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Aliases for NSUN4 Gene

Aliases for NSUN4 Gene

  • NOP2/Sun RNA Methyltransferase Family Member 4 2 3 5
  • Sperm Head And Tail Associated Protein 2 3
  • NOL1/NOP2/Sun Domain Family Member 4 3 4
  • NOP2/Sun Domain Family, Member 4 2 3
  • 5-Methylcytosine RRNA Methyltransferase NSUN4 3
  • NOL1/NOP2/Sun Domain Family, Member 4 2
  • Putative Methyltransferase NSUN4 3
  • EC 2.1.1.29 56
  • EC 2.1.1.- 4
  • EC 2.1.1 56
  • SHTAP 3

External Ids for NSUN4 Gene

Previous GeneCards Identifiers for NSUN4 Gene

  • GC01P046518
  • GC01P046578
  • GC01P046805
  • GC01P044939

Summaries for NSUN4 Gene

GeneCards Summary for NSUN4 Gene

NSUN4 (NOP2/Sun RNA Methyltransferase Family Member 4) is a Protein Coding gene. Among its related pathways are Gene Expression and rRNA processing in the mitochondrion. Gene Ontology (GO) annotations related to this gene include methyltransferase activity and small ribosomal subunit rRNA binding. An important paralog of this gene is NSUN3.

UniProtKB/Swiss-Prot for NSUN4 Gene

  • Involved in mitochondrial ribosome assembly. 5-methylcytosine rRNA methyltransferase that probably is involved in mitochondrial ribosome small subunit (SSU) maturation by methylation of mitochondrial 12S rRNA; the function is independent of MTERFD2/MTERF4 and assembled mitochondrial ribosome large subunit (LSU). Targeted to LSU by MTERFD2/MTERF4 and probably is involved in a final step in ribosome biogenesis to ensure that SSU and LSU are assembled. In vitro can methylate 16S rRNA of the LSU; the methylation is enhanced by MTERFD/MTERF4.

Additional gene information for NSUN4 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NSUN4 Gene

Genomics for NSUN4 Gene

GeneHancer (GH) Regulatory Elements for NSUN4 Gene

Promoters and enhancers for NSUN4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I046338 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 601.4 +1.4 1371 5.5 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC NSUN4 LRRC41 GPBP1L1 LURAP1 RPL7AP16 EFCAB14-AS1 UQCRH RPS15AP10 MOB3C PIK3R3
GH01I046393 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 38.5 +54.4 54396 1.7 ARNT ZFP64 ARID4B NEUROD1 SIN3A ZNF2 YY1 CBX5 KLF13 SP3 FAAH NSUN4 LRRC41 NASP FAAHP1
GH01I046246 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 28 -92.2 -92167 3.1 HDGF PKNOX1 SMAD1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 GC01M046246 RAD54L TOE1 LRRC41 GPBP1L1 EFCAB14-AS1 NSUN4 RPL7AP16 NASP MOB3C
GH01I045489 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 28.6 -849.3 -849268 2.2 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 TESK2 CCDC163 NSUN4 PRDX1 LRRC41 TOE1 IPP GPBP1L1 KIF2C ZSWIM5
GH01I046717 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 23.4 +378.6 378608 3.3 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 EFCAB14 PIR52630 LRRC41 EFCAB14-AS1 NSUN4 TEX38 LINC01389 CYP4B1 MOB3C NENFP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NSUN4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NSUN4 gene promoter:

Genomic Locations for NSUN4 Gene

Genomic Locations for NSUN4 Gene
chr1:46,340,177-46,365,152
(GRCh38/hg38)
Size:
24,976 bases
Orientation:
Plus strand
chr1:46,805,849-46,830,824
(GRCh37/hg19)

Genomic View for NSUN4 Gene

Genes around NSUN4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NSUN4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NSUN4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NSUN4 Gene

Proteins for NSUN4 Gene

  • Protein details for NSUN4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96CB9-NSUN4_HUMAN
    Recommended name:
    5-methylcytosine rRNA methyltransferase NSUN4
    Protein Accession:
    Q96CB9
    Secondary Accessions:
    • A8K6S6
    • B3KQ50
    • B4DHA4
    • Q5TDF7
    • Q96AN8
    • Q9HAJ8

