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

    Gene ID: 27037, updated on 10-Dec-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (20111875..20117226, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (20490925..20496276, complement)
    RS_2024_09 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. Human TRMT2A methylates tRNA and contributes to translation fidelity. Witzenberger M, et al. Nucleic Acids Res, 2023 Sep 8. PMID 37395448, Free PMC Article
    2. TRMT2A is a novel cell cycle regulator that suppresses cell proliferation. Chang YH, et al. Biochem Biophys Res Commun, 2019 Jan 8. PMID 30502085
    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. 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
    5. Chemical tagging for sensitive determination of uridine modifications in RNA. Cheng QY, et al. Chem Sci, 2020 Jan 8. PMID 34123281, Free PMC Article

    See all (65) 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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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