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TRMT2A tRNA methyltransferase 2 homolog A [ Homo sapiens (human) ]

Gene ID: 27037, updated on 5-Mar-2024

Summary

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Official Symbol
TRMT2Aprovided by HGNC
Official Full Name
tRNA methyltransferase 2 homolog Aprovided by HGNC
Primary source
HGNC:HGNC:24974
See related
Ensembl:ENSG00000099899 MIM:611151; AllianceGenome:HGNC:24974
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HTF9C
Summary
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]
Expression
Ubiquitous expression in spleen (RPKM 11.1), testis (RPKM 10.2) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See TRMT2A in Genome Data Viewer
Location:
22q11.21
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (20111875..20117226, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (20490925..20496276, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (20099398..20104749, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene DGCR8 microprocessor complex subunit Neighboring gene microRNA 3618 Neighboring gene microRNA 1306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20099501-20100000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13476 Neighboring gene microRNA 6816 Neighboring gene RAN binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18671 Neighboring gene small nucleolar RNA, H/ACA box 77B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20119547-20120200 Neighboring gene zinc finger DHHC-type palmitoyltransferase 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20125107-20125706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13481 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13482

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Chemical tagging for sensitive determination of uridine modifications in RNA. Cheng QY, et al. Chem Sci, 2020 Jan 8. PMID 34123281, Free PMC Article
  2. m(5)U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs. Pereira M, et al. Int J Mol Sci, 2021 Mar 14. PMID 33799331, Free PMC Article
  3. FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA. Carter JM, et al. Nucleic Acids Res, 2019 Nov 4. PMID 31361898, Free PMC Article
  4. TRMT2A is a novel cell cycle regulator that suppresses cell proliferation. Chang YH, et al. Biochem Biophys Res Commun, 2019 Jan 8. PMID 30502085
  5. The expression of TRMT2A, a novel cell cycle regulated protein, identifies a subset of breast cancer patients with HER2 over-expression that are at an increased risk of recurrence. Hicks DG, et al. BMC Cancer, 2010 Mar 22. PMID 20307320, Free PMC Article

See all (56) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Human TRMT2A methylates tRNA and contributes to translation fidelity.
    Title: Human TRMT2A methylates tRNA and contributes to translation fidelity.
  2. m(5)U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs.
    Title: m(5)U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs.
  3. Our associated finding of extensive irreversible TRMT2A-tRNA crosslinking in vivo following 5-Fluorouracil exposure is also intriguing, as it suggests a tangible mechanism for a previously suspected RNA-dependent route of Fluorouracil-mediated cytotoxicity.
    Title: FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA.
  4. tRNA methyltransferase 2 homolog A (TRMT2A) protein harbors an RNA recognition motif in the N-terminus and the conserved uracil-C5-methyltransferase domain of the TrmA family in the C-terminus. TRMT2A predominantly localizes to the nucleus in HeLa cells. TRMT2A-overexpressing cells display decreased cell proliferation and altered DNA content, while TRMT2A-deficient cells exhibit increased growth.
    Title: TRMT2A is a novel cell cycle regulator that suppresses cell proliferation.
  5. TRMT2A staining showed a strong correlation with likelihood of recurrence at five years in 67 HER2+ breast cancer.
    Title: The expression of TRMT2A, a novel cell cycle regulated protein, identifies a subset of breast cancer patients with HER2 over-expression that are at an increased risk of recurrence.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: HTF9C gene of 22q11.21 region associates with schizophrenia having deficit-sustained attention.
  7. Single nucleotid polymorphisms of this gene may be associated with a deficit in sustained attention within schizophrenia, in a Taiwanese cohort.
    Title: HTF9C gene of 22q11.21 region associates with schizophrenia having deficit-sustained attention.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC102728

