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Aliases for NSUN3 Gene

Aliases for NSUN3 Gene

  • NOP2/Sun RNA Methyltransferase Family Member 3 2 3 5
  • NOL1/NOP2/Sun Domain Family Member 3 3 4
  • TRNA (Cytosine(34)-C(5))-Methyltransferase, Mitochondrial 3
  • NOL1/NOP2/Sun Domain Family, Member 3 2
  • NOP2/Sun Domain Family, Member 3 2
  • Putative Methyltransferase NSUN3 3
  • EC 2.1.1.- 4
  • EC 2.1.1 61
  • MSTP077 3
  • MST077 3

External Ids for NSUN3 Gene

Previous GeneCards Identifiers for NSUN3 Gene

  • GC03P095264
  • GC03P093781
  • GC03P091144

Summaries for NSUN3 Gene

GeneCards Summary for NSUN3 Gene

NSUN3 (NOP2/Sun RNA Methyltransferase Family Member 3) is a Protein Coding gene. GO annotations related to this gene include RNA binding and methyltransferase activity. An important paralog of this gene is NSUN4.

UniProtKB/Swiss-Prot for NSUN3 Gene

  • Mitochondrial tRNA methyltransferase that mediates methylation of cytosine to 5-methylcytosine (m5C) at position 34 of mt-tRNA(Met) (PubMed:27497299, PubMed:27214402, PubMed:27356879). mt-tRNA(Met) methylation at cytosine(34) takes place at the wobble position of the anticodon and initiates the formation of 5-formylcytosine (f(5)c) at this position (PubMed:27497299, PubMed:27214402, PubMed:27356879). mt-tRNA(Met) containing the f(5)c modification at the wobble position enables recognition of the AUA codon in addition to the AUG codon, expanding codon recognition in mitochondrial translation (PubMed:27497299, PubMed:27356879).

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NSUN3 Gene

Genomics for NSUN3 Gene

Regulatory Elements for NSUN3 Gene

Enhancers for NSUN3 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
GH03G094004 1 Ensembl ENCODE 11.5 -58.4 -58422 0.6 CTCF ZNF654 IRF2 TEAD1 TRIM22 REST RAD21 YY1 RFX5 TEAD3 DHFR2 NSUN3 HMGN1P7 STX19
GH03G093979 1 ENCODE 10.6 -82.3 -82252 2.5 HDGF PKNOX1 ATF1 ARID4B SIN3A FEZF1 DMAP1 BRCA1 ZNF2 ZNF48 DHFR2 NSUN3 ARL13B GC03M093988
GH03G094061 1.1 ENCODE 0.7 +0.4 433 2.9 HDGF CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 YY1 CBX5 NFYC REST STX19 DHFR2 NSUN3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NSUN3 on UCSC Golden Path with GeneCards custom track

Promoters for NSUN3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000155264 -16 1801 HDGF CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 YY1 CBX5 NFYC REST

Genomic Location for NSUN3 Gene

Chromosome:
3
Start:
94,062,916 bp from pter
End:
94,128,545 bp from pter
Size:
65,630 bases
Orientation:
Plus strand

Genomic View for NSUN3 Gene

Genes around NSUN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NSUN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NSUN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NSUN3 Gene

Proteins for NSUN3 Gene

  • Protein details for NSUN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H649-NSUN3_HUMAN
    Recommended name:
    tRNA (cytosine(34)-C(5))-methyltransferase, mitochondrial
    Protein Accession:
    Q9H649
    Secondary Accessions:
    • Q6PG41
    • Q8IXG9
    • Q9H6M2

    Protein attributes for NSUN3 Gene

    Size:
    340 amino acids
    Molecular mass:
    38244 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAN76512.1; Type=Miscellaneous discrepancy; Note=Chimera.; Evidence={ECO:0000305}; Sequence=AAQ13600.1; Type=Frameshift; Positions=98; Evidence={ECO:0000305}; Sequence=BAB15234.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for NSUN3 Gene

