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    NSUN4 NOP2/Sun RNA methyltransferase 4 [ Homo sapiens (human) ]

    Gene ID: 387338, updated on 10-Dec-2024

    Summary

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    Official Symbol
    NSUN4provided by HGNC
    Official Full Name
    NOP2/Sun RNA methyltransferase 4provided by HGNC
    Primary source
    HGNC:HGNC:31802
    See related
    Ensembl:ENSG00000117481 MIM:615394; AllianceGenome:HGNC:31802
    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
    SHTAP
    Summary
    Enables rRNA (cytosine-C5-)-methyltransferase activity. Involved in rRNA methylation. Located in mitochondrion. Part of mitochondrial large ribosomal subunit. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in testis (RPKM 13.3), thyroid (RPKM 4.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NSUN4 in Genome Data Viewer
    Location:
    1p33
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (46340807..46385199)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (46218025..46262412)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (46806479..46850871)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RAD54 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46750956-46751580 Neighboring gene leucine rich repeat containing 41 Neighboring gene NANOG hESC enhancer GRCh37_chr1:46764257-46764758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46766628-46767210 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46767211-46767793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 844 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:46768959-46769542 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:46769543-46770124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 998 Neighboring gene ubiquinol-cytochrome c reductase hinge protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46794429-46795157 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:46795158-46795887 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46795888-46796616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46797347-46798076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 845 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:46804880-46805679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1000 Neighboring gene MPRA-validated peak205 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr1:46837735-46837899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:46859877-46860390 Neighboring gene fatty acid amide hydrolase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1001 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:46898417-46899137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1003 Neighboring gene fatty acid amide hydrolase pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. m5C RNA methyltransferase-related gene NSUN4 stimulates malignant progression of hepatocellular carcinoma and can be a prognostic marker. Cui M, et al. Cancer Biomark, 2022. PMID 34744073
    2. NSUN4 mediated RNA 5-methylcytosine promotes the malignant progression of glioma through improving the CDC42 mRNA stabilization. Zhao Z, et al. Cancer Lett, 2024 Aug 10. PMID 38876383
    3. Structure of the human MTERF4-NSUN4 protein complex that regulates mitochondrial ribosome biogenesis. Spåhr H, et al. Proc Natl Acad Sci U S A, 2012 Sep 18. PMID 22949673, Free PMC Article
    4. Global changes in DNA methylation and hydroxymethylation in Alzheimer's disease human brain. Coppieters N, et al. Neurobiol Aging, 2014 Jun. PMID 24387984
    5. RNA 5-methylcytosine marks mitochondrial double-stranded RNAs for degradation and cytosolic release. Kim S, et al. Mol Cell, 2024 Aug 8. PMID 39019044,

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NSUN4 mediated RNA 5-methylcytosine promotes the malignant progression of glioma through improving the CDC42 mRNA stabilization.
      Title: NSUN4 mediated RNA 5-methylcytosine promotes the malignant progression of glioma through improving the CDC42 mRNA stabilization.
    2. m5C RNA methyltransferase-related gene NSUN4 stimulates malignant progression of hepatocellular carcinoma and can be a prognostic marker.
      Title: m5C RNA methyltransferase-related gene NSUN4 stimulates malignant progression of hepatocellular carcinoma and can be a prognostic marker.
    3. It involves in epigenetic changes during the progression of Alzheimer disease pathology.
      Title: Global changes in DNA methylation and hydroxymethylation in Alzheimer's disease human brain.
    4. analysis of the 3D crystal structure of the human MTERF4-NSUN4 complex
      Title: Structure of the human MTERF4-NSUN4 protein complex that regulates mitochondrial ribosome biogenesis.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment.
    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

    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

    Potential readthrough

    Included gene: FAAH

    Homology

    Clone Names

    • FLJ18051, MGC22960

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables mRNA (cytidine-5-)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables rRNA (cytosine-C5-)-methyltransferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables rRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables rRNA methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA (cytidine-5-)-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mitochondrial RNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitochondrial RNA modification IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in rRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in rRNA methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in rRNA methylation TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    part_of mitochondrial large ribosomal subunit IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of mitochondrial large ribosomal subunit IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 

    General protein information

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    Preferred Names
    5-methylcytosine rRNA methyltransferase NSUN4
    Names
    5-methylcytosine tRNA methyltransferase NSUN4
    NOL1/NOP2/Sun domain family member 4
    NOP2/Sun RNA methyltransferase family member 4
    NOP2/Sun domain family, member 4
    putative methyltransferase NSUN4
    sperm head and tail associated protein
    NP_001243056.1
    NP_001243057.1
    NP_001374194.1
    NP_001374195.1
    NP_001374196.1
    NP_001374197.1
    NP_001374198.1
    NP_001374199.1
    NP_001374200.1
    NP_001374201.1
    NP_950245.2

    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_001256127.3 → NP_001243056.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform b

      See identical proteins and their annotated locations for NP_001243056.1

      Status: VALIDATED

      Source sequence(s)
      AL122001
      Consensus CDS
      CCDS57996.1
      UniProtKB/TrEMBL
      A8K8I8
      Related
      ENSP00000437758.1, ENST00000537428.2
      Conserved Domains (1) summary
      COG0144
      Location:106 → 333
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    2. NM_001256128.3 → NP_001243057.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform b

      See identical proteins and their annotated locations for NP_001243057.1

      Status: VALIDATED

      Source sequence(s)
      AL122001
      Consensus CDS
      CCDS57996.1
      UniProtKB/TrEMBL
      A8K8I8
      Conserved Domains (1) summary
      COG0144
      Location:106 → 333
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    3. NM_001387265.1 → NP_001374194.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform c

      Status: VALIDATED

      Source sequence(s)
      AL122001
      UniProtKB/TrEMBL
      A8K8I8
      Conserved Domains (1) summary
      COG0144
      Location:155 → 381
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    4. NM_001387266.1 → NP_001374195.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform d

      Status: VALIDATED

      Source sequence(s)
      AL122001
      Conserved Domains (1) summary
      COG0144
      Location:155 → 326
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    5. NM_001387267.1 → NP_001374196.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform e

      Status: VALIDATED

      Source sequence(s)
      AL122001
      UniProtKB/TrEMBL
      A8K8I8
      Conserved Domains (1) summary
      COG0144
      Location:3 → 358
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    6. NM_001387268.1 → NP_001374197.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform f

      Status: VALIDATED

      Source sequence(s)
      AL122001
      UniProtKB/TrEMBL
      A8K8I8
      Conserved Domains (1) summary
      COG0144
      Location:155 → 326
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    7. NM_001387269.1 → NP_001374198.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform g

      Status: VALIDATED

      Source sequence(s)
      AL122001
      UniProtKB/TrEMBL
      A8K8I8
      Conserved Domains (1) summary
      COG0144
      Location:155 → 326
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    8. NM_001387270.1 → NP_001374199.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform h

      Status: VALIDATED

      Source sequence(s)
      AL122001
      Conserved Domains (1) summary
      COG0144
      Location:155 → 259
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    9. NM_001387271.1 → NP_001374200.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform i

      Status: VALIDATED

      Source sequence(s)
      AL122001
      Conserved Domains (1) summary
      COG0144
      Location:155 → 252
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    10. NM_001387272.1 → NP_001374201.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform j

      Status: VALIDATED

      Source sequence(s)
      AL122001
      Conserved Domains (1) summary
      COG0144
      Location:155 → 259
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    11. NM_199044.4 → NP_950245.2  5-methylcytosine rRNA methyltransferase NSUN4 isoform a

      See identical proteins and their annotated locations for NP_950245.2

      Status: VALIDATED

      Source sequence(s)
      AL122001
      Consensus CDS
      CCDS534.1
      UniProtKB/Swiss-Prot
      A8K6S6, B3KQ50, B4DHA4, Q5TDF7, Q96AN8, Q96CB9, Q9HAJ8
      UniProtKB/TrEMBL
      A8K8I8
      Related
      ENSP00000419740.1, ENST00000474844.6
      Conserved Domains (1) summary
      COG0144
      Location:155 → 382
      RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

    RNA

    1. NR_045789.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001

    2. NR_045790.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001
      Related
      ENST00000307089.7

    3. NR_045791.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001

    4. NR_170617.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001

    5. NR_170618.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001

    6. NR_170619.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001

    7. NR_170620.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001

    8. NR_170621.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001

    9. NR_170622.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001

    10. NR_170623.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001

    11. NR_170624.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL122001

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      46340807..46385199
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      46218025..46262412
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96CB9.2 GenPept UniProtKB/Swiss-Prot:Q96CB9

    Gene LinkOut

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

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