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    MRM3 mitochondrial rRNA methyltransferase 3 [ Homo sapiens (human) ]

    Gene ID: 55178, updated on 5-Mar-2024

    Summary

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    Official Symbol
    MRM3provided by HGNC
    Official Full Name
    mitochondrial rRNA methyltransferase 3provided by HGNC
    Primary source
    HGNC:HGNC:18485
    See related
    Ensembl:ENSG00000171861 MIM:612600; AllianceGenome:HGNC:18485
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RMTL1; RNMTL1
    Summary
    Efficient translation of mitochondrial-derived transcripts requires proper assembly of the large subunit of the mitochondrial ribosome. Central to the biogenesis of this large subunit is the A-loop of mitochondrial 16S rRNA, which is modified by three rRNA methyltransferases located near mtDNA nucleoids. The protein encoded by this gene methylates G(1370) of 16S rRNA, and this modification is necessary for proper ribosomal large subnit assembly. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]
    Expression
    Ubiquitous expression in testis (RPKM 12.8), bone marrow (RPKM 6.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MRM3 in Genome Data Viewer
    Location:
    17p13.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (782353..792509)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (668784..678768)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (685593..695749)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7943 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7945 Neighboring gene TLC domain containing 3A Neighboring gene gem nuclear organelle associated protein 4 Neighboring gene diazepam binding inhibitor-like 5, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11440 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:685572-686120 Neighboring gene glyoxalase domain containing 4 Neighboring gene Sharpr-MPRA regulatory region 8532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11442 Neighboring gene nucleoredoxin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:736782-737522 Neighboring gene Sharpr-MPRA regulatory region 9814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:746053-747038 Neighboring gene uncharacterized LOC124903894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:753668-754242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:754898-755398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:773909-774736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:790499-790998 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:800010-801209 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:801761-802401 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:802905-803406 Neighboring gene uncharacterized LOC101927727 Neighboring gene Sharpr-MPRA regulatory region 13189

    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
    • 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. The ATF/CREB site is the key element for transcription of the human RNA methyltransferase like 1(RNMTL1) gene, a newly discovered 17p13.3 gene. Xu J, et al. Cell Res, 2002 Sep. PMID 12296377
    2. MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome. Rorbach J, et al. Mol Biol Cell, 2014 Sep 1. PMID 25009282, Free PMC Article
    3. A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit. Rebelo-Guiomar P, et al. Nat Commun, 2022 Feb 17. PMID 35177605, Free PMC Article
    4. Assignment of 2'-O-methyltransferases to modification sites on the mammalian mitochondrial large subunit 16 S ribosomal RNA (rRNA). Lee KW, et al. J Biol Chem, 2014 Sep 5. PMID 25074936, Free PMC Article
    5. Mitochondrial ribosomal RNA (rRNA) methyltransferase family members are positioned to modify nascent rRNA in foci near the mitochondrial DNA nucleoid. Lee KW, et al. J Biol Chem, 2013 Oct 25. PMID 24036117, Free PMC Article

    See all (74) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MRM2 and MRM3 are human mitochondrial methyltransferases involved in the modification of 16S rRNA and are important factors for the biogenesis and function of the large subunit of the mitochondrial ribosome.
      Title: MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome.
    2. Data show that 2'-O-methyltransferases MRM1, MRM2, and RNMTL1 are responsible for modification of large subunit rRNA at residues G1145, U1369, and G1370, respectively.
      Title: Assignment of 2'-O-methyltransferases to modification sites on the mammalian mitochondrial large subunit 16 S ribosomal RNA (rRNA).
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    4. The ATF/CREB site is the key element for transcription of this protein found on human chromosome 17.
      Title: The ATF/CREB site is the key element for transcription of the human RNA methyltransferase like 1(RNMTL1) gene, a newly discovered 17p13.3 gene.
    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

    EBI GWAS Catalog

    Description
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog

    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

    • FLJ10581

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables rRNA (guanosine-2'-O-)-methyltransferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables rRNA (guanosine-2'-O-)-methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in rRNA 2'-O-methylation TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    rRNA methyltransferase 3, mitochondrial
    Names
    16S rRNA (guanosine(1370)-2'-O)-methyltransferase
    16S rRNA [Gm1370] 2'-O-methyltransferase
    RNA methyltransferase like 1
    RNA methyltransferase-like protein 1
    putative RNA methyltransferase
    NP_001304876.1
    NP_060616.1

    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_001317947.2 → NP_001304876.1  rRNA methyltransferase 3, mitochondrial isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate internal exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AF177344, AK222900, BI830018
      UniProtKB/Swiss-Prot
      Q9HC36
      Conserved Domains (1) summary
      pfam00588
      Location:13 → 204
      SpoU_methylase; SpoU rRNA Methylase family

    2. NM_018146.4 → NP_060616.1  rRNA methyltransferase 3, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_060616.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AF177344, AK222900
      Consensus CDS
      CCDS10997.1
      UniProtKB/Swiss-Prot
      Q53GN1, Q86VC3, Q96F76, Q9HC36, Q9NVQ5
      Related
      ENSP00000306080.4, ENST00000304478.9
      Conserved Domains (2) summary
      smart00967
      Location:125 → 191
      SpoU_sub_bind; RNA 2'-O ribose methyltransferase substrate binding
      cd18106
      Location:210 → 402
      SpoU-like_RNMTL1; SAM-dependent rRNA methylase related to RNMTL1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      782353..792509
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      668784..678768
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HC36.2 GenPept UniProtKB/Swiss-Prot:Q9HC36

    Gene LinkOut

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

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