TRMT1 (tRNA methyltransferase 1) - Rat Genome Database
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Gene: TRMT1 (tRNA methyltransferase 1) Homo sapiens
Analyze
Symbol: TRMT1
Name: tRNA methyltransferase 1
RGD ID: 1601995
HGNC Page HGNC
Description: Exhibits tRNA (guanine-N2-)-methyltransferase activity. Predicted to be involved in tRNA N2-guanine methylation. Predicted to localize to nucleus. Implicated in autosomal recessive non-syndromic intellectual disability.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: FLJ20244; MRT68; N(2),N(2)-dimethylguanosine tRNA methyltransferase; TRM1; TRM1 tRNA methyltransferase 1 homolog; tRNA (guanine(26)-N(2))-dimethyltransferase; tRNA 2,2-dimethylguanosine-26 methyltransferase; tRNA methyltransferase 1 homolog; tRNA(guanine-26,N(2)-N(2)) methyltransferase; tRNA(m(2,2)G26)dimethyltransferase
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: TRMT1P1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1913,104,902 - 13,117,567 (-)EnsemblGRCh38hg38GRCh38
GRCh381913,104,907 - 13,116,740 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371913,215,714 - 13,227,573 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361913,076,715 - 13,088,332 (-)NCBINCBI36hg18NCBI36
Celera1913,106,119 - 13,117,969 (-)NCBI
Cytogenetic Map19p13.13NCBI
HuRef1912,788,354 - 12,799,966 (-)NCBIHuRef
CHM1_11913,216,745 - 13,228,558 (-)NCBICHM1_1
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
nucleoplasm  (TAS)
nucleus  (IBA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Abnormal corpus callosum morphology  (IAGP)
Abnormal facial shape  (IAGP)
Aortic root aneurysm  (IAGP)
Aphasia  (IAGP)
Astigmatism  (IAGP)
Attention deficit hyperactivity disorder  (IAGP)
Autistic behavior  (IAGP)
Autosomal recessive inheritance  (IAGP)
Blepharophimosis  (IAGP)
Broad eyebrow  (IAGP)
Broad hallux  (IAGP)
Broad thumb  (IAGP)
Cafe-au-lait spot  (IAGP)
Cerebellar atrophy  (IAGP)
Clinodactyly of hallux  (IAGP)
Conductive hearing impairment  (IAGP)
Congenital nystagmus  (IAGP)
Cryptorchidism  (IAGP)
Decreased body weight  (IAGP)
Delayed ability to walk  (IAGP)
Delayed gross motor development  (IAGP)
Delayed speech and language development  (IAGP)
Depressed nasal bridge  (IAGP)
Disproportionate tall stature  (IAGP)
Down-sloping shoulders  (IAGP)
Downslanted palpebral fissures  (IAGP)
Duane anomaly  (IAGP)
Feeding difficulties  (IAGP)
Frontal cortical atrophy  (IAGP)
Frontal upsweep of hair  (IAGP)
Generalized hypotonia  (IAGP)
Global developmental delay  (IAGP)
High forehead  (IAGP)
High palate  (IAGP)
Highly arched eyebrow  (IAGP)
Hip dysplasia  (IAGP)
Hypertelorism  (IAGP)
Impaired tandem gait  (IAGP)
Incisor macrodontia  (IAGP)
Infantile onset  (IAGP)
Intellectual disability, mild  (IAGP)
Joint hypermobility  (IAGP)
Kyphosis  (IAGP)
Long face  (IAGP)
Long philtrum  (IAGP)
Macrotia  (IAGP)
Microcephaly  (IAGP)
Micrognathia  (IAGP)
Muscular hypotonia  (IAGP)
Narrow face  (IAGP)
Narrow mouth  (IAGP)
Narrow palpebral fissure  (IAGP)
Nasal speech  (IAGP)
Panic attack  (IAGP)
Papilledema  (IAGP)
Periventricular leukomalacia  (IAGP)
Pes cavus  (IAGP)
Pes planus  (IAGP)
Precocious puberty  (IAGP)
Prominent fingertip pads  (IAGP)
Prominent forehead  (IAGP)
Ptosis  (IAGP)
Pulmonary artery dilatation  (IAGP)
Receptive language delay  (IAGP)
Relative macrocephaly  (IAGP)
Retinal atrophy  (IAGP)
Scoliosis  (IAGP)
Seizure  (IAGP)
Severe global developmental delay  (IAGP)
Short hallux  (IAGP)
Sleep disturbance  (IAGP)
Small for gestational age  (IAGP)
Small scrotum  (IAGP)
Smooth philtrum  (IAGP)
Speech apraxia  (IAGP)
Synophrys  (IAGP)
Thin vermilion border  (IAGP)
Visual impairment  (IAGP)
Wide nasal bridge  (IAGP)
