Wybutosine (yW) is a hypermodified guanosine at the 3-prime position adjacent to the anticodon of phenylalanine tRNA that stabilizes codon-anticodon interactions during decoding on the ribosome. TRMT12 is the human homolog of a yeast gene essential for yW synthesis (Noma and Suzuki, 2006).[supplied by OMIM, Mar 2008] See more...

Aliases for TRMT12 Gene

Aliases for TRMT12 Gene

  • TRNA Methyltransferase 12 Homolog 2 3 5
  • TYW2 2 3 4
  • TRNA(Phe) (4-Demethylwyosine(37)-C(7)) Aminocarboxypropyltransferase 3 4
  • TRNA Wybutosine-Synthesizing Protein 2 Homolog 3 4
  • TRNA-YW-Synthesizing Protein 2 3 4
  • TRM12 3 4
  • TRNA Methyltransferase 12 Homolog (S. Cerevisiae) 2
  • TRNA Methyltranferase 12 Homolog (S. Cerevisiae) 2
  • Alpha-Amino-Alpha-Carboxypropyl Transferase TYW2 3
  • Homolog Of Yeast TRNA Methyltransferase 3
  • TRNA Methyltranferase 12 Homolog 3
  • TRNA-YW Synthesizing Protein 2 2
  • EC 2.5.1.114 4
  • EC 2.1.1.32 51
  • FLJ20772 2
  • EC 2.1.1 51
  • TRMT12 5
  • Trm12 2

External Ids for TRMT12 Gene

Previous GeneCards Identifiers for TRMT12 Gene

  • GC08P125534
  • GC08P125463
  • GC08P120788

Summaries for TRMT12 Gene

Entrez Gene Summary for TRMT12 Gene

  • Wybutosine (yW) is a hypermodified guanosine at the 3-prime position adjacent to the anticodon of phenylalanine tRNA that stabilizes codon-anticodon interactions during decoding on the ribosome. TRMT12 is the human homolog of a yeast gene essential for yW synthesis (Noma and Suzuki, 2006).[supplied by OMIM, Mar 2008]

GeneCards Summary for TRMT12 Gene

TRMT12 (TRNA Methyltransferase 12 Homolog) is a Protein Coding gene. Diseases associated with TRMT12 include Noma. Among its related pathways are Gene Expression and tRNA processing. Gene Ontology (GO) annotations related to this gene include transferase activity. An important paralog of this gene is TRMT5.

UniProtKB/Swiss-Prot Summary for TRMT12 Gene

  • S-adenosyl-L-methionine-dependent transferase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the transfer of the alpha-amino-alpha-carboxypropyl (acp) group from S-adenosyl-L-methionine to the C-7 position of 4-demethylwyosine (imG-14) to produce wybutosine-86.

Gene Wiki entry for TRMT12 Gene

Additional gene information for TRMT12 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRMT12 Gene

Genomics for TRMT12 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TRMT12 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRMT12 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRMT12

Top Transcription factor binding sites by QIAGEN in the TRMT12 gene promoter:
  • AREB6
  • c-Myc
  • GATA-2
  • Max
  • Max1
  • Nkx5-1
  • Pbx1a
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for TRMT12 Gene

Genomic Locations for TRMT12 Gene
chr8:124,450,820-124,462,150
(GRCh38/hg38)
Size:
11,331 bases
Orientation:
Plus strand
chr8:125,463,048-125,474,391
(GRCh37/hg19)
Size:
11,344 bases
Orientation:
Plus strand

Genomic View for TRMT12 Gene

Genes around TRMT12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRMT12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRMT12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRMT12 Gene

Proteins for TRMT12 Gene

  • Protein details for TRMT12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q53H54-TYW2_HUMAN
    Recommended name:
    tRNA wybutosine-synthesizing protein 2 homolog
    Protein Accession:
    Q53H54
    Secondary Accessions:
    • Q6PKB9
    • Q96F21
    • Q9NWK6

    Protein attributes for TRMT12 Gene

    Size:
    448 amino acids
    Molecular mass:
    50236 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH03057.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=AAH03057.2; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence starting in position 371.; Evidence={ECO:0000305};

neXtProt entry for TRMT12 Gene

Selected DME Specific Peptides for TRMT12 Gene

Q53H54:
  • LLSEDCFQA
  • GGILHIHQNVESF
  • VHACEWNP
  • GEVLVDLYAGIGYFTLPFLVHA
  • NLEINGV
  • GNITEKLR

Post-translational modifications for TRMT12 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TRMT12 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for TRMT12 Gene

Gene Families for TRMT12 Gene

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

Protein Domains for TRMT12 Gene

InterPro:
Blocks:
  • Family of unknown function Met10
ProtoNet:

Suggested Antigen Peptide Sequences for TRMT12 Gene

GenScript: Design optimal peptide antigens:
  • Alpha-amino-alpha-carboxypropyl transferase TYW2 (TYW2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q53H54

UniProtKB/Swiss-Prot:

TYW2_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 TRMT12: view

Function for TRMT12 Gene

Molecular function for TRMT12 Gene

UniProtKB/Swiss-Prot Function:
S-adenosyl-L-methionine-dependent transferase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the transfer of the alpha-amino-alpha-carboxypropyl (acp) group from S-adenosyl-L-methionine to the C-7 position of 4-demethylwyosine (imG-14) to produce wybutosine-86.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=4-demethylwyosine(37) in tRNA(Phe) + S-adenosyl-L-methionine = 4-demethyl-7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in tRNA(Phe) + H(+) + S-methyl-5'-thioadenosine; Xref=Rhea:RHEA:36355, Rhea:RHEA-COMP:10164, Rhea:RHEA-COMP:10378, ChEBI:CHEBI:15378, ChEBI:CHEBI:17509, ChEBI:CHEBI:59789, ChEBI:CHEBI:64315, ChEBI:CHEBI:73550; EC=2.5.1.114; Evidence={ECO:0000269|PubMed:22761755};.

