Dnmt3l (DNA methyltransferase 3 like) - Rat Genome Database

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Gene: Dnmt3l (DNA methyltransferase 3 like) Rattus norvegicus
Analyze
Symbol: Dnmt3l
Name: DNA methyltransferase 3 like
RGD ID: 1303239
Description: Predicted to enable enzyme activator activity and enzyme binding activity. Involved in response to ethanol. Predicted to be located in condensed nuclear chromosome and heterochromatin. Predicted to be part of ESC/E(Z) complex. Predicted to be active in cytoplasm and nucleus. Biomarker of choline deficiency disease. Orthologous to human DNMT3L (DNA methyltransferase 3 like); PARTICIPATES IN cysteine and methionine metabolic pathway; INTERACTS WITH bisphenol A; cadmium dichloride; chlorpyrifos.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DNA (cytosine-5)-methyltransferase 3-like; DNA (cytosine-5-)-methyltransferase 3-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22010,614,933 - 10,629,516 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2010,614,934 - 10,629,516 (-)Ensembl
Rnor_6.02011,344,513 - 11,359,090 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2011,344,514 - 11,359,090 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02013,514,653 - 13,529,169 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42010,958,957 - 10,973,422 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12010,959,183 - 10,973,649 (-)NCBI
Celera2012,120,702 - 12,135,281 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Effect of DNA Demethylation in Experimental Encapsulating Peritoneal Sclerosis. Kim KH, etal., Ther Apher Dial. 2014 Sep 26. doi: 10.1111/1744-9987.12186.
3. Gestational choline deficiency causes global and Igf2 gene DNA hypermethylation by up-regulation of Dnmt1 expression. Kovacheva VP, etal., J Biol Chem. 2007 Oct 26;282(43):31777-88. Epub 2007 Aug 27.
4. Identification of 11 pseudogenes in the DNA methyltransferase gene family in rodents and humans and implications for the functional loci. Lees-Murdock DJ, etal., Genomics 2004 Jul;84(1):193-204.
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Effects of acute ethanol exposure on anxiety measures and epigenetic modifiers in the extended amygdala of adolescent rats. Sakharkar AJ, etal., Int J Neuropsychopharmacol. 2014 Dec;17(12):2057-67. doi: 10.1017/S1461145714001047. Epub 2014 Jun 26.
Additional References at PubMed
PMID:11934864   PMID:12202768   PMID:15057822   PMID:15318244   PMID:16543361   PMID:16780588   PMID:16920095   PMID:18042343   PMID:24074865   PMID:25503965   PMID:27856912  


