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Aliases for TRMT2A Gene

Aliases for TRMT2A Gene

  • TRNA Methyltransferase 2 Homolog A 2 3 5
  • HpaII Tiny Fragments Locus 9c Protein 3 4
  • HTF9C 3 4
  • TRNA Methyltransferase 2 Homolog A (S. Cerevisiae) 2
  • TRNA (Uracil-5-)-Methyltransferase Homolog A 3
  • TRM2 TRNA Methyltransferase 2 Homolog A 3
  • HpaII Tiny Fragments Locus 9C 2
  • EC 2.1.1.- 4

External Ids for TRMT2A Gene

Previous GeneCards Identifiers for TRMT2A Gene

  • GC22M018479
  • GC22M003720

Summaries for TRMT2A Gene

Entrez Gene Summary for TRMT2A Gene

  • The protein encoded by this gene is of unknown function. However, it is orthologous to the mouse Trmt2a gene and contains an RNA methyltransferase domain. Expression of this gene varies during the cell cycle, with aberrant expression being a possible biomarker in certain breast cancers. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

GeneCards Summary for TRMT2A Gene

TRMT2A (TRNA Methyltransferase 2 Homolog A) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is TRMT2B.

UniProtKB/Swiss-Prot for TRMT2A Gene

  • May be involved in nucleic acid metabolism and/or modifications.

Additional gene information for TRMT2A Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRMT2A Gene

Genomics for TRMT2A Gene

GeneHancer (GH) Regulatory Elements for TRMT2A Gene

Promoters and enhancers for TRMT2A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22I020114 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 581.2 +0.1 146 4.6 CLOCK MLX ZFP64 FEZF1 DMAP1 SLC30A9 E2F8 ZNF143 ZNF263 SP3 TRMT2A RANBP1 MED15 RPL7AP70 LZTR1 ZDHHC8 UFD1 DGCR8 SCARF2 THAP7
GH22I020494 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 82.5 -378.5 -378451 2.7 CLOCK FEZF1 YBX1 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 MED15 KLHL22 LOC101928824 LZTR1 DGCR8 RPL7AP70 TRMT2A RPL8P5 LOC100420177 THAP7
GH22I020078 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 69 +35.9 35871 5.2 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 DGCR8 LZTR1 TRMT2A MED15 RPL7AP70 RPL8P5 UFD1 ENSG00000273300 LOC100420177 ENSG00000243762
GH22I019947 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 72.8 +166.7 166668 7.3 HDGF PKNOX1 FOXA2 MLX ZFP64 ARID4B FEZF1 DMAP1 ZNF2 POLR2B COMT DGCR8 TRMT2A ENSG00000273300 RPL8P5 LOC100420177 LINC01311 MED15 DGCR11 RPL7AP70
GH22I019477 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 44.1 +638.1 638142 3.8 HDGF HNRNPUL1 PKNOX1 CLOCK SMAD1 FOXA2 ARNT ARID4B SIN3A YBX1 UFD1 CDC45 DGCR8 TRMT2A RPL7AP70 DGCR11 ENSG00000273300 RPL8P5 LINC01311 RANBP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TRMT2A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TRMT2A gene promoter:

Genomic Locations for TRMT2A Gene

Genomic Locations for TRMT2A Gene
5,527 bases
Minus strand

Genomic View for TRMT2A Gene

Genes around TRMT2A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRMT2A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRMT2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRMT2A Gene

Proteins for TRMT2A Gene

  • Protein details for TRMT2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    tRNA (uracil-5-)-methyltransferase homolog A
    Protein Accession:
    Secondary Accessions:
    • D3DX25
    • Q32P57
    • Q96ME6
    • Q9H732

    Protein attributes for TRMT2A Gene

    625 amino acids
    Molecular mass:
    68726 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for TRMT2A Gene


neXtProt entry for TRMT2A Gene

Post-translational modifications for TRMT2A Gene

  • Ubiquitination at isoforms=2187, posLast=242242, isoforms=2290, posLast=314314, and posLast=346346
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TRMT2A Gene

Domains & Families for TRMT2A Gene

Gene Families for TRMT2A Gene

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

Suggested Antigen Peptide Sequences for TRMT2A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.
genes like me logo Genes that share domains with TRMT2A: view

Function for TRMT2A Gene

Molecular function for TRMT2A Gene

UniProtKB/Swiss-Prot Function:
May be involved in nucleic acid metabolism and/or modifications.

