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

    Gene ID: 54482, updated on 2-Nov-2024

    Summary

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    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, Nov 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 6.2), appendix (RPKM 5.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    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

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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. A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription. Li H, et al. EMBO J, 2022 Mar 15. PMID 34850409, Free PMC Article
    2. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Weinmann AS, et al. Genes Dev, 2002 Jan 15. PMID 11799066, Free PMC Article
    3. The DNA sequence and biological annotation of human chromosome 1. Gregory SG, et al. Nature, 2006 May 18. PMID 16710414
    4. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Fei T, et al. Proc Natl Acad Sci U S A, 2017 Jun 27. PMID 28611215, Free PMC Article
    5. Ubiquitin-mediated proteolysis of HuR by heat shock. Abdelmohsen K, et al. EMBO J, 2009 May 6. PMID 19322201, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription.
      Title: A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription.
    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

    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

    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

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    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)

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

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (3) summary
      pfam05206
      Location:151 → 455
      TRM13; Methyltransferase TRM13
      pfam05253
      Location:59 → 80
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:17 → 45
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein

    2. NM_001393410.1 → NP_001380339.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (2) summary
      pfam05206
      Location:127 → 431
      TRM13; Methyltransferase TRM13
      pfam11722
      Location:17 → 45
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein

    3. NM_001393411.1 → NP_001380340.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (3) summary
      pfam05253
      Location:59 → 80
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:17 → 45
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
      cl17173
      Location:165 → 273
      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_001393412.1 → NP_001380341.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (3) summary
      pfam05253
      Location:59 → 80
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:17 → 45
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
      cl17173
      Location:151 → 259
      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_001393413.1 → NP_001380342.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (3) summary
      pfam05253
      Location:59 → 80
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:17 → 45
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
      cl17173
      Location:165 → 274
      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_001393414.1 → NP_001380343.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform 7

      Status: VALIDATED

      Source sequence(s)
      AL445928
      Conserved Domains (3) summary
      pfam05253
      Location:59 → 80
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:17 → 45
      zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein
      cl17173
      Location:151 → 260
      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_019083.3 → NP_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:165 → 469
      TRM13; Methyltransferase TRM13
      pfam05253
      Location:59 → 80
      zf-U11-48K; U11-48K-like CHHC zinc finger
      pfam11722
      Location:17 → 45
      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_047422780.1 → XP_047278736.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X2

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

      UniProtKB/TrEMBL
      B4DQS9

    3. XM_047422783.1 → XP_047278739.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X4

      Related
      ENSP00000432616.1, ENST00000482437.5

    4. XM_047422784.1 → XP_047278740.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X5

    5. XM_047422773.1 → XP_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_054337112.1 → XP_054193087.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X2

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

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

      UniProtKB/TrEMBL
      B4DGS0

    4. XM_054337115.1 → XP_054193090.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X5

      UniProtKB/TrEMBL
      B4DIY2

    5. XM_054337111.1 → XP_054193086.1  tRNA:m(4)X modification enzyme TRM13 homolog isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NUP7.2 GenPept UniProtKB/Swiss-Prot:Q9NUP7

    Gene LinkOut

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

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