References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10982862   PMID:12477932   PMID:14702039   PMID:15057824   PMID:15489334   PMID:16189514   PMID:16344560   PMID:16964243   PMID:21044950   PMID:21516116   PMID:21873635   PMID:22658674  
PMID:22863883   PMID:22939629   PMID:24778252   PMID:25416956   PMID:26186194   PMID:26308914   PMID:26344197   PMID:27499296   PMID:28514442   PMID:28515276   PMID:28784718   PMID:28986522  
PMID:29568061   PMID:29669786   PMID:29955894   PMID:30110629   PMID:30289604   PMID:31091453   PMID:31586073   PMID:32296183   PMID:32353859   PMID:32457219   PMID:32694731   PMID:32877691  
PMID:33060197  


Genomics

Comparative Map Data
TRMT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1913,104,902 - 13,117,567 (-)EnsemblGRCh38hg38GRCh38
GRCh381913,104,907 - 13,116,740 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371913,215,714 - 13,227,573 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361913,076,715 - 13,088,332 (-)NCBINCBI36hg18NCBI36
Celera1913,106,119 - 13,117,969 (-)NCBI
Cytogenetic Map19p13.13NCBI
HuRef1912,788,354 - 12,799,966 (-)NCBIHuRef
CHM1_11913,216,745 - 13,228,558 (-)NCBICHM1_1
Trmt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,412,953 - 85,426,437 (+)NCBIGRCm39mm39
GRCm38884,686,324 - 84,699,808 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,686,307 - 84,699,808 (+)EnsemblGRCm38mm10GRCm38
MGSCv37887,213,146 - 87,223,707 (+)NCBIGRCm37mm9NCBIm37
MGSCv36887,579,383 - 87,589,892 (+)NCBImm8
Celera888,989,136 - 88,999,879 (+)NCBICelera
Cytogenetic Map8C3NCBI
cM Map841.02NCBI
Trmt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01925,798,262 - 25,813,458 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,803,262 - 25,813,467 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,775,694 - 36,789,077 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,119,864 - 25,130,026 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11925,124,689 - 25,134,852 (-)NCBI
Celera1923,010,440 - 23,020,602 (-)NCBICelera
Cytogenetic Map19q11NCBI
Trmt1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541532,126,444 - 32,135,516 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541532,126,630 - 32,136,770 (-)NCBIChiLan1.0ChiLan1.0
TRMT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11913,410,882 - 13,413,172 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01912,666,426 - 12,679,454 (-)NCBIMhudiblu_PPA_v0panPan3
TRMT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2049,101,158 - 49,108,732 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12049,100,794 - 49,108,734 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Trmt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366592,142,151 - 2,149,373 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRMT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl265,940,123 - 65,949,324 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1265,940,122 - 65,949,324 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2266,237,279 - 66,245,843 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TRMT1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl611,785,730 - 11,799,730 (-)Ensembl
ChlSab1.1611,786,279 - 11,799,270 (-)NCBI
Trmt1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624901650,444 - 659,921 (-)NCBI

Position Markers
RH80493  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371913,215,747 - 13,216,168UniSTSGRCh37
Build 361913,076,747 - 13,077,168RGDNCBI36
Celera1913,106,152 - 13,106,573RGD
Cytogenetic Map19p13.2UniSTS
HuRef1912,788,387 - 12,788,808UniSTS
GeneMap99-GB4 RH Map1974.42UniSTS
D19S694E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371913,227,001 - 13,227,112UniSTSGRCh37
