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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
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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

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