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Aliases for NT5M Gene

Aliases for NT5M Gene

  • 5',3'-Nucleotidase, Mitochondrial 2
  • 5,3-Nucleotidase, Mitochondrial 2 3 4 5
  • 5 Nucleotidase, Mitochondrial 2 3
  • Deoxy-5-Nucleotidase 2 3 4
  • DNT-2 3 4
  • DNT2 3 4
  • Mitochondrial 5 Nucleotidase 3
  • 5(3)-Deoxyribonucleotidase 3
  • EC 3.1.3.- 4
  • EC 3.1.3 63
  • MdN 3

External Ids for NT5M Gene

Previous GeneCards Identifiers for NT5M Gene

  • GC17P017521
  • GC17P018565
  • GC17P017149
  • GC17P017407
  • GC17P017147
  • GC17P016959
  • GC17P017206

Summaries for NT5M Gene

Entrez Gene Summary for NT5M Gene

  • This gene encodes a 5' nucleotidase that localizes to the mitochondrial matrix. This enzyme dephosphorylates the 5'- and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides. The gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]

GeneCards Summary for NT5M Gene

NT5M (5',3'-Nucleotidase, Mitochondrial) is a Protein Coding gene. Diseases associated with NT5M include dentin sensitivity. Among its related pathways are Metabolism and Purine metabolism. GO annotations related to this gene include nucleotide binding and nucleotidase activity. An important paralog of this gene is NT5C.

UniProtKB/Swiss-Prot for NT5M Gene

  • Dephosphorylates specifically the 5 and 2(3)-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NT5M Gene

Genomics for NT5M Gene

Regulatory Elements for NT5M Gene

Promoters for NT5M Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around NT5M on UCSC Golden Path with GeneCards custom track

Genomic Location for NT5M Gene

Chromosome:
17
Start:
17,303,335 bp from pter
End:
17,347,663 bp from pter
Size:
44,329 bases
Orientation:
Plus strand

Genomic View for NT5M Gene

Genes around NT5M on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NT5M Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NT5M Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NT5M Gene

Proteins for NT5M Gene

  • Protein details for NT5M Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NPB1-NT5M_HUMAN
    Recommended name:
    5(3)-deoxyribonucleotidase, mitochondrial
    Protein Accession:
    Q9NPB1

    Protein attributes for NT5M Gene

    Size:
    228 amino acids
    Molecular mass:
    25862 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for NT5M Gene

neXtProt entry for NT5M Gene

Proteomics data for NT5M Gene at MOPED

Selected DME Specific Peptides for NT5M Gene

Post-translational modifications for NT5M Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NT5M Gene

Domains & Families for NT5M Gene

Gene Families for NT5M Gene

Protein Domains for NT5M Gene

Suggested Antigen Peptide Sequences for NT5M Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NPB1

UniProtKB/Swiss-Prot:

NT5M_HUMAN :
  • Belongs to the 5(3)-deoxyribonucleotidase family.
Family:
  • Belongs to the 5(3)-deoxyribonucleotidase family.
genes like me logo Genes that share domains with NT5M: view

Function for NT5M Gene

Molecular function for NT5M Gene

UniProtKB/Swiss-Prot Function:
Dephosphorylates specifically the 5 and 2(3)-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.

Enzyme Numbers (IUBMB) for NT5M Gene

Gene Ontology (GO) - Molecular Function for NT5M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008253 5-nucleotidase activity EXP,IEA 10899995
genes like me logo Genes that share ontologies with NT5M: view
genes like me logo Genes that share phenotypes with NT5M: view

Animal Model Products

miRNA for NT5M Gene

miRTarBase miRNAs that target NT5M

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NT5M Gene

Localization for NT5M Gene

Subcellular locations from UniProtKB/Swiss-Prot for NT5M Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for NT5M Gene COMPARTMENTS Subcellular localization image for NT5M gene
Compartment Confidence
mitochondrion 5
nucleus 2
peroxisome 2
cytosol 1