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables C-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in tRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytosol TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
tRNA (uracil-5-)-methyltransferase homolog A
Names
TRM2 tRNA methyltransferase 2 homolog A
hpaII tiny fragments locus 9c protein
mRNA (uracil-5-)-methyltransferase TRMT2A
NP_001244923.1
NP_001317968.1
NP_073564.3
NP_892029.2
XP_011528441.1
XP_011528444.1
XP_054181515.1
XP_054181516.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001257994.2 → NP_001244923.1  tRNA (uracil-5-)-methyltransferase homolog A isoform b

    See identical proteins and their annotated locations for NP_001244923.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice junction at the 5' end of a coding exon compared to variant 1. The resulting isoform (b) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC006547, AI539558, AK057029
    Consensus CDS
    CCDS58793.1
    UniProtKB/Swiss-Prot
    Q8IZ69
    Related
    ENSP00000384968.3, ENST00000404751.7
    Conserved Domains (4) summary
    COG0724
    Location:70 → 161
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    COG2265
    Location:179 → 540
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cd12439
    Location:68 → 146
    RRM_TRMT2A; RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins
    cl17173
    Location:385 → 541
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  2. NM_001331039.2 → NP_001317968.1  tRNA (uracil-5-)-methyltransferase homolog A isoform c

    Status: REVIEWED

    Source sequence(s)
    AC006547, CA440188
    Consensus CDS
    CCDS82693.1
    UniProtKB/TrEMBL
    F2Z2W7
    Related
    ENSP00000395738.2, ENST00000439169.2
    Conserved Domains (4) summary
    COG0724
    Location:70 → 161
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    COG2265
    Location:179 → 599
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cd12439
    Location:68 → 146
    RRM_TRMT2A; RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins
    cl17173
    Location:385 → 606
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  3. NM_022727.6 → NP_073564.3  tRNA (uracil-5-)-methyltransferase homolog A isoform a

    See identical proteins and their annotated locations for NP_073564.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AC006547, AI539558, BC017184, BX349795
    Consensus CDS
    CCDS13774.1
    UniProtKB/Swiss-Prot
    D3DX25, Q32P57, Q8IZ69, Q96ME6, Q9H732
    Related
    ENSP00000252136.7, ENST00000252136.12
    Conserved Domains (2) summary
    COG2265
    Location:179 → 581
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cd12439
    Location:68 → 146
    RRM_TRMT2A; RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

  4. NM_182984.5 → NP_892029.2  tRNA (uracil-5-)-methyltransferase homolog A isoform a

    See identical proteins and their annotated locations for NP_892029.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AI539558, BC017184, BX349795
    Consensus CDS
    CCDS13774.1
    UniProtKB/Swiss-Prot
    D3DX25, Q32P57, Q8IZ69, Q96ME6, Q9H732
    Related
    ENSP00000385807.3, ENST00000403707.7
    Conserved Domains (2) summary
    COG2265
    Location:179 → 581
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cd12439
    Location:68 → 146
    RRM_TRMT2A; RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    20111875..20117226 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011530139.4 → XP_011528441.1  tRNA (uracil-5-)-methyltransferase homolog A isoform X1

    UniProtKB/TrEMBL
    F2Z2W7
    Conserved Domains (4) summary
    COG0724
    Location:70 → 161
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    COG2265
    Location:179 → 599
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cd12439
    Location:68 → 146
    RRM_TRMT2A; RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins
    cl17173
    Location:385 → 606
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  2. XM_011530142.4 → XP_011528444.1  tRNA (uracil-5-)-methyltransferase homolog A isoform X2

    See identical proteins and their annotated locations for XP_011528444.1

    Conserved Domains (2) summary
    COG2265
    Location:63 → 273
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cl17173
    Location:59 → 280
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    20490925..20496276 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054325540.1 → XP_054181515.1  tRNA (uracil-5-)-methyltransferase homolog A isoform X1

    UniProtKB/TrEMBL
    F2Z2W7

  2. XM_054325541.1 → XP_054181516.1  tRNA (uracil-5-)-methyltransferase homolog A isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IZ69.2 GenPept UniProtKB/Swiss-Prot:Q8IZ69

Gene LinkOut

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