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

    Gene ID: 54482, updated on 10-Dec-2024

    Summary

    Official Symbol
    TRMT13provided by HGNC
    Official Full Name
    tRNA methyltransferase 13 homologprovided by HGNC
    Primary source
    HGNC:HGNC:25502
    See related
    Ensembl:ENSG00000122435 AllianceGenome:HGNC:25502
    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
    Summary
    Predicted to enable tRNA methyltransferase activity. Predicted to be involved in tRNA methylation. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 6.2), appendix (RPKM 5.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TRMT13 in Genome Data Viewer
    Location:
    1p21.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (100133163..100150496)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (99981278..99998611)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (100598719..100616052)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:100503123-100503725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:100514024-100514739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1370 Neighboring gene major facilitator superfamily domain containing 14A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1372 Neighboring gene SAS-6 centriolar assembly protein Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100578889-100579078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1373 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100598108-100598271 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:100598267-100598869 Neighboring gene Sharpr-MPRA regulatory region 13340 Neighboring gene leucine rich repeat containing 39 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:100665653-100666490 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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10287, FLJ11219

    Gene Ontology Provided by GOA

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

    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_001380338.1
    NP_001380339.1
    NP_001380340.1
    NP_001380341.1
    NP_001380342.1
    NP_001380343.1
    NP_061956.2
    XP_047278729.1
    XP_047278736.1
    XP_047278738.1
    XP_047278739.1
    XP_047278740.1
    XP_054193086.1
    XP_054193087.1
    XP_054193088.1
    XP_054193089.1
    XP_054193090.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001393409.1NP_001380338.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL445928
      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. NM_001393410.1NP_001380339.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (2) summary
      pfam05206
      Location:127431
      TRM13; Methyltransferase TRM13
      pfam11722
      Location:1745
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
    3. NM_001393411.1NP_001380340.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (3) summary
      pfam05253
      Location:5980
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:1745
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
      cl17173
      Location:165273
      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. NM_001393412.1NP_001380341.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (3) summary
      pfam05253
      Location:5980
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:1745
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
      cl17173
      Location:151259
      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_001393413.1NP_001380342.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (3) summary
      pfam05253
      Location:5980
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:1745
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
      cl17173
      Location:165274
      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_001393414.1NP_001380343.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 7

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (3) summary
      pfam05253
      Location:5980
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:1745
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
      cl17173
      Location:151260
      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_019083.3NP_061956.2  tRNA:m(4)X modification enzyme TRM13 homolog isoform 1

      See identical proteins and their annotated locations for NP_061956.2

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Consensus CDS
      CCDS765.1
      UniProtKB/Swiss-Prot
      Q5VVL0, Q9NUP7, Q9NW65
      Related
      ENSP00000359160.2, ENST00000370141.8
      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_135078.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AK002081, AK298941, AL699548

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      100133163..100150496
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422780.1XP_047278736.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X2

    2. XM_047422782.1XP_047278738.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X3

      UniProtKB/TrEMBL
      B4DQS9
    3. XM_047422783.1XP_047278739.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X4

      UniProtKB/TrEMBL
      A8K039
      Related
      ENSP00000432616.1, ENST00000482437.5
    4. XM_047422784.1XP_047278740.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X5

      UniProtKB/TrEMBL
      A8K039
    5. XM_047422773.1XP_047278729.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      99981278..99998611
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337112.1XP_054193087.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X2

    2. XM_054337113.1XP_054193088.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X3

    3. XM_054337114.1XP_054193089.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X4

      UniProtKB/TrEMBL
      A8K039, B4DGS0
    4. XM_054337115.1XP_054193090.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X5

      UniProtKB/TrEMBL
      A8K039, B4DIY2
    5. XM_054337111.1XP_054193086.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X1