    Protein attributes for NSUN4 Gene

    Size:
    384 amino acids
    Molecular mass:
    43089 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for NSUN4 Gene

    Alternative splice isoforms for NSUN4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NSUN4 Gene

Selected DME Specific Peptides for NSUN4 Gene

Q96CB9:
  • VYSTCSL
  • QFGDLWPSIR
  • CAAPGGK
  • EQKYGALVNNF
  • TYDRVLVDVPCTTDRHSL
  • AASLLPVLAL

Post-translational modifications for NSUN4 Gene

  • Ubiquitination at isoforms=237, Lys215, isoforms=3, 4240, and isoforms=3, 4274

Domains & Families for NSUN4 Gene

Gene Families for NSUN4 Gene

Graphical View of Domain Structure for InterPro Entry

Q96CB9

UniProtKB/Swiss-Prot:

NSUN4_HUMAN :
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family.
Family:
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family.
genes like me logo Genes that share domains with NSUN4: view

Function for NSUN4 Gene

Molecular function for NSUN4 Gene

UniProtKB/Swiss-Prot Function:
Involved in mitochondrial ribosome assembly. 5-methylcytosine rRNA methyltransferase that probably is involved in mitochondrial ribosome small subunit (SSU) maturation by methylation of mitochondrial 12S rRNA; the function is independent of MTERFD2/MTERF4 and assembled mitochondrial ribosome large subunit (LSU). Targeted to LSU by MTERFD2/MTERF4 and probably is involved in a final step in ribosome biogenesis to ensure that SSU and LSU are assembled. In vitro can methylate 16S rRNA of the LSU; the methylation is enhanced by MTERFD/MTERF4.

Enzyme Numbers (IUBMB) for NSUN4 Gene

Phenotypes From GWAS Catalog for NSUN4 Gene

Gene Ontology (GO) - Molecular Function for NSUN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21531335
GO:0008168 methyltransferase activity IDA 23022348
GO:0009383 rRNA (cytosine-C5-)-methyltransferase activity EXP 21531335
GO:0016740 transferase activity IEA --
GO:0019843 rRNA binding IEA --
genes like me logo Genes that share ontologies with NSUN4: view
genes like me logo Genes that share phenotypes with NSUN4: view

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NSUN4 Gene

Localization for NSUN4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NSUN4 Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NSUN4 gene
Compartment Confidence
mitochondrion 5
plasma membrane 1
peroxisome 1
nucleus 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for NSUN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005759 mitochondrial matrix TAS --
GO:0005762 mitochondrial large ribosomal subunit IDA 21531335
genes like me logo Genes that share ontologies with NSUN4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NSUN4 Gene

Pathways & Interactions for NSUN4 Gene

genes like me logo Genes that share pathways with NSUN4: view

Pathways by source for NSUN4 Gene

Gene Ontology (GO) - Biological Process for NSUN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing IEA --
GO:0031167 rRNA methylation TAS --
GO:0032259 methylation IEA --
GO:0042254 ribosome biogenesis IEA --
GO:0042256 mature ribosome assembly IEA --
genes like me logo Genes that share ontologies with NSUN4: view

No data available for SIGNOR curated interactions for NSUN4 Gene

Drugs & Compounds for NSUN4 Gene

(1) Additional Compounds for NSUN4 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
29908-03-0
genes like me logo Genes that share compounds with NSUN4: view

Transcripts for NSUN4 Gene

Unigene Clusters for NSUN4 Gene

NOP2/Sun domain family, member 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NSUN4 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c · 6d · 6e · 6f · 6g ^ 7a · 7b ^ 8a ·
SP1: - - - - - - - - - - - - -
SP2: - -
SP3: - - - -
SP4: - - - - - - - - - - - - - - -
SP5: - - - - - - - - - - - - - - -
SP6: - - - - - - - - - - - -
SP7: - - - - - - - - - -
SP8: - - - - - -
SP9: - - - - - -
SP10: -
SP11: - -
SP12: - - - - - - - -
SP13: - - -
SP14: - - -
SP15: -

ExUns: 8b ^ 9a · 9b ^ 10a · 10b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for NSUN4 Gene

GeneLoc Exon Structure for
NSUN4
ECgene alternative splicing isoforms for
NSUN4

Expression for NSUN4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NSUN4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NSUN4 Gene

This gene is overexpressed in Testis (x8.0).

