Tmlhe (trimethyllysine hydroxylase, epsilon) - Rat Genome Database
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Gene: Tmlhe (trimethyllysine hydroxylase, epsilon) Rattus norvegicus
Analyze
Symbol: Tmlhe
Name: trimethyllysine hydroxylase, epsilon
RGD ID: 620629
Description: Exhibits trimethyllysine dioxygenase activity. Predicted to be involved in carnitine biosynthetic process and negative regulation of oxidoreductase activity. Localizes to mitochondrion. Human ortholog(s) of this gene implicated in autistic disorder. Orthologous to human TMLHE (trimethyllysine hydroxylase, epsilon); PARTICIPATES IN carnitine biosynthetic pathway; lysine degradation pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: epsilon-trimethyllysine 2-oxoglutarate dioxygenase; epsilon-trimethyllysine hydroxylase; MGC94841; TML dioxygenase; TML hydroxylase; TML-alpha-ketoglutarate dioxygenase; TMLD; Tmlh; trimethyllysine dioxygenase, mitochondrial
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
Rnor_6.020237,461 - 285,125 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl20237,506 - 284,943 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.020231,244 - 279,207 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4208,623 - 56,125 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12019,571 - 56,039 (+)NCBI
Celera20963,069 - 1,011,108 (+)NCBICelera
Cytogenetic Map20p12NCBI
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
mitochondrial matrix  (IEA)
mitochondrion  (IBA,IDA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12121276   PMID:12477932   PMID:15489334   PMID:15754339   PMID:23092983  


Genomics

Comparative Map Data
Tmlhe
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.020237,461 - 285,125 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl20237,506 - 284,943 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.020231,244 - 279,207 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4208,623 - 56,125 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12019,571 - 56,039 (+)NCBI
Celera20963,069 - 1,011,108 (+)NCBICelera
Cytogenetic Map20p12NCBI
TMLHE
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX155,489,011 - 155,719,098 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 EnsemblX155,489,011 - 155,669,944 (-)EnsemblGRCh38hg38GRCh38
GRCh38X155,489,011 - 155,612,952 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X154,718,672 - 154,842,622 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X154,372,967 - 154,495,791 (-)NCBINCBI36hg18NCBI36
Build 34X154,283,476 - 154,406,301NCBI
CeleraX154,736,459 - 154,739,995 (+)NCBI
CeleraX154,903,691 - 154,996,305 (-)NCBI
Cytogenetic MapXq28NCBI
HuRefX143,232,719 - 143,323,711 (-)NCBIHuRef
CHM1_1X154,630,300 - 154,754,464 (-)NCBICHM1_1
Tmlhe
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Cytogenetic MapX NCBI
Tmlhe
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955594272,646 - 331,757 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955594272,668 - 329,997 (+)NCBIChiLan1.0ChiLan1.0
TMLHE
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X154,870,199 - 154,976,780 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0X144,956,906 - 145,081,204 (-)NCBIMhudiblu_PPA_v0panPan3
TMLHE
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX123,324,729 - 123,438,947 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X123,322,773 - 123,438,999 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tmlhe
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493695864,713 - 113,627 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMLHE
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX125,598,105 - 125,673,680 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X125,601,920 - 125,673,716 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X142,728,254 - 142,800,047 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMLHE
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X129,628,788 - 129,729,616 (-)NCBI
ChlSab1.1 EnsemblX129,626,286 - 129,729,592 (-)Ensembl
Tmlhe
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624980310,630 - 407,364 (+)NCBI

Position Markers
BF389672  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.020255,090 - 255,309NCBIRnor6.0
Rnor_5.020249,062 - 249,281UniSTSRnor5.0
RGSC_v3.42026,248 - 26,467UniSTSRGSC3.4
Celera20981,266 - 981,485UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2015192000Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:104
Count of miRNA genes:79
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000000956, ENSRNOT00000049573
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 34 52 41 14 41 4 7 59 35 34 11 4
Low 9 5 5 4 4 15 7 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000049573   ⟹   ENSRNOP00000044070
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20248,410 - 284,832 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076655   ⟹   ENSRNOP00000068322
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20237,506 - 284,943 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076901   ⟹   ENSRNOP00000068031
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20237,506 - 284,943 (+)Ensembl
RefSeq Acc Id: NM_133387   ⟹   NP_596878
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.020237,506 - 284,943 (+)NCBI
Rnor_5.020231,244 - 279,207 (+)NCBI
RGSC_v3.4208,623 - 56,125 (+)RGD
Celera20963,069 - 1,011,108 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255855   ⟹   XP_006255917
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.020237,461 - 285,125 (+)NCBI
Rnor_5.020231,244 - 279,207 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_596878 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255917 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH85923 (Get FASTA)   NCBI Sequence Viewer  
  AAL01252 (Get FASTA)   NCBI Sequence Viewer  
  EDL84655 (Get FASTA)   NCBI Sequence Viewer  
  Q91ZW6 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_596878   ⟸   NM_133387
- UniProtKB: Q91ZW6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006255917   ⟸   XM_006255855
- Peptide Label: isoform X1
- UniProtKB: Q91ZW6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000044070   ⟸   ENSRNOT00000049573
RefSeq Acc Id: ENSRNOP00000068031   ⟸   ENSRNOT00000076901
RefSeq Acc Id: ENSRNOP00000068322   ⟸   ENSRNOT00000076655