Build 361913,088,001 - 13,088,112RGDNCBI36
Celera1913,117,407 - 13,117,518RGD
Cytogenetic Map19p13.2UniSTS
HuRef1912,799,404 - 12,799,515UniSTS
WI-19708  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371913,215,721 - 13,215,810UniSTSGRCh37
Build 361913,076,721 - 13,076,810RGDNCBI36
Celera1913,106,126 - 13,106,215RGD
Cytogenetic Map19p13.2UniSTS
HuRef1912,788,361 - 12,788,450UniSTS
GeneMap99-GB4 RH Map1973.49UniSTS
Whitehead-RH Map1965.2UniSTS
RH47064  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371913,215,752 - 13,215,874UniSTSGRCh37
Build 361913,076,752 - 13,076,874RGDNCBI36
Celera1913,106,157 - 13,106,279RGD
Cytogenetic Map19p13.2UniSTS
HuRef1912,788,392 - 12,788,514UniSTS
GeneMap99-GB4 RH Map1972.87UniSTS
NCBI RH Map1987.9UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:6433
Count of miRNA genes:1007
Interacting mature miRNAs:1295
Transcripts:ENST00000221504, ENST00000357720, ENST00000437766, ENST00000585435, ENST00000585622, ENST00000586224, ENST00000586830, ENST00000587487, ENST00000587633, ENST00000588229, ENST00000588511, ENST00000588746, ENST00000588813, ENST00000590812, ENST00000591425, ENST00000591717, ENST00000592062, ENST00000592606, ENST00000592729, ENST00000592814, ENST00000592892, ENST00000593157, ENST00000593257
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 sensory system adipose tissue appendage entire extraembryonic component
High 1
Medium 2426 2439 1660 563 1706 405 4252 1858 3408 388 1444 1601 171 1204 2687 3
Low 6 545 63 59 242 59 103 335 301 30 3 7 101 1
Below cutoff 2 2 1 13 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_054900 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001136035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001142554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001351760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001351761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001351762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_017722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC005546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF075055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF196479 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK000251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK292377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK295245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK304636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC002492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC018302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC034242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC040126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF798026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ212049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA202329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DC313999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DC344734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DC364503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DC365548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DC373552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000221504   ⟹   ENSP00000221504
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,104,907 - 13,116,657 (-)Ensembl
RefSeq Acc Id: ENST00000357720   ⟹   ENSP00000350352
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,104,902 - 13,116,749 (-)Ensembl
RefSeq Acc Id: ENST00000437766   ⟹   ENSP00000416149
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,104,902 - 13,116,649 (-)Ensembl
RefSeq Acc Id: ENST00000585435
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,107,602 - 13,109,642 (-)Ensembl
