Dnmt3b (DNA methyltransferase 3 beta) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Dnmt3b (DNA methyltransferase 3 beta) Rattus norvegicus
Analyze
Symbol: Dnmt3b
Name: DNA methyltransferase 3 beta
RGD ID: 1303274
Description: Enables DNA binding activity; chromatin binding activity; and histone deacetylase binding activity. Involved in several processes, including cellular response to dexamethasone stimulus; cellular response to hyperoxia; and response to alkaloid. Located in cytoplasm and nucleus. Biomarker of anxiety disorder; congenital heart disease; hepatocellular carcinoma; and prostatitis. Human ortholog(s) of this gene implicated in several diseases, including acute myeloid leukemia; autoimmune disease (multiple); carcinoma (multiple); immunodeficiency-centromeric instability-facial anomalies syndrome 1; and thymoma. Orthologous to human DNMT3B (DNA methyltransferase 3 beta); PARTICIPATES IN DNA modification pathway; methionine cycle/metabolic pathway; cysteine and methionine metabolic pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 5-aza-2'-deoxycytidine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DNA (cytosine-5)-methyltransferase 3B; DNA (cytosine-5-)-methyltransferase 3 beta; DNA methyltransferase 3B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Dnmt3b-ps1   Dnmt3b-ps2  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23142,130,592 - 142,169,124 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3142,130,592 - 142,169,124 (+)Ensembl
Rnor_6.03149,131,541 - 149,170,061 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3149,131,785 - 149,208,786 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03155,510,828 - 155,591,435 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43144,030,737 - 144,069,265 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13143,936,358 - 143,974,887 (+)NCBI
Celera3140,873,202 - 140,910,431 (+)NCBICelera
Cytogenetic Map3q41NCBI
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
(+)-catechin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3'-diindolylmethane  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-phenylprop-2-enal  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-nonylphenol  (ISO)
4-tert-Octylphenol  (ISO)
5-aza-2'-deoxycytidine  (EXP,ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
8-hydroxy-2'-deoxyguanosine  (ISO)
acetic acid  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
amphetamine  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzophenanthridine  (ISO)
berberine  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
bromochloroacetic acid  (ISO)
buta-1,3-diene  (ISO)
Butylparaben  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
cocaine  (ISO)
copper(II) sulfate  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
D-penicillamine  (ISO)
DDT  (EXP)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (EXP,ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
diphenylcyclopropenone  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP,ISO)
entinostat  (ISO)
ethanol  (ISO)
etoposide  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
gibberellin A3  (EXP)
glycine betaine  (ISO)
guggulsterone  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
indole-3-methanol  (EXP)
isoprenaline  (ISO)
ketamine  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
LY294002  (ISO)
menadione  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP)
microcystin-LR  (ISO)
Monobutylphthalate  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
ozone  (EXP,ISO)
p-tert-Amylphenol  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PCB138  (ISO)
pelargonidin  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP,ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
procyanidin B2  (ISO)
pterostilbene  (ISO)
quartz  (ISO)
quinoline  (ISO)
resveratrol  (EXP,ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
streptozocin  (ISO)
sulforaphane  (ISO)
tamoxifen  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (ISO)
tributylstannane  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
uranium atom  (EXP)
valproic acid  (ISO)
vanillin  (ISO)
vinclozolin  (EXP)
vinyl carbamate  (ISO)
withaferin A  (ISO)
wortmannin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Azad AK, etal., Cancer. 2012 Mar 15;118(6):1554-65. doi: 10.1002/cncr.26446. Epub 2011 Aug 25.
2. Bai S, etal., J Biol Chem. 2006 May 12;281(19):13604-11. Epub 2006 Mar 14.
3. Bai S, etal., Mol Cell Biol. 2005 Jan;25(2):751-66.
4. 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.
