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TRDMT1 tRNA aspartic acid methyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 1787, updated on 2-Nov-2024

Summary

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Official Symbol
TRDMT1provided by HGNC
Official Full Name
tRNA aspartic acid methyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:2977
See related
Ensembl:ENSG00000107614 MIM:602478; AllianceGenome:HGNC:2977
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
DMNT2; DNMT2; PUMET; RNMT1; MHSAIIP
Summary
This gene encodes a protein responsible for the methylation of aspartic acid transfer RNA, specifically at the cytosine-38 residue in the anticodon loop. This enzyme also possesses residual DNA-(cytosine-C5) methyltransferase activity. While similar in sequence and structure to DNA cytosine methyltransferases, this gene is distinct and highly conserved in its function among taxa. [provided by RefSeq, Jun 2010]
Expression
Ubiquitous expression in thyroid (RPKM 1.0), endometrium (RPKM 0.6) and 25 other tissues See more
Orthologs
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Genomic context

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See TRDMT1 in Genome Data Viewer
Location:
10p13
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (17137336..17201672, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (17155855..17220211, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (17179335..17243671, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3107 Neighboring gene uncharacterized LOC105376435 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:16864864-16865015 Neighboring gene MPRA-validated peak881 silencer Neighboring gene MPRA-validated peak882 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:16933270-16934469 Neighboring gene cubilin Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:16942960-16943677 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:16970960-16971553 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:17010389-17010952 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:17026880-17027039 Neighboring gene GATA motif-containing MPRA enhancer 283 Neighboring gene Sharpr-MPRA regulatory region 1431 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:17104252-17105451 Neighboring gene MPRA-validated peak883 silencer Neighboring gene MPRA-validated peak884 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:17157167-17158366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2181 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:17268719-17268933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2182 Neighboring gene Sharpr-MPRA regulatory region 14556 Neighboring gene VIM antisense RNA 1 Neighboring gene vimentin Neighboring gene MPRA-validated peak886 silencer Neighboring gene ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6 Neighboring gene ST8SIA6 antisense RNA 1

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. Cloning and analysis of a novel human putative DNA methyltransferase. Van den Wyngaert I, et al. FEBS Lett, 1998 Apr 17. PMID 9599025
  2. Novel nucleotide substitutions within the coding region of DNMT2 are in strong linkage disequilibrium in Caucasians and Japanese. Franchina M, et al. Hum Hered, 2001. PMID 11713417
  3. Mapping the tRNA binding site on the surface of human DNMT2 methyltransferase. Jurkowski TP, et al. Biochemistry, 2012 Jun 5. PMID 22591353
  4. Structure and function of eukaryotic DNA methyltransferases. Chen T, et al. Curr Top Dev Biol, 2004. PMID 15094296
  5. Five novel alternatively spliced transcripts of DNA (cytosine-5) methyltransferase 2 in human peripheral blood leukocytes. Franchina M, et al. Int J Biochem Cell Biol, 2001 Nov. PMID 11551826