Selected DME Specific Peptides for NSUN3 Gene

Q9H649:
  • LVYSTCTL
  • CAAPGGK
  • AASLLPVLAL
  • DKVLVDAPCSNDRSWL

Post-translational modifications for NSUN3 Gene

  • Ubiquitination at Lys67
  • Modification sites at PhosphoSitePlus

Other Protein References for NSUN3 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for NSUN3 Gene

Gene Families for NSUN3 Gene

Suggested Antigen Peptide Sequences for NSUN3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H649

UniProtKB/Swiss-Prot:

NSUN3_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 NSUN3: view

Function for NSUN3 Gene

Molecular function for NSUN3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + cytosine(34) in mitochondrial tRNA(Met) = S-adenosyl-L-homocysteine + 5-methylcytosine(34) in mitochondrial tRNA(Met).
UniProtKB/Swiss-Prot Function:
Mitochondrial tRNA methyltransferase that mediates methylation of cytosine to 5-methylcytosine (m5C) at position 34 of mt-tRNA(Met) (PubMed:27497299, PubMed:27214402, PubMed:27356879). mt-tRNA(Met) methylation at cytosine(34) takes place at the wobble position of the anticodon and initiates the formation of 5-formylcytosine (f(5)c) at this position (PubMed:27497299, PubMed:27214402, PubMed:27356879). mt-tRNA(Met) containing the f(5)c modification at the wobble position enables recognition of the AUA codon in addition to the AUG codon, expanding codon recognition in mitochondrial translation (PubMed:27497299, PubMed:27356879).

Enzyme Numbers (IUBMB) for NSUN3 Gene

Gene Ontology (GO) - Molecular Function for NSUN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000049 tRNA binding IEA --
GO:0003723 RNA binding IEA --
GO:0008168 methyltransferase activity IBA --
GO:0016428 tRNA (cytosine-5-)-methyltransferase activity IDA 27214402
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with NSUN3: view

Phenotypes for NSUN3 Gene

genes like me logo Genes that share phenotypes with NSUN3: view

Animal Model Products

CRISPR Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NSUN3 Gene

Localization for NSUN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NSUN3 Gene

Mitochondrion matrix.

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 NSUN3 gene
Compartment Confidence
mitochondrion 5
nucleus 2
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for NSUN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA,IDA 27214402
GO:0005759 mitochondrial matrix IEA,IDA 27497299
GO:0005762 mitochondrial large ribosomal subunit IBA --
genes like me logo Genes that share ontologies with NSUN3: view

Pathways & Interactions for NSUN3 Gene

SuperPathways for NSUN3 Gene

No Data Available

Interacting Proteins for NSUN3 Gene

Gene Ontology (GO) - Biological Process for NSUN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002127 wobble base cytosine methylation IDA 27214402
GO:0031167 rRNA methylation IBA --
GO:0032259 methylation IEA --
GO:0070129 regulation of mitochondrial translation IMP 27356879
genes like me logo Genes that share ontologies with NSUN3: view

No data available for Pathways by source and SIGNOR curated interactions for NSUN3 Gene

Drugs & Compounds for NSUN3 Gene

(1) Drugs for NSUN3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-Adenosylmethionine Approved Nutra 0
genes like me logo Genes that share compounds with NSUN3: view

Transcripts for NSUN3 Gene

Unigene Clusters for NSUN3 Gene

NOP2/Sun domain family, member 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NSUN3 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7
SP1: - -
SP2: -
SP3:

Relevant External Links for NSUN3 Gene

GeneLoc Exon Structure for
NSUN3
ECgene alternative splicing isoforms for
NSUN3

Expression for NSUN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NSUN3 Gene

Protein differential expression in normal tissues from HIPED for NSUN3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (38.6), Cervix (23.2), and Serum (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NSUN3 Gene



Protein tissue co-expression partners for NSUN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of NSUN3 Gene:

NSUN3

SOURCE GeneReport for Unigene cluster for NSUN3 Gene:

Hs.448003

Evidence on tissue expression from TISSUES for NSUN3 Gene

  • Intestine(4.2)
  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with NSUN3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NSUN3 Gene