5. Chen MF, etal., Cancer. 2012 Aug 15;118(16):4074-89. doi: 10.1002/cncr.26736. Epub 2011 Dec 27.
6. Chen WC, etal., PLoS One. 2014 Mar 13;9(3):e89956. doi: 10.1371/journal.pone.0089956. eCollection 2014.
7. Coppede F, etal., PLoS One. 2013 Nov 19;8(11):e80846. doi: 10.1371/journal.pone.0080846. eCollection 2013.
8. Cowin PA, etal., Endocrinology. 2010 Feb;151(2):783-92. doi: 10.1210/en.2009-0982. Epub 2010 Jan 7.
9. Dawson MA and Kouzarides T, Cell. 2012 Jul 6;150(1):12-27. doi: 10.1016/j.cell.2012.06.013.
10. de Vogel S, etal., Cancer Epidemiol Biomarkers Prev. 2009 Nov;18(11):3086-96. doi: 10.1158/1055-9965.EPI-09-0289. Epub 2009 Oct 20.
11. Delatte B, etal., EMBO J. 2014 Jun 2;33(11):1198-211. doi: 10.15252/embj.201488290. Epub 2014 May 13.
12. Elsner VR, etal., Exp Gerontol. 2013 Feb;48(2):136-9. doi: 10.1016/j.exger.2012.11.011. Epub 2012 Nov 30.
13. Fan H, etal., J Exp Clin Cancer Res. 2008 Jul 28;27:24. doi: 10.1186/1756-9966-27-24.
14. Feng Y, etal., J Nutr Biochem. 2013 Jul;24(7):1373-80. doi: 10.1016/j.jnutbio.2012.11.005. Epub 2013 Jan 17.
15. Feng YJ, etal., Zhonghua Yi Xue Za Zhi. 2013 Dec 24;93(48):3822-5.
16. Fonseca-Silva T, etal., Pathobiology. 2012;79(1):18-23. doi: 10.1159/000330171. Epub 2012 Jan 12.
17. Guo X, etal., Mol Biol Rep. 2010 Jan;37(1):219-25. doi: 10.1007/s11033-009-9626-z. Epub 2009 Jul 22.
18. Hayette S, etal., PLoS One. 2012;7(12):e51527. doi: 10.1371/journal.pone.0051527. Epub 2012 Dec 10.
19. Hernandez-Sotelo D, etal., Mol Biol Rep. 2013 Jul;40(7):4275-80. doi: 10.1007/s11033-013-2511-9. Epub 2013 May 16.
20. Khorshied MM and El-Ghamrawy MK, Gene. 2012 Dec 10;511(1):34-7. doi: 10.1016/j.gene.2012.09.024. Epub 2012 Sep 18.
21. Kn H, etal., Cancer Biol Ther. 2004 Oct;3(10):989-94. Epub 2004 Oct 2.
22. Lee SJ, etal., Carcinogenesis. 2005 Feb;26(2):403-9. Epub 2004 Nov 4.
23. Lees-Murdock DJ, etal., Genomics 2004 Jul;84(1):193-204.
24. Li Y, etal., Diabetes Res Clin Pract. 2011 Nov;94(2):242-8. doi: 10.1016/j.diabres.2011.07.027. Epub 2011 Aug 23.
25. Li Y, etal., Zhonghua Nei Ke Za Zhi. 2005 Aug;44(8):588-91.
26. Liu X and Guo SW, Gynecol Obstet Invest. 2012;74(2):100-8. Epub 2012 May 4.
27. Liu Z, etal., Cancer Lett. 2008 Sep 8;268(1):158-65. doi: 10.1016/j.canlet.2008.03.034. Epub 2008 May 1.
28. Loree J, etal., Int J Radiat Biol. 2006 Nov;82(11):805-15.
29. Majumder S, etal., J Biol Chem. 2002 May 3;277(18):16048-58. Epub 2002 Feb 13.
30. Meunier L, etal., Endocrinology. 2012 Apr;153(4):1936-47. doi: 10.1210/en.2011-1109. Epub 2012 Feb 14.
31. MGD data from the GO Consortium
32. Mizuno S, etal., Blood. 2001 Mar 1;97(5):1172-9.
33. Morey SR, etal., Cancer Res. 2006 Dec 15;66(24):11659-67.
34. Nam EJ, etal., Rheumatol Int. 2010 Aug;30(10):1299-303. doi: 10.1007/s00296-009-1141-y. Epub 2009 Sep 24.
35. Nguyen T, etal., Epigenetics. 2011 Mar;6(3):388-94. Epub 2011 Mar 1.
36. OMIM Disease Annotation Pipeline
37. Park HJ, etal., Cancer Lett. 2006 Feb 28;233(2):271-8.
38. Pazienza V, etal., PPAR Res. 2012;2012:461784. doi: 10.1155/2012/461784. Epub 2012 Aug 8.
39. Ping J, etal., Toxicology. 2014 Jul 3;321:53-61. doi: 10.1016/j.tox.2014.03.011. Epub 2014 Apr 6.
40. Pipeline to import KEGG annotations from KEGG into RGD
41. Pol Bodetto S, etal., Neuropharmacology. 2013 Oct;73:31-40. doi: 10.1016/j.neuropharm.2013.05.005. Epub 2013 May 18.
42. Qin W, etal., Nutr Cancer. 2014;66(2):270-7. doi: 10.1080/01635581.2014.868910. Epub 2014 Jan 21.
43. RGD automated data pipeline
44. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