No data available for Gene Ontology (GO) - Cellular Components for NT5M Gene

Pathways & Interactions for NT5M Gene

genes like me logo Genes that share pathways with NT5M: view

Pathways by source for NT5M Gene

Interacting Proteins for NT5M Gene

Gene Ontology (GO) - Biological Process for NT5M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009223 pyrimidine deoxyribonucleotide catabolic process TAS 10899995
GO:0009264 deoxyribonucleotide catabolic process IEA --
GO:0044281 small molecule metabolic process TAS --
GO:0055086 nucleobase-containing small molecule metabolic process TAS --
genes like me logo Genes that share ontologies with NT5M: view

No data available for SIGNOR curated interactions for NT5M Gene

Drugs & Compounds for NT5M Gene

(17) Drugs for NT5M Gene - From: HMDB, DrugBank, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine Approved, Investigational Pharma Agonist 363
Adenosine monophosphate Approved Nutra 0
thymidine Experimental Pharma 0
cyclic 3',5'-thymidine monophosphate Experimental Pharma Target 0
Dpb-T Experimental Pharma Target 0

(17) Additional Compounds for NT5M Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
beta-nicotinamide D-ribonucleotide
Cytidine monophosphate
  • 5'-CMP
  • 5-Cytidylate
  • 5-Cytidylic acid
  • CMP
  • Cytidine 5'-monophosphate
63-37-6
deoxyadenosine
  • 1-(6-Amino-9H-purin-9-yl)-1,2-dideoxy-b-D-Ribofuranose
  • 1-(6-Amino-9H-purin-9-yl)-1,2-dideoxy-beta-D-Ribofuranose
  • 1-(6-Amino-9H-purin-9-yl)-1,2-dideoxy-beta-delta-Ribofuranose
  • 2'-Deoxyadenosine
  • 2-Deoxyadenosine
958-09-8
Deoxyadenosine monophosphate
  • 2'-dAMP
  • 2'-Deoxy-5'-adenylate
  • 2'-Deoxy-5'-adenylic acid
  • 2'-Deoxy-Adenosine 5'-phosphorate
  • 2'-Deoxy-Adenosine 5'-phosphoric acid
653-63-4
deoxyguanosine
  • 2'-Deoxy-Guanosine
  • 2'-Deoxyguanosine
  • 2-Deoxyguanosine
  • 9-(2-Deoxy-b-D-erythro-pentofuranosyl)-Guanine
  • 9-(2-Deoxy-b-D-erythro-pentofuranosyl)guanine
961-07-9
genes like me logo Genes that share compounds with NT5M: view

Transcripts for NT5M Gene

Unigene Clusters for NT5M Gene

5,3-nucleotidase, mitochondrial:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NT5M Gene

No ASD Table

Relevant External Links for NT5M Gene

GeneLoc Exon Structure for
NT5M
ECgene alternative splicing isoforms for
NT5M

Expression for NT5M Gene

mRNA expression in normal human tissues for NT5M Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

SOURCE GeneReport for Unigene cluster for NT5M Gene Hs.513977

mRNA Expression by UniProt/SwissProt for NT5M Gene

Q9NPB1-NT5M_HUMAN
Tissue specificity: Highly expressed in heart, brain and skeletal muscle. Detected at very low levels in kidney and pancreas.
genes like me logo Genes that share expression patterns with NT5M: view

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for NT5M Gene

Orthologs for NT5M Gene

This gene was present in the common ancestor of chordates.

