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Aliases for NUDT16 Gene

Aliases for NUDT16 Gene

  • Nudix (Nucleoside Diphosphate Linked Moiety X)-Type Motif 16 2 3
  • Nucleoside Diphosphate-Linked Moiety X Motif 16 3 4
  • Inosine Diphosphate Phosphatase 3 4
  • U8 SnoRNA-Binding Protein H29K 3 4
  • M7GpppN-MRNA Hydrolase 3 4
  • IDP Phosphatase 3 4
  • Nudix Motif 16 3 4
  • IDPase 3 4
  • U8 SnoRNA-Decapping Enzyme 3
  • EC 3.6.1.62 4
  • EC 3.6.1.- 4
  • EC 3.6.1 63

External Ids for NUDT16 Gene

Previous GeneCards Identifiers for NUDT16 Gene

  • GC03P132584
  • GC03P131100
  • GC03P128485

Summaries for NUDT16 Gene

GeneCards Summary for NUDT16 Gene

NUDT16 (Nudix (Nucleoside Diphosphate Linked Moiety X)-Type Motif 16) is a Protein Coding gene. Among its related pathways are Metabolism and Purine metabolism (REACTOME). GO annotations related to this gene include protein homodimerization activity and magnesium ion binding. An important paralog of this gene is NUDT16L1.

UniProtKB/Swiss-Prot for NUDT16 Gene

  • RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal-dependent manner. Part of the U8 snoRNP complex that is required for the accumulation of mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G and/or m227G caps from U8 snoRNA and leaves a 5monophosphate on the RNA. Catalyzes also the cleavage of the cap structure on mRNAs. Does not hydrolyze cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with less efficiencies. Has broad substrate specificity with manganese or cobalt as cofactor and can act on various RNA species. Binds to the U8 snoRNA; metal is not required for RNA-binding. May play a role in the regulation of snoRNAs and mRNAs degradation. Acts also as a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate (ITP) to their respective monophosphate derivatives and does not distinguish between the deoxy- and ribose forms. The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP. Binds strongly to GTP, ITP and XTP. Participates in the hydrolysis of dIDP/IDP and probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NUDT16 Gene

Genomics for NUDT16 Gene

Regulatory Elements for NUDT16 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for NUDT16 Gene

Start:
131,381,671 bp from pter
End:
131,388,830 bp from pter
Size:
7,160 bases
Orientation:
Plus strand

Genomic View for NUDT16 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for NUDT16 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NUDT16 Gene

Proteins for NUDT16 Gene

  • Protein details for NUDT16 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96DE0-NUD16_HUMAN
    Recommended name:
    U8 snoRNA-decapping enzyme
    Protein Accession:
    Q96DE0
    Secondary Accessions:
    • B4E3B4
    • E9PED4
    • F5GYJ1
    • Q96N82

    Protein attributes for NUDT16 Gene

    Size:
    195 amino acids
    Molecular mass:
    21273 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Name=Co(2+); Xref=ChEBI:CHEBI:48828; Note=Binds 3 or 4 divalent metal cations. Acts specifically on U8 snoRNA with magnesium as cofactor. Has broad substrate specificity with bound manganese or cobalt (in vitro).;
    Quaternary structure:
    • Homodimer.
    SequenceCaution:
    • Sequence=BAB71024.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NUDT16 Gene

    Alternative splice isoforms for NUDT16 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NUDT16 Gene

Proteomics data for NUDT16 Gene at MOPED

Selected DME Specific Peptides for NUDT16 Gene

Post-translational modifications for NUDT16 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NUDT16 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Domains for NUDT16 Gene

Gene Families for NUDT16 Gene

HGNC:
  • NUDT :Nudix motif containing

Protein Domains for NUDT16 Gene

Suggested Antigen Peptide Sequences for NUDT16 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96DE0

UniProtKB/Swiss-Prot:

NUD16_HUMAN :
  • Q96DE0
Domain:
  • Contains 1 nudix hydrolase domain.
Family:
  • Belongs to the Nudix hydrolase family. NUDT16 subfamily.
genes like me logo Genes that share domains with NUDT16: view