Enzyme Numbers (IUBMB) for TRMT2A Gene

Phenotypes From GWAS Catalog for TRMT2A Gene

Gene Ontology (GO) - Molecular Function for TRMT2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,HDA 22658674
GO:0008168 methyltransferase activity IEA --
GO:0008173 RNA methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with TRMT2A: view
genes like me logo Genes that share phenotypes with TRMT2A: view

Animal Models for TRMT2A Gene

MGI Knock Outs for TRMT2A:

Animal Model Products

CRISPR Products

miRNA for TRMT2A Gene

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TRMT2A Gene

Localization for TRMT2A Gene

Subcellular locations from

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 TRMT2A gene
Compartment Confidence
cytosol 3
nucleus 2

Subcellular locations from the

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

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for TRMT2A Gene

Pathways & Interactions for TRMT2A Gene

SuperPathways for TRMT2A Gene

No Data Available

Interacting Proteins for TRMT2A Gene

Gene Ontology (GO) - Biological Process for TRMT2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001510 RNA methylation IEA --
GO:0006396 RNA processing IEA --
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with TRMT2A: view

No data available for Pathways by source and SIGNOR curated interactions for TRMT2A Gene

Drugs & Compounds for TRMT2A Gene

No Compound Related Data Available

Transcripts for TRMT2A Gene

Unigene Clusters for TRMT2A Gene

TRNA methyltransferase 2 homolog A (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRMT2A Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^
SP1: - - - - - - -
SP2: - - - -
SP3: - - - -
SP4: - - -
SP6: - -
SP7: - - - -
SP8: - -
SP9: -
SP12: - - -
SP13: -

ExUns: 13a · 13b ^ 14 ^ 15a · 15b · 15c · 15d · 15e
SP1: - -
SP2: -
SP3: - -
SP11: -

Relevant External Links for TRMT2A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for TRMT2A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TRMT2A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRMT2A Gene

This gene is overexpressed in Lung (49.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TRMT2A Gene

Protein tissue co-expression partners for TRMT2A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TRMT2A Gene:


SOURCE GeneReport for Unigene cluster for TRMT2A Gene:


Evidence on tissue expression from TISSUES for TRMT2A Gene

  • Intestine(4.3)
  • Kidney(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with TRMT2A: view

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 TRMT2A Gene

Orthologs for TRMT2A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TRMT2A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia TRMT2A 33 34
  • 99.36 (n)
(Canis familiaris)
Mammalia TRMT2A 33 34
  • 86.38 (n)
(Mus musculus)
Mammalia Trmt2a 33 16 34
  • 82.82 (n)
(Rattus norvegicus)
Mammalia Trmt2a 33
  • 82.4 (n)
(Bos Taurus)
Mammalia TRMT2A 33 34
  • 80.91 (n)
(Monodelphis domestica)
Mammalia TRMT2A 34
  • 67 (a)
(Gallus gallus)
Aves TRMT2A 33 34
  • 68.34 (n)
(Anolis carolinensis)
Reptilia TRMT2A 34
  • 56 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia trmt2a 33
  • 62.46 (n)
Str.15843 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8434 33
(Danio rerio)
Actinopterygii trmt2a 33 34
  • 63.75 (n)
wufa10b06 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13964 33
fruit fly
(Drosophila melanogaster)
Insecta CG3808 33 34
  • 49.35 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012408 33
  • 48.01 (n)
(Caenorhabditis elegans)
Secernentea H24K24.4 33 34
  • 44.31 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRM2 34 36
  • 14 (a)
Species where no ortholog for TRMT2A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TRMT2A Gene

Gene Tree for TRMT2A (if available)
Gene Tree for TRMT2A (if available)

Paralogs for TRMT2A Gene

Paralogs for TRMT2A Gene

(1) SIMAP similar genes for TRMT2A Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with TRMT2A: view

Variants for TRMT2A Gene

Sequence variations from dbSNP and Humsavar for TRMT2A Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
VAR_035482 A breast cancer sample p.Pro604Ser
rs1000172388 -- 20,117,260(-) C/A 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000722261 -- 20,112,872(-) G/A intron_variant
rs1001019119 -- 20,116,097(-) A/G 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, synonymous_variant, upstream_transcript_variant
rs1001068662 -- 20,111,718(-) C/G downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for TRMT2A Gene

Variant ID Type Subtype PubMed ID
dgv4480n100 CNV gain 25217958
dgv4481n100 CNV gain 25217958
dgv726n67 CNV gain 20364138
dgv7983n54 CNV gain 21841781
esv2758825 CNV loss 17122850
esv3647284 CNV gain 21293372
esv3647287 CNV insertion 21293372
esv3893434 CNV gain 25118596
nsv471183 CNV loss 18288195
nsv828938 CNV gain 20364138
nsv828939 CNV loss 20364138
nsv834133 CNV loss 17160897
nsv953027 CNV deletion 24416366

Variation tolerance for TRMT2A Gene

Residual Variation Intolerance Score: 58.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.00; 49.93% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRMT2A Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRMT2A Gene

Disorders for TRMT2A Gene

Additional Disease Information for TRMT2A

No disorders were found for TRMT2A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TRMT2A Gene

Publications for TRMT2A Gene

  1. HTF9C gene of 22q11.21 region associates with schizophrenia having deficit-sustained attention. (PMID: 18075473) Liu YL … Hwu HG (Psychiatric genetics 2007) 2 3 22 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4 58
  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 58
  5. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 3 4 58

Products for TRMT2A Gene

Sources for TRMT2A Gene

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