Orthologs for NSUN3 Gene

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

Orthologs for NSUN3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NSUN3 34 35
  • 99.41 (n)
cow
(Bos Taurus)
Mammalia NSUN3 34 35
  • 91.2 (n)
dog
(Canis familiaris)
Mammalia NSUN3 34 35
  • 88.82 (n)
mouse
(Mus musculus)
Mammalia Nsun3 34 16 35
  • 84.17 (n)
rat
(Rattus norvegicus)
Mammalia Nsun3 34
  • 82.16 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 78 (a)
OneToMany
-- 35
  • 76 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia NSUN3 35
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves NSUN3 34 35
  • 68.59 (n)
lizard
(Anolis carolinensis)
Reptilia NSUN3 35
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nsun3 34
  • 66.04 (n)
zebrafish
(Danio rerio)
Actinopterygii nsun3 34 35
  • 56.6 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NOP2 35
  • 12 (a)
OneToMany
Species where no ortholog for NSUN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for NSUN3 Gene

ENSEMBL:
Gene Tree for NSUN3 (if available)
TreeFam:
Gene Tree for NSUN3 (if available)

Paralogs for NSUN3 Gene

Paralogs for NSUN3 Gene

(1) SIMAP similar genes for NSUN3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with NSUN3: view

Variants for NSUN3 Gene

Sequence variations from dbSNP and Humsavar for NSUN3 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1000038209 -- 94,065,212(+) CATGC(C/T)GTCTA intron-variant, upstream-variant-2KB
rs1000070825 -- 94,064,771(+) TGTTA(C/T)GCCTT intron-variant, upstream-variant-2KB
rs1000074520 -- 94,101,771(+) ATACT(A/G)TATAA intron-variant
rs1000211876 -- 94,070,093(+) CAGTA(A/G)ATAGA intron-variant
rs1000277127 -- 94,092,026(+) GTGCC(A/G)GGTGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for NSUN3 Gene

Variant ID Type Subtype PubMed ID
esv2678302 CNV deletion 23128226
esv3597014 CNV loss 21293372
esv3597015 CNV loss 21293372
esv3893746 CNV loss 25118596
nsv963341 CNV duplication 23825009

Variation tolerance for NSUN3 Gene

Residual Variation Intolerance Score: 27.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.31; 41.22% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NSUN3 Gene

Human Gene Mutation Database (HGMD)
NSUN3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NSUN3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NSUN3 Gene

Disorders for NSUN3 Gene

UniProtKB/Swiss-Prot

NSUN3_HUMAN
  • Note=Mitochondrial complex deficiency (PubMed:27356879). A disorder of the mitochondrial respiratory chain resulting in a highly variable phenotype depending on which tissues are affected (PubMed:27356879). Clinical features include combined developmental disability, microcephaly, failure to thrive, recurrent increased lactate levels in plasma, muscular weakness, proximal accentuated, external ophthalmoplegia and convergence nystagmus (PubMed:27356879). Defects are probably caused by deficient methylation and formylation of mt-tRNA(Met) wobble cytosine (PubMed:27356879). The disease may be caused by mutations affecting the gene represented in this entry. {ECO:0000269 PubMed:27356879}.

Relevant External Links for NSUN3

Genetic Association Database (GAD)
NSUN3
Human Genome Epidemiology (HuGE) Navigator
NSUN3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NSUN3

No disorders were found for NSUN3 Gene.

No data available for MalaCards and Genatlas for NSUN3 Gene

Publications for NSUN3 Gene

  1. NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNA(Met). (PMID: 27214402) Nakano S. … Suzuki T. (Nat. Chem. Biol. 2016) 3 4 64
  2. Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3. (PMID: 27356879) Van Haute L. … Minczuk M. (Nat. Commun. 2016) 3 4 64
  3. NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. (PMID: 27497299) Haag S. … Bohnsack M.T. (EMBO J. 2016) 3 4 64
  4. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G. … Wijmenga C. (Gut 2009) 3 46 64
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 2 3 64

Products for NSUN3 Gene

Sources for NSUN3 Gene

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