RefSeq Acc Id: ENST00000585622
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,115,702 - 13,116,721 (-)Ensembl
RefSeq Acc Id: ENST00000586224   ⟹   ENSP00000468377
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,115,464 - 13,116,748 (-)Ensembl
RefSeq Acc Id: ENST00000586830
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,107,775 - 13,109,732 (-)Ensembl
RefSeq Acc Id: ENST00000587487   ⟹   ENSP00000465370
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,109,645 - 13,116,702 (-)Ensembl
RefSeq Acc Id: ENST00000587633   ⟹   ENSP00000466716
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,110,186 - 13,116,027 (-)Ensembl
RefSeq Acc Id: ENST00000588229   ⟹   ENSP00000467984
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,115,871 - 13,116,736 (-)Ensembl
RefSeq Acc Id: ENST00000588511
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,104,939 - 13,116,725 (-)Ensembl
RefSeq Acc Id: ENST00000588746   ⟹   ENSP00000468031
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,115,458 - 13,116,736 (-)Ensembl
RefSeq Acc Id: ENST00000588813
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,115,379 - 13,116,733 (-)Ensembl
RefSeq Acc Id: ENST00000590812
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,115,836 - 13,116,759 (-)Ensembl
RefSeq Acc Id: ENST00000591425
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,115,423 - 13,116,736 (-)Ensembl
RefSeq Acc Id: ENST00000591717   ⟹   ENSP00000466966
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,113,001 - 13,116,749 (-)Ensembl
RefSeq Acc Id: ENST00000592062   ⟹   ENSP00000466967
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,104,907 - 13,117,567 (-)Ensembl
RefSeq Acc Id: ENST00000592606
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,115,947 - 13,116,759 (-)Ensembl
RefSeq Acc Id: ENST00000592729
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,115,441 - 13,116,622 (-)Ensembl
RefSeq Acc Id: ENST00000592814   ⟹   ENSP00000467938
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,110,158 - 13,116,712 (-)Ensembl
RefSeq Acc Id: ENST00000592892
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,115,627 - 13,116,748 (-)Ensembl
RefSeq Acc Id: ENST00000593157
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,104,907 - 13,116,740 (-)Ensembl
RefSeq Acc Id: ENST00000593257
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1913,112,955 - 13,116,159 (-)Ensembl
RefSeq Acc Id: NM_001136035   ⟹   NP_001129507
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,104,907 - 13,116,740 (-)NCBI
GRCh371913,215,714 - 13,227,573 (-)NCBI
Celera1913,106,119 - 13,117,969 (-)RGD
HuRef1912,788,354 - 12,799,966 (-)ENTREZGENE
CHM1_11913,216,745 - 13,228,558 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001142554   ⟹   NP_001136026
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,104,907 - 13,116,740 (-)NCBI
GRCh371913,215,714 - 13,227,573 (-)NCBI
Celera1913,106,119 - 13,117,969 (-)RGD
HuRef1912,788,354 - 12,799,966 (-)ENTREZGENE
CHM1_11913,216,745 - 13,228,458 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001351760   ⟹   NP_001338689
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,104,907 - 13,116,740 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001351761   ⟹   NP_001338690
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,104,907 - 13,116,740 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001351762   ⟹   NP_001338691
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,104,907 - 13,116,740 (-)NCBI
Sequence:
RefSeq Acc Id: NM_017722   ⟹   NP_060192
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,104,907 - 13,116,740 (-)NCBI
GRCh371913,215,714 - 13,227,573 (-)NCBI
Build 361913,076,715 - 13,088,332 (-)NCBI Archive
