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

    Gene ID: 1787, updated on 28-Oct-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
    mouse all
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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 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 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

    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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