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DNMT2/TRDMT1 gene knockout compromises doxorubicin-induced unfolded protein response and sensitizes cancer cells to ER stress-induced apoptosis.
    Title: DNMT2/TRDMT1 gene knockout compromises doxorubicin-induced unfolded protein response and sensitizes cancer cells to ER stress-induced apoptosis.
  2. Position 34 of tRNA is a discriminative element for m5C38 modification by human DNMT2.
    Title: Position 34 of tRNA is a discriminative element for m5C38 modification by human DNMT2.
  3. Decoding the Genetic Alterations in Genes of DNMT Family (DNA Methyl-Transferase) and their Association with Head and Neck Squamous Cell Carcinoma.
    Title: Decoding the Genetic Alterations in Genes of DNMT Family (DNA Methyl-Transferase) and their Association with Head and Neck Squamous Cell Carcinoma.
  4. The lack of functional DNMT2/TRDMT1 gene modulates cancer cell responses during drug-induced senescence.
    Title: The lack of functional DNMT2/TRDMT1 gene modulates cancer cell responses during drug-induced senescence.
  5. TRDMT1 participates in the DNA damage repair of granulosa cells in premature ovarian failure.
    Title: TRDMT1 participates in the DNA damage repair of granulosa cells in premature ovarian failure.
  6. Trdmt1 3'-untranslated region functions as a competing endogenous RNA in leukemia HL-60 cell differentiation.
    Title: Trdmt1 3'-untranslated region functions as a competing endogenous RNA in leukemia HL-60 cell differentiation.
  7. TRDMT1 has a role in 5-methylcytosine modification of mRNA and in HEK293 cell proliferation and migration
    Title: Depletion of TRDMT1 affects 5-methylcytosine modification of mRNA and inhibits HEK293 cell proliferation and migration.
  8. Data suggest that, upon HIV-1 infection, DNMT2 is re-localized from the nucleus to cytoplasmic stress granules where DNMT2 methylates HIV-1 messenger RNA; this methylation increases the stability of the HIV-1 RNA genome and up-regulates virus replication; thus, DNMT2 appears to facilitate HIV-1 infection.
    Title: Cytosine methylation by DNMT2 facilitates stability and survival of HIV-1 RNA in the host cell during infection.
  9. The strong effect of some of the somatic cancer mutations on DNMT2 activity suggests that these mutations have a functional role in tumorigenesis.
    Title: Somatic cancer mutations in the DNMT2 tRNA methyltransferase alter its catalytic properties.
  10. DNMT1, DNMT2 and DNMT3A may play important roles in gastric cancer carcinogenesis.
    Title: Risk-association of DNA methyltransferases polymorphisms with gastric cancer in the Southern Chinese population.
Submit: New GeneRIF Correction See all GeneRIFs (20)

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

EBI GWAS Catalog

Description
Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.
EBI GWAS Catalog
Genome wide association and linkage analyses identified three loci-4q25, 17q23.2, and 10q11.21-associated with variation in leukocyte telomere length: the Long Life Family Study.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables tRNA (cytidine-5-)-methyltransferase activity EXP
Inferred from Experiment
more info
 PubMed 
enables tRNA (cytidine-5-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA (cytidine-5-)-methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables tRNA methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in response to amphetamine IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within tRNA methylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in tRNA modification IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in tRNA modification TAS
Traceable Author Statement
more info
  
involved_in tRNA stabilization ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
tRNA (cytosine(38)-C(5))-methyltransferase
Names
DNA (cytosine-5)-methyltransferase-like protein 2
DNA MTase homolog HsaIIP
DNA cytosine-5 methyltransferase 2
DNA methyltransferase-2
tRNA (cytosine-5-)-methyltransferase
NP_001307935.1
NP_001307936.1
NP_001338148.1
NP_001338149.1
NP_001338150.1
NP_001338151.1
NP_001338152.1
NP_004403.1
XP_005252431.1
XP_016871290.1
XP_024303623.1
XP_047280649.1
XP_047280650.1
XP_047280651.1
XP_047280652.1
XP_047280653.1
XP_047280654.1
XP_054220922.1
XP_054220923.1
XP_054220924.1
XP_054220925.1
XP_054220926.1
XP_054220927.1
XP_054220928.1
XP_054220929.1
XP_054220930.1

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_001321006.2 → NP_001307935.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform f

    Status: REVIEWED

    Source sequence(s)
    AC067747, AJ223333, AK299027, AW136056
    UniProtKB/TrEMBL
    B4DQZ2
    Conserved Domains (1) summary
    cl17173
    Location:25 → 310
    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_001321007.2 → NP_001307936.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform g

    Status: REVIEWED

    Source sequence(s)
    AC067747, AJ223333, AK299027, AL133415, AW136056, BX537961
    UniProtKB/TrEMBL
    B7Z1Y7
    Conserved Domains (1) summary
    cl17173
    Location:1 → 320
    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_001351219.2 → NP_001338148.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform h

    Status: REVIEWED

    Source sequence(s)
    AC067747, AF329941, AJ223333, AW136056, HY167774
    UniProtKB/TrEMBL
    A0A0U1U562
    Conserved Domains (1) summary
    cd00315
    Location:4 → 384
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...