45. RGD automated import pipeline for gene-chemical interactions
46. Sharma D, etal., Mol Endocrinol. 2013 Jul;27(7):1142-52. doi: 10.1210/me.2013-1079. Epub 2013 May 13.
47. Su PH, etal., Oncogene. 2013 Jan 3;32(1):15-26. doi: 10.1038/onc.2012.29. Epub 2012 Feb 13.
48. Su X, etal., Oncol Rep. 2010 Mar;23(3):819-26.
49. Tao J, etal., J Clin Immunol. 2008 Sep;28(5):432-9. doi: 10.1007/s10875-008-9223-2. Epub 2008 Aug 6.
50. Tryndyak VP, etal., Carcinogenesis. 2006 Aug;27(8):1713-20. Epub 2006 Apr 22.
51. Wang X, etal., Mol Neurobiol. 2013 Dec;48(3):544-55. doi: 10.1007/s12035-013-8444-4. Epub 2013 Mar 26.
52. Wu Y, etal., Fertil Steril. 2007 Jan;87(1):24-32. Epub 2006 Nov 1.
53. Xiong L, etal., FEBS J. 2012 Dec;279(23):4318-26. doi: 10.1111/febs.12021. Epub 2012 Nov 7.
54. Xiong Y, etal., Gynecol Oncol. 2005 Mar;96(3):601-9.
55. Xu GL, etal., Nature. 1999 Nov 11;402(6758):187-91.
56. Zhang C, etal., Neurosci Lett. 2009 Oct 25;462(3):308-11. doi: 10.1016/j.neulet.2009.06.085. Epub 2009 Jul 2.
57. Zhang C, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2010 Dec;27(6):697-9. doi: 10.3760/cma.j.issn.1003-9406.2010.06.022.
58. Zhang Q, etal., Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2013 Feb;31(2):92-5.
59. Zheng Q, etal., PLoS One. 2013 Sep 17;8(9):e74626. doi: 10.1371/journal.pone.0074626. eCollection 2013.
Additional References at PubMed
PMID:9662389   PMID:10555141   PMID:11919202   PMID:11934864   PMID:14519686   PMID:15456878   PMID:16543361   PMID:17303076   PMID:17938196   PMID:18056424   PMID:18413740   PMID:18567530  
PMID:18814855   PMID:19796622   PMID:20548288   PMID:21378119   PMID:22133874   PMID:23754746   PMID:25190601   PMID:25416223   PMID:27856912  


Genomics

Comparative Map Data
Dnmt3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23142,130,592 - 142,169,124 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl3142,130,592 - 142,169,124 (+)Ensembl
Rnor_6.03149,131,541 - 149,170,061 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3149,131,785 - 149,208,786 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03155,510,828 - 155,591,435 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43144,030,737 - 144,069,265 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13143,936,358 - 143,974,887 (+)NCBI
Celera3140,873,202 - 140,910,431 (+)NCBICelera
Cytogenetic Map3q41NCBI
DNMT3B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2032,762,385 - 32,809,356 (+)EnsemblGRCh38hg38GRCh38
GRCh382032,762,385 - 32,809,356 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372031,350,191 - 31,397,162 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362030,813,852 - 30,860,823 (+)NCBINCBI36hg18NCBI36
Celera2028,104,119 - 28,151,087 (+)NCBI
Cytogenetic Map20q11.21NCBI
HuRef2028,137,312 - 28,184,284 (+)NCBIHuRef
CHM1_12031,253,633 - 31,300,607 (+)NCBICHM1_1
Dnmt3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392153,491,332 - 153,529,650 (+)NCBIGRCm39mm39
GRCm39 Ensembl2153,491,370 - 153,529,650 (+)Ensembl
GRCm382153,649,411 - 153,687,730 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2153,649,450 - 153,687,730 (+)EnsemblGRCm38mm10GRCm38
MGSCv372153,475,190 - 153,513,466 (+)NCBIGRCm37mm9NCBIm37
MGSCv362153,340,895 - 153,379,168 (+)NCBImm8
Celera2159,495,468 - 159,534,017 (+)NCBICelera
Cytogenetic Map2H1NCBI
Dnmt3b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542228,380,591 - 28,421,301 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542228,380,595 - 28,427,012 (-)NCBIChiLan1.0ChiLan1.0
