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    TRMT6 tRNA methyltransferase 6 non-catalytic subunit [ Homo sapiens (human) ]

    Gene ID: 51605, updated on 11-Apr-2024

    Summary

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    Official Symbol
    TRMT6provided by HGNC
    Official Full Name
    tRNA methyltransferase 6 non-catalytic subunitprovided by HGNC
    Primary source
    HGNC:HGNC:20900
    See related
    Ensembl:ENSG00000089195 AllianceGenome:HGNC:20900
    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
    GCD10; CGI-09; Gcd10p
    Summary
    This gene encodes a member of the tRNA methyltransferase 6 protein family. A similar protein in yeast is part of a two component methyltransferase, which is involved in the posttranslational modification that produces the modified nucleoside 1-methyladenosine in tRNAs. Modified 1-methyladenosine influences initiator methionine stability and may be involved in the replication of human immunodeficiency virus type 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
    Expression
    Ubiquitous expression in testis (RPKM 9.9), bone marrow (RPKM 9.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    20p12.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (5937228..5950533, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (5977563..5990868, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (5917874..5931179, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12659 Neighboring gene chromogranin B Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:5904456-5905655 Neighboring gene KN motif and ankyrin repeat domains 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12660 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:5920579-5920767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17533 Neighboring gene minichromosome maintenance 8 homologous recombination repair factor Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:5950104-5950670 Neighboring gene MCM8 antisense RNA 1 Neighboring gene RNA, 7SL, cytoplasmic 498, pseudogene

    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. Clinical Significance of TRMT6 in Hepatocellular Carcinoma: A Bioinformatics-Based Study. Wang Y, et al. Med Sci Monit, 2019 May 25. PMID 31128068, Free PMC Article
    2. Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA(3)(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target. Finer-Moore J, et al. J Mol Biol, 2015 Dec 4. PMID 26470919, Free PMC Article
    3. N(1)-methyladenosine methylation in tRNA drives liver tumourigenesis by regulating cholesterol metabolism. Wang Y, et al. Nat Commun, 2021 Nov 2. PMID 34728628, Free PMC Article
    4. Base-Resolution Mapping Reveals Distinct m(1)A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts. Li X, et al. Mol Cell, 2017 Dec 7. PMID 29107537, Free PMC Article
    5. The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution. Safra M, et al. Nature, 2017 Nov 9. PMID 29072297

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of hepatoblastoma susceptibility loci in the TRMT6 gene from a seven-center case-control study.
      Title: Identification of hepatoblastoma susceptibility loci in the TRMT6 gene from a seven-center case-control study.
    2. TRMT6 gene rs236110 C > A polymorphism increases the risk of Wilms tumor.
      Title: TRMT6 gene rs236110 C > A polymorphism increases the risk of Wilms tumor.
    3. N(1)-methyladenosine methylation in tRNA drives liver tumourigenesis by regulating cholesterol metabolism.
      Title: N(1)-methyladenosine methylation in tRNA drives liver tumourigenesis by regulating cholesterol metabolism.
    4. TRMT6 was upregulated in HCC tissues, and higher TRMT6 expression levels was correlated with reduced OS and RFS in patients with primary HCC.
      Title: Clinical Significance of TRMT6 in Hepatocellular Carcinoma: A Bioinformatics-Based Study.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association studies identify loci associated with age at menarche and age at natural menopause.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of tRNA methyltransferase 6 homolog (TRMT6) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • MGC5029

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA modification IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of tRNA (m1A) methyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of tRNA (m1A) methyltransferase complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
    Names
    mRNA methyladenosine-N(1)-methyltransferase non-catalytic subunit TRM6
    tRNA methyltransferase 6 homolog
    tRNA(m1A58)MTase subunit TRM6

    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_001281467.2 → NP_001268396.1  tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 isoform 2

      See identical proteins and their annotated locations for NP_001268396.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in its 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AI291549, AK300812, AL035461, BC001262, DC348968
      Consensus CDS
      CCDS63225.1
      UniProtKB/Swiss-Prot
      Q9UJA5
      Related
      ENSP00000392070.2, ENST00000453074.6
      Conserved Domains (1) summary
      pfam04189
      Location:1 → 95
      Gcd10p; Gcd10p family

    2. NM_015939.5 → NP_057023.2  tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 isoform 1

      See identical proteins and their annotated locations for NP_057023.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AI291549, AL035461, BC001262, DC348968
      Consensus CDS
      CCDS13093.1
      UniProtKB/Swiss-Prot
      B4DUV6, Q76P92, Q9BQV5, Q9UJA5, Q9ULR7, Q9Y2Z8
      Related
      ENSP00000203001.2, ENST00000203001.7
      Conserved Domains (1) summary
      pfam04189
      Location:19 → 252
      Gcd10p; Gcd10p family

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      5937228..5950533 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      5977563..5990868 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UJA5.1 GenPept UniProtKB/Swiss-Prot:Q9UJA5

    Gene LinkOut

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

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