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METTL15 methyltransferase 15, mitochondrial 12S rRNA N4-cytidine [ Homo sapiens (human) ]

Gene ID: 196074, updated on 3-Apr-2024

Summary

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Official Symbol
METTL15provided by HGNC
Official Full Name
methyltransferase 15, mitochondrial 12S rRNA N4-cytidineprovided by HGNC
Primary source
HGNC:HGNC:26606
See related
Ensembl:ENSG00000169519 MIM:618711; AllianceGenome:HGNC:26606
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
METT5D1
Summary
Predicted to enable rRNA (cytosine-N4-)-methyltransferase activity. Predicted to be involved in rRNA base methylation. Predicted to be located in mitochondrial matrix. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 2.9), adrenal (RPKM 2.8) and 25 other tissues See more
Orthologs
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Genomic context

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See METTL15 in Genome Data Viewer
Location:
11p14.1
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (28108388..28532475)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (28248905..28667716)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (28129935..28355054)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902655 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:28128916-28129440 Neighboring gene kinesin family member 18A Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:28129441-28129964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4549 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:28131476-28131976 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:28161954-28163153 Neighboring gene microRNA 610 Neighboring gene MPRA-validated peak1236 silencer Neighboring gene ATP synthase membrane subunit g pseudogene 8 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:28314740-28314932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3212 Neighboring gene RN7SK pseudogene 158 Neighboring gene ribosomal protein S15a pseudogene 31 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:28533666-28534166 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:28542087-28543286 Neighboring gene microRNA 8068 Neighboring gene long intergenic non-protein coding RNA 2758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:28628021-28628558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:28628559-28629095 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:28649825-28650547 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:28758360-28758514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:28787885-28788386 Neighboring gene NANOG hESC enhancer GRCh37_chr11:28795368-28795892 Neighboring gene uncharacterized LOC105376604 Neighboring gene long intergenic non-protein coding RNA 2742

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 human mitochondrial 12S rRNA m(4)C methyltransferase METTL15 is required for mitochondrial function. Chen H, et al. J Biol Chem, 2020 Jun 19. PMID 32371392, Free PMC Article
  2. METTL15 interacts with the assembly intermediate of murine mitochondrial small ribosomal subunit to form m4C840 12S rRNA residue. Laptev I, et al. Nucleic Acids Res, 2020 Aug 20. PMID 32573735, Free PMC Article
  3. METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis. Van Haute L, et al. Nucleic Acids Res, 2019 Nov 4. PMID 31665743, Free PMC Article
  4. KCMF1 (potassium channel modulatory factor 1) Links RAD6 to UBR4 (ubiquitin N-recognin domain-containing E3 ligase 4) and lysosome-mediated degradation. Hong JH, et al. Mol Cell Proteomics, 2015 Mar. PMID 25582440, Free PMC Article
  5. mTOR Inhibition via Rapamycin Treatment Partially Reverts the Deficit in Energy Metabolism Caused by FH Loss in RPE Cells. Merle DA, et al. Antioxidants (Basel), 2021 Dec 3. PMID 34943047, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circular RNA METTL15/miR-374a-5p/ESCO2 axis induces colorectal cancer development.
    Title: Circular RNA METTL15/miR-374a-5p/ESCO2 axis induces colorectal cancer development.
  2. The human mitochondrial 12S rRNA m(4)C methyltransferase METTL15 is required for mitochondrial function.
    Title: The human mitochondrial 12S rRNA m(4)C methyltransferase METTL15 is required for mitochondrial function.
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
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ33979

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables rRNA (cytosine-N4-)-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables rRNA (cytosine-N4-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in rRNA base methylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in rRNA base methylation IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in mitochondrial matrix IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
12S rRNA N4-methylcytidine (m4C) methyltransferase
Names
12S rRNA m4C methyltransferase
methyltransferase 5 domain containing 1
methyltransferase 5 domain-containing protein 1
methyltransferase like 15
methyltransferase-like protein 15
probable S-adenosyl-L-methionine-dependent methyltransferase METT5D1
probable methyltransferase-like protein 15
putative S-adenosyl-L-methionine-dependent methyltransferase METT5D1
NP_001107000.1
NP_001284704.1
NP_689849.2
XP_011518242.1
XP_011518243.1
XP_047282471.1
XP_047282472.1
XP_047282473.1
XP_047282474.1
XP_054223915.1
XP_054223916.1
XP_054223917.1
XP_054223918.1
XP_054223919.1
XP_054223920.1
XP_054223921.1
XP_054223922.1
XP_054223923.1

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_001113528.2 → NP_001107000.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform 1

    See identical proteins and their annotated locations for NP_001107000.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC087376, AK091298, AL832668, DB327106, DB458698
    Consensus CDS
    CCDS44559.1
    UniProtKB/Swiss-Prot
    A6NJ78, A8MRS5, B7WNU2, Q3MHD3, Q8N601, Q8NBA7
    Related
    ENSP00000384369.3, ENST00000407364.8
    Conserved Domains (2) summary
    COG0286
    Location:81 → 128
    HsdM; Type I restriction-modification system, DNA methylase subunit [Defense mechanisms]
    PRK00050
    Location:72 → 407
    PRK00050; 16S rRNA m(4)C1402 methyltranserfase; Provisional

  2. NM_001297775.2 → NP_001284704.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform 3

    See identical proteins and their annotated locations for NP_001284704.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC023206, AC087376, AC104978, BC066900, DA800481
    Consensus CDS
    CCDS73269.1
    UniProtKB/Swiss-Prot
    P0C7V9
    Related
    ENSP00000385507.3, ENST00000406787.7
    Conserved Domains (2) summary
    COG0286
    Location:81 → 128
    HsdM; Type I restriction-modification system, DNA methylase subunit [Defense mechanisms]
    cl17173
    Location:67 → 197
    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_152636.3 → NP_689849.2  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform 2

    See identical proteins and their annotated locations for NP_689849.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has multiple differences in the 3' coding region, compared to variant 1, one of which results in a premature termination codon. The encoded protein (isoform 2) has a novel shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AC087376, AK091298, AL832668, DB327106, DB458698
    Consensus CDS
    CCDS31450.1
    UniProtKB/TrEMBL
    A0A0U1RR76
    Related
    ENSP00000307251.6, ENST00000303459.10
    Conserved Domains (2) summary
    COG0286
    Location:81 → 128
    HsdM; Type I restriction-modification system, DNA methylase subunit [Defense mechanisms]
    cl17173
    Location:72 → 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). ...

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    28108388..28532475
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011519940.4 → XP_011518242.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X3

    UniProtKB/Swiss-Prot
    P0C7V9
    Conserved Domains (2) summary
    COG0286
    Location:81 → 128
    HsdM; Type I restriction-modification system, DNA methylase subunit [Defense mechanisms]
    cl17173
    Location:67 → 203
    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. XM_011519941.3 → XP_011518243.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X4

    Conserved Domains (2) summary
    COG0286
    Location:81 → 128
    HsdM; Type I restriction-modification system, DNA methylase subunit [Defense mechanisms]
    cl17173
    Location:72 → 129
    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. XM_047426516.1 → XP_047282472.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X1

  4. XM_047426515.1 → XP_047282471.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X1

  5. XM_047426518.1 → XP_047282474.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X2

  6. XM_047426517.1 → XP_047282473.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X2

RNA

  1. XR_007062458.1 RNA Sequence

  2. XR_930849.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    28248905..28667716
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367940.1 → XP_054223915.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X5

  2. XM_054367948.1 → XP_054223923.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X4

  3. XM_054367941.1 → XP_054223916.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X5

  4. XM_054367947.1 → XP_054223922.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X3

  5. XM_054367944.1 → XP_054223919.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X6

  6. XM_054367943.1 → XP_054223918.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X1

  7. XM_054367942.1 → XP_054223917.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X1

  8. XM_054367946.1 → XP_054223921.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X2

  9. XM_054367945.1 → XP_054223920.1  12S rRNA N4-methylcytidine (m4C) methyltransferase isoform X2

RNA

  1. XR_008488356.1 RNA Sequence

  2. XR_008488357.1 RNA Sequence

  3. XR_008488354.1 RNA Sequence

  4. XR_008488353.1 RNA Sequence

  5. XR_008488355.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A6NJ78.1 GenPept UniProtKB/Swiss-Prot:A6NJ78

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