Transcriptome

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

Promoters
RGD ID:13701267
Promoter ID:EPDNEW_R11786
Type:initiation region
Name:Tmlhe_1
Description:trimethyllysine hydroxylase, epsilon
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_6.020237,501 - 237,561EPDNEW

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)
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
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 (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 (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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 242216 242217 C G snv F344/DuCrlCrlj (KyushuU), KFRS3B/Kyo (KyushuU), DOB/Oda (KyushuU), F344/Jcl (KyushuU), LEC/Tj (KyushuU), HWY/Slc (KyushuU), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), ZFDM (KyushuU), F344/NSlc (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU)
20 242219 242220 A C snv SBN/Ygl (MCW), RCS/Kyo (KyushuU), SBH/Ygl (MCW), HTX/Kyo (KyushuU), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 248433 248434 C G snv FHH/EurMcwi (MCW), CDR, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), GH/OmrMcwi (MCW), CDS
20 248436 248437 A C snv SBH/Ygl (MCW), SBN/Ygl (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 19551 19552 C G snv SHR/OlaIpcv (ICL), FHH/EurMcwi (MDC), SS/JrHsdMcwi (ICL), SS/Jr (ICL), SR/JrHsd (ICL), SHRSP/Gcrc (ICL), SHR/NHsd (ICL), SHR/OlaIpcv (ICL), LN/MavRrrc (ICL), LL/MavRrrc (ICL), SHRSP/Gcrc (MDC), SS/JrHsdMcwi (MDC), SHR/OlaIpcv (KNAW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), GH/OmrMcwi (MCW), BBDP/WorN (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), GK/Ox (ICL), LH/MavRrrc (ICL)
20 19554 19555 A C snv SBN/Ygl (ICL), SBH/Ygl (ICL), MNS/Gib (ICL), ACI/EurMcwi (MCW), WAG/Rij (ICL), ACI/N (KNAW), MHS/Gib (ICL), COP/CrCrl (MCW & UW), ACI/EurMcwi (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620629 AgrOrtholog
Ensembl Genes ENSRNOG00000000729 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000044070 UniProtKB/Swiss-Prot
  ENSRNOP00000068031 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000068322 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000049573 UniProtKB/Swiss-Prot
  ENSRNOT00000076655 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000076901 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.2020.30 UniProtKB/Swiss-Prot
  3.60.130.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7109209 IMAGE-MGC_LOAD
InterPro GBBH-like_N_sf UniProtKB/Swiss-Prot
  GBH-like_N UniProtKB/Swiss-Prot
  TauD-like_sf UniProtKB/Swiss-Prot
  TauD/TfdA-like UniProtKB/Swiss-Prot
  Trimethyllysine_dOase UniProtKB/Swiss-Prot
KEGG Report rno:170898 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94841 IMAGE-MGC_LOAD
NCBI Gene 170898 ENTREZGENE
Pfam DUF971 UniProtKB/Swiss-Prot
  TauD UniProtKB/Swiss-Prot
PhenoGen Tmlhe PhenoGen
TIGRFAMs carnitine_TMLD UniProtKB/Swiss-Prot
UniGene Rn.3607 ENTREZGENE
UniProt Q91ZW6 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5U2P7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Tmlhe  trimethyllysine hydroxylase, epsilon      Symbol and Name status set to approved 625702 APPROVED
2003-04-28 Tmlhe  trimethyllysine hydroxylase, epsilon  Tmlh  epsilon-trimethyllysine hydroxylase  Symbol and Name updated to reflect Human and Mouse nomenclature 629477 PROVISIONAL
2002-08-07 Tmlh  epsilon-trimethyllysine hydroxylase      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in liver and kidney 70558
gene_function catalyzes the formation of beta-hydroxy-N-epsilon-trimethyl-lysine from epsilon-N-trimethyllysine 70558
gene_process functions in L-carnitine biosynthetic pathway 70558
gene_product 47.5kDa protein 70558