Celera1913,106,119 - 13,117,969 (-)RGD
HuRef1912,788,354 - 12,799,966 (-)ENTREZGENE
CHM1_11913,216,745 - 13,228,458 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001129507   ⟸   NM_001136035
- Peptide Label: isoform 1
- UniProtKB: Q9NXH9 (UniProtKB/Swiss-Prot),   A0A024R7I5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001136026   ⟸   NM_001142554
- Peptide Label: isoform 2
- UniProtKB: Q9NXH9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_060192   ⟸   NM_017722
- Peptide Label: isoform 1
- UniProtKB: Q9NXH9 (UniProtKB/Swiss-Prot),   A0A024R7I5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001338690   ⟸   NM_001351761
- Peptide Label: isoform 3
- Sequence:
RefSeq Acc Id: NP_001338689   ⟸   NM_001351760
- Peptide Label: isoform 2
- Sequence:
RefSeq Acc Id: NP_001338691   ⟸   NM_001351762
- Peptide Label: isoform 4
- Sequence:
RefSeq Acc Id: ENSP00000416149   ⟸   ENST00000437766
RefSeq Acc Id: ENSP00000468377   ⟸   ENST00000586224
RefSeq Acc Id: ENSP00000466716   ⟸   ENST00000587633
RefSeq Acc Id: ENSP00000465370   ⟸   ENST00000587487
RefSeq Acc Id: ENSP00000467984   ⟸   ENST00000588229
RefSeq Acc Id: ENSP00000468031   ⟸   ENST00000588746
RefSeq Acc Id: ENSP00000221504   ⟸   ENST00000221504
RefSeq Acc Id: ENSP00000466966   ⟸   ENST00000591717
RefSeq Acc Id: ENSP00000467938   ⟸   ENST00000592814
RefSeq Acc Id: ENSP00000466967   ⟸   ENST00000592062
RefSeq Acc Id: ENSP00000350352   ⟸   ENST00000357720
Protein Domains
C3H1-type   Trm1 methyltransferase

Promoters
RGD ID:6796150
Promoter ID:HG_KWN:29053
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000221504,   NM_001136035,   NM_001142554,   NM_017722
Position:
Human AssemblyChrPosition (strand)Source
Build 361913,088,376 - 13,088,876 (-)MPROMDB
RGD ID:6852036
Promoter ID:EP73824
Type:initiation region
Name:HS_FLJ20244
Description:Hypothetical protein FLJ20244.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:NEDO full length human cDNA sequencing project.; Oligo-capping
Position:
Human AssemblyChrPosition (strand)Source
Build 361913,088,550 - 13,088,610EPD
RGD ID:7238779
Promoter ID:EPDNEW_H25134
Type:initiation region
Name:TRMT1_1
Description:tRNA methyltransferase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381913,116,736 - 13,116,796EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NC_000019.9:g.(?_13106632)_(13428155_?)del deletion Marshall-Smith syndrome [RCV000543828] Chr19:13106632..13428155 [GRCh37]
Chr19:19p13.2		 pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:8831147-13331227)x3 copy number gain See cases [RCV000052908] Chr19:8831147..13331227 [GRCh38]
Chr19:8941823..13442041 [GRCh37]
Chr19:8802823..13303041 [NCBI36]
Chr19:19p13.2-13.13		 likely pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:10315258-14048994)x3 copy number gain See cases [RCV000052909] Chr19:10315258..14048994 [GRCh38]
Chr19:10425934..14159806 [GRCh37]
Chr19:10286934..14020806 [NCBI36]
Chr19:19p13.2-13.12		 pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:12132052-14751798)x3 copy number gain See cases [RCV000052910] Chr19:12132052..14751798 [GRCh38]
Chr19:12242867..14862610 [GRCh37]
Chr19:12103867..14723610 [NCBI36]
Chr19:19p13.2-13.12		 pathogenic
GRCh38/hg38 19p13.13(chr19:12850595-13290954)x3 copy number gain See cases [RCV000052911] Chr19:12850595..13290954 [GRCh38]
Chr19:12961409..13401768 [GRCh37]
Chr19:12822409..13262768 [NCBI36]
Chr19:19p13.13		 pathogenic
GRCh38/hg38 19p13.13(chr19:12813597-13119698)x3 copy number gain See cases [RCV000054144] Chr19:12813597..13119698 [GRCh38]
Chr19:12924411..13230512 [GRCh37]
Chr19:12785411..13091512 [NCBI36]
Chr19:19p13.13		 uncertain significance
