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    NSUN2 NOP2/Sun RNA methyltransferase 2 [ Homo sapiens (human) ]

    Gene ID: 54888, updated on 3-Nov-2024

    Summary

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    Official Symbol
    NSUN2provided by HGNC
    Official Full Name
    NOP2/Sun RNA methyltransferase 2provided by HGNC
    Primary source
    HGNC:HGNC:25994
    See related
    Ensembl:ENSG00000037474 MIM:610916; AllianceGenome:HGNC:25994
    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
    MISU; MRT5; SAKI; TRM4
    Summary
    This gene encodes a methyltransferase that catalyzes the methylation of cytosine to 5-methylcytosine (m5C) at position 34 of intron-containing tRNA(Leu)(CAA) precursors. This modification is necessary to stabilize the anticodon-codon pairing and correctly translate the mRNA. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Mar 2011]
    Expression
    Ubiquitous expression in lymph node (RPKM 14.3), appendix (RPKM 14.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NSUN2 in Genome Data Viewer
    Location:
    5p15.31
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (6599239..6633044, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (6529664..6563719, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (6599352..6633157, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374639 Neighboring gene ubiquitin conjugating enzyme E2 QL1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22334 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:6583428-6583589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15898 Neighboring gene long intergenic non-protein coding RNA 1018 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:6633253-6633764 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:6633765-6634276 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:6648951-6649644 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:6649645-6650336 Neighboring gene steroid 5 alpha-reductase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22335 Neighboring gene uncharacterized LOC124900934

    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 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. Whole exome sequencing identifies a splicing mutation in NSUN2 as a cause of a Dubowitz-like syndrome. Martinez FJ, et al. J Med Genet, 2012 Jun. PMID 22577224, Free PMC Article
    2. NSun2 promotes cell migration through methylating autotaxin mRNA. Xu X, et al. J Biol Chem, 2020 Dec 25. PMID 33093178, Free PMC Article
    3. N(6)-methyladenosine modification of circNSUN2 facilitates cytoplasmic export and stabilizes HMGA2 to promote colorectal liver metastasis. Chen RX, et al. Nat Commun, 2019 Oct 16. PMID 31619685, Free PMC Article
    4. Genomic gain of 5p15 leads to over-expression of Misu (NSUN2) in breast cancer. Frye M, et al. Cancer Lett, 2010 Mar 1. PMID 19740597
    5. Methylation by NSun2 represses the levels and function of microRNA 125b. Yuan S, et al. Mol Cell Biol, 2014 Oct 1. PMID 25047833, Free PMC Article

    See all (214) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NSUN2/YBX1 promotes the progression of breast cancer by enhancing HGH1 mRNA stability through m[5]C methylation.
      Title: NSUN2/YBX1 promotes the progression of breast cancer by enhancing HGH1 mRNA stability through m(5)C methylation.
    2. NSUN2 affects diabetic retinopathy progression by regulating MUC1 expression through RNA m[5]C methylation.
      Title: NSUN2 affects diabetic retinopathy progression by regulating MUC1 expression through RNA m(5)C methylation.
    3. 5-Methylcytosine transferase NSUN2 drives NRF2-mediated ferroptosis resistance in non-small cell lung cancer.
      Title: 5-Methylcytosine transferase NSUN2 drives NRF2-mediated ferroptosis resistance in non-small cell lung cancer.
    4. NSUN2 promotes lung adenocarcinoma progression through stabilizing PIK3R2 mRNA in an m[5]C-dependent manner.
      Title: NSUN2 promotes lung adenocarcinoma progression through stabilizing PIK3R2 mRNA in an m(5)C-dependent manner.
    5. NSUN2-Mediated m[5]C Methylation Impairs Endometrial Receptivity.
      Title: NSUN2-Mediated m(5)C Methylation Impairs Endometrial Receptivity.
    6. LncRNA HOST2 promotes NSUN2-mediated breast cancer progression via interaction with ELAVL1.
      Title: LncRNA HOST2 promotes NSUN2-mediated breast cancer progression via interaction with ELAVL1.
    7. NSUN2-mediated mRNA m[5]C Modification Regulates the Progression of Hepatocellular Carcinoma.
      Title: NSUN2-mediated mRNA m(5)C Modification Regulates the Progression of Hepatocellular Carcinoma.
    8. NSUN2-mediated m5C modification of HBV RNA positively regulates HBV replication.
      Title: NSUN2-mediated m5C modification of HBV RNA positively regulates HBV replication.
    9. NSUN2 is a glucose sensor suppressing cGAS/STING to maintain tumorigenesis and immunotherapy resistance.
      Title: NSUN2 is a glucose sensor suppressing cGAS/STING to maintain tumorigenesis and immunotherapy resistance.
    10. NSUN2-mediated m[5] C RNA methylation dictates retinoblastoma progression through promoting PFAS mRNA stability and expression.
      Title: NSUN2-mediated m(5) C RNA methylation dictates retinoblastoma progression through promoting PFAS mRNA stability and expression.
    Submit: New GeneRIF Correction See all GeneRIFs (57)