  4. NM_001351220.2 → NP_001338149.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform i

    Status: REVIEWED

    Source sequence(s)
    AA399591, AC067747, AJ223333, AK294100, BF435781, BX117729, CN304214
    UniProtKB/TrEMBL
    A0A0U1U562
    Conserved Domains (1) summary
    cl17173
    Location:4 → 359
    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). ...

  5. NM_001351221.2 → NP_001338150.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform j

    Status: REVIEWED

    Source sequence(s)
    AC067747, AF329941, AJ223333, AW136056
    UniProtKB/TrEMBL
    A0A0U1U562
    Conserved Domains (1) summary
    cl17173
    Location:4 → 338
    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). ...

  6. NM_001351222.2 → NP_001338151.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform k

    Status: REVIEWED

    Source sequence(s)
    AC067747, AJ223333, AK294100, BF435781, BX494949, CN304214, DC416110
    UniProtKB/TrEMBL
    B7Z1Y7
    Conserved Domains (1) summary
    cl17173
    Location:1 → 281
    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). ...

  7. NM_001351223.2 → NP_001338152.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform k

    Status: REVIEWED

    Source sequence(s)
    AC067747, AJ223333, AK294100, BF435781, CN304214, DC416110
    UniProtKB/TrEMBL
    B7Z1Y7
    Conserved Domains (1) summary
    cl17173
    Location:1 → 281
    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). ...

  8. NM_004412.7 → NP_004403.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform a

    See identical proteins and their annotated locations for NP_004403.1

    Status: REVIEWED

    Source sequence(s)
    AC067747, AJ223333, AW136056
    Consensus CDS
    CCDS7114.1
    UniProtKB/Swiss-Prot
    B0YJ02, B0YJ03, B0YJ07, B0YJ08, O14717, O43669, Q86WW6
    UniProtKB/TrEMBL
    A0A0U1U562, Q6ICS7
    Related
    ENSP00000367030.3, ENST00000377799.8
    Conserved Domains (1) summary
    cd00315
    Location:4 → 391
    Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    17137336..17201672 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047424697.1 → XP_047280653.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X8

  2. XM_047424695.1 → XP_047280651.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X5

  3. XM_005252374.5 → XP_005252431.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X2

    UniProtKB/TrEMBL
    A0A0U1U562
    Conserved Domains (1) summary
    cl17173
    Location:4 → 359
    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). ...

  4. XM_047424696.1 → XP_047280652.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X7

  5. XM_017015801.2 → XP_016871290.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X6

    UniProtKB/TrEMBL
    A0A0U1U562

  6. XM_047424694.1 → XP_047280650.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X4

  7. XM_047424693.1 → XP_047280649.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X3

  8. XM_024447855.2 → XP_024303623.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X1

    UniProtKB/TrEMBL
    A0A0U1U562
    Conserved Domains (1) summary
    cl17173
    Location:4 → 352
    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). ...

  9. XM_047424698.1 → XP_047280654.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    17155855..17220211 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054364954.1 → XP_054220929.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X8

  2. XM_054364951.1 → XP_054220926.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X5

  3. XM_054364948.1 → XP_054220923.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X2

  4. XM_054364953.1 → XP_054220928.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X7

  5. XM_054364952.1 → XP_054220927.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X6

  6. XM_054364950.1 → XP_054220925.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X4

  7. XM_054364949.1 → XP_054220924.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X3

  8. XM_054364947.1 → XP_054220922.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X1

  9. XM_054364955.1 → XP_054220930.1  tRNA (cytosine(38)-C(5))-methyltransferase isoform X9

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_176081.2: Suppressed sequence

    Description
    NM_176081.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

  2. NM_176083.2: Suppressed sequence

    Description
    NM_176083.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

  3. NM_176084.1: Suppressed sequence

    Description
    NM_176084.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  4. NM_176085.1: Suppressed sequence

    Description
    NM_176085.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  5. NM_176086.1: Suppressed sequence

    Description
    NM_176086.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14717.1 GenPept UniProtKB/Swiss-Prot:O14717

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