GRCh38/hg38 19p13.2-13.12(chr19:11227942-14532135)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053944]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053944]|See cases [RCV000053944] Chr19:11227942..14532135 [GRCh38]
Chr19:11338618..14642947 [GRCh37]
Chr19:11199618..14503947 [NCBI36]
Chr19:19p13.2-13.12		 pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:11517825-13225287)x1 copy number loss See cases [RCV000053945] Chr19:11517825..13225287 [GRCh38]
Chr19:11628640..13336101 [GRCh37]
Chr19:11489640..13197101 [NCBI36]
Chr19:19p13.2-13.13		 pathogenic
NM_017722.4(TRMT1):c.967C>T (p.Arg323Cys) single nucleotide variant not provided [RCV000171278] Chr19:13110210 [GRCh38]
Chr19:13221024 [GRCh37]
Chr19:19p13.13		 likely pathogenic
GRCh38/hg38 19p13.2-q13.31(chr19:11227942-44626354)x3 copy number gain See cases [RCV000133888] Chr19:11227942..44626354 [GRCh38]
Chr19:11338618..45129651 [GRCh37]
Chr19:11199618..49821491 [NCBI36]
Chr19:19p13.2-q13.31		 pathogenic
GRCh38/hg38 19p13.13(chr19:13034666-13283686)x1 copy number loss See cases [RCV000135352] Chr19:13034666..13283686 [GRCh38]
Chr19:13145480..13394500 [GRCh37]
Chr19:13006480..13255500 [NCBI36]
Chr19:19p13.13		 pathogenic
GRCh38/hg38 19p13.13(chr19:12978943-13236134)x3 copy number gain See cases [RCV000136559] Chr19:12978943..13236134 [GRCh38]
Chr19:13089757..13346948 [GRCh37]
Chr19:12950757..13207948 [NCBI36]
Chr19:19p13.13		 likely pathogenic|uncertain significance
GRCh38/hg38 19p13.2-13.12(chr19:12580427-14742673)x1 copy number loss See cases [RCV000135937] Chr19:12580427..14742673 [GRCh38]
Chr19:12691241..14853485 [GRCh37]
Chr19:12552241..14714485 [NCBI36]
Chr19:19p13.2-13.12		 pathogenic|likely pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:11525163-14155021)x1 copy number loss See cases [RCV000136909] Chr19:11525163..14155021 [GRCh38]
Chr19:11635978..14265833 [GRCh37]
Chr19:11496978..14126833 [NCBI36]
Chr19:19p13.2-13.12		 pathogenic
GRCh38/hg38 19p13.13(chr19:12974394-13408586)x1 copy number loss See cases [RCV000138197] Chr19:12974394..13408586 [GRCh38]
Chr19:13085208..13519400 [GRCh37]
Chr19:12946208..13380400 [NCBI36]
Chr19:19p13.13		 pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:10319474-13777860)x1 copy number loss See cases [RCV000141568] Chr19:10319474..13777860 [GRCh38]
Chr19:10430150..13888674 [GRCh37]
Chr19:10291150..13749674 [NCBI36]
Chr19:19p13.2-13.13		 pathogenic
GRCh37/hg19 19p13.2(chr19:13180583-13319148)x3 copy number gain See cases [RCV000449427] Chr19:13180583..13319148 [GRCh37]
Chr19:19p13.2		 likely pathogenic
GRCh37/hg19 19p13.2(chr19:12204632-13497073)x1 copy number loss See cases [RCV000449161] Chr19:12204632..13497073 [GRCh37]
Chr19:19p13.2		 pathogenic
GRCh37/hg19 19p13.2-13.12(chr19:9678768-14853426) copy number gain See cases [RCV000446985] Chr19:9678768..14853426 [GRCh37]
Chr19:19p13.2-13.12		 pathogenic
GRCh37/hg19 19p13.2-13.12(chr19:12574343-14726197)x1 copy number loss See cases [RCV000511130] Chr19:12574343..14726197 [GRCh37]
Chr19:19p13.2-13.12		 pathogenic
GRCh37/hg19 19p13.2-13.12(chr19:11608072-14543046)x3 copy number gain See cases [RCV000511013] Chr19:11608072..14543046 [GRCh37]
Chr19:19p13.2-13.12		 uncertain significance
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888)x3 copy number gain See cases [RCV000511289] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43		 pathogenic|uncertain significance
GRCh37/hg19 19p13.3-q13.43(chr19:260912-58956888) copy number gain See cases [RCV000512296] Chr19:260912..58956888 [GRCh37]
Chr19:19p13.3-q13.43		 pathogenic
NM_017722.4(TRMT1):c.1107-2A>G single nucleotide variant not provided [RCV000513125] Chr19:13109840 [GRCh38]
Chr19:13220654 [GRCh37]
Chr19:19p13.13		 likely pathogenic
