Trdmt1 (tRNA aspartic acid methyltransferase 1) - Rat Genome Database

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Gene: Trdmt1 (tRNA aspartic acid methyltransferase 1) Rattus norvegicus
Analyze
Symbol: Trdmt1
Name: tRNA aspartic acid methyltransferase 1
RGD ID: 1306292
Description: Predicted to have tRNA (cytosine-5-)-methyltransferase activity. Involved in response to amphetamine. Predicted to localize to cytoplasm. Orthologous to human TRDMT1 (tRNA aspartic acid methyltransferase 1); PARTICIPATES IN homocysteine metabolic pathway; methionine cycle/metabolic pathway; cysteine and methionine metabolic pathway; INTERACTS WITH aflatoxin B1; allethrin; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DNA (cytosine-5)-methyltransferase-like protein 2; DNA methyltransferase 2; Dnmt2; LOC291324; MGC112666; tRNA (cytosine(38)-C(5))-methyltransferase; tRNA (cytosine-5-)-methyltransferase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21776,601,966 - 76,646,104 (-)NCBI
Rnor_6.0 Ensembl1780,826,846 - 80,860,195 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01780,824,652 - 80,859,585 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01782,445,133 - 82,478,017 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41787,791,647 - 87,824,484 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11787,802,488 - 87,835,316 (-)NCBI
Celera1775,981,585 - 76,014,443 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:16424344   PMID:18567810   PMID:22885326  


Genomics

Comparative Map Data
Trdmt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21776,601,966 - 76,646,104 (-)NCBI
Rnor_6.0 Ensembl1780,826,846 - 80,860,195 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01780,824,652 - 80,859,585 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01782,445,133 - 82,478,017 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41787,791,647 - 87,824,484 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11787,802,488 - 87,835,316 (-)NCBI
Celera1775,981,585 - 76,014,443 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
TRDMT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1017,137,336 - 17,202,054 (-)EnsemblGRCh38hg38GRCh38
GRCh381017,137,336 - 17,202,066 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371017,179,335 - 17,243,671 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361017,224,988 - 17,283,687 (-)NCBINCBI36hg18NCBI36
Celera1017,118,228 - 17,177,333 (-)NCBI
Cytogenetic Map10p13NCBI
HuRef1017,098,163 - 17,157,293 (-)NCBIHuRef
CHM1_11017,179,480 - 17,244,194 (-)NCBICHM1_1
Trdmt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39213,509,690 - 13,549,618 (-)NCBIGRCm39mm39
GRCm39 Ensembl213,513,825 - 13,549,479 (-)Ensembl
GRCm38213,504,879 - 13,544,797 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl213,509,014 - 13,544,668 (-)EnsemblGRCm38mm10GRCm38
MGSCv37213,431,788 - 13,466,291 (-)NCBIGRCm37mm9NCBIm37
MGSCv36213,428,017 - 13,462,517 (-)NCBImm8
Celera213,420,290 - 13,454,789 (-)NCBICelera
Cytogenetic Map2A1NCBI
Trdmt1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542910,742,097 - 10,771,877 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542910,741,512 - 10,774,268 (+)NCBIChiLan1.0ChiLan1.0
TRDMT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11017,726,701 - 17,791,345 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1017,738,374 - 17,791,345 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01017,460,091 - 17,518,855 (-)NCBIMhudiblu_PPA_v0panPan3
TRDMT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1219,702,561 - 19,763,744 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl219,677,444 - 19,763,741 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha216,806,079 - 16,867,665 (+)NCBI
ROS_Cfam_1.0219,994,579 - 20,056,169 (+)NCBI
UMICH_Zoey_3.1217,196,915 - 17,258,530 (+)NCBI
UNSW_CanFamBas_1.0218,035,155 - 18,097,023 (+)NCBI
UU_Cfam_GSD_1.0218,653,004 - 18,714,640 (+)NCBI
Trdmt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934417,839,758 - 17,856,427 (-)NCBI
SpeTri2.0NW_00493652010,104,050 - 10,122,057 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRDMT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1043,434,444 - 43,516,094 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11043,434,148 - 43,494,924 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21048,148,992 - 48,157,057 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TRDMT1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1917,098,086 - 17,166,267 (-)NCBI
ChlSab1.1 Ensembl917,100,491 - 17,155,826 (-)Ensembl
Vero_WHO_p1.0NW_02366605122,733,372 - 22,794,872 (-)NCBI
Trdmt1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479610,630,982 - 10,712,689 (+)NCBI

