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: Enables trimethyllysine dioxygenase activity. Predicted to be involved in carnitine biosynthetic process and negative regulation of oxidoreductase activity. Predicted to be located in mitochondrial matrix. Predicted to be active in 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: VALIDATED
Previously 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 Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82096,561 - 144,414 (+)NCBIGRCr8
mRatBN7.22091,234 - 138,942 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2091,272 - 140,386 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx20100,768 - 153,428 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.020104,240 - 156,894 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02099,724 - 147,338 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12019,571 - 56,039 (+)NCBI
Celera20963,069 - 1,011,108 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
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. Molecular and Biochemical Characterization of Rat epsilon -N-Trimethyllysine Hydroxylase, the First Enzyme of Carnitine Biosynthesis. Vaz FM, etal., J Biol Chem 2001 Sep 7;276(36):33512-7.
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:15754339   PMID:23092983  


Genomics

Comparative Map Data
Tmlhe
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82096,561 - 144,414 (+)NCBIGRCr8
mRatBN7.22091,234 - 138,942 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2091,272 - 140,386 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx20100,768 - 153,428 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.020104,240 - 156,894 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02099,724 - 147,338 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38X155,489,011 - 155,612,952 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX155,489,011 - 155,719,098 (-)EnsemblGRCh38hg38GRCh38
GRCh37X154,718,672 - 154,842,613 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X154,372,967 - 154,495,791 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X154,283,476 - 154,406,301NCBI
CeleraX154,736,459 - 154,739,995 (+)NCBICelera
CeleraX154,903,691 - 154,996,305 (-)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX143,232,719 - 143,323,711 (-)NCBIHuRef
CHM1_1X154,630,300 - 154,754,464 (-)NCBICHM1_1
T2T-CHM13v2.0X153,718,334 - 153,838,175 (-)NCBIT2T-CHM13v2.0
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
NHGRI_mPanPan1-v2X155,455,887 - 155,580,231 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X155,447,729 - 155,583,817 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X144,956,906 - 145,081,204 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X154,870,199 - 154,976,780 (-)NCBIpanpan1.1PanPan1.1panPan2
TMLHE
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X123,322,773 - 123,438,999 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX123,324,729 - 123,438,947 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX108,309,388 - 108,425,608 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X126,454,187 - 126,569,036 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1X122,191,346 - 122,307,568 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X124,713,751 - 124,830,273 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X124,445,149 - 124,561,391 (-)NCBIUU_Cfam_GSD_1.0
Tmlhe
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X120,209,145 - 120,330,205 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493695864,713 - 113,627 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMLHE
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX125,598,116 - 125,673,669 (-)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X129,628,788 - 129,729,616 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX129,626,286 - 129,729,592 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606567,704,658 - 67,816,724 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmlhe
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624980310,426 - 406,972 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624980310,630 - 407,364 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tmlhe
1189 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126123605Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
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
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013624629Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
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
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat

Markers in Region
BF389672  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.220108,897 - 109,117 (+)MAPPERmRatBN7.2
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000049573   ⟹   ENSRNOP00000044070
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2091,272 - 140,386 (+)Ensembl
Rnor_6.0 Ensembl20248,410 - 284,832 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076655   ⟹   ENSRNOP00000068322
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2091,315 - 140,386 (+)Ensembl
Rnor_6.0 Ensembl20237,506 - 284,943 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076901   ⟹   ENSRNOP00000068031
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2091,272 - 140,386 (+)Ensembl
Rnor_6.0 Ensembl20237,506 - 284,943 (+)Ensembl
RefSeq Acc Id: NM_133387   ⟹   NP_596878
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82096,613 - 144,235 (+)NCBI
mRatBN7.22091,311 - 138,942 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82096,561 - 144,414 (+)NCBI
mRatBN7.22091,234 - 138,942 (+)NCBI
Rnor_6.020237,461 - 285,125 (+)NCBI
Rnor_5.020231,244 - 279,207 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098398   ⟹   XP_038954326
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr820107,564 - 144,414 (+)NCBI
mRatBN7.220102,262 - 138,942 (+)NCBI
RefSeq Acc Id: XM_039098401   ⟹   XP_038954329
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr820107,564 - 144,414 (+)NCBI
mRatBN7.220102,269 - 138,942 (+)NCBI
RefSeq Acc Id: XM_063278944   ⟹   XP_063135014
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr820107,558 - 144,414 (+)NCBI
RefSeq Acc Id: NP_596878   ⟸   NM_133387
- UniProtKB: Q91ZW6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006255917   ⟸   XM_006255855
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000044070   ⟸   ENSRNOT00000049573
Ensembl Acc Id: ENSRNOP00000068031   ⟸   ENSRNOT00000076901
Ensembl Acc Id: ENSRNOP00000068322   ⟸   ENSRNOT00000076655
RefSeq Acc Id: XP_038954326   ⟸   XM_039098398
- Peptide Label: isoform X1
- UniProtKB: A0A8L2QMT7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954329   ⟸   XM_039098401
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063135014   ⟸   XM_063278944
- Peptide Label: isoform X1
Protein Domains
Gamma-butyrobetaine hydroxylase-like N-terminal   TauD/TfdA-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q91ZW6-F1-model_v2 AlphaFold Q91ZW6 1-421 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620629 AgrOrtholog
BioCyc Gene G2FUF-5098 BioCyc
BioCyc Pathway PWY-6100 [L-carnitine biosynthesis] BioCyc
BioCyc Pathway Image PWY-6100 BioCyc
Ensembl Genes ENSRNOG00000000729 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00065032616 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000049573.5 UniProtKB/TrEMBL
  ENSRNOT00000076655.3 UniProtKB/Swiss-Prot
  ENSRNOT00000076901.3 UniProtKB/Swiss-Prot
  ENSRNOT00065056107 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.2020.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.60.130.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7109209 IMAGE-MGC_LOAD
InterPro AlphaKG_dependent_hydroxylases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GBBH-like_N UniProtKB/TrEMBL
  GBBH-like_N_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GBH-like_N UniProtKB/Swiss-Prot
  TauD-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TauD/TfdA-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Trimethyllysine_dOase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:170898 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94841 IMAGE-MGC_LOAD
NCBI Gene 170898 ENTREZGENE
PANTHER GAMMA-BUTYROBETAINE HYDROXYLASE-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF971 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TauD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tmlhe PhenoGen
RatGTEx ENSRNOG00000000729 RatGTEx
  ENSRNOG00065032616 RatGTEx
Superfamily-SCOP Clavaminate synthase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2QMT7 ENTREZGENE, UniProtKB/TrEMBL
  A6KR34 ENTREZGENE, UniProtKB/TrEMBL
  Q5U2P7 ENTREZGENE
  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