniProtKB/Swiss-Prot
  ENSRNOT00000089093 UniProtKB/Swiss-Prot
InterPro ADD UniProtKB/Swiss-Prot
  ADD_DNMT3A UniProtKB/Swiss-Prot
  C5_DNA_meth_AS UniProtKB/Swiss-Prot
  C5_MeTfrase UniProtKB/Swiss-Prot
  DNMT3_ADD UniProtKB/Swiss-Prot
  DNMT3A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PWWP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM-dependent_MTases UniProtKB/Swiss-Prot
KEGG Report rno:444984 UniProtKB/Swiss-Prot
NCBI Gene 444984 ENTREZGENE
PANTHER PTHR23068:SF10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ADD_DNMT3 UniProtKB/Swiss-Prot
  DNA_methylase UniProtKB/Swiss-Prot
  PWWP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Dnmt3a PhenoGen
PROSITE ADD UniProtKB/Swiss-Prot
  C5_MTASE_1 UniProtKB/Swiss-Prot
  PWWP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM_MT_C5 UniProtKB/Swiss-Prot
SMART PWWP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53335 UniProtKB/Swiss-Prot
UniProt DNM3A_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q5FVL1_RAT UniProtKB/TrEMBL
UniProt Secondary Q1LZ52 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-29 Dnmt3a  DNA methyltransferase 3 alpha  Dnmt3a  DNA (cytosine-5-)-methyltransferase 3 alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-11 Dnmt3a  DNA (cytosine-5-)-methyltransferase 3 alpha  Dnmt3a  DNA methyltransferase 3A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-02-14 Dnmt3a  DNA methyltransferase 3A      Symbol and Name status set to provisional 70820 PROVISIONAL