TRMT2A Gene (Protein Coding)

TRNA Methyltransferase 2 Homolog A

GC22M020099
GIFtS:
38
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. [... See more...

Aliases for TRMT2A Gene

Aliases for TRMT2A Gene

  • TRNA Methyltransferase 2 Homolog A 2 3 5
  • HTF9C 2 3 4
  • TRNA (Uracil-5-)-Methyltransferase Homolog A 3 4
  • HpaII Tiny Fragments Locus 9c Protein 3 4
  • TRNA Methyltransferase 2 Homolog A (S. Cerevisiae) 2
  • TRM2 TRNA Methyltransferase 2 Homolog A 3
  • HpaII Tiny Fragments Locus 9C 2
  • EC 2.1.1.- 4
  • TRMT2A 5

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. Diseases associated with TRMT2A include Thymic Dysplasia and Breast Cancer. 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 Summary for TRMT2A Gene

Additional gene information for TRMT2A Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRMT2A Gene

Genomics for TRMT2A Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TRMT2A 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
GH22J020114 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 647.4 +0.2 226 4.7 ZNF221 BRCA1 ARHGAP35 SP1 CREB1 HNRNPL TEAD4 PRDM10 ZNF629 TFE3 TRMT2A RANBP1 lnc-CCDC188-3-001 lnc-CCDC188-3-002 LZTR1 DGCR8 LINC01311 MED15 THAP7-AS1 ENSG00000215493
GH22J020494 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 94.3 -378.3 -378309 3.4 RNF2 ARHGAP35 CREB1 GATAD2A CTCF HNRNPL ATF7 PRDM10 ZNF629 TFE3 MED15 KLHL22 LOC101928824 lnc-MED15-1 DGCR8 LZTR1 TRMT2A RPL7AP70 ENSG00000215493 THAP7-AS1
GH22J020078 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 62.1 +35.9 35871 5.2 RNF2 ARHGAP35 SP1 HNRNPL GATAD2A ATF7 TEAD4 PRDM10 ZNF629 REST DGCR8 lnc-TRMT2A-3 TRMT2A LZTR1 MED15 UFD1 RPL7AP70 RPL8P5 RANBP1 LINC01311
GH22J020506 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 44.8 -392.1 -392110 5.8 CEBPG HNRNPL CREB1 PRDM10 ZNF629 TFE3 SIX5 SMAD2 ZNF692 POLR2A MED15 piR-38716-094 piR-41245-161 piR-58557-056 LZTR1 TRMT2A DGCR8 RPL7AP70 RPL8P5 ENSG00000215493
GH22J019947 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 49.7 +166.7 166668 7.3 HNRNPL CREB1 GATAD2A CTCF ATF7 PRDM10 ZNF629 TFE3 ZNF512 SOX13 COMT DGCR8 TRMT2A ENSG00000215493 LINC01311 RPL7AP70 ZDHHC8 RPL8P5 ENSG00000273300 MED15
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRMT2A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRMT2A

Top Transcription factor binding sites by QIAGEN in the TRMT2A gene promoter:
  • CREB
  • deltaCREB
  • Pax-5
  • Spz1
  • SRF
  • YY1

Genomic Locations for TRMT2A Gene

Genomic Locations for TRMT2A Gene
chr22:20,111,872-20,117,392
(GRCh38/hg38)
Size:
5,521 bases
Orientation:
Minus strand
chr22:20,099,389-20,104,915
(GRCh37/hg19)
Size:
5,527 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for TRMT2A Gene

Proteins for TRMT2A Gene

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

    Protein Symbol:
    Q8IZ69-TRM2A_HUMAN
    Recommended name:
    tRNA (uracil-5-)-methyltransferase homolog A
    Protein Accession:
    Q8IZ69
    Secondary Accessions:
    • D3DX25
    • Q32P57
    • Q96ME6
    • Q9H732

    Protein attributes for TRMT2A Gene

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

    Alternative splice isoforms for TRMT2A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRMT2A Gene

Protein Expression for TRMT2A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TRMT2A Gene

  • Ubiquitination at Lys187, Lys242, Lys290, Lys314, and Lys346
  • Modification sites at PhosphoSitePlus

Other Protein References for TRMT2A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TRMT2A Gene