Function for NUDT16 Gene

Molecular function for NUDT16 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties: Kinetic parameters: KM=0.062 uM for IDP (at 37 degrees Celsius) {ECO:0000269 PubMed:20385596}; KM=0.088 uM for dIDP (at 37 degrees Celsius) {ECO:0000269 PubMed:20385596}; KM=0.330 uM for GDP (at 37 degrees Celsius) {ECO:0000269 PubMed:20385596}; KM=0.319 mM for dGDP (at 37 degrees Celsius) {ECO:0000269 PubMed:20385596}; KM=15.7 mM for XDP (at 37 degrees Celsius) {ECO:0000269 PubMed:20385596}; KM=22.1 mM for ITP (at 37 degrees Celsius) {ECO:0000269 PubMed:20385596}; KM=24.1 mM for dITP (at 37 degrees Celsius) {ECO:0000269 PubMed:20385596}; Note=kcat is 0.931 sec(-1) with IDP. kcat is 0.966 sec(-1) with dIDP. kcat is 0.518 sec(-1) with GDP. kcat is 0.492 sec(-1) with dGDP. kcat is 2.6 sec(-1) with XDP. kcat is 3.06 sec(-1) with ITP. kcat is 3.2 sec(-1) with dITP. The catalytic efficiency for IDP is at least 1.3-fold higher than for dIDP, 9.6-fold higher than for GDP and dGDP, 100-fold higher than for XDP, ITP and dITP.; pH dependence: Gradually increased from pH 6.5 to 8.5 in its IDP hydrolyzing activity. {ECO:0000269 PubMed:20385596}; Temperature dependence: Exhibited a temperature-dependent increase in its IDP hydrolyzing activity up to 60 degrees Celsius. {ECO:0000269 PubMed:20385596};
UniProtKB/Swiss-Prot CatalyticActivity: 5-(N(7)-methylguanosine 5-triphospho)-(mRNA) + H(2)O = N(7)-methylguanosine 5-diphosphate + 5-phospho-(mRNA)
UniProtKB/Swiss-Prot CatalyticActivity: IDP + H(2)O = IMP + phosphate
UniProtKB/Swiss-Prot Function: RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal-dependent manner. Part of the U8 snoRNP complex that is required for the accumulation of mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G and/or m227G caps from U8 snoRNA and leaves a 5monophosphate on the RNA. Catalyzes also the cleavage of the cap structure on mRNAs. Does not hydrolyze cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with less efficiencies. Has broad substrate specificity with manganese or cobalt as cofactor and can act on various RNA species. Binds to the U8 snoRNA; metal is not required for RNA-binding. May play a role in the regulation of snoRNAs and mRNAs degradation. Acts also as a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate (ITP) to their respective monophosphate derivatives and does not distinguish between the deoxy- and ribose forms. The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP. Binds strongly to GTP, ITP and XTP. Participates in the hydrolysis of dIDP/IDP and probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.

Enzyme Numbers (IUBMB) for NUDT16 Gene

Gene Ontology (GO) - Molecular Function for NUDT16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding IDA 17567574
GO:0003729 mRNA binding IDA 21337011
GO:0005525 GTP binding IDA 20385596
GO:0008235 metalloexopeptidase activity IDA 21337011
GO:0016787 hydrolase activity --
genes like me logo Genes that share ontologies with NUDT16: view

Animal Model Products

CRISPR Products

miRNA for NUDT16 Gene

miRTarBase miRNAs that target NUDT16

No data available for Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for NUDT16 Gene

Localization for NUDT16 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NUDT16 Gene

Nucleus. Nucleus, nucleoplasm. Nucleus, nucleolus. Cytoplasm. Note=Localized predominantly in the cytoplasm. Localized in nucleolus, and in a minor proportion in distinct foci in the nucleoplasm (By similarity). {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for NUDT16 Gene COMPARTMENTS Subcellular localization image for NUDT16 gene
Compartment Confidence
nucleus 5
mitochondrion 3
cytosol 1

Gene Ontology (GO) - Cellular Components for NUDT16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IDA 20385596
genes like me logo Genes that share ontologies with NUDT16: view

Pathways for NUDT16 Gene

genes like me logo Genes that share pathways with NUDT16: view

Pathways by source for NUDT16 Gene

2 KEGG pathways for NUDT16 Gene

Interacting Proteins for NUDT16 Gene

Gene Ontology (GO) - Biological Process for NUDT16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006382 adenosine to inosine editing IMP 20385596
GO:0006402 mRNA catabolic process IDA 21070968
GO:0006508 proteolysis IDA 21337011
GO:0008284 positive regulation of cell proliferation IMP 20385596
GO:0016077 snoRNA catabolic process IDA 15053875
genes like me logo Genes that share ontologies with NUDT16: view

Compounds for NUDT16 Gene

(3) HMDB Compounds for NUDT16 Gene

Compound Synonyms Cas Number PubMed IDs
Cobalt
  • Co
7440-48-4
Magnesium
  • Magnesium
7439-95-4
Manganese
  • manganese
7439-96-5
genes like me logo Genes that share compounds with NUDT16: view