DNMT3B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12030,169,081 - 30,215,487 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2030,186,069 - 30,215,487 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02029,049,993 - 29,096,957 (+)NCBIMhudiblu_PPA_v0panPan3
DNMT3B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12422,096,386 - 22,123,378 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2422,096,349 - 22,122,900 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2421,724,710 - 21,769,260 (+)NCBI
ROS_Cfam_1.02422,765,878 - 22,810,458 (+)NCBI
UMICH_Zoey_3.12422,042,034 - 22,086,566 (+)NCBI
UNSW_CanFamBas_1.02422,150,746 - 22,195,021 (+)NCBI
UU_Cfam_GSD_1.02422,581,755 - 22,626,058 (+)NCBI
Dnmt3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640171,116,001 - 171,139,372 (+)NCBI
SpeTri2.0NW_00493648519,547,836 - 19,570,716 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DNMT3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1736,332,801 - 36,386,074 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11736,345,715 - 36,386,076 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21741,282,731 - 41,322,908 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DNMT3B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1237,128,635 - 37,176,033 (+)NCBI
ChlSab1.1 Ensembl237,146,538 - 37,174,570 (+)Ensembl
Vero_WHO_p1.0NW_02366605089,724,034 - 89,772,846 (-)NCBI
Dnmt3b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248426,450,972 - 6,505,929 (-)NCBI

Position Markers
UniSTS:472909  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23142,158,376 - 142,158,451 (+)MAPPERmRatBN7.2
mRatBN7.23142,195,729 - 142,195,804 (+)MAPPERmRatBN7.2
Rnor_6.03149,198,110 - 149,198,184NCBIRnor6.0
Rnor_6.03149,159,316 - 149,159,390NCBIRnor6.0
Rnor_5.03155,576,334 - 155,576,408UniSTSRnor5.0
Rnor_5.03155,538,611 - 155,538,685UniSTSRnor5.0
RGSC_v3.43144,058,520 - 144,058,594UniSTSRGSC3.4
RGSC_v3.43144,097,377 - 144,097,451UniSTSRGSC3.4
Celera3140,937,252 - 140,937,326UniSTS
Celera3140,899,686 - 140,899,760UniSTS
Cytogenetic Map3q41UniSTS
UniSTS:525685  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23142,153,093 - 142,154,418 (+)MAPPERmRatBN7.2
Rnor_6.03149,154,033 - 149,155,357NCBIRnor6.0
Rnor_5.03155,533,328 - 155,534,652UniSTSRnor5.0
RGSC_v3.43144,053,237 - 144,054,561UniSTSRGSC3.4
Celera3140,894,403 - 140,895,727UniSTS
Cytogenetic Map3q41UniSTS
UniSTS:525686  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23142,165,241 - 142,165,985 (+)MAPPERmRatBN7.2
mRatBN7.23142,205,382 - 142,206,153 (+)MAPPERmRatBN7.2
Rnor_6.03149,207,898 - 149,208,668NCBIRnor6.0
Rnor_6.03149,166,179 - 149,166,922NCBIRnor6.0
Rnor_5.03155,586,122 - 155,586,892UniSTSRnor5.0
Rnor_5.03155,545,474 - 155,546,217UniSTSRnor5.0
RGSC_v3.43144,065,383 - 144,066,126UniSTSRGSC3.4
RGSC_v3.43144,107,027 - 144,107,797UniSTSRGSC3.4
Celera3140,946,902 - 140,947,672UniSTS
Celera3140,906,549 - 140,907,292UniSTS
Cytogenetic Map3q41UniSTS
Dnmt3b  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23142,159,601 - 142,159,993 (+)MAPPERmRatBN7.2
Rnor_6.03149,160,541 - 149,160,932NCBIRnor6.0
Rnor_5.03155,539,836 - 155,540,227UniSTSRnor5.0
RGSC_v3.43144,059,745 - 144,060,136UniSTSRGSC3.4
Celera3140,900,911 - 140,901,302UniSTS
Cytogenetic Map3q41UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3140069424146976080Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141339013162184794Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141339236155617360Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:192
Count of miRNA genes:116