    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 disability, autosomal recessive 5
    MedGen: C1970199 OMIM: 611091 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag Interaction of HIV-1 Gag with NOP2/Sun RNA methyltransferase family, member 2 (NSUN2) is identified in a series of six affinity purification/mass spectrometry screens PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ20303

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mRNA (cytidine-5-)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tRNA (cytidine-5-)-methyltransferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables tRNA (cytidine-5-)-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tRNA (cytidine-5-)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in hair follicle maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in meiotic cell cycle checkpoint signaling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of mRNA export from nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of stem cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in spermatid development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA modification TAS
    Traceable Author Statement
    more info
    		  
    involved_in tRNA stabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatoid body IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in spindle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    RNA cytosine C(5)-methyltransferase NSUN2
    Names
    5-methycytoisine methyltransferase
    Myc-induced SUN-domain-containing protein
    NOL1/NOP2/Sun domain family, member 2
    NOP2/Sun RNA methyltransferase family member 2
    NOP2/Sun domain family, member 2
    mRNA cytosine C(5)-methyltransferase
    myc-induced SUN domain-containing protein
    substrate of AIM1/Aurora kinase B
    tRNA (cytosine(34)-C(5))-methyltransferase
    tRNA (cytosine-5-)-methyltransferase NSUN2
    tRNA cytosine C(5)-methyltransferase
    tRNA methyltransferase 4 homolog
    NP_001180384.1
    NP_060225.4
    XP_054208843.1

    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.

    Genomic

    1. NG_028215.1 RefSeqGene

      Range
      5317..39122
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001193455.2 → NP_001180384.1  RNA cytosine C(5)-methyltransferase NSUN2 isoform 2

      See identical proteins and their annotated locations for NP_001180384.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame coding exon in the 5' region compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
      Source sequence(s)
      AK298980, BC001041, BF000644, BG387061
      Consensus CDS
      CCDS54832.1
      UniProtKB/Swiss-Prot
      Q08J23
      Related
      ENSP00000420957.1, ENST00000506139.5
      Conserved Domains (1) summary
      COG0144
      Location:28 → 396
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    2. NM_017755.6 → NP_060225.4  RNA cytosine C(5)-methyltransferase NSUN2 isoform 1

      See identical proteins and their annotated locations for NP_060225.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB255451, BC001041, BF000644
      Consensus CDS
      CCDS3869.1
      UniProtKB/Swiss-Prot
      A8K529, B2RNR4, B3KP09, B4DQW2, G3V1R4, Q08J23, Q9BVN4, Q9H858, Q9NXD9
      Related
      ENSP00000264670.6, ENST00000264670.11
      Conserved Domains (1) summary
      COG0144
      Location:28 → 431
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    RNA

    1. NR_037947.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an internal exon compared to variant 1. This causes a frame-shift and premature translation termination, rendering this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB255451, BC001041
      Related
      ENST00000504374.5

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      6599239..6633044 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      6529664..6563719 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352868.1 → XP_054208843.1  RNA cytosine C(5)-methyltransferase NSUN2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q08J23.2 GenPept UniProtKB/Swiss-Prot:Q08J23

    Gene LinkOut

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

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