Genomics

Comparative Map Data
Dnmt3l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22010,614,933 - 10,629,516 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2010,614,934 - 10,629,516 (-)Ensembl
Rnor_6.02011,344,513 - 11,359,090 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2011,344,514 - 11,359,090 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02013,514,653 - 13,529,169 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42010,958,957 - 10,973,422 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12010,959,183 - 10,973,649 (-)NCBI
Celera2012,120,702 - 12,135,281 (-)NCBICelera
Cytogenetic Map20p12NCBI
DNMT3L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382144,246,339 - 44,261,897 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2144,246,339 - 44,262,216 (-)EnsemblGRCh38hg38GRCh38
GRCh372145,666,222 - 45,681,780 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362144,490,651 - 44,506,527 (-)NCBINCBI36hg18NCBI36
Build 342144,490,650 - 44,506,527NCBI
Celera2130,771,480 - 30,787,356 (-)NCBI
Cytogenetic Map21q22.3NCBI
HuRef2131,036,675 - 31,052,591 (-)NCBIHuRef
CHM1_12145,226,863 - 45,242,733 (-)NCBICHM1_1
T2T-CHM13v2.02142,600,400 - 42,615,957 (-)NCBI
Dnmt3l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391077,878,121 - 77,899,456 (+)NCBIGRCm39mm39
GRCm39 Ensembl1077,877,781 - 77,899,456 (+)Ensembl
GRCm381078,042,287 - 78,063,622 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1078,041,947 - 78,063,622 (+)EnsemblGRCm38mm10GRCm38
MGSCv371077,505,032 - 77,526,360 (+)NCBIGRCm37mm9NCBIm37
MGSCv361077,452,971 - 77,466,744 (+)NCBImm8
Celera1079,081,287 - 79,102,649 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Dnmt3l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540741,177,582 - 41,186,965 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540741,177,582 - 41,186,965 (+)NCBIChiLan1.0ChiLan1.0
DNMT3L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12143,798,778 - 43,814,283 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2143,798,778 - 43,814,283 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02130,503,194 - 30,520,237 (-)NCBIMhudiblu_PPA_v0panPan3
DNMT3L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13138,099,100 - 38,111,432 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3137,256,521 - 37,272,413 (-)NCBI
ROS_Cfam_1.03137,646,747 - 37,659,063 (-)NCBI
ROS_Cfam_1.0 Ensembl3137,645,326 - 37,659,391 (-)Ensembl
UMICH_Zoey_3.13137,513,901 - 37,526,213 (-)NCBI
UNSW_CanFamBas_1.03137,497,879 - 37,510,191 (-)NCBI
UU_Cfam_GSD_1.03137,992,522 - 38,008,421 (-)NCBI
Dnmt3l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497137,307,350 - 37,324,745 (-)NCBI
SpeTri2.0NW_004936500143,078 - 160,318 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DNMT3L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13207,119,051 - 207,132,538 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113207,119,025 - 207,141,990 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213216,998,088 - 217,011,839 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DNMT3L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1287,991,868 - 88,006,399 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl287,991,936 - 88,005,459 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605416,105,634 - 16,119,773 (-)NCBIVero_WHO_p1.0
Dnmt3l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474529,869,196 - 29,878,169 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462474529,869,174 - 29,878,189 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:39
Interacting mature miRNAs:42
Transcripts:ENSRNOT00000001610
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 4
Low 3 15 14 6 14 6 14 8 16 9
Below cutoff 23 13 13 5 13 3 3 19 27 15 2 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001610   ⟹   ENSRNOP00000001610
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2010,614,934 - 10,629,516 (-)Ensembl
Rnor_6.0 Ensembl2011,344,514 - 11,359,090 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110206   ⟹   ENSRNOP00000080143
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2010,614,934 - 10,629,275 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111099   ⟹   ENSRNOP00000092377
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2010,614,934 - 10,629,275 (-)Ensembl
RefSeq Acc Id: NM_001003964   ⟹   NP_001003964
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22010,614,934 - 10,629,516 (-)NCBI
Rnor_6.02011,344,514 - 11,359,090 (-)NCBI
Rnor_5.02013,514,653 - 13,529,169 (-)NCBI
RGSC_v3.42010,958,957 - 10,973,422 (-)RGD
Celera2012,120,702 - 12,135,281 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256250   ⟹   XP_006256312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22010,614,933 - 10,629,331 (-)NCBI
Rnor_6.02011,344,513 - 11,359,003 (-)NCBI
Rnor_5.02013,514,653 - 13,529,169 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098728   ⟹   XP_038954656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22010,614,933 - 10,623,611 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001003964 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256312 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954656 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAE52320 (Get FASTA)   NCBI Sequence Viewer  
  EDL97062 (Get FASTA)   NCBI Sequence Viewer  
  Q1LZ50 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001003964   ⟸   NM_001003964
- Sequence:
RefSeq Acc Id: XP_006256312   ⟸   XM_006256250
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000001610   ⟸   ENSRNOT00000001610
RefSeq Acc Id: XP_038954656   ⟸   XM_039098728
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000092377   ⟸   ENSRNOT00000111099
RefSeq Acc Id: ENSRNOP00000080143   ⟸   ENSRNOT00000110206
Protein Domains
ADD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q1LZ50-F1-model_v2 AlphaFold Q1LZ50 1-422 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
BUF/N (2020)
Visual CSV TAB Printer
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
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
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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
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
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
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/Stm (2019)
Visual CSV TAB Printer
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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
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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
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
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
LEW/Crl (2019)
Visual CSV TAB Printer
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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)
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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)
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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)
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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)
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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)
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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)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
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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)
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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/NRrrcMcwi (2019)
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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
MR/N (2020)
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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
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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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
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
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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/N (2020)
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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/NCrl (2019)
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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
WN/N (2020)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 11355818 11355819 C G snv WKY/NCrl (RGD), WKY/NCrl (2019), WKY/NHsd (RGD), WKY/Gcrc (RGD), WKY/N (2020)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 13525897 13525898 C G snv WKY/Gcrc (KNAW), WKY/N (KNAW), NIG-III/Hok (KyushuU), WKY/NHsd (KNAW), WKY/NCrl (KNAW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 10626242 10626243 C G snv WKY/N (2020), WKY/NCrl (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303239 AgrOrtholog
BioCyc Gene G2FUF-4275 BioCyc
Ensembl Genes ENSRNOG00000001212 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001610 ENTREZGENE
  ENSRNOP00000001610.8 UniProtKB/TrEMBL
  ENSRNOP00000080143.1 UniProtKB/TrEMBL
  ENSRNOP00000092377 ENTREZGENE
  ENSRNOP00000092377.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001610 ENTREZGENE
  ENSRNOT00000001610.8 UniProtKB/TrEMBL
  ENSRNOT00000110206.1 UniProtKB/TrEMBL
  ENSRNOT00000111099 ENTREZGENE
  ENSRNOT00000111099.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ADD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNMT3_ADD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNMT3L UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM-dependent_MTases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:309680 UniProtKB/Swiss-Prot
NCBI Gene 309680 ENTREZGENE
PANTHER PTHR23068:SF13 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ADD_DNMT3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Dnmt3l PhenoGen
PROSITE ADD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZPM6_RAT UniProtKB/TrEMBL
  A0A8I6AHQ5_RAT UniProtKB/TrEMBL
  DNM3L_RAT UniProtKB/Swiss-Prot
  F1LQE0_RAT UniProtKB/TrEMBL
  Q1LZ50 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-29 Dnmt3l  DNA methyltransferase 3 like  Dnmt3l  DNA (cytosine-5-)-methyltransferase 3-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Dnmt3l  DNA (cytosine-5-)-methyltransferase 3-like      Symbol and Name status set to approved 1299863 APPROVED
2005-07-14 Dnmt3l  DNA (cytosine-5-)-methyltransferase 3-like      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_product appears to be a pseudogene 1304004