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Aliases for TRMT5 Gene

Aliases for TRMT5 Gene

  • TRNA Methyltransferase 5 2 3 5
  • KIAA1393 2 3 4
  • TRNA (Guanine(37)-N1)-Methyltransferase 2 3
  • TRNA [GM37] Methyltransferase 3 4
  • M1G-Methyltransferase 3 4
  • TRM5 3 4
  • TRNA Methyltransferase 5 Homolog (S. Cerevisiae) 2
  • TRNA (Guanine-N(1)-)-Methyltransferase 3
  • TRM5 TRNA Methyltransferase 5 Homolog 3
  • TRNA Methyltransferase 5 Homolog 4
  • TRNA-N1G37 Methyltransferase 3
  • EC 2.1.1.228 4
  • COXPD26 3

External Ids for TRMT5 Gene

Previous HGNC Symbols for TRMT5 Gene

  • KIAA1393

Previous GeneCards Identifiers for TRMT5 Gene

  • GC14M060508
  • GC14M061438
  • GC14M041601

Summaries for TRMT5 Gene

Entrez Gene Summary for TRMT5 Gene

  • tRNAs contain as many as 13 or 14 nucleotides that are modified posttranscriptionally by enzymes that are highly specific for particular nucleotides in the tRNA structure. TRMT5 methylates the N1 position of guanosine-37 (G37) in selected tRNAs using S-adenosyl methionine (Brule et al., 2004 [PubMed 15248782]).[supplied by OMIM, Mar 2008]

GeneCards Summary for TRMT5 Gene

TRMT5 (TRNA Methyltransferase 5) is a Protein Coding gene. Diseases associated with TRMT5 include Combined Oxidative Phosphorylation Deficiency 26. Among its related pathways are Gene Expression and tRNA processing. Gene Ontology (GO) annotations related to this gene include tRNA (guanine(37)-N(1))-methyltransferase activity.

UniProtKB/Swiss-Prot for TRMT5 Gene

  • Involved in mitochondrial tRNA methylation (PubMed:26189817). Specifically methylates the N1 position of guanosine-37 in various tRNAs. Methylation is not dependent on the nature of the nucleoside 5 of the target nucleoside. This is the first step in the biosynthesis of wybutosine (yW), a modified base adjacent to the anticodon of tRNAs and required for accurate decoding.

Additional gene information for TRMT5 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRMT5 Gene

Genomics for TRMT5 Gene

GeneHancer (GH) Regulatory Elements for TRMT5 Gene

Promoters and enhancers for TRMT5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14I060979 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.1 148 3.9 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 SLC30A9 SLC38A6 TRMT5 ENSG00000258892
GH14I060640 Promoter/Enhancer 2.9 VISTA EPDnew Ensembl ENCODE dbSUPER 45.6 +331.2 331174 19.2 PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 SIX1 TRMT5 SLC38A6 PCNX4 C14orf39 LOC101927702 SIX4 TMEM30B MNAT1 SIX6
GH14I061320 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 26 -356.1 -356055 33.6 HDGF PKNOX1 FOXA2 ARNT SIN3A YBX1 FEZF1 ZNF2 IRF4 ZNF213 PRKCH TRMT5 TMEM30B SLC38A6 LOC105370527 ENSG00000247287 GC14M061347
GH14I060734 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 20.7 +245.7 245650 3.1 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 MNAT1 TRMT5 PCNX4 SLC38A6 RBM8B RNU6-398P MAD2L1P1
GH14I060720 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 14.8 +258.6 258627 4.6 PKNOX1 CLOCK FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B POLR2B SIX4 GC14M060376 TRMT5 MNAT1 SCOCP1 RTN1 PPM1A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TRMT5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TRMT5 gene promoter:

Genomic Locations for TRMT5 Gene

Genomic Locations for TRMT5 Gene
chr14:60,971,441-60,981,358
(GRCh38/hg38)
Size:
9,918 bases
Orientation:
Minus strand
chr14:61,438,159-61,448,076
(GRCh37/hg19)

Genomic View for TRMT5 Gene

Genes around TRMT5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRMT5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRMT5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRMT5 Gene

Proteins for TRMT5 Gene

  • Protein details for TRMT5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q32P41-TRM5_HUMAN
    Recommended name:
    tRNA (guanine(37)-N1)-methyltransferase
    Protein Accession:
    Q32P41
    Secondary Accessions:
    • B2RN19
    • Q9P2F4

