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Aliases for NUDT16 Gene

Aliases for NUDT16 Gene

  • Nudix Hydrolase 16 2 3 4 5
  • 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
  • Testicular Tissue Protein Li 129 3
  • U8 SnoRNA-Decapping Enzyme 3
  • EC 3.6.1.62 4
  • EC 3.6.1.64 4
  • EC 3.6.1 56

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 Hydrolase 16) is a Protein Coding gene. Among its related pathways are Purine metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and hydrolase activity. 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 (PubMed:20385596, PubMed:26121039). The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP (PubMed:20385596). 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 (PubMed:20385596).

Additional gene information for NUDT16 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 NUDT16 Gene

Genomics for NUDT16 Gene

GeneHancer (GH) Regulatory Elements for NUDT16 Gene

Promoters and enhancers for NUDT16 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
GH03I131380 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 557.4 -0.2 -150 2.6 HDGF ATF1 ARID4B SIN3A FEZF1 DMAP1 ZBTB7B ZNF48 YY1 POLR2B NUDT16 LOC339874 PIK3R4 ATP2C1 MRPL3 ASTE1
GH03I131349 Enhancer 0.8 Ensembl ENCODE 11.4 -31.5 -31489 1.4 ESRRA RXRA ZFP37 MAFG NR2F2 JUND GATA3 NFE2 CUX1 FOS LOC339874 NUDT16 GC03P131359 RNU6-726P GC03M131093 NEK11
GH03I131385 Enhancer 1 Ensembl ENCODE dbSUPER 5.5 +5.3 5282 3.7 JUN MAX RAD21 NR2F2 GABPA JUND POLR2A HNF4G KDM1A HNF4A GC03P131387 NUDT16
GH03I131371 Enhancer 0.8 FANTOM5 Ensembl dbSUPER 6.7 -10.0 -9971 1 MNT KDM1A SNORA58 NEK11 NUDT16 NUDT16P1 LOC339874
GH03I131215 Enhancer 1 Ensembl ENCODE 4.6 -164.2 -164242 2.9 NFIB FEZF1 ZNF335 FOS SP3 ZNF398 ZEB2 ZNF843 ZFP69B NFIC NUDT16P1 NUDT16 GC03M131093 RNU6-726P GC03P131359 NEK11
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NUDT16 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NUDT16 gene promoter:

Genomic Locations for NUDT16 Gene

Genomic Locations for NUDT16 Gene
chr3:131,381,671-131,388,830
(GRCh38/hg38)
Size:
7,160 bases
Orientation:
Plus strand
chr3:131,100,515-131,107,674
(GRCh37/hg19)

Genomic View for NUDT16 Gene

Genes around NUDT16 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NUDT16 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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;
    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

Selected DME Specific Peptides for NUDT16 Gene

Q96DE0:
  • HACHALL
  • MRFDGRLGFPGGFVD

Post-translational modifications for NUDT16 Gene

No Post-translational modifications

Other Protein References for NUDT16 Gene

Domains & Families for NUDT16 Gene

Gene Families for NUDT16 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

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 :
  • Belongs to the Nudix hydrolase family. NUDT16 subfamily.
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. {ECO:0000269 PubMed:20385596}; 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 CatalyticActivity:
dIDP + H(2)O = dIMP + phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
The phosphatase activity is inhibited by the product IMP.
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 (PubMed:20385596, PubMed:26121039). The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP (PubMed:20385596). 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 (PubMed:20385596).

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:0003723 RNA binding IEA --
GO:0003729 mRNA binding IDA 21337011
GO:0005525 GTP binding IDA 20385596
GO:0008235 metalloexopeptidase activity IDA 21337011
genes like me logo Genes that share ontologies with NUDT16: view
genes like me logo Genes that share phenotypes with NUDT16: view

Animal Model Products

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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 (PubMed:21070968). Localized in nucleolus, and in a minor proportion in distinct foci in the nucleoplasm (By similarity). {ECO:0000250 UniProtKB:Q6TEC1, ECO:0000269 PubMed:21070968}.

