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    TRMO tRNA methyltransferase O [ Homo sapiens (human) ]

    Gene ID: 51531, updated on 5-Mar-2024

    Summary

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    Official Symbol
    TRMOprovided by HGNC
    Official Full Name
    tRNA methyltransferase Oprovided by HGNC
    Primary source
    HGNC:HGNC:30967
    See related
    Ensembl:ENSG00000136932 AllianceGenome:HGNC:30967
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NAP1; HSPC219; C9orf156
    Summary
    Enables tRNA (adenine-N6-)-methyltransferase activity. Involved in tRNA methylation. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 2.2), lymph node (RPKM 1.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    9q22.33
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (97896855..97922500, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (110061668..110094437, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100659137..100684782, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100465986-100467185 Neighboring gene keratin 18 pseudogene 13 Neighboring gene papillary thyroid carcinoma susceptibility candidate 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28678 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100520047-100521246 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:100534165-100534666 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:100534667-100535166 Neighboring gene VISTA enhancer hs1595 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20103 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100571176-100572375 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100589760-100589981 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100613975-100614476 Neighboring gene VISTA enhancer hs1596 Neighboring gene VISTA enhancers hs1597 and hs1717 Neighboring gene forkhead box E1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28679 Neighboring gene hemogen Neighboring gene Sharpr-MPRA regulatory region 4249 Neighboring gene CRISPRi-validated cis-regulatory element chr9.1594 Neighboring gene uncharacterized LOC124902226 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100745493-100746375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20109 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20110 Neighboring gene uncharacterized LOC124902225 Neighboring gene acidic nuclear phosphoprotein 32 family member B

    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. Binding of HIV-1 Nef to a novel thioesterase enzyme correlates with Nef-mediated CD4 down-regulation. Liu LX, et al. J Biol Chem, 1997 May 23. PMID 9153233
    2. FOXE1 association with both isolated cleft lip with or without cleft palate, and isolated cleft palate. Moreno LM, et al. Hum Mol Genet, 2009 Dec 15. PMID 19779022, Free PMC Article
    3. The FOXE1 locus is a major genetic determinant for radiation-related thyroid carcinoma in Chernobyl. Takahashi M, et al. Hum Mol Genet, 2010 Jun 15. PMID 20350937
    4. Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. Letra A, et al. Am J Med Genet A, 2010 Jul. PMID 20583170, Free PMC Article
    5. Discovery of the β-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs. Kimura S, et al. Nucleic Acids Res, 2014 Aug. PMID 25063302, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate.
    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
    Novel associations for hypothyroidism include known autoimmune risk loci.
    EBI GWAS Catalog
    The FOXE1 locus is a major genetic determinant for radiation-related thyroid carcinoma in Chernobyl.
    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

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tRNA (L-threonylcarbamoyladenosine(37)-C2) methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in tRNA methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    tRNA (adenine(37)-N6)-methyltransferase
    Names
    Nef (lentivirus myristoylated factor) associated protein 1
    Nef associated protein 1
    nef-associated protein 1
    thioesterase NAP1

    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_001330725.2 → NP_001317654.1  tRNA (adenine(37)-N6)-methyltransferase isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL499604
      Consensus CDS
      CCDS83387.1
      UniProtKB/TrEMBL
      Q5T114
      Conserved Domains (2) summary
      pfam18389
      Location:189 → 257
      TrmO_C; TrmO C-terminal domain
      cl00749
      Location:1 → 18
      UPF0066; Escherichia coli YaeB and related proteins

    2. NM_001371657.1 → NP_001358586.1  tRNA (adenine(37)-N6)-methyltransferase isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL499604
      Consensus CDS
      CCDS6730.1
      UniProtKB/Swiss-Prot
      Q5T113, Q86SK0, Q9BU70, Q9NXJ7, Q9P0Q7
      Conserved Domains (2) summary
      pfam18389
      Location:335 → 403
      TrmO_C; TrmO C-terminal domain
      pfam01980
      Location:45 → 164
      UPF0066; Uncharacterized protein family UPF0066

    3. NM_001371658.1 → NP_001358587.1  tRNA (adenine(37)-N6)-methyltransferase isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL499604
      Conserved Domains (1) summary
      pfam01980
      Location:45 → 164
      UPF0066; Uncharacterized protein family UPF0066

    4. NM_001371659.1 → NP_001358588.1  tRNA (adenine(37)-N6)-methyltransferase isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL499604
      Conserved Domains (2) summary
      pfam18389
      Location:261 → 329
      TrmO_C; TrmO C-terminal domain
      pfam01980
      Location:2 → 90
      UPF0066; Uncharacterized protein family UPF0066

    5. NM_001371660.1 → NP_001358589.1  tRNA (adenine(37)-N6)-methyltransferase isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL499604
      Consensus CDS
      CCDS83387.1
      UniProtKB/TrEMBL
      Q5T114
      Conserved Domains (2) summary
      pfam18389
      Location:189 → 257
      TrmO_C; TrmO C-terminal domain
      cl00749
      Location:1 → 18
      UPF0066; Escherichia coli YaeB and related proteins

    6. NM_001371661.1 → NP_001358590.1  tRNA (adenine(37)-N6)-methyltransferase isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL499604
      Consensus CDS
      CCDS83387.1
      UniProtKB/TrEMBL
      Q5T114
      Related
      ENSP00000364259.1, ENST00000375118.1
      Conserved Domains (2) summary
      pfam18389
      Location:189 → 257
      TrmO_C; TrmO C-terminal domain
      cl00749
      Location:1 → 18
      UPF0066; Escherichia coli YaeB and related proteins

    7. NM_016481.5 → NP_057565.3  tRNA (adenine(37)-N6)-methyltransferase isoform 1

      See identical proteins and their annotated locations for NP_057565.3

      Status: VALIDATED

      Source sequence(s)
      AL499604
      Consensus CDS
      CCDS6730.1
      UniProtKB/Swiss-Prot
      Q5T113, Q86SK0, Q9BU70, Q9NXJ7, Q9P0Q7
      Related
      ENSP00000364260.3, ENST00000375119.8
      Conserved Domains (2) summary
      pfam18389
      Location:335 → 403
      TrmO_C; TrmO C-terminal domain
      pfam01980
      Location:45 → 164
      UPF0066; Uncharacterized protein family UPF0066

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      97896855..97922500 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011518776.4 → XP_011517078.1  tRNA (adenine(37)-N6)-methyltransferase isoform X1

      Conserved Domains (1) summary
      cd09281
      Location:32 → 159
      UPF0066; Escherichia coli YaeB and related proteins

    2. XM_047423465.1 → XP_047279421.1  tRNA (adenine(37)-N6)-methyltransferase isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      110061668..110094437 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363085.1 → XP_054219060.1  tRNA (adenine(37)-N6)-methyltransferase isoform X1

    2. XM_054363086.1 → XP_054219061.1  tRNA (adenine(37)-N6)-methyltransferase isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BU70.2 GenPept UniProtKB/Swiss-Prot:Q9BU70

    Gene LinkOut

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

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