Orthologs for NT5M Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NT5M 35
  • 99.56 (n)
  • 99.12 (a)
NT5M 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NT5M 36
  • 73 (a)
OneToOne
NT5M 35
  • 88.69 (n)
  • 87.95 (a)
dog
(Canis familiaris)
Mammalia NT5M 35
  • 90.01 (n)
  • 85.46 (a)
NT5M 36
  • 71 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nt5m 16
Nt5m 36
  • 85 (a)
OneToOne
Nt5m 35
  • 90.83 (n)
  • 93.65 (a)
oppossum
(Monodelphis domestica)
Mammalia NT5M 36
  • 61 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NT5M 36
  • 63 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nt5m 35
  • 85.25 (n)
  • 86.78 (a)
chicken
(Gallus gallus)
Aves NT5M 35
  • 80.95 (n)
  • 86.24 (a)
NT5M 36
  • 63 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NT5M 36
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nt5m 35
  • 74.96 (n)
  • 80.95 (a)
Species with no ortholog for NT5M:
  • 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)
  • 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)
  • zebrafish (Danio rerio)

Evolution for NT5M Gene

ENSEMBL:
Gene Tree for NT5M (if available)
TreeFam:
Gene Tree for NT5M (if available)

Paralogs for NT5M Gene

Paralogs for NT5M Gene

(1) SIMAP similar genes for NT5M Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with NT5M: view

Variants for NT5M Gene

Sequence variations from dbSNP and Humsavar for NT5M Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1860552 -- 17,328,566(+) GTCTC(A/G)GGGCA intron-variant
rs1860553 -- 17,332,223(+) GGGAC(C/T)GTGTC intron-variant
rs2064060 -- 17,345,402(+) CGTGG(C/T)GACTC intron-variant
rs3203918 -- 17,347,394(+) CCCCT(C/T)TTGGT utr-variant-3-prime
rs3826302 -- 17,344,210(-) GGGCA(C/T)CCCTA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for NT5M Gene

Variant ID Type Subtype PubMed ID
nsv155 OTHER Inversion 15895083
nsv499114 OTHER Inversion 21111241
nsv833380 CNV Loss 17160897
nsv833382 CNV Loss 17160897
nsv469777 CNV Complex 16826518
esv33859 CNV Loss 17666407
esv2715716 CNV Deletion 23290073
esv2715717 CNV Deletion 23290073
esv2715719 CNV Deletion 23290073
esv5295 CNV Deletion 18987735
esv2673352 CNV Deletion 23128226
esv1198553 CNV Deletion 17803354
esv2813 CNV Deletion 18987735
esv6568 CNV Loss 19470904
esv2715720 CNV Deletion 23290073
nsv112007 CNV Loss 16902084
esv26411 CNV Loss 19812545
nsv9500 CNV Loss 18304495
esv2659771 CNV Deletion 23128226

Variation tolerance for NT5M Gene

Residual Variation Intolerance Score: 65.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.81; 17.10% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NT5M Gene

HapMap Linkage Disequilibrium report
NT5M

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NT5M Gene

Disorders for NT5M Gene

MalaCards: The human disease database

(1) MalaCards diseases for NT5M Gene - From: DISEASES

Disorder Aliases PubMed IDs
dentin sensitivity
  • sensitive dentin
- elite association - COSMIC cancer census association via MalaCards
Search NT5M in MalaCards View complete list of genes associated with diseases

Relevant External Links for NT5M

Genetic Association Database (GAD)
NT5M
Human Genome Epidemiology (HuGE) Navigator
NT5M
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NT5M
genes like me logo Genes that share disorders with NT5M: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NT5M Gene

Publications for NT5M Gene

  1. A deoxyribonucleotidase in mitochondria: involvement in regulation of dNTP pools and possible link to genetic disease. (PMID: 10899995) Rampazzo C. … Bianchi V. (Proc. Natl. Acad. Sci. U.S.A. 2000) 2 3 4 67
  2. Crystal structure of a human mitochondrial deoxyribonucleotidase. (PMID: 12352955) Rinaldo-Matthis A. … Nordlund P. (Nat. Struct. Biol. 2002) 3 23
  3. Human mitochondrial 5'-deoxyribonucleotidase. Overproduction in cultured cells and functional aspects. (PMID: 12124385) Gallinaro L. … Bianchi V. (J. Biol. Chem. 2002) 3 23
  4. Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase. (PMID: 24506201) Pachl P. … A9ezA!A8ovA! P. (J Enzyme Inhib Med Chem 2015) 3
  5. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3

Products for NT5M Gene

Sources for NT5M Gene

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