NM_001351762.2(TRMT1):c.-382_-381del deletion not provided [RCV000513415] Chr19:13115689..13115690 [GRCh38]
Chr19:13226503..13226504 [GRCh37]
Chr19:19p13.13		 likely pathogenic
NM_001351762.2(TRMT1):c.-114_-83del deletion INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 68 [RCV000754765] Chr19:13112965..13112996 [GRCh38]
Chr19:13223779..13223810 [GRCh37]
Chr19:19p13.13		 pathogenic
NM_017722.4(TRMT1):c.1506+1G>T single nucleotide variant INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 68 [RCV000754766] Chr19:13107750 [GRCh38]
Chr19:13218564 [GRCh37]
Chr19:19p13.13		 pathogenic
NM_001136035.3(TRMT1):c.1332_1333del (p.Tyr445fs) deletion INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 68 [RCV000754767] Chr19:13109445..13109446 [GRCh38]
Chr19:13220259..13220260 [GRCh37]
Chr19:19p13.13		 pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:260912-59097160)x3 copy number gain not provided [RCV000752444] Chr19:260912..59097160 [GRCh37]
Chr19:19p13.3-q13.43		 pathogenic
GRCh37/hg19 19p13.3-q13.43(chr19:68029-59110290)x3 copy number gain not provided [RCV000752439] Chr19:68029..59110290 [GRCh37]
Chr19:19p13.3-q13.43		 pathogenic
NM_001136035.4(TRMT1):c.1554A>G (p.Pro518=) single nucleotide variant not provided [RCV000963183] Chr19:13107603 [GRCh38]
Chr19:13218417 [GRCh37]
Chr19:19p13.13		 benign
NM_001136035.4(TRMT1):c.1778A>G (p.Asp593Gly) single nucleotide variant not provided [RCV000895071] Chr19:13105322 [GRCh38]
Chr19:13216136 [GRCh37]
Chr19:19p13.13		 likely benign
NM_001136035.4(TRMT1):c.1509G>A (p.Glu503=) single nucleotide variant not provided [RCV000964038] Chr19:13107648 [GRCh38]
Chr19:13218462 [GRCh37]
Chr19:19p13.13		 benign
NM_001136035.4(TRMT1):c.672G>A (p.Ser224=) single nucleotide variant not provided [RCV000928540] Chr19:13112981 [GRCh38]
Chr19:13223795 [GRCh37]
Chr19:19p13.13		 likely benign
NM_001136035.4(TRMT1):c.174C>T (p.Thr58=) single nucleotide variant not provided [RCV000925576] Chr19:13116226 [GRCh38]
Chr19:13227040 [GRCh37]
Chr19:19p13.13		 likely benign
NM_001136035.4(TRMT1):c.1353G>C (p.Leu451=) single nucleotide variant not provided [RCV000902559] Chr19:13109425 [GRCh38]
Chr19:13220239 [GRCh37]
Chr19:19p13.13		 likely benign
NM_001136035.4(TRMT1):c.1177-8G>A single nucleotide variant not provided [RCV000903814] Chr19:13109692 [GRCh38]
Chr19:13220506 [GRCh37]
Chr19:19p13.13		 benign
NM_001136035.4(TRMT1):c.1032G>C (p.Leu344=) single nucleotide variant not provided [RCV000905452] Chr19:13109989 [GRCh38]
Chr19:13220803 [GRCh37]
Chr19:19p13.13		 benign
NM_001136035.4(TRMT1):c.1943dup (p.Gly649fs) duplication not provided [RCV001065939] Chr19:13104971..13104972 [GRCh38]
Chr19:13215785..13215786 [GRCh37]
Chr19:19p13.13		 pathogenic
NM_001136035.4(TRMT1):c.1404C>T (p.Ala468=) single nucleotide variant not provided [RCV000886265] Chr19:13107853 [GRCh38]
Chr19:13218667 [GRCh37]
Chr19:19p13.13		 likely benign
NM_001136035.4(TRMT1):c.48G>T (p.Arg16=) single nucleotide variant not provided [RCV000975990] Chr19:13116352 [GRCh38]
Chr19:13227166 [GRCh37]
Chr19:19p13.13		 likely benign
GRCh37/hg19 19p13.2(chr19:12354642-13424014)x1 copy number loss not provided [RCV000846538] Chr19:12354642..13424014 [GRCh37]
Chr19:19p13.2		 pathogenic
NM_001136035.4(TRMT1):c.1086G>A (p.Ala362=) single nucleotide variant not provided [RCV000960081] Chr19:13109935 [GRCh38]
Chr19:13220749 [GRCh37]
Chr19:19p13.13		 benign
NM_001136035.4(TRMT1):c.816G>A (p.Thr272=) single nucleotide variant not provided [RCV000887265] Chr19:13112759 [GRCh38]
Chr19:13223573 [GRCh37]
Chr19:19p13.13		 benign
NM_001136035.4(TRMT1):c.1312-4G>A single nucleotide variant not provided [RCV000953084] Chr19:13109470 [GRCh38]
Chr19:13220284 [GRCh37]