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 NUDT16 gene
Compartment Confidence
nucleus 5
mitochondrion 3
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NUDT16 Gene

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

Pathways & Interactions 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 IEA --
GO:0008284 positive regulation of cell proliferation IMP 20385596
GO:0009117 nucleotide metabolic process IEA --
genes like me logo Genes that share ontologies with NUDT16: view

No data available for SIGNOR curated interactions for NUDT16 Gene

Drugs & Compounds for NUDT16 Gene

(4) Drugs for NUDT16 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Magnesium Approved Nutra 0
Manganese Approved Nutra 37
Cobalt Pharma 174
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:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for NUDT16 Gene

Protein differential expression in normal tissues from HIPED for NUDT16 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (9.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NUDT16 Gene



Protein tissue co-expression partners for NUDT16 Gene

NURSA nuclear receptor signaling pathways regulating expression of NUDT16 Gene:

NUDT16

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.

Evidence on tissue expression from TISSUES for NUDT16 Gene

  • Nervous system(4.7)
  • Kidney(4.5)
  • Liver(4.3)
  • Pancreas(4.2)
  • Lung(2.2)
genes like me logo Genes that share expression patterns with NUDT16: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 87.15 (n)
mouse
(Mus musculus)
Mammalia Nudt16 33 16 34
  • 81.08 (n)
1700080E11Rik 34
  • 49 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Nudt16 33
  • 79.69 (n)
cow
(Bos Taurus)
Mammalia NUDT16 34
  • 61 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NUDT16 34
  • 54 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NUDT16 34
  • 53 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NUDT16 34
  • 46 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nudt16 33
  • 58.2 (n)
zebrafish
(Danio rerio)
Actinopterygii zgc:103759 33 34
  • 56.92 (n)
FP015790.3 34
  • 35 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3699 34
  • 22 (a)
OneToMany
Species where no ortholog for NUDT16 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)
  • 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

(1) 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 Variation AA Info Type
rs1000018026 -- 131,380,083(+) T/C upstream_transcript_variant
rs1000149039 -- 131,386,589(+) T/C/G 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000260423 -- 131,381,777(+) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000317911 -- 131,382,069(+) C/T coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs1000514650 -- 131,384,415(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant

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

Variant ID Type Subtype PubMed ID
nsv829724 CNV gain 17160897
nsv1006656 CNV gain 25217958
esv3597788 CNV gain 21293372
esv3597785 CNV gain 21293372
esv3597781 CNV gain 21293372
dgv934e214 CNV loss 21293372

Variation tolerance for NUDT16 Gene

Residual Variation Intolerance Score: 75.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.78; 47.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NUDT16 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NUDT16

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

Disorders for NUDT16 Gene

Additional Disease Information for NUDT16

No disorders were found for NUDT16 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NUDT16 Gene

Publications for NUDT16 Gene

  1. Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate. (PMID: 26121039) Trésaugues L … Nordlund P (PloS one 2015) 3 4 58
  2. hNUDT16: a universal decapping enzyme for small nucleolar RNA and cytoplasmic mRNA. (PMID: 21337011) Lu G … Yan J (Protein & cell 2011) 3 4 58
  3. NUDT16 is a (deoxy)inosine diphosphatase, and its deficiency induces accumulation of single-strand breaks in nuclear DNA and growth arrest. (PMID: 20385596) Iyama T … Nakabeppu Y (Nucleic acids research 2010) 3 4 58
  4. Multiple mRNA decapping enzymes in mammalian cells. (PMID: 21070968) Song MG … Kiledjian M (Molecular cell 2010) 3 4 58
  5. Evolutionary conservation supports ancient origin for Nudt16, a nuclear-localized, RNA-binding, RNA-decapping enzyme. (PMID: 18820299) Taylor MJ … Peculis BA (Nucleic acids research 2008) 3 4 58

Products for NUDT16 Gene

Sources for NUDT16 Gene

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