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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
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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

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