Interacting mature miRNAs:155
Transcripts:ENSRNOT00000015482
Prediction methods:Miranda, 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 10 12 6 6 6 8 12 18
Low 3 32 45 35 13 35 4 5 66 22 23 11 4
Below cutoff 1 4 6 1 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015482   ⟹   ENSRNOP00000015482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3142,130,592 - 142,169,124 (+)Ensembl
Rnor_6.0 Ensembl3149,144,795 - 149,168,760 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090321   ⟹   ENSRNOP00000070758
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3142,130,592 - 142,168,823 (+)Ensembl
Rnor_6.0 Ensembl3149,131,785 - 149,208,786 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000097170   ⟹   ENSRNOP00000096797
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3142,130,592 - 142,169,124 (+)Ensembl
RefSeq Acc Id: NM_001003959   ⟹   NP_001003959
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23142,130,592 - 142,169,124 (+)NCBI
Rnor_6.03149,131,541 - 149,170,061 (+)NCBI
Rnor_5.03155,510,828 - 155,591,435 (+)NCBI
RGSC_v3.43144,030,737 - 144,069,265 (+)RGD
Celera3140,873,202 - 140,910,431 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001003959 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAE52319 (Get FASTA)   NCBI Sequence Viewer  
  EDL85992 (Get FASTA)   NCBI Sequence Viewer  
  EDL85993 (Get FASTA)   NCBI Sequence Viewer  
  EDL85994 (Get FASTA)   NCBI Sequence Viewer  
  EDL85995 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001003959   ⟸   NM_001003959
- UniProtKB: Q1LZ51 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070758   ⟸   ENSRNOT00000090321
RefSeq Acc Id: ENSRNOP00000015482   ⟸   ENSRNOT00000015482
RefSeq Acc Id: ENSRNOP00000096797   ⟸   ENSRNOT00000097170
Protein Domains
PHD-type   PWWP

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:1303274 AgrOrtholog
Ensembl Genes ENSRNOG00000010625 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015482 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070758 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015482 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000090321 UniProtKB/TrEMBL
InterPro ADD UniProtKB/TrEMBL
  C5_DNA_meth_AS UniProtKB/TrEMBL
  C5_MeTfrase UniProtKB/TrEMBL
  DNMT3_ADD UniProtKB/TrEMBL
  DNMT3B UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
  SAM-dependent_MTases-like UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
KEGG Report rno:444985 UniProtKB/TrEMBL
NCBI Gene 444985 ENTREZGENE
Pfam ADD_DNMT3 UniProtKB/TrEMBL
  DNA_methylase UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
PhenoGen Dnmt3b PhenoGen
PROSITE ADD UniProtKB/TrEMBL
  C5_MTASE_1 UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
  SAM_MT_C5 UniProtKB/TrEMBL
SMART PWWP UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
  SSF53335 UniProtKB/TrEMBL
UniProt A0A0G2JYR2_RAT UniProtKB/TrEMBL
  Q1LZ51 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1LQ40 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-29 Dnmt3b  DNA methyltransferase 3 beta  Dnmt3b  DNA (cytosine-5-)-methyltransferase 3 beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-20 Dnmt3b  DNA (cytosine-5-)-methyltransferase 3 beta  Dnmt3b  DNA methyltransferase 3B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Dnmt3b  DNA methyltransferase 3B      Symbol and Name status set to approved 1299863 APPROVED
2005-07-14 Dnmt3b  DNA methyltransferase 3B      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression mouse homolog is expressed in oocytes 1304004