Enzyme Numbers (IUBMB) for TRMT12 Gene

Phenotypes From GWAS Catalog for TRMT12 Gene

Gene Ontology (GO) - Molecular Function for TRMT12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0008175 tRNA methyltransferase activity IBA 21873635
GO:0016740 transferase activity IEA --
GO:0102522 tRNA 4-demethylwyosine alpha-amino-alpha-carboxypropyltransferase activity IEA --
genes like me logo Genes that share ontologies with TRMT12: view
genes like me logo Genes that share phenotypes with TRMT12: view

Animal Model Products

CRISPR Products

miRNA for TRMT12 Gene

miRTarBase miRNAs that target TRMT12

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRMT12

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TRMT12 Gene

Localization for TRMT12 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 TRMT12 gene
Compartment Confidence
nucleus 3
cytosol 3
mitochondrion 2
extracellular 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRMT12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
genes like me logo Genes that share ontologies with TRMT12: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for TRMT12 Gene

Pathways & Interactions for TRMT12 Gene

genes like me logo Genes that share pathways with TRMT12: view

UniProtKB/Swiss-Prot Q53H54-TYW2_HUMAN

  • Pathway: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.

Gene Ontology (GO) - Biological Process for TRMT12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008033 tRNA processing IEA --
GO:0030488 tRNA methylation IBA 21873635
GO:0031591 wybutosine biosynthetic process IBA --
genes like me logo Genes that share ontologies with TRMT12: view

No data available for SIGNOR curated interactions for TRMT12 Gene

Drugs & Compounds for TRMT12 Gene

(1) Additional Compounds for TRMT12 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with TRMT12: view

Transcripts for TRMT12 Gene

mRNA/cDNA for TRMT12 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRMT12

Alternative Splicing Database (ASD) splice patterns (SP) for TRMT12 Gene

No ASD Table

Relevant External Links for TRMT12 Gene

GeneLoc Exon Structure for
TRMT12

Expression for TRMT12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRMT12 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRMT12 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRMT12

SOURCE GeneReport for Unigene cluster for TRMT12 Gene:

Hs.9925

Evidence on tissue expression from TISSUES for TRMT12 Gene

  • Skin(4.3)
  • Intestine(4.2)
  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with TRMT12: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRMT12 Gene

Orthologs for TRMT12 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TRMT12 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TRMT12 30 31
  • 99.48 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TRMT12 30 31
  • 88.66 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TRMT12 30 31
  • 86.83 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Trmt12 30
  • 84.97 (n)
Mouse
(Mus musculus)
Mammalia Trmt12 30 17 31
  • 82.53 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TRMT12 31
  • 68 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 67 (a)
OneToMany
-- 31
  • 62 (a)
OneToMany
Chicken
(Gallus gallus)
Aves TRMT12 30 31
  • 63.93 (n)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia trmt12 30
  • 59.8 (n)
Str.3891 30
Zebrafish
(Danio rerio)
Actinopterygii zgc:153361 30
  • 55.87 (n)
TRMT12 (2 of 2) 31
  • 50 (a)
OneToMany
TRMT12 (1 of 2) 31
  • 50 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea F40F9.10 31
  • 23 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRM12 31 33
  • 19 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT4G04670 30
  • 52.89 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 52 (a)
OneToOne
Species where no ortholog for TRMT12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • 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 (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 TRMT12 Gene

ENSEMBL:
Gene Tree for TRMT12 (if available)
TreeFam:
Gene Tree for TRMT12 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRMT12: view image

Paralogs for TRMT12 Gene

Paralogs for TRMT12 Gene

Pseudogenes.org Pseudogenes for TRMT12 Gene

genes like me logo Genes that share paralogs with TRMT12: view

Variants for TRMT12 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRMT12 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
rs3812475 - p.Trp28Arg

Additional dbSNP identifiers (rs#s) for TRMT12 Gene

Structural Variations from Database of Genomic Variants (DGV) for TRMT12 Gene

Variant ID Type Subtype PubMed ID
dgv1414e214 CNV gain 21293372
esv2762769 CNV gain 21179565
nsv1017848 CNV gain 25217958
nsv1034768 CNV gain 25217958

Variation tolerance for TRMT12 Gene

Residual Variation Intolerance Score: 46% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.79; 33.71% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRMT12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRMT12

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRMT12 Gene

Disorders for TRMT12 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TRMT12 Gene - From: GeneCards

Disorder Aliases PubMed IDs
noma
  • cancrum oris
- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with TRMT12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TRMT12 Gene

Publications for TRMT12 Gene

  1. Ribonucleome analysis identified enzyme genes responsible for wybutosine synthesis. (PMID: 17150819) Noma A … Suzuki T (Nucleic acids symposium series (2004) 2006) 2 3
  2. A novel methyltransferase required for the formation of the hypermodified nucleoside wybutosine in eucaryotic tRNA. (PMID: 16005430) Kalhor HR … Clarke S (Biochemical and biophysical research communications 2005) 2 3
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. 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
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for TRMT12 Gene

  • Signalway Proteins for TRMT12

Sources for TRMT12 Gene