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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 58
  • EC 2.1.1.- 4
  • EC 2.1.1 58
  • 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 rRNA processing in the nucleus and cytosol and Gene Expression. 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

Regulatory Elements for NSUN4 Gene

Enhancers for NSUN4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H046338 1.4 ENCODE dbSUPER 51.4 +1.4 1372 5 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A MEF2D NSUN4 LRRC41 GPBP1L1 LURAP1 UQCRH EFCAB14-AS1 CYP4B1 RPL7AP16 FAAH PIR34500
GH01H046347 1 ENCODE 47.8 +7.9 7901 0 HDGF PKNOX1 ATF1 ARNT ARID4B SIN3A YBX1 ZNF143 ATF7 RUNX3 NSUN4 LRRC41 EFCAB14-AS1 GPBP1L1 UQCRH RPL7AP16 CYP4B1 LURAP1 GC01M046344 ENSG00000225779
GH01H046170 1.8 FANTOM5 Ensembl ENCODE dbSUPER 25.1 -166.8 -166849 5 HDGF PKNOX1 ATF1 SIN3A GLIS2 ATF7 YY2 REST SREBF1 MEF2D LRRC41 TOE1 NASP NSUN4 MUTYH TEX38 LURAP1 RPL7AP16 RPS15AP10 CCDC163
GH01H046369 1.1 Ensembl ENCODE 38.8 +29.9 29915 1 HDAC1 PKNOX1 KLF1 ARNT TAL1 BATF FOSL1 TCF12 ZNF766 CTBP1 NSUN4 ENSG00000225779 GC01M046344
GH01H046246 1.4 FANTOM5 ENCODE 28 -92.2 -92168 3 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 LRRC41 TOE1 GPBP1L1 EFCAB14-AS1 NSUN4 NASP MUTYH RPL7AP16 IPP RPS15AP10
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NSUN4 on UCSC Golden Path with GeneCards custom track

Promoters for NSUN4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000005950 523 1801 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A MEF2D

Genomic Location for NSUN4 Gene

Chromosome:
1
Start:
46,340,177 bp from pter
End:
46,365,152 bp from pter
Size:
24,976 bases
Orientation:
Plus strand

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 Lys37, posLast=215215, Lys240, and posLast=274274
  • Modification sites at PhosphoSitePlus

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for NSUN4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for NSUN4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

Primer Products

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 Sequence Context AA Info Type
rs1000083703 -- 46,357,908(+) CAAAT(G/T)ATTAT intron-variant
rs1000303679 -- 46,364,714(+) CACTG(C/G)TCACT nc-transcript-variant, utr-variant-3-prime
rs1000379367 -- 46,351,969(+) TTCCA(C/G)TCTCT intron-variant
rs1000536722 -- 46,357,236(+) GTGCA(A/G)TGGCA intron-variant
rs1000562071 -- 46,364,025(+) TAGGC(C/T)AGGCA nc-transcript-variant, utr-variant-3-prime

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

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

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)

Relevant External Links 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

Relevant External Links for NSUN4

Genetic Association Database (GAD)
NSUN4
Human Genome Epidemiology (HuGE) Navigator
NSUN4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NSUN4

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 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 60
  2. 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 60
  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 60
  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 45 60
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60

Products for NSUN4 Gene

Sources for NSUN4 Gene

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