Transcripts for NUDT16 Gene

Unigene Clusters for NUDT16 Gene

Nudix (nucleoside diphosphate linked moiety X)-type motif 16:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for NUDT16

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for NUDT16 Gene

No ASD Table

Relevant External Links for NUDT16 Gene

GeneLoc Exon Structure for
NUDT16
ECgene alternative splicing isoforms for
NUDT16

Expression for NUDT16 Gene

mRNA expression in normal human tissues for NUDT16 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for NUDT16 Gene

SOURCE GeneReport for Unigene cluster for NUDT16 Gene Hs.282050

mRNA Expression by UniProt/SwissProt for NUDT16 Gene

Q96DE0-NUD16_HUMAN
Tissue specificity: Expressed strongly in lung, kidney, adrenal gland, testis, heart and brain.
genes like me logo Genes that share expressions with NUDT16: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for NUDT16 Gene

Orthologs for NUDT16 Gene

This gene was present in the common ancestor of chordates.

Orthologs for NUDT16 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NUDT16 35
  • 87.15 (n)
  • 82.81 (a)
NUDT16 36
  • 62 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NUDT16 36
  • 61 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NUDT16 36
  • 54 (a)
OneToOne
mouse
(Mus musculus)
Mammalia 1700080E11Rik 36
  • 49 (a)
OneToMany
Nudt16 35
  • 81.08 (n)
  • 80.73 (a)
Nudt16 16
Nudt16 36
  • 61 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia NUDT16 36
  • 53 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nudt16 35
  • 79.69 (n)
  • 78.12 (a)
lizard
(Anolis carolinensis)
Reptilia NUDT16 36
  • 46 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nudt16 35
  • 58.2 (n)
  • 59.79 (a)
zebrafish
(Danio rerio)
Actinopterygii FP015790.3 36
  • 35 (a)
ManyToMany
zgc:103759 35
  • 56.92 (n)
  • 55.56 (a)
zgc:103759 36
  • 38 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3699 36
  • 22 (a)
OneToMany
Species with no ortholog for NUDT16:
  • 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for NUDT16 Gene

ENSEMBL:
Gene Tree for NUDT16 (if available)
TreeFam:
Gene Tree for NUDT16 (if available)

Paralogs for NUDT16 Gene

Paralogs for NUDT16 Gene

Selected SIMAP similar genes for NUDT16 Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for NUDT16 Gene

genes like me logo Genes that share paralogs with NUDT16: view

Variants for NUDT16 Gene

Sequence variations from dbSNP and Humsavar for NUDT16 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs2874 -- 131,384,240(-) TTAAC(A/G)TGCCT utr-variant-3-prime, nc-transcript-variant
rs1054161 -- 131,386,684(+) AAGAT(G/T)TTCCC utr-variant-3-prime, nc-transcript-variant
rs3749390 -- 131,385,828(-) TGACT(G/T)AGAAC utr-variant-3-prime, nc-transcript-variant
rs6767434 -- 131,388,615(+) GAATG(C/T)ACAGA utr-variant-3-prime, nc-transcript-variant
rs10656610 -- 131,388,791(+) ATAAA(-/TAAT)TATTT utr-variant-3-prime, nc-transcript-variant

Structural Variations from Database of Genomic Variants (DGV) for NUDT16 Gene

Variant ID Type Subtype PubMed ID
nsv829724 CNV Gain 17160897

Relevant External Links for NUDT16 Gene

HapMap Linkage Disequilibrium report
NUDT16

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NUDT16 Gene

Disorders for NUDT16 Gene

No disorders were found for NUDT16 Gene.

No data available for UniProtKB/Swiss-Prot for NUDT16 Gene

Publications for NUDT16 Gene

  1. 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
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  3. Xenopus U8 snoRNA binding protein is a conserved nuclear decapping enzyme. (PMID: 15053875) Ghosh T. … Peculis B.A. (Mol. Cell 2004) 3 4
  4. Metal determines efficiency and substrate specificity of the nuclear NUDIX decapping proteins X29 and H29K (Nudt16). (PMID: 17567574) Peculis B.A. … Cleland M. (J. Biol. Chem. 2007) 3 4
  5. Crystallization and crystallographic analysis of human NUDT16. (PMID: 18607096) Zhang J. … Yan J. (Acta Crystallogr. F 2008) 3 4

Products for NUDT16 Gene

Sources for NUDT16 Gene

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