Chr19:19p13.13		 benign
NM_001136035.4(TRMT1):c.1515A>T (p.Glu505Asp) single nucleotide variant not provided [RCV000911705] Chr19:13107642 [GRCh38]
Chr19:13218456 [GRCh37]
Chr19:19p13.13		 likely benign
NM_001136035.4(TRMT1):c.1430C>T (p.Ser477Leu) single nucleotide variant Inborn genetic diseases [RCV001265910] Chr19:13107827 [GRCh38]
Chr19:13218641 [GRCh37]
Chr19:19p13.13		 uncertain significance
NM_001136035.4(TRMT1):c.312del (p.Lys105fs) deletion INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 68 [RCV001262708] Chr19:13115767 [GRCh38]
Chr19:13226581 [GRCh37]
Chr19:19p13.13		 pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:25980 AgrOrtholog
COSMIC TRMT1 COSMIC
Ensembl Genes ENSG00000104907 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000221504 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000350352 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000416149 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000465370 UniProtKB/TrEMBL
  ENSP00000466716 UniProtKB/TrEMBL
  ENSP00000466966 UniProtKB/TrEMBL
  ENSP00000466967 UniProtKB/Swiss-Prot
  ENSP00000467938 UniProtKB/TrEMBL
  ENSP00000467984 UniProtKB/TrEMBL
  ENSP00000468031 UniProtKB/TrEMBL
  ENSP00000468377 UniProtKB/TrEMBL
Ensembl Transcript ENST00000221504 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000357720 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000437766 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000586224 UniProtKB/TrEMBL
  ENST00000587487 UniProtKB/TrEMBL
  ENST00000587633 UniProtKB/TrEMBL
  ENST00000588229 UniProtKB/TrEMBL
  ENST00000588511 ENTREZGENE
  ENST00000588746 UniProtKB/TrEMBL
  ENST00000591717 UniProtKB/TrEMBL
  ENST00000592062 UniProtKB/Swiss-Prot
  ENST00000592814 UniProtKB/TrEMBL
  ENST00000593157 ENTREZGENE
Gene3D-CATH 3.30.56.70 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000104907 GTEx
HGNC ID HGNC:25980 ENTREZGENE
Human Proteome Map TRMT1 Human Proteome Map
InterPro SAM-dependent_MTases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Trm1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  tRNA_met_Trm1_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_CCCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_CCCH_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:55621 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 55621 ENTREZGENE
OMIM 611669 OMIM
  618302 OMIM
PANTHER PTHR10631 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-CCCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134867808 PharmGKB
PROSITE SAM_MT_TRM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_C3H1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ZnF_C3H1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53335 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF90229 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs TRM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Hs.515169 ENTREZGENE
UniProt A0A024R7G3_HUMAN UniProtKB/TrEMBL
  A0A024R7I5 ENTREZGENE, UniProtKB/TrEMBL
  K7EJX9_HUMAN UniProtKB/TrEMBL
  K7EMZ2_HUMAN UniProtKB/TrEMBL
  K7ENI9_HUMAN UniProtKB/TrEMBL
  K7EQQ8_HUMAN UniProtKB/TrEMBL
  K7EQU7_HUMAN UniProtKB/TrEMBL
  K7EQY6_HUMAN UniProtKB/TrEMBL
  K7ERR5_HUMAN UniProtKB/TrEMBL
  Q9NXH9 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O76103 UniProtKB/Swiss-Prot
  Q548Y5 UniProtKB/Swiss-Prot
  Q8WVA6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-09-29 TRMT1  tRNA methyltransferase 1    tRNA methyltransferase 1 homolog (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED
2012-06-19 TRMT1  tRNA methyltransferase 1 homolog (S. cerevisiae)  TRMT1  TRM1 tRNA methyltransferase 1 homolog (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED