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Trmt2a TRM2 tRNA methyltransferase 2A [ Mus musculus (house mouse) ]

Gene ID: 15547, updated on 28-Oct-2024

Summary

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Official Symbol
Trmt2aprovided by MGI
Official Full Name
TRM2 tRNA methyltransferase 2Aprovided by MGI
Primary source
MGI:MGI:96270
See related
Ensembl:ENSMUSG00000022721 AllianceGenome:MGI:96270
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Htf9c
Summary
Predicted to enable C-methyltransferase activity and tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent. Predicted to be involved in mRNA processing; methylation; and tRNA processing. Predicted to be located in cytosol. Is expressed in several structures, including brain; cardiovascular system; forelimb bud; gut; and sensory organ. Orthologous to human TRMT2A (tRNA methyltransferase 2 homolog A). [provided by Alliance of Genome Resources, Oct 2024]
Expression
Ubiquitous expression in limb E14.5 (RPKM 20.3), CNS E14 (RPKM 18.8) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Trmt2a in Genome Data Viewer
Location:
16 A3; 16 11.31 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (18066747..18072636)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (18248847..18254772)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene zinc finger, DHHC domain containing 8 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:18231149-18231350 Neighboring gene predicted gene, 25777 Neighboring gene RAN binding protein 1 Neighboring gene STARR-positive B cell enhancer ABC_E8621 Neighboring gene DGCR8, microprocessor complex subunit Neighboring gene microRNA 1306 Neighboring gene microRNA 3618

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Cell type-specific interactions of transcription factors with a housekeeping promoter in vivo. Stapleton G, et al. Nucleic Acids Res, 1993 May 25. PMID 8389443, Free PMC Article
  2. Binding of proteins from embryonic and differentiated cells to a bidirectional promoter contained within a CpG island. Tyndall C, et al. J Mol Biol, 1992 Jul 20. PMID 1640448
  3. Expression of the murine RanBP1 and Htf9-c genes is regulated from a shared bidirectional promoter during cell cycle progression. Guarguaglini G, et al. Biochem J, 1997 Jul 1. PMID 9224656, Free PMC Article
  4. Transcriptional control of the Htf9-A/RanBP-1 gene during the cell cycle. Di Matteo G, et al. Cell Growth Differ, 1995 Oct. PMID 8845298
  5. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Bird A, et al. Cell, 1985 Jan. PMID 2981636

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (3) 

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

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables C-methyltransferase activity ISO
Inferred from Sequence Orthology
more info
  
enables C-methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent ISO
Inferred from Sequence Orthology
more info
  
enables tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in tRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
tRNA (uracil-5-)-methyltransferase homolog A
Names
TRM2 tRNA methyltransferase 2 homolog A
hpaII tiny fragments locus 9c protein
mRNA (uracil-5-)-methyltransferase TRMT2A
NP_001074468.1
NP_001074469.1
NP_001182134.1
NP_001344075.1
NP_001412031.1
NP_001412032.1
NP_001412033.1
XP_036015680.1

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_001080999.2 → NP_001074468.1  tRNA (uracil-5-)-methyltransferase homolog A isoform 2

    See identical proteins and their annotated locations for NP_001074468.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks a segment of the 5' UTR and 5' coding region, and uses an upstream start codon, compared to variant 1. The resulting isoform (2) has a distinct N-terminus and is the same length as isoform 1.
    Source sequence(s)
    AC084822, AK080170, AK134368
    Consensus CDS
    CCDS37281.1
    UniProtKB/Swiss-Prot
    P70221, P70222, Q3UYU2, Q78E15, Q80VN8, Q8BNV1
    UniProtKB/TrEMBL
    Q3UJM1
    Related
    ENSMUSP00000111304.2, ENSMUST00000115640.8
    Conserved Domains (4) summary
    COG0724
    Location:60 → 201
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    COG2265
    Location:169 → 571
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cd12439
    Location:58 → 136
    RRM_TRMT2A; RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins
    cl17173
    Location:375 → 578
    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). ...

  2. NM_001081000.2 → NP_001074469.1  tRNA (uracil-5-)-methyltransferase homolog A isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
    Source sequence(s)
    AC084822, AK080170, AK134368, BY090144
    Consensus CDS
    CCDS37282.1
    UniProtKB/TrEMBL
    E9PUQ7, Q3UJM1
    Related
    ENSMUSP00000111303.3, ENSMUST00000100099.10
    Conserved Domains (4) summary
    COG0724
    Location:60 → 201
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    COG2265
    Location:169 → 571
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cd12439
    Location:58 → 136
    RRM_TRMT2A; RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins
    cl17173
    Location:375 → 578
    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). ...

  3. NM_001195205.1 → NP_001182134.1  tRNA (uracil-5-)-methyltransferase homolog A isoform 4

    See identical proteins and their annotated locations for NP_001182134.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks a segment of the 5' UTR and 5' coding region, uses an upstream start codon, and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (4) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC084822, AK080170, CJ049472
    Consensus CDS
    CCDS57020.1
    UniProtKB/TrEMBL
    Q3UJM1
    Related
    ENSMUSP00000121216.2, ENSMUST00000140206.8
    Conserved Domains (4) summary
    COG0724
    Location:60 → 201
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    COG2265
    Location:169 → 532
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cd12439
    Location:58 → 136
    RRM_TRMT2A; RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins
    cl17173
    Location:375 → 539
    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_001357146.1 → NP_001344075.1  tRNA (uracil-5-)-methyltransferase homolog A isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC084822
    UniProtKB/TrEMBL
    Q05BM5, Q3UJM1
    Conserved Domains (2) summary
    COG2265
    Location:158 → 560
    TrmA; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]
    cd12439
    Location:47 → 125
    RRM_TRMT2A; RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

  5. NM_001425102.1 → NP_001412031.1  tRNA (uracil-5-)-methyltransferase homolog A isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC084822

  6. NM_001425103.1 → NP_001412032.1  tRNA (uracil-5-)-methyltransferase homolog A isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC084822

  7. NM_001425104.1 → NP_001412033.1  tRNA (uracil-5-)-methyltransferase homolog A isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC084822

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    18066747..18072636
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036159787.1 → XP_036015680.1  tRNA (uracil-5-)-methyltransferase homolog A isoform X4

    Related
    ENSMUST00000153292.8
    Conserved Domains (1) summary
    cl17173
    Location:99 → 307
    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). ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_008307.2: Suppressed sequence

    Description
    NM_008307.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which retains an intron.
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8BNV1.2 GenPept UniProtKB/Swiss-Prot:Q8BNV1

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