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Aliases for NSUN3 Gene

Aliases for NSUN3 Gene

  • NOP2/Sun RNA Methyltransferase 3 2 3
  • NOP2/Sun RNA Methyltransferase Family Member 3 2 3 5
  • TRNA (Cytosine(34)-C(5))-Methyltransferase, Mitochondrial 3 4
  • NOL1/NOP2/Sun Domain Family Member 3 3 4
  • NOL1/NOP2/Sun Domain Family, Member 3 2
  • Putative Methyltransferase NSUN3 3
  • EC 2.1.1.- 4
  • EC 2.1.1 56
  • 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 3) is a Protein Coding gene. Gene Ontology (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).

Additional gene information for NSUN3 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 NSUN3 Gene

Genomics for NSUN3 Gene

GeneHancer (GH) Regulatory Elements for NSUN3 Gene

Promoters and enhancers for NSUN3 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
GH03J094061 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 600.7 +0.2 221 3.6 CC2D1A ELF3 NKRF POLR2A CEBPG ZNF687 ZSCAN21 MAFK TFE3 ELF1 STX19 DHFR2 NSUN3
GH03J093979 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 20.5 -82.3 -82279 3 SP1 ELF3 NKRF POLR2A CSDE1 ZNF384 FOS CREM MLLT1 MTA1 PROS1 ARL13B RBBP4P2 NSUN3 WDR82P1 DHFR2 GC03M093988
GH03J094028 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 11.5 -35.0 -34979 2.4 CTBP1 DPF2 GATA3 ELF1 JUND ZBTB40 ZNF217 SMARCE1 STX19 NSUN3 DHFR2 HMGN1P7 ARL13B
GH03J094004 Enhancer 0.7 ENCODE 11.6 -58.5 -58499 0.6 CTCF ZNF24 RAD21 REST SP1 TRIM22 IRF2 KMT2B SMARCA5 TEAD1 NSUN3 DHFR2 HMGN1P7 ARL13B STX19
GH03J093989 Promoter 0.5 Ensembl 11.1 -73.4 -73380 0.4 GC03M093988 HMGN1P7 NSUN3 DHFR2 ARL13B STX19
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NSUN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NSUN3 gene promoter:
  • AML1a
  • AP-1
  • C/EBPalpha
  • FOXO1
  • FOXO1a
  • NF-kappaB
  • NF-kappaB1
  • NF-kappaB2
  • RORalpha1
  • S8

Genomic Locations for NSUN3 Gene

Genomic Locations for NSUN3 Gene
chr3:94,062,980-94,131,832
(GRCh38/hg38)
Size:
68,853 bases
Orientation:
Plus strand
chr3:93,781,760-93,847,389
(GRCh37/hg19)
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 isoforms=67
  • Modification sites at PhosphoSitePlus

Other Protein References for NSUN3 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for NSUN3 Gene

Gene Families for NSUN3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for NSUN3 Gene

Suggested Antigen Peptide Sequences for NSUN3 Gene

GenScript: Design optimal peptide antigens:
  • NOL1/NOP2/Sun domain family member 3 (NSUN3_HUMAN)

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 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).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=cytidine(34) in mitochondrial tRNA + S-adenosyl-L-methionine = 5-methylcytidine(34) in mitochondrial tRNA + H(+) + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:53076, Rhea:RHEA-COMP:13451, Rhea:RHEA-COMP:13453, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; Evidence={ECO:0000269 PubMed:27214402, ECO:0000269 PubMed:27356879, ECO:0000269 PubMed:27497299};.

Enzyme Numbers (IUBMB) for NSUN3 Gene

Phenotypes From GWAS Catalog 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 21873635
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
genes like me logo Genes that share phenotypes with NSUN3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NSUN3

Clone Products

  • Applied Biological Materials (abm): Clones for NSUN3 - Now 50% OFF >
  • * NSUN3 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * NSUN3 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear membrane (2)
  • Nucleoplasm (2)
See all subcellular structures

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 IDA,IEA 27497299
GO:0005762 mitochondrial large ribosomal subunit IBA 21873635
genes like me logo Genes that share ontologies with NSUN3: view

Pathways & Interactions for NSUN3 Gene

PathCards logo

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 tRNA wobble base cytosine methylation IDA 27214402
GO:0031167 rRNA methylation IBA 21873635
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) Additional Compounds for NSUN3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with NSUN3: view

Transcripts for NSUN3 Gene

mRNA/cDNA for NSUN3 Gene

Unigene Clusters for NSUN3 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NSUN3

Clone Products

  • Applied Biological Materials (abm): Clones for NSUN3 - Now 50% OFF >
  • * NSUN3 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * NSUN3 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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, 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

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 35 34
  • 99.41 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NSUN3 35 34
  • 91.2 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NSUN3 35 34
  • 88.82 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nsun3 17 35 34
  • 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 35 34
  • 68.59 (n)
OneToOne
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 35 34
  • 56.6 (n)
OneToOne
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)
Aminode:
Evolutionary constrained regions (ECRs) for NSUN3: view image

Paralogs for NSUN3 Gene

Paralogs for NSUN3 Gene

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

  • NSUN3_HUMAN
  • F8WF52_HUMAN
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 Variation AA Info Type
rs1000038209 -- 94,065,212(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000070825 -- 94,064,771(+) C/A/T genic_upstream_transcript_variant, intron_variant
rs1000074520 -- 94,101,771(+) A/G intron_variant
rs1000211876 -- 94,070,093(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000277127 -- 94,092,026(+) A/G 5_prime_UTR_variant, 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)

Additional Variant Information for NSUN3 Gene

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

SNP Genotyping and Copy Number Assay Products

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}.

Additional Disease Information for NSUN3

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

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 (Nature chemical biology 2016) 2 3 4 58
  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 (Nature communications 2016) 2 3 4 58
  3. NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. (PMID: 27497299) Haag S … Bohnsack MT (The EMBO journal 2016) 3 4 58
  4. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 45 58
  5. The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation. (PMID: 29845934) Faust TB … Frankel AD (eLife 2018) 3 58

Products for NSUN3 Gene

Sources for NSUN3 Gene

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