Domains & Families for TRMT2A Gene

Gene Families for TRMT2A Gene

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

Protein Domains for TRMT2A Gene

InterPro:
Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)
  • (Uracil-5)-methyltransferase
ProtoNet:

Suggested Antigen Peptide Sequences for TRMT2A Gene

GenScript: Design optimal peptide antigens:
  • HpaII tiny fragments locus 9c protein (TRM2A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IZ69

UniProtKB/Swiss-Prot:

TRM2A_HUMAN :
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.
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

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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:
  • Trmt2a Trmt2a<tm2b(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

miRNA for TRMT2A Gene

miRTarBase miRNAs that target TRMT2A

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRMT2A

Clone Products

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

Localization for TRMT2A 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 TRMT2A gene
Compartment Confidence
cytosol 3
nucleus 2
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (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

PathCards logo

SuperPathways for TRMT2A Gene

No Data Available

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

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  1. Drug
No Compound Related Data Available

Transcripts for TRMT2A Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for TRMT2A Gene

4 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
20 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 TRMT2A

Clone 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: - - -
SP5:
SP6: - -
SP7: - - - -
SP8: - -
SP9: -
SP10:
SP11:
SP12: - - -
SP13: -

ExUns: 13a · 13b ^ 14 ^ 15a · 15b · 15c · 15d · 15e
SP1: - -
SP2: -
SP3: - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11: -
SP12:
SP13:

Relevant External Links for TRMT2A Gene

GeneLoc Exon Structure for
TRMT2A

Expression for TRMT2A Gene

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  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for TRMT2A Gene
mRNA expression by BioGPS for TRMT2A GenemRNA expression by GTEx 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, MaxQB, and MOPED for TRMT2A Gene



Protein tissue co-expression partners for TRMT2A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRMT2A

SOURCE GeneReport for Unigene cluster for TRMT2A Gene:

Hs.713579

Evidence on tissue expression from TISSUES for TRMT2A Gene

  • Intestine(4.3)
  • Nervous system(4.3)
  • Kidney(4.2)
  • Skin(2.2)
  • Blood(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
Chimpanzee
(Pan troglodytes)
 Mammalia TRMT2A 30 31
  • 99.36 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia TRMT2A 30 31
  • 86.38 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Trmt2a 30 17 31
  • 82.82 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Trmt2a 30
  • 82.4 (n)
Cow
(Bos Taurus)
 Mammalia TRMT2A 30 31
  • 80.91 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia TRMT2A 31
  • 67 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves TRMT2A 30 31
  • 68.34 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia TRMT2A 31
  • 56 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia trmt2a 30
  • 62.46 (n)
Str.15843 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.8434 30
Zebrafish
(Danio rerio)
 Actinopterygii trmt2a 30 31
  • 63.75 (n)
 OneToOne
wufa10b06 30
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.13964 30
Fruit Fly
(Drosophila melanogaster)
 Insecta CG3808 30 31
  • 49.35 (n)
 OneToMany
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP012408 30
  • 48.01 (n)
Worm
(Caenorhabditis elegans)
 Secernentea H24K24.4 30 31
  • 44.31 (n)
 OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes TRM2 31 33
  • 14 (a)
 OneToMany
Species where no ortholog for TRMT2A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for TRMT2A (if available)
TreeFam:
Gene Tree for TRMT2A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRMT2A: view image

Paralogs for TRMT2A Gene

Paralogs for TRMT2A Gene

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

  • TRM2A_HUMAN
  • C9K041_HUMAN
  • F2Z2W7_HUMAN
  • H7BZZ4_HUMAN
  • H7C100_HUMAN
genes like me logo Genes that share paralogs with TRMT2A: view

Variants for TRMT2A Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRMT2A Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
VAR_035482 A breast cancer sample p.Pro604Ser
rs447017 - p.Ser602Arg

Additional dbSNP identifiers (rs#s) for TRMT2A Gene

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)
TRMT2A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRMT2A

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

Disorders for TRMT2A Gene

MalaCards: The human disease database

(3) MalaCards diseases for TRMT2A Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
thymic dysplasia
breast cancer
  • breast lobular carcinoma
digeorge syndrome
  • cayler cardiofacial syndrome
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TRMT2A

Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with TRMT2A: view

No data available for 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 23
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 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. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 3 4

ExternalLinks

View latest publications for TRMT2A gene in Mastermind

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