    Protein attributes for TRMT5 Gene

    Size:
    509 amino acids
    Molecular mass:
    58246 Da
    Quaternary structure:
    • Monomer.

neXtProt entry for TRMT5 Gene

Post-translational modifications for TRMT5 Gene

No Post-translational modifications

Other Protein References for TRMT5 Gene

No data available for DME Specific Peptides for TRMT5 Gene

Domains & Families for TRMT5 Gene

Gene Families for TRMT5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

Q32P41

UniProtKB/Swiss-Prot:

TRM5_HUMAN :
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM5/TYW2 family.
Family:
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM5/TYW2 family.
genes like me logo Genes that share domains with TRMT5: view

Function for TRMT5 Gene

Molecular function for TRMT5 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA.
UniProtKB/Swiss-Prot Function:
Involved in mitochondrial tRNA methylation (PubMed:26189817). Specifically methylates the N1 position of guanosine-37 in various tRNAs. Methylation is not dependent on the nature of the nucleoside 5 of the target nucleoside. This is the first step in the biosynthesis of wybutosine (yW), a modified base adjacent to the anticodon of tRNAs and required for accurate decoding.

Enzyme Numbers (IUBMB) for TRMT5 Gene

Phenotypes From GWAS Catalog for TRMT5 Gene

Gene Ontology (GO) - Molecular Function for TRMT5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008168 methyltransferase activity IEA --
GO:0009019 tRNA (guanine-N1-)-methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0052906 tRNA (guanine(37)-N(1))-methyltransferase activity IEA --
genes like me logo Genes that share ontologies with TRMT5: view
genes like me logo Genes that share phenotypes with TRMT5: view

Human Phenotype Ontology for TRMT5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for TRMT5 Gene

miRTarBase miRNAs that target TRMT5

Inhibitory RNA Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for TRMT5 Gene

Localization for TRMT5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRMT5 Gene

Mitochondrion matrix. Nucleus. Cytoplasm. Note=Predominantly in the mitochondria and in the nucleus. {ECO:0000255 HAMAP-Rule:MF_03152}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TRMT5 gene
Compartment Confidence
mitochondrion 5
nucleus 4
cytosol 2
plasma membrane 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRMT5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IEA --
GO:0005759 mitochondrial matrix IEA,IDA 26189817
genes like me logo Genes that share ontologies with TRMT5: view

Pathways & Interactions for TRMT5 Gene

genes like me logo Genes that share pathways with TRMT5: view

Interacting Proteins for TRMT5 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 13)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000261249%0d%0a9606.ENSP00000438349%0d%0a9606.ENSP00000472299%0d%0a9606.ENSP00000353741%0d%0a9606.ENSP00000330054%0d%0a9606.ENSP00000401191%0d%0a
Selected Interacting proteins: Q32P41-TRM5_HUMAN ENSP00000261249 for TRMT5 Gene via IID STRING

Gene Ontology (GO) - Biological Process for TRMT5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008033 tRNA processing IEA --
GO:0030488 tRNA methylation IEA --
GO:0032259 methylation IEA --
GO:0070901 mitochondrial tRNA methylation IMP 26189817
genes like me logo Genes that share ontologies with TRMT5: view

No data available for SIGNOR curated interactions for TRMT5 Gene

Drugs & Compounds for TRMT5 Gene

(1) Drugs for TRMT5 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for TRMT5 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
29908-03-0
genes like me logo Genes that share compounds with TRMT5: view

Transcripts for TRMT5 Gene

Unigene Clusters for TRMT5 Gene

TRNA methyltransferase 5 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRMT5 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5
SP1: -
SP2:

Relevant External Links for TRMT5 Gene

GeneLoc Exon Structure for
TRMT5
ECgene alternative splicing isoforms for
TRMT5

Expression for TRMT5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TRMT5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRMT5 Gene

This gene is overexpressed in Stomach (19.1), Lung (10.3), and Heart (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TRMT5 Gene



Protein tissue co-expression partners for TRMT5 Gene

NURSA nuclear receptor signaling pathways regulating expression of TRMT5 Gene:

TRMT5

SOURCE GeneReport for Unigene cluster for TRMT5 Gene:

Hs.380159

Evidence on tissue expression from TISSUES for TRMT5 Gene

  • Nervous system(4.2)
  • Bone(4)
genes like me logo Genes that share expression patterns with TRMT5: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRMT5 Gene

Orthologs for TRMT5 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRMT5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TRMT5 33 34
  • 99.41 (n)
dog
(Canis familiaris)
Mammalia TRMT5 33 34
  • 88.25 (n)
cow
(Bos Taurus)
Mammalia TRMT5 33 34
  • 87.9 (n)
rat
(Rattus norvegicus)
Mammalia Trmt5 33
  • 82.05 (n)
mouse
(Mus musculus)
Mammalia Trmt5 33 16 34
  • 81.7 (n)
oppossum
(Monodelphis domestica)
Mammalia TRMT5 34
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves TRMT5 33 34
  • 68.69 (n)
lizard
(Anolis carolinensis)
Reptilia TRMT5 34
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia trmt5 33
  • 65.45 (n)
zebrafish
(Danio rerio)
Actinopterygii trmt5 33 34
  • 59.16 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32281 33 34
  • 50.17 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006124 33
  • 49.49 (n)
worm
(Caenorhabditis elegans)
Secernentea C53A5.17 33 34
  • 47.55 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRM5 33 34 36
  • 50.89 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E12761g 33
  • 48.83 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAL033W 33
  • 46.82 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G56120 33
  • 51.18 (n)
rice
(Oryza sativa)
Liliopsida Os02g0606301 33
  • 55.98 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes trm5 33
  • 52.9 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU09311 33
  • 48.01 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 40 (a)
OneToOne
Species where no ortholog for TRMT5 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TRMT5 Gene

ENSEMBL:
Gene Tree for TRMT5 (if available)
TreeFam:
Gene Tree for TRMT5 (if available)

Paralogs for TRMT5 Gene

No data available for Paralogs for TRMT5 Gene

Variants for TRMT5 Gene

Sequence variations from dbSNP and Humsavar for TRMT5 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1057517685 pathogenic, Combined oxidative phosphorylation deficiency 26 60,975,763(-) T/C coding_sequence_variant, missense_variant
rs746738473 pathogenic, Combined oxidative phosphorylation deficiency 26 60,976,047(-) C/T coding_sequence_variant, missense_variant
rs755184077 pathogenic, Combined oxidative phosphorylation deficiency 26, not provided 60,979,583(-) TATTT/T coding_sequence_variant, frameshift
VAR_075655 Combined oxidative phosphorylation deficiency 26 (COXPD26) [MIM:616539] p.Arg291His
VAR_075656 Combined oxidative phosphorylation deficiency 26 (COXPD26) [MIM:616539] p.Met386Val

Structural Variations from Database of Genomic Variants (DGV) for TRMT5 Gene

Variant ID Type Subtype PubMed ID
esv2748755 CNV deletion 23290073
nsv1037387 CNV gain 25217958
nsv1049936 CNV loss 25217958
nsv564881 CNV gain 21841781
nsv974345 CNV duplication 23825009

Variation tolerance for TRMT5 Gene

Residual Variation Intolerance Score: 87.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.72; 46.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRMT5 Gene

Human Gene Mutation Database (HGMD)
TRMT5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRMT5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRMT5 Gene

Disorders for TRMT5 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TRMT5 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
combined oxidative phosphorylation deficiency 26
  • coxpd26
- elite association - COSMIC cancer census association via MalaCards
Search TRMT5 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TRM5_HUMAN
  • Combined oxidative phosphorylation deficiency 26 (COXPD26) [MIM:616539]: A mitochondrial disorder characterized by lactic acidosis, multiple mitochondrial respiratory-chain-complex deficiencies in skeletal muscle, and additional variable features including hypertrophic cardiomyopathy, exercise intolerance, and failure to thrive. {ECO:0000269 PubMed:26189817}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TRMT5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TRMT5: view

No data available for Genatlas for TRMT5 Gene

Publications for TRMT5 Gene

  1. Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein. (PMID: 15248782) Brulé H … Holmes WM (Biochemistry 2004) 2 3 4 22 58
  2. TRMT5 Mutations Cause a Defect in Post-transcriptional Modification of Mitochondrial tRNA Associated with Multiple Respiratory-Chain Deficiencies. (PMID: 26189817) Powell CA … Minczuk M (American journal of human genetics 2015) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4 58
  5. Conservation of structure and mechanism by Trm5 enzymes. (PMID: 23887145) Christian T … Hou YM (RNA (New York, N.Y.) 2013) 3 58

Products for TRMT5 Gene

Sources for TRMT5 Gene

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