Position Markers
RH128044  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21776,612,780 - 76,612,970 (+)MAPPER
Rnor_6.01780,826,895 - 80,827,084NCBIRnor6.0
Rnor_5.01782,445,279 - 82,445,468UniSTSRnor5.0
RGSC_v3.41787,791,793 - 87,791,982UniSTSRGSC3.4
Celera1775,981,731 - 75,981,920UniSTS
RH 3.4 Map17773.0UniSTS
Cytogenetic Map17q12.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)174117605786176057Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)174117605786176057Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)174173108086731080Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174254187285446768Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174435615789356157Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175347518090690466Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)175387148890843779Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175399194790843779Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175622429686731080Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)176219582286194199Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176549735982019219Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176751265790843779Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176933327285183543Rat
1300129Rf25Renal function QTL 253.03blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)177485263085183543Rat
12904736Cm121Cardiac mass QTL 1210.043heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)177570542786731080Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:274
Count of miRNA genes:170
Interacting mature miRNAs:192
Transcripts:ENSRNOT00000038651
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 9 2 16 2 71 20 32 10
Low 3 43 48 39 3 39 8 11 3 15 9 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000038651   ⟹   ENSRNOP00000038279
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1780,826,846 - 80,860,195 (-)Ensembl
RefSeq Acc Id: NM_001031643   ⟹   NP_001026813
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21776,612,635 - 76,645,471 (-)NCBI
Rnor_6.01780,826,749 - 80,859,585 (-)NCBI
Rnor_5.01782,445,133 - 82,478,017 (-)NCBI
RGSC_v3.41787,791,647 - 87,824,484 (-)RGD
Celera1775,981,585 - 76,014,443 (-)RGD
Sequence:
RefSeq Acc Id: XM_017600497   ⟹   XP_017455986
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01780,824,652 - 80,855,860 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039095552   ⟹   XP_038951480
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21776,610,538 - 76,646,100 (-)NCBI
RefSeq Acc Id: XM_039095553   ⟹   XP_038951481
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21776,601,966 - 76,646,104 (-)NCBI
RefSeq Acc Id: XM_039095554   ⟹   XP_038951482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21776,610,538 - 76,645,358 (-)NCBI
RefSeq Acc Id: XM_039095555   ⟹   XP_038951483
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21776,610,538 - 76,624,455 (-)NCBI
RefSeq Acc Id: XM_039095556   ⟹   XP_038951484
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21776,610,538 - 76,624,492 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001026813   ⟸   NM_001031643
- UniProtKB: Q4G073 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017455986   ⟸   XM_017600497
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000038279   ⟸   ENSRNOT00000038651
RefSeq Acc Id: XP_038951481   ⟸   XM_039095553
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951480   ⟸   XM_039095552
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951482   ⟸   XM_039095554
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038951484   ⟸   XM_039095556
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038951483   ⟸   XM_039095555
- Peptide Label: isoform X4
Protein Domains
SAM-dependent MTase C5-type

Transcriptome

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

Promoters
RGD ID:13700595
Promoter ID:EPDNEW_R11119
Type:single initiation site
Name:Trdmt1_1
Description:tRNA aspartic acid methyltransferase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01780,859,582 - 80,859,642EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306292 AgrOrtholog
Ensembl Genes ENSRNOG00000026132 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000038279 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000038651 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7387075 IMAGE-MGC_LOAD
InterPro C5_MeTfrase UniProtKB/Swiss-Prot
  C5_meth_CS UniProtKB/Swiss-Prot
  SAM-dependent_MTases UniProtKB/Swiss-Prot
KEGG Report rno:291324 UniProtKB/Swiss-Prot
MGC_CLONE MGC:112666 IMAGE-MGC_LOAD
NCBI Gene 291324 ENTREZGENE
Pfam DNA_methylase UniProtKB/Swiss-Prot
PhenoGen Trdmt1 PhenoGen
PRINTS C5METTRFRASE UniProtKB/Swiss-Prot
PROSITE C5_MTASE_2 UniProtKB/Swiss-Prot
  SAM_MT_C5 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53335 UniProtKB/Swiss-Prot
TIGRFAMs dcm UniProtKB/Swiss-Prot
UniProt Q4G073 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Trdmt1  tRNA aspartic acid methyltransferase 1  Dnmt2  DNA methyltransferase 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Dnmt2  DNA methyltransferase 2  Dnmt2_predicted  DNA methyltransferase 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Dnmt2_predicted  DNA methyltransferase 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED