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

Gene ID: 221078, updated on 17-Jun-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 (cytosine-5-)-methyltransferase activity and tRNA binding activity. Involved in tRNA C5-cytosine methylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 4.8), liver (RPKM 4.1) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (18545561..18659327, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (18531853..18678450, complement)
105.20220307 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 ADP ribosylation factor 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. 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
  3. Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6. Liu RJ, et al. Nucleic Acids Res, 2017 Jun 20. PMID 28531330, Free PMC Article
  4. Sequence-specific and Shape-selective RNA Recognition by the Human RNA 5-Methylcytosine Methyltransferase NSun6. Long T, et al. J Biol Chem, 2016 Nov 11. PMID 27703015, 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 (25) 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)

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

  • 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_2023_10

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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