Trmt10c (tRNA methyltransferase 10C, mitochondrial RNase P subunit) - Rat Genome Database

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Gene: Trmt10c (tRNA methyltransferase 10C, mitochondrial RNase P subunit) Rattus norvegicus
Analyze
Symbol: Trmt10c
Name: tRNA methyltransferase 10C, mitochondrial RNase P subunit
RGD ID: 1306333
Description: Predicted to enable identical protein binding activity; tRNA binding activity; and tRNA methyltransferase activity. Predicted to be involved in RNA processing and positive regulation of mitochondrial translation. Predicted to be located in mitochondrial nucleoid. Predicted to be part of mitochondrial ribonuclease P complex and tRNA methyltransferase complex. Predicted to be active in mitochondrion and nucleoplasm. Human ortholog(s) of this gene implicated in combined oxidative phosphorylation deficiency 30. Orthologous to human TRMT10C (tRNA methyltransferase 10C, mitochondrial RNase P subunit); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC304012; MGC94708; mitochondrial ribonuclease P protein 1; mitochondrial RNase P protein 1; mRNA methyladenosine-N(1)-methyltransferase; Rg9mtd1; RNA (guanine-9-) methyltransferase domain containing 1; RNA (guanine-9-)-methyltransferase domain-containing protein 1; tRNA (adenine(9)-N(1))-methyltransferase; tRNA (guanine(9)-N(1))-methyltransferase; tRNA methyltransferase 10 homolog C; tRNA methyltransferase 10 homolog C (S. cerevisiae)
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
GRCr81158,053,455 - 58,058,533 (+)NCBIGRCr8
mRatBN7.21144,584,388 - 44,589,466 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1144,584,113 - 44,589,568 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1153,360,710 - 53,365,798 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01146,022,325 - 46,027,413 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01145,146,488 - 45,151,576 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01147,047,342 - 47,052,420 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1147,047,342 - 47,052,418 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01150,229,232 - 50,234,310 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41145,559,299 - 45,564,377 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11145,616,887 - 45,621,964 (+)NCBI
Celera1144,334,937 - 44,340,015 (+)NCBICelera
Cytogenetic Map11q12NCBI
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

Cellular Component

Molecular Function

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:18614015   PMID:21593607   PMID:22658674   PMID:22681889   PMID:23042678   PMID:24703694   PMID:25931508   PMID:27132592   PMID:29040705   PMID:29072297   PMID:29880640  


Genomics

Comparative Map Data
Trmt10c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81158,053,455 - 58,058,533 (+)NCBIGRCr8
mRatBN7.21144,584,388 - 44,589,466 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1144,584,113 - 44,589,568 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1153,360,710 - 53,365,798 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01146,022,325 - 46,027,413 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01145,146,488 - 45,151,576 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01147,047,342 - 47,052,420 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1147,047,342 - 47,052,418 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01150,229,232 - 50,234,310 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41145,559,299 - 45,564,377 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11145,616,887 - 45,621,964 (+)NCBI
Celera1144,334,937 - 44,340,015 (+)NCBICelera
Cytogenetic Map11q12NCBI
TRMT10C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383101,561,868 - 101,566,446 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3101,561,868 - 101,566,446 (+)EnsemblGRCh38hg38GRCh38
GRCh373101,280,712 - 101,285,290 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363102,763,402 - 102,767,779 (+)NCBINCBI36Build 36hg18NCBI36
Build 343102,763,402 - 102,767,777NCBI
Celera399,673,048 - 99,677,425 (+)NCBICelera
Cytogenetic Map3q12.3NCBI
HuRef398,649,589 - 98,654,197 (+)NCBIHuRef
CHM1_13101,243,751 - 101,248,361 (+)NCBICHM1_1
T2T-CHM13v2.03104,274,164 - 104,278,741 (+)NCBIT2T-CHM13v2.0
Trmt10c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391655,854,083 - 55,858,149 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1655,852,972 - 55,858,182 (-)EnsemblGRCm39 Ensembl
GRCm381656,033,720 - 56,037,786 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1656,032,609 - 56,037,819 (-)EnsemblGRCm38mm10GRCm38
MGSCv371656,033,833 - 56,037,887 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361655,958,671 - 55,962,727 (-)NCBIMGSCv36mm8
Celera1656,349,120 - 56,353,174 (-)NCBICelera
Cytogenetic Map16C1.1NCBI
cM Map1633.79NCBI
Trmt10c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554273,135,518 - 3,136,786 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554273,133,225 - 3,137,070 (+)NCBIChiLan1.0ChiLan1.0
TRMT10C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2299,519,074 - 99,523,476 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1399,523,856 - 99,528,459 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0398,671,176 - 98,675,743 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13105,350,939 - 105,355,548 (+)NCBIpanpan1.1PanPan1.1panPan2
TRMT10C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1337,944,675 - 7,949,402 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl337,945,929 - 7,949,272 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha338,099,240 - 8,103,577 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0338,083,913 - 8,088,266 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl338,084,141 - 8,088,264 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1337,971,544 - 7,975,882 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0338,017,896 - 8,022,436 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0338,358,192 - 8,362,532 (+)NCBIUU_Cfam_GSD_1.0
Trmt10c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602148,925,151 - 148,942,864 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366301,823,302 - 1,824,564 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366301,823,045 - 1,827,050 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRMT10C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13157,496,170 - 157,504,418 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113157,495,075 - 157,522,349 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213166,980,770 - 167,002,275 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TRMT10C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12279,307,124 - 79,311,496 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2279,307,444 - 79,308,658 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604187,251,890 - 87,256,421 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Trmt10c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478915,422,758 - 15,424,002 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478915,420,199 - 15,424,401 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Trmt10c
16 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:339
Count of miRNA genes:207
Interacting mature miRNAs:252
Transcripts:ENSRNOT00000002198
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat

Markers in Region
AI013863  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map11332.4UniSTS
Cytogenetic Map11q12UniSTS


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 33 52 36 19 36 8 8 74 35 34 11 8
Low 10 5 5 5 3 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002198   ⟹   ENSRNOP00000002198
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1144,584,113 - 44,589,568 (+)Ensembl
Rnor_6.0 Ensembl1147,047,342 - 47,052,418 (+)Ensembl
RefSeq Acc Id: NM_001008337   ⟹   NP_001008338
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81158,053,455 - 58,058,533 (+)NCBI
mRatBN7.21144,584,388 - 44,589,466 (+)NCBI
Rnor_6.01147,047,342 - 47,052,420 (+)NCBI
Rnor_5.01150,229,232 - 50,234,310 (+)NCBI
RGSC_v3.41145,559,299 - 45,564,377 (+)RGD
Celera1144,334,937 - 44,340,015 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001008338 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH85895 (Get FASTA)   NCBI Sequence Viewer  
  EDM11053 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002198
  ENSRNOP00000002198.3
GenBank Protein Q5U2R4 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001008338   ⟸   NM_001008337
- Peptide Label: precursor
- UniProtKB: Q5U2R4 (UniProtKB/Swiss-Prot),   A6IQQ0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002198   ⟸   ENSRNOT00000002198
Protein Domains
SAM-dependent MTase TRM10-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5U2R4-F1-model_v2 AlphaFold Q5U2R4 1-414 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306333 AgrOrtholog
BioCyc Gene G2FUF-21515 BioCyc
Ensembl Genes ENSRNOG00000039567 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002198 ENTREZGENE
  ENSRNOT00000002198.6 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.1280.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7193162 IMAGE-MGC_LOAD
InterPro MT_TRM10-typ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MT_TRM10-typ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRM10_SAM-dep_MTase_dom UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
  tRNA_m1G_MeTrfase_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  tRNA_MeTrfase_TRMD/TRM10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:304012 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:94708 IMAGE-MGC_LOAD
NCBI Gene 304012 ENTREZGENE
PANTHER PTHR13563 UniProtKB/Swiss-Prot
  PTHR13563:SF5 UniProtKB/Swiss-Prot
  TRNA (GUANINE-9-) METHYLTRANSFERASE UniProtKB/TrEMBL
  TRNA METHYLTRANSFERASE 10 HOMOLOG C UniProtKB/TrEMBL
Pfam tRNA_m1G_MT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Trmt10c PhenoGen
PROSITE SAM_MT_TRM10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039567 RatGTEx
UniProt A6IQQ0 ENTREZGENE, UniProtKB/TrEMBL
  Q5U2R4 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-10-04 Trmt10c  tRNA methyltransferase 10C, mitochondrial RNase P subunit  Trmt10c  tRNA methyltransferase 10 homolog C (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-10 Trmt10c  tRNA methyltransferase 10 homolog C (S. cerevisiae)  Rg9mtd1  RNA (guanine-9-) methyltransferase domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Rg9mtd1  RNA (guanine-9-) methyltransferase domain containing 1  Rg9mtd1_predicted  RNA (guanine-9-) methyltransferase domain containing 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Rg9mtd1_predicted  RNA (guanine-9-) methyltransferase domain containing 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED