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Aliases for TRMT1 Gene

Aliases for TRMT1 Gene

  • TRNA Methyltransferase 1 2 3 5
  • TRNA 2,2-Dimethylguanosine-26 Methyltransferase 3 4
  • TRNA(Guanine-26,N(2)-N(2)) Methyltransferase 3 4
  • TRNA(M(2,2)G26)Dimethyltransferase 3 4
  • N(2),N(2)-Dimethylguanosine TRNA Methyltransferase 3
  • TRNA Methyltransferase 1 Homolog (S. Cerevisiae) 2
  • TRNA (Guanine(26)-N(2))-Dimethyltransferase 3
  • TRM1 TRNA Methyltransferase 1 Homolog 3
  • TRNA Methyltransferase 1 Homolog 3
  • EC 2.1.1.216 4
  • EC 2.1.1.32 56
  • TRM1 3

External Ids for TRMT1 Gene

Previous GeneCards Identifiers for TRMT1 Gene

  • GC22P044944
  • GC22P045052
  • GC19M013077
  • GC19M013215
  • GC19M012788

Summaries for TRMT1 Gene

Entrez Gene Summary for TRMT1 Gene

  • This gene encodes a tRNA-modifying enzyme that acts as a dimethyltransferase, modifying a single guanine residue at position 26 of the tRNA. The encoded enzyme has both mono- and dimethylase activity when exogenously expressed, and uses S-adenosyl methionine as a methyl donor. The C-terminal region of the encoded protein has both a zinc finger motif, and an arginine/proline-rich region. Mutations in this gene have been implicated in autosomal recessive intellectual disorder (ARID). Alternative splicing results in multiple transcript variants encoding different isoforms. There is a pseudogene of this gene on the X chromosome. [provided by RefSeq, May 2017]

GeneCards Summary for TRMT1 Gene

TRMT1 (TRNA Methyltransferase 1) is a Protein Coding gene. Diseases associated with TRMT1 include Cataract 7. Among its related pathways are Gene Expression and tRNA processing. Gene Ontology (GO) annotations related to this gene include tRNA binding. An important paralog of this gene is TRMT1L.

UniProtKB/Swiss-Prot for TRMT1 Gene

  • Dimethylates a single guanine residue at position 26 of most tRNAs using S-adenosyl-L-methionine as donor of the methyl groups.

Additional gene information for TRMT1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRMT1 Gene

Genomics for TRMT1 Gene

GeneHancer (GH) Regulatory Elements for TRMT1 Gene

Promoters and enhancers for TRMT1 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
GH19I013115 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 595.2 -1.4 -1369 7.7 DMAP1 YBX1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC MEF2D ZNF610 TRMT1 NACC1 ZNF791 ZNF136 ZNF442 CCDC130 MRI1 ZNF564 WDR83OS ZNF44
GH19I013148 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 62.8 -36.1 -36128 10.2 MLX DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 STX10 ENSG00000267598 IER2 CCDC130 ZNF136 ZNF44 TRMT1 ZNF709 ZNF564 ZNF791
GH19I012781 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 62.2 +328.3 328269 16 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 JUNB CCDC130 ZNF136 ZNF44 ZNF791 ZNF564 WDR83OS TRMT1 ZNF700 TRIR
GH19I012936 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 51.1 +178.4 178435 5.8 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARNT ARID4B NEUROD1 SIN3A DMAP1 CALR MIR6515 ZNF136 CCDC130 TRMT1 ZNF625 RPS6P25 ZNF44 ZNF844 ZNF564
GH19I013011 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 43 +97.4 97372 17.2 HDGF FOXA2 MLX ARNT ARID4B FEZF1 DMAP1 ZNF2 YY1 ZNF213 NFIX ZNF136 ZNF709 ZNF791 TRMT1 CCDC130 MRI1 ZNF44 ZNF564 ZNF625
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TRMT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TRMT1 gene promoter:

Genomic Locations for TRMT1 Gene

Genomic Locations for TRMT1 Gene
chr19:13,104,900-13,117,567
(GRCh38/hg38)
Size:
12,668 bases
Orientation:
Minus strand
chr19:13,215,714-13,228,381
(GRCh37/hg19)

Genomic View for TRMT1 Gene

Genes around TRMT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRMT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRMT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRMT1 Gene

Proteins for TRMT1 Gene

  • Protein details for TRMT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NXH9-TRM1_HUMAN
    Recommended name:
    tRNA (guanine(26)-N(2))-dimethyltransferase
    Protein Accession:
    Q9NXH9
    Secondary Accessions:
    • O76103
    • Q548Y5
    • Q8WVA6

    Protein attributes for TRMT1 Gene

    Size:
    659 amino acids
    Molecular mass:
    72234 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for TRMT1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRMT1 Gene

Selected DME Specific Peptides for TRMT1 Gene

Q9NXH9:
  • DFYVRVFV
  • VFYNPVQEFNRDL

Post-translational modifications for TRMT1 Gene

  • Ubiquitination at isoforms=2371 and isoforms=2487

Domains & Families for TRMT1 Gene

Gene Families for TRMT1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for TRMT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NXH9

UniProtKB/Swiss-Prot:

TRM1_HUMAN :
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. Trm1 family.
Family:
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. Trm1 family.
genes like me logo Genes that share domains with TRMT1: view

Function for TRMT1 Gene

Molecular function for TRMT1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
2 S-adenosyl-L-methionine + guanine(26) in tRNA = 2 S-adenosyl-L-homocysteine + N(2)-dimethylguanine(26) in tRNA.
UniProtKB/Swiss-Prot Function:
Dimethylates a single guanine residue at position 26 of most tRNAs using S-adenosyl-L-methionine as donor of the methyl groups.

Enzyme Numbers (IUBMB) for TRMT1 Gene

Phenotypes From GWAS Catalog for TRMT1 Gene

Gene Ontology (GO) - Molecular Function for TRMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000049 tRNA binding IEA --
GO:0003723 RNA binding HDA,IDA 22658674
GO:0004809 tRNA (guanine-N2-)-methyltransferase activity IBA --
GO:0005515 protein binding IPI 16189514
GO:0008168 methyltransferase activity IEA --
genes like me logo Genes that share ontologies with TRMT1: view
genes like me logo Genes that share phenotypes with TRMT1: view

Animal Models for TRMT1 Gene

MGI Knock Outs for TRMT1:

Animal Model Products

CRISPR Products

miRNA for TRMT1 Gene

miRTarBase miRNAs that target TRMT1

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TRMT1 Gene

Localization for TRMT1 Gene

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 TRMT1 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 3
plasma membrane 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleus (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005654 nucleoplasm TAS --
GO:0005739 mitochondrion IBA --
genes like me logo Genes that share ontologies with TRMT1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for TRMT1 Gene

Pathways & Interactions for TRMT1 Gene

genes like me logo Genes that share pathways with TRMT1: view

Pathways by source for TRMT1 Gene

Gene Ontology (GO) - Biological Process for TRMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002940 tRNA N2-guanine methylation IBA --
GO:0006400 tRNA modification TAS --
GO:0008033 tRNA processing IEA --
GO:0030488 tRNA methylation IEA --
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with TRMT1: view

No data available for SIGNOR curated interactions for TRMT1 Gene

Drugs & Compounds for TRMT1 Gene

(1) Drugs for TRMT1 Gene - From: HMDB

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

(1) Additional Compounds for TRMT1 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 TRMT1: view

Transcripts for TRMT1 Gene

Unigene Clusters for TRMT1 Gene

TRNA methyltransferase 1 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRMT1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g · 2h ^ 3a · 3b · 3c · 3d ^ 4a · 4b · 4c ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b ·
SP1: - - - - - -
SP2: - - - -
SP3: - - - -
SP4: - - - - - - - - - - - - - - -
SP5:
SP6: - - - - - - - -
SP7: - - - - - -
SP8: - - - - - - -
SP9: - - - - -
SP10:
SP11:
SP12: - - - - - - - - -
SP13:
SP14: - - - - -
SP15: - - - - - - - -
SP16: - - - - - - - - - - -
SP17: - - -
SP18:
SP19: - - - -
SP20: - - - - -
SP21: - - - -
SP22: - - - - - -
SP23: - - - - - - - - -
SP24: - -
SP25: - - -

ExUns: 7c · 7d ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^ 18
SP1:
SP2:
SP3: -
SP4:
SP5: -
SP6:
SP7: - -
SP8:
SP9:
SP10: -
SP11:
SP12:
SP13: -
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:
SP22:
SP23:
SP24:
SP25:

