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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. 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.

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

Regulatory Elements for TRMT5 Gene

Enhancers for TRMT5 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14G061320 2 FANTOM5 Ensembl ENCODE dbSUPER 15.5 -356.1 -356055 33.6 HDGF PKNOX1 FOXA2 ARNT WRNIP1 SIN3A YBX1 FEZF1 ZNF2 ZNF143 PRKCH TMEM30B TRMT5 LOC105370527 ENSG00000247287 GC14M061347
GH14G061100 2 FANTOM5 Ensembl ENCODE dbSUPER 10.1 -121.5 -121545 4.6 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 FEZF1 ZBTB7B YY1 FOS SLC38A6 TRMT5 C14orf39 SIX1 PPM1A LOC105378182 LOC101927756
GH14G061186 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.7 -207.4 -207385 4.1 ELF3 ZSCAN4 ARID4B SIN3A ZNF48 RAD21 ZNF121 GATA2 ZNF366 SCRT2 PRKCH TRMT5 TMEM30B
GH14G060090 1.6 Ensembl ENCODE dbSUPER 11.1 +887.6 887639 6.2 HDGF PKNOX1 MLX WRNIP1 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF143 DHRS7 L3HYPDH PCNX4 TRMT5 GC14P060140
GH14G061660 1.6 FANTOM5 Ensembl ENCODE 11.1 -680.9 -680935 4.5 HDGF PKNOX1 SIN3A ZBTB7B YY1 CBX5 ZNF143 ZNF207 FOS CEBPZ FLJ22447 HIF1A TRMT5 LOC101927780 GC14P061694 GC14P061590
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TRMT5 on UCSC Golden Path with GeneCards custom track

Promoters for TRMT5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000069280 58 2201 HDGF CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF766 ZNF143
ENSR00000069280 -130 2201 HDGF CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF766 ZNF143

Genomic Location for TRMT5 Gene

Chromosome:
14
Start:
60,971,441 bp from pter
End:
60,981,358 bp from pter
Size:
9,918 bases
Orientation:
Minus strand

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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TRMT5 Gene

No data available for DME Specific Peptides for TRMT5 Gene

Domains & Families for TRMT5 Gene

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

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

Inhibitory RNA Products

Clone Products

Flow Cytometry 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

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 IDA,IEA 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://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000261249%0d%0a9606.ENSP00000472299%0d%0a9606.ENSP00000438349%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

(2) Drugs for TRMT5 Gene - From: HMDB

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

Clone Products

Flow Cytometry 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 34 35
  • 99.41 (n)
dog
(Canis familiaris)
Mammalia TRMT5 34 35
  • 88.25 (n)
cow
(Bos Taurus)
Mammalia TRMT5 34 35
  • 87.9 (n)
rat
(Rattus norvegicus)
Mammalia Trmt5 34
  • 82.05 (n)
mouse
(Mus musculus)
Mammalia Trmt5 34 16 35
  • 81.7 (n)
oppossum
(Monodelphis domestica)
Mammalia TRMT5 35
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves TRMT5 34 35
  • 68.69 (n)
lizard
(Anolis carolinensis)
Reptilia TRMT5 35
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia trmt5 34
  • 65.45 (n)
zebrafish
(Danio rerio)
Actinopterygii trmt5 34 35
  • 59.16 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32281 34 35
  • 50.17 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006124 34
  • 49.49 (n)
worm
(Caenorhabditis elegans)
Secernentea C53A5.17 34 35
  • 47.55 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRM5 34 35 37
  • 50.89 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E12761g 34
  • 48.83 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAL033W 34
  • 46.82 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G56120 34
  • 51.18 (n)
rice
(Oryza sativa)
Liliopsida Os02g0606301 34
  • 55.98 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes trm5 34
  • 52.9 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU09311 34
  • 48.01 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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 Sequence Context AA Info Type
VAR_075655 Combined oxidative phosphorylation deficiency 26 (COXPD26) [MIM:616539]
VAR_075656 Combined oxidative phosphorylation deficiency 26 (COXPD26) [MIM:616539]
rs1057517685 Pathogenic 60,975,763(-) TTGTC(A/G)TGAAC reference, missense
rs746738473 Pathogenic 60,976,047(+) TGATA(C/T)GGCTG reference, missense
rs755184077 Pathogenic 60,979,583(+) CTGAC(-/TATT)TCTTT upstream-variant-2KB, reference, frameshift-variant

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)

Relevant External Links 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: OMIM, ClinVar, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
combined oxidative phosphorylation deficiency 26
  • combined oxidative phosphorylation deficiency type 26
- 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.

Relevant External Links for TRMT5

Genetic Association Database (GAD)
TRMT5
Human Genome Epidemiology (HuGE) Navigator
TRMT5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TRMT5
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) Brule H. … Holmes W.M. (Biochemistry 2004) 2 3 4 22 64
  2. TRMT5 Mutations Cause a Defect in Post-transcriptional Modification of Mitochondrial tRNA Associated with Multiple Respiratory-Chain Deficiencies. (PMID: 26189817) Powell C.A. … Minczuk M. (Am. J. Hum. Genet. 2015) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  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 Res. 2000) 3 4 64
  5. Conservation of structure and mechanism by Trm5 enzymes. (PMID: 23887145) Christian T. … Hou Y.M. (RNA 2013) 3 64

Products for TRMT5 Gene

Sources for TRMT5 Gene

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