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    NSUN6 NOP2/Sun RNA methyltransferase 6 [ Homo sapiens (human) ]

    Gene ID: 221078, updated on 27-Nov-2024

    Summary

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    Official Symbol
    NSUN6provided by HGNC
    Official Full Name
    NOP2/Sun RNA methyltransferase 6provided by HGNC
    Primary source
    HGNC:HGNC:23529
    See related
    Ensembl:ENSG00000241058 MIM:617199; AllianceGenome:HGNC:23529
    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
    MRT82; NOPD1; ARL5B-AS1; 4933414E04Rik
    Summary
    Enables tRNA (cytidine-5-)-methyltransferase activity and tRNA binding activity. Involved in tRNA C5-cytosine methylation. Located in cytoplasm. Implicated in autosomal recessive intellectual developmental disorder 82. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 4.8), liver (RPKM 4.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NSUN6 in Genome Data Viewer
    Location:
    10p12.31
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (18545561..18659327, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (18531853..18678450, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (18834490..18948167, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene calcium voltage-gated channel auxiliary subunit beta 2 Neighboring gene uncharacterized LOC107984213 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:18629448-18629653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3112 Neighboring gene uncharacterized LOC124902386 Neighboring gene uncharacterized LOC124902387 Neighboring gene NANOG hESC enhancer GRCh37_chr10:18841481-18841982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3116 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2184 Neighboring gene uncharacterized LOC105376440 Neighboring gene ARF like GTPase 5B Neighboring gene AIFM1 pseudogene 1

    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 RNA methyltransferase NSUN6 suppresses pancreatic cancer development by regulating cell proliferation. Yang R, et al. EBioMedicine, 2021 Jan. PMID 33418496, Free PMC Article
    2. Biallelic variants in NSUN6 cause an autosomal recessive neurodevelopmental disorder. Mattioli F, et al. Genet Med, 2023 Sep. PMID 37226891
    3. NSUN6 Regulates NM23-H1 Expression in an m5C Manner to Affect Epithelial-Mesenchymal Transition in Lung Cancer. Lu Z, et al. Med Princ Pract, 2024. PMID 38029727, Free PMC Article
    4. Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6. Selmi T, et al. Nucleic Acids Res, 2021 Jan 25. PMID 33330931, Free PMC Article
    5. NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs. Haag S, et al. RNA, 2015 Sep. PMID 26160102, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NSUN6 Regulates NM23-H1 Expression in an m5C Manner to Affect Epithelial-Mesenchymal Transition in Lung Cancer.
      Title: NSUN6 Regulates NM23-H1 Expression in an m5C Manner to Affect Epithelial-Mesenchymal Transition in Lung Cancer.
    2. Biallelic variants in NSUN6 cause an autosomal recessive neurodevelopmental disorder.
      Title: Biallelic variants in NSUN6 cause an autosomal recessive neurodevelopmental disorder.
    3. NSUN6, an RNA methyltransferase of 5-mC controls glioblastoma response to temozolomide (TMZ) via NELFB and RPS6KB2 interaction.
      Title: NSUN6, an RNA methyltransferase of 5-mC controls glioblastoma response to temozolomide (TMZ) via NELFB and RPS6KB2 interaction.
    4. The RNA methyltransferase NSUN6 suppresses pancreatic cancer development by regulating cell proliferation.
      Title: The RNA methyltransferase NSUN6 suppresses pancreatic cancer development by regulating cell proliferation.
    5. Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6.
      Title: Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6.
    6. The structures of NSun6, a human tRNA:m5C methyltransferase, in the apo form and in complex with a full-length tRNA substrate.
      Title: Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6.
    7. findings suggest that human NSun6 relies on a delicate network for RNA recognition, which involves both the primary sequence and tertiary structure of tRNA substrates.
      Title: Sequence-specific and Shape-selective RNA Recognition by the Human RNA 5-Methylcytosine Methyltransferase NSun6.
    8. Findings identified NSUN6 as a novel mammalian m5C tRNA methyltransferase and suggest that methylation of tRNAs by NSUN6 occurs during a late step of tRNA biogenesis, after the addition of the CCA tail and export of the tRNA from the nucleus.
      Title: NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: An integrative method for scoring candidate genes from association studies: application to warfarin dosing.
    10. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    Associated conditions

    Description Tests
    Intellectual developmental disorder, autosomal recessive 82
    MedGen: CN377626 OMIM: 620779 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    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)

    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

    • FLJ23743, DKFZp686G10106

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables tRNA (cytidine-5-)-methyltransferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables tRNA (cytidine-5-)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA C5-cytosine methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA modification IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA modification TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
    Names
    ARL5B antisense RNA 1
    NOL1/NOP2/Sun and PUA domain-containing protein 1
    NOL1/NOP2/Sun domain family, member 6
    NOP2/Sun RNA methyltransferase family member 6
    NOP2/Sun domain family, member 6
    nucleolar protein (NOL1/NOP2/sun) and PUA domains 1
    putative methyltransferase NSUN6

    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_001351115.2 → NP_001338044.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AA347409, BC035778, DB012566, HY169016
      Conserved Domains (2) summary
      smart00359
      Location:114 → 201
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:214 → 464
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    2. NM_001351116.2 → NP_001338045.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL600949, BC035778
      Conserved Domains (2) summary
      smart00359
      Location:103 → 190
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:203 → 453
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    3. NM_001351117.2 → NP_001338046.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform 4

      Status: VALIDATED

      Source sequence(s)
      BC035778, DB012566, HY169016
      Conserved Domains (2) summary
      smart00359
      Location:63 → 150
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:163 → 413
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    4. NM_001351118.2 → NP_001338047.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform 5

      Status: VALIDATED

      Source sequence(s)
      BC035778, BQ224447, HY169016
      Conserved Domains (1) summary
      COG0144
      Location:74 → 324
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    5. NM_182543.5 → NP_872349.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform 1

      See identical proteins and their annotated locations for NP_872349.1

      Status: VALIDATED

      Source sequence(s)
      BC035778, DB012566, HY169016
      Consensus CDS
      CCDS7130.1
      UniProtKB/Swiss-Prot
      B0YJ54, Q8TEA1
      Related
      ENSP00000366519.4, ENST00000377304.7
      Conserved Domains (2) summary
      smart00359
      Location:115 → 202
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:215 → 465
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      18545561..18659327 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024447884.2 → XP_024303652.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X4

      Conserved Domains (2) summary
      smart00359
      Location:103 → 190
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:203 → 453
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    2. XM_011519385.2 → XP_011517687.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X3

      See identical proteins and their annotated locations for XP_011517687.1

      Conserved Domains (2) summary
      smart00359
      Location:103 → 194
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:207 → 457
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    3. XM_011519386.3 → XP_011517688.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X3

      See identical proteins and their annotated locations for XP_011517688.1

      Conserved Domains (2) summary
      smart00359
      Location:103 → 194
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:207 → 457
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    4. XM_047424778.1 → XP_047280734.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X4

    5. XM_011519384.2 → XP_011517686.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X3

      See identical proteins and their annotated locations for XP_011517686.1

      Conserved Domains (2) summary
      smart00359
      Location:103 → 194
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:207 → 457
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    6. XM_047424779.1 → XP_047280735.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X5

    7. XM_017015907.3 → XP_016871396.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X3

      Conserved Domains (2) summary
      smart00359
      Location:103 → 194
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:207 → 457
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    8. XM_011519387.3 → XP_011517689.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X9

      Conserved Domains (2) summary
      smart00359
      Location:63 → 154
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:167 → 417
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    9. XM_011519383.2 → XP_011517685.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X2

      Conserved Domains (2) summary
      smart00359
      Location:114 → 205
      PUA; Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase
      COG0144
      Location:218 → 468
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    10. XM_047424777.1 → XP_047280733.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X1

    11. XM_047424781.1 → XP_047280737.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X10

    12. XM_047424783.1 → XP_047280739.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X11

    13. XM_017015912.3 → XP_016871401.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X11

      Conserved Domains (1) summary
      COG0144
      Location:78 → 328
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    14. XM_047424782.1 → XP_047280738.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X7

    15. XM_047424780.1 → XP_047280736.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X6

    16. XM_047424784.1 → XP_047280740.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      18531853..18678450 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365122.1 → XP_054221097.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X4

    2. XM_054365119.1 → XP_054221094.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X4

    3. XM_054365116.1 → XP_054221091.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X13

    4. XM_054365115.1 → XP_054221090.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X13

    5. XM_054365111.1 → XP_054221086.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X2

    6. XM_054365113.1 → XP_054221088.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X12

      UniProtKB/Swiss-Prot
      B0YJ54, Q8TEA1

    7. XM_054365114.1 → XP_054221089.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X12

      UniProtKB/Swiss-Prot
      B0YJ54, Q8TEA1

    8. XM_054365112.1 → XP_054221087.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X12

      UniProtKB/Swiss-Prot
      B0YJ54, Q8TEA1

    9. XM_054365108.1 → XP_054221083.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X1

    10. XM_054365109.1 → XP_054221084.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X1

    11. XM_054365110.1 → XP_054221085.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X1

    12. XM_054365118.1 → XP_054221093.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X4

    13. XM_054365121.1 → XP_054221096.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X4

    14. XM_054365120.1 → XP_054221095.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X4

    15. XM_054365117.1 → XP_054221092.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X3

    16. XM_054365123.1 → XP_054221098.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X5

    17. XM_054365125.1 → XP_054221100.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X14

    18. XM_054365124.1 → XP_054221099.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X14

    19. XM_054365127.1 → XP_054221102.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X7

    20. XM_054365126.1 → XP_054221101.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X6

    21. XM_054365128.1 → XP_054221103.1  tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TEA1.1 GenPept UniProtKB/Swiss-Prot:Q8TEA1

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