Relevant External Links for TRMT1 Gene

GeneLoc Exon Structure for
TRMT1
ECgene alternative splicing isoforms for
TRMT1

Expression for TRMT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TRMT1 Gene

Protein differential expression in normal tissues from HIPED for TRMT1 Gene

This gene is overexpressed in Lung (52.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TRMT1 Gene



Protein tissue co-expression partners for TRMT1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TRMT1 Gene:

TRMT1

SOURCE GeneReport for Unigene cluster for TRMT1 Gene:

Hs.515169

Evidence on tissue expression from TISSUES for TRMT1 Gene

  • Nervous system(5)
  • Intestine(4.7)
  • Spleen(3.3)
  • Kidney(2.9)
  • Lung(2.5)
genes like me logo Genes that share expression patterns with TRMT1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRMT1 Gene

Orthologs for TRMT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRMT1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TRMT1 33 34
  • 99.44 (n)
dog
(Canis familiaris)
Mammalia TRMT1 33 34
  • 87.63 (n)
cow
(Bos Taurus)
Mammalia TRMT1 33 34
  • 87.46 (n)
rat
(Rattus norvegicus)
Mammalia Trmt1 33
  • 83.33 (n)
mouse
(Mus musculus)
Mammalia Trmt1 33 16 34
  • 81.58 (n)
oppossum
(Monodelphis domestica)
Mammalia TRMT1 34
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TRMT1 34
  • 43 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TRMT1 34
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia trmt1 33
  • 66.26 (n)
zebrafish
(Danio rerio)
Actinopterygii trmt1 33 34
  • 65.07 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009740 33
  • 55.46 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6388 33 34
  • 54.5 (n)
worm
(Caenorhabditis elegans)
Secernentea trm-1 33 34
  • 46.91 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR075W 33
  • 47.88 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRM1 33 34 36
  • 45.81 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F19404g 33
  • 45.48 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G15810 33
  • 49.14 (n)
rice
(Oryza sativa)
Liliopsida Os03g0786700 33
  • 50.5 (n)
Os.14753 33
bread mold
(Neurospora crassa)
Ascomycetes NCU06336 33
  • 47.91 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes trm1 33
  • 46.86 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6910 34
  • 46 (a)
OneToMany
Species where no ortholog for TRMT1 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)
  • chicken (Gallus gallus)
  • 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)
  • 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 TRMT1 Gene

ENSEMBL:
Gene Tree for TRMT1 (if available)
TreeFam:
Gene Tree for TRMT1 (if available)

Paralogs for TRMT1 Gene

Paralogs for TRMT1 Gene

Pseudogenes.org Pseudogenes for TRMT1 Gene

genes like me logo Genes that share paralogs with TRMT1: view

Variants for TRMT1 Gene

Sequence variations from dbSNP and Humsavar for TRMT1 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs542184779 likely-pathogenic, not provided 13,110,210(-) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs868289171 likely-pathogenic, not provided 13,115,689(-) TTT/T 5_prime_UTR_variant, coding_sequence_variant, frameshift, intron_variant
rs1000109060 -- 13,114,259(-) C/A/T intron_variant
rs1000198492 -- 13,108,897(-) A/G intron_variant
rs1000250873 -- 13,108,763(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TRMT1 Gene

Variant ID Type Subtype PubMed ID
nsv578635 CNV loss 21841781

Variation tolerance for TRMT1 Gene

Residual Variation Intolerance Score: 16.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.81; 34.04% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRMT1 Gene

Human Gene Mutation Database (HGMD)
TRMT1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRMT1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRMT1 Gene

Disorders for TRMT1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TRMT1 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
cataract 7
  • ctrct7
- elite association - COSMIC cancer census association via MalaCards
Search TRMT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TRMT1

genes like me logo Genes that share disorders with TRMT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TRMT1 Gene

Publications for TRMT1 Gene

  1. The human tRNA(m(2)(2)G(26))dimethyltransferase: functional expression and characterization of a cloned hTRM1 gene. (PMID: 10982862) Liu J … Strâby KB (Nucleic acids research 2000) 2 3 4 58
  2. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil SA … Gygi SP (Nature biotechnology 2006) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4 58
  5. 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

Products for TRMT1 Gene