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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81158,053,455 - 58,058,533 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1158,033,201 - 58,059,062 (+)EnsemblGRCr8
mRatBN7.21144,584,388 - 44,589,466 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1144,584,113 - 44,589,568 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1153,360,710 - 53,365,798 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01146,022,325 - 46,027,413 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01145,146,488 - 45,151,576 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01147,047,342 - 47,052,420 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1147,047,342 - 47,052,418 (+)Ensemblrn6Rnor6.0
Rnor_5.01150,229,232 - 50,234,310 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41145,559,299 - 45,564,377 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1144,334,937 - 44,340,015 (+)NCBICelera
RGSC_v3.11145,616,887 - 45,621,964 (+)NCBI
Cytogenetic Map11q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
mitochondrial matrix  (IEA,ISO)
mitochondrial nucleoid  (IEA,ISO,ISS)
mitochondrion  (IBA,IEA,ISO,ISS)
nucleoplasm  (IBA)
nucleus  (IBA)

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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1158,033,201 - 58,059,062 (+)EnsemblGRCr8
mRatBN7.21144,584,388 - 44,589,466 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1144,584,113 - 44,589,568 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1153,360,710 - 53,365,798 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01146,022,325 - 46,027,413 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01145,146,488 - 45,151,576 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01147,047,342 - 47,052,420 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1147,047,342 - 47,052,418 (+)Ensemblrn6Rnor6.0
Rnor_5.01150,229,232 - 50,234,310 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41145,559,299 - 45,564,377 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1144,334,937 - 44,340,015 (+)NCBICelera
RGSC_v3.11145,616,887 - 45,621,964 (+)NCBI
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 (+)Ensemblhg38GRCh38
GRCh373101,280,712 - 101,285,290 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363102,763,402 - 102,767,779 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381656,033,720 - 56,037,786 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1656,032,609 - 56,037,819 (-)Ensemblmm10GRCm38
MGSCv371656,033,833 - 56,037,887 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (+)Ensembl
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha338,099,240 - 8,103,577 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0338,083,913 - 8,088,266 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (-)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462478915,420,199 - 15,424,401 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Trmt10c
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1440,166,208 - 40,170,553 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Trmt10c
23 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
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)112252474682951192Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)113330600878306008Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)114644316891443168Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113330600878306008Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113294306789836615Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113191546976915469Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)113642841681428416Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)113461876079618760Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)115441539196071021Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)115775483796071021Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112019354996351019Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)113674945981749459Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)113674945981749459Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)115107102196071021Rat
631510Spl2Serum phospholipid level QTL 24.1blood phospholipid amount (VT:0006084)serum phospholipid level (CMO:0001171)112755668572556685Rat

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


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000002198   ⟹   ENSRNOP00000002198
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1158,033,201 - 58,059,062 (+)Ensembl
mRatBN7.2 Ensembl1144,584,113 - 44,589,568 (+)Ensembl
Rnor_6.0 Ensembl1147,047,342 - 47,052,418 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000162601   ⟹   ENSRNOP00000112229
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1158,051,054 - 58,057,297 (+)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 ENSRNOP00000002198.3
  ENSRNOP00000112229
GenBank Protein Q5U2R4 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001008338   ⟸   NM_001008337
- Peptide Label: precursor
- UniProtKB: Q5U2R4 (UniProtKB/Swiss-Prot),   A6IQQ0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000002198   ⟸   ENSRNOT00000002198
Ensembl Acc Id: ENSRNOP00000112229   ⟸   ENSRNOT00000162601
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 ENSRNOT00000002198.6 UniProtKB/Swiss-Prot
  ENSRNOT00000162601 ENTREZGENE
Gene3D-CATH 3.40.1280.30 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7193162 IMAGE-MGC_LOAD
InterPro MT_TRM10-typ UniProtKB/Swiss-Prot
  MT_TRM10-typ_sf UniProtKB/Swiss-Prot
  TRM10C UniProtKB/Swiss-Prot
  tRNA_m1G_MeTrfase_euk UniProtKB/Swiss-Prot
  tRNA_MeTrfase_TRMD/TRM10 UniProtKB/Swiss-Prot
KEGG Report rno:304012 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94708 IMAGE-MGC_LOAD
NCBI Gene 304012 ENTREZGENE
PANTHER PTHR13563 UniProtKB/Swiss-Prot
  PTHR13563:SF5 UniProtKB/Swiss-Prot
Pfam tRNA_m1G_MT UniProtKB/Swiss-Prot
PhenoGen Trmt10c PhenoGen
PROSITE SAM_MT_TRM10 UniProtKB/Swiss-Prot
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