Protein differential expression in normal tissues from HIPED for NSUN4 Gene

This gene is overexpressed in Heart (50.2) and Breast (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NSUN4 Gene



Protein tissue co-expression partners for NSUN4 Gene

NURSA nuclear receptor signaling pathways regulating expression of NSUN4 Gene:

NSUN4

SOURCE GeneReport for Unigene cluster for NSUN4 Gene:

Hs.163424

Evidence on tissue expression from TISSUES for NSUN4 Gene

  • Nervous system(4.3)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with NSUN4: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NSUN4 Gene

Orthologs for NSUN4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for NSUN4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NSUN4 33 34
  • 99.83 (n)
dog
(Canis familiaris)
Mammalia NSUN4 33 34
  • 89.05 (n)
cow
(Bos Taurus)
Mammalia NSUN4 33 34
  • 88.63 (n)
mouse
(Mus musculus)
Mammalia Nsun4 33 16 34
  • 87.11 (n)
rat
(Rattus norvegicus)
Mammalia Nsun4 33
  • 86.32 (n)
oppossum
(Monodelphis domestica)
Mammalia NSUN4 34
  • 68 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NSUN4 34
  • 53 (a)
OneToOne
chicken
(Gallus gallus)
Aves NSUN4 33 34
  • 64.46 (n)
lizard
(Anolis carolinensis)
Reptilia NSUN4 34
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nsun4 33
  • 62.54 (n)
Str.15258 33
zebrafish
(Danio rerio)
Actinopterygii nsun4 33 34
  • 56.39 (n)
Dr.5991 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008523 33
  • 50.94 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4749 33 34
  • 50.04 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_Y39G10AR.21 33
  • 49.85 (n)
Y39G10AR.21 34
  • 31 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NOP2 34
  • 12 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
OneToOne
Species where no ortholog for NSUN4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NSUN4 Gene

ENSEMBL:
Gene Tree for NSUN4 (if available)
TreeFam:
Gene Tree for NSUN4 (if available)

Paralogs for NSUN4 Gene

Paralogs for NSUN4 Gene

(1) SIMAP similar genes for NSUN4 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with NSUN4: view

Variants for NSUN4 Gene

Sequence variations from dbSNP and Humsavar for NSUN4 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000083703 -- 46,357,908(+) T/G intron_variant
rs1000303679 -- 46,364,714(+) G/C 3_prime_UTR_variant, non_coding_transcript_variant
rs1000379367 -- 46,351,969(+) G/C intron_variant
rs1000536722 -- 46,357,236(+) A/G intron_variant
rs1000562071 -- 46,364,025(+) T/C 3_prime_UTR_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for NSUN4 Gene

Variant ID Type Subtype PubMed ID
nsv829748 CNV loss 17160897
nsv546162 CNV loss 21841781
nsv470711 CNV gain 18288195
nsv159955 CNV deletion 16902084
nsv1113114 CNV deletion 24896259
esv3577837 CNV loss 25503493
esv2761743 CNV gain 21179565
esv22272 CNV loss 19812545
dgv258n54 CNV loss 21841781

Variation tolerance for NSUN4 Gene

Residual Variation Intolerance Score: 64.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.78; 96.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NSUN4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NSUN4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NSUN4 Gene

Disorders for NSUN4 Gene

Additional Disease Information for NSUN4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for NSUN4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NSUN4 Gene

Publications for NSUN4 Gene

  1. Structure of the essential MTERF4:NSUN4 protein complex reveals how an MTERF protein collaborates to facilitate rRNA modification. (PMID: 23022348) Yakubovskaya E … Garcia-Diaz M (Structure (London, England : 1993) 2012) 3 4 58
  2. Structure of the human MTERF4-NSUN4 protein complex that regulates mitochondrial ribosome biogenesis. (PMID: 22949673) Spåhr H … Hallberg BM (Proceedings of the National Academy of Sciences of the United States of America 2012) 3 4 58
  3. MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome. (PMID: 21531335) Cámara Y … Larsson NG (Cell metabolism 2011) 3 4 58
  4. 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. (PMID: 19086053) Gratacòs M … Psychiatric Genetics Network Group (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2009) 3 44 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for NSUN4 Gene

Sources for NSUN4 Gene

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