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

Gene ID: 387338, updated on 18-Nov-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, Nov 2024]
Expression
Broad expression in testis (RPKM 13.3), thyroid (RPKM 4.5) and 25 other tissues See more
Orthologs
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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: 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. 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 Variation Viewer (GRCh37.p13)

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

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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