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    TRMT13 tRNA methyltransferase 13 homolog [ Homo sapiens (human) ]

    Gene ID: 54482, updated on 17-Jun-2019

    Summary

    Official Symbol
    TRMT13provided by HGNC
    Official Full Name
    tRNA methyltransferase 13 homologprovided by HGNC
    Primary source
    HGNC:HGNC:25502
    See related
    Ensembl:ENSG00000122435
    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
    CCDC76
    Expression
    Ubiquitous expression in lymph node (RPKM 6.2), appendix (RPKM 5.4) and 25 other tissues See more
    Orthologs

    Genomic context

    See TRMT13 in Genome Data Viewer
    Location:
    1p21.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (100133080..100150498)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (100598669..100616054)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene solute carrier family 35 member A3 Neighboring gene RNA, U6 small nuclear 1318, pseudogene Neighboring gene major facilitator superfamily domain containing 14A Neighboring gene SAS-6 centriolar assembly protein Neighboring gene leucine rich repeat containing 39 Neighboring gene ribosomal protein L23a pseudogene 90 Neighboring gene dihydrolipoamide branched chain transacylase E2 Neighboring gene brain protein I3 pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    Pathways from BioSystems

    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • tRNA modification in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
      tRNA modification in the nucleus and cytosol, organism-specific biosystemAt least 92 distinct tRNA nucleotide base modifications have been found. The modifications are made post-transcriptionally by a large group of disparate enzymes located in the nucleus, cytosol, and m...
    • tRNA processing, organism-specific biosystem (from REACTOME)
      tRNA processing, organism-specific biosystemGenes encoding transfer RNAs (tRNAs) are transcribed by RNA polymerase III in the nucleus and by mitochondrial RNA polymerase in the mitochondrion.In the nucleus transcription reactions produce precu...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ10287, FLJ11219

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    tRNA 2'-O-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    tRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    tRNA:m(4)X modification enzyme TRM13 homolog
    Names
    coiled-coil domain containing 76
    coiled-coil domain-containing protein 76
    tRNA [Gm4] methyltransferase
    tRNA guanosine-2'-O-methyltransferase TRM13 homolog
    NP_061956.2
    XP_005271002.1
    XP_005271003.1
    XP_016856993.1
    XP_016856994.1

    NCBI Reference Sequences (RefSeq)

    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_019083.2NP_061956.2  tRNA:m(4)X modification enzyme TRM13 homolog

      See identical proteins and their annotated locations for NP_061956.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the supported protein.
      Source sequence(s)
      AK002081, AL699548, CR745287
      Consensus CDS
      CCDS765.1
      UniProtKB/Swiss-Prot
      Q9NUP7
      Related
      ENSP00000359160.2, ENST00000370141.7
      Conserved Domains (3) summary
      pfam05206
      Location:165469
      TRM13; Methyltransferase TRM13
      pfam05253
      Location:5980
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:1745
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein

    RNA

    1. NR_135078.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK002081, AK298941, AL699548, CR745287

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      100133080..100150498
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005270945.3XP_005271002.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X1

      Conserved Domains (3) summary
      pfam05206
      Location:151455
      TRM13; Methyltransferase TRM13
      pfam05253
      Location:5980
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:1745
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
    2. XM_017001505.1XP_016856994.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X4

    3. XM_005270946.2XP_005271003.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X2

      Conserved Domains (1) summary
      pfam05206
      Location:24328
      TRM13; Methyltransferase TRM13
    4. XM_017001504.1XP_016856993.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X3

    RNA

    1. XR_001737237.1 RNA Sequence

    2. XR_246276.3 RNA Sequence

    3. XR_001737241.1 RNA Sequence

    4. XR_002956838.1 RNA Sequence

    5. XR_001737239.1 RNA Sequence

    6. XR_001737238.1 RNA Sequence

    7. XR_001737240.1 RNA Sequence

    8. XR_246275.3 RNA Sequence

    9. XR_001737236.1 RNA Sequence

    10. XR_246273.4 RNA Sequence

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