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

    Gene ID: 196074, updated on 27-Nov-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
    Enables rRNA (cytosine-N4-)-methyltransferase activity. Involved in rRNA base methylation. Is active in mitochondrial matrix. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 2.9), adrenal (RPKM 2.8) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (28108388..28532475)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (28248905..28667716)
    RS_2024_09 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 catalytic activity of methyltransferase METTL15 is dispensable for its role in mitochondrial ribosome biogenesis. Mutti CD, et al. RNA Biol, 2024 Jan. PMID 38913872, Free PMC Article
    2. 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
    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. 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
    5. Circular RNA METTL15/miR-374a-5p/ESCO2 axis induces colorectal cancer development. Guo F, et al. Acta Biochim Pol, 2023 Sep 16. PMID 37715994

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The catalytic activity of methyltransferase METTL15 is dispensable for its role in mitochondrial ribosome biogenesis.
      Title: The catalytic activity of methyltransferase METTL15 is dispensable for its role in mitochondrial ribosome biogenesis.
    2. 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.
    3. 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)

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 
    located_in mitochondrial matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP 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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    NEW Try the new Transcript table

    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

      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

      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

      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_2024_08

    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

    Gene LinkOut

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

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