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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
  • 5(3)-Deoxyribonucleotidase, Mitochondrial 3
  • Mitochondrial 5 Nucleotidase 3
  • 5(3)-Deoxyribonucleotidase 3
  • EC 3.1.3.- 4
  • EC 3.1.3 61
  • 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 Adiaspiromycosis and Ametropic Amblyopia. Among its related pathways are NAD metabolism and Purine metabolism (KEGG). 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 CIViC summary , 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

Enhancers for NT5M 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
GH17G017234 1.4 ENCODE dbSUPER 34 -66.6 -66578 3.5 HDGF FOXA2 MLX ARNT WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 FLCN NT5M UPF3AP1 SMCR5 LOC644422 LOC100419436 PLD6 ENSG00000264187 ENSG00000266498
GH17G017279 1.1 ENCODE 37.5 -22.4 -22427 2.6 PKNOX1 CREB3L1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 FLCN NT5M MPRIP-AS1 COPS3 PLD6 ATPAF2 GC17P017245
GH17G017275 0.9 Ensembl ENCODE 37.6 -27.0 -27035 1.0 HDGF PKNOX1 JUNB SIN3A TBX21 JUND TARDBP IKZF1 NBN RELB FLCN NT5M COPS3 ATPAF2 GC17P017245
GH17G017302 1.5 FANTOM5 ENCODE 13.1 +1.0 1046 3.7 HDGF PKNOX1 CREB3L1 MLX ARNT ARID4B SIN3A DMAP1 FEZF1 ZNF2 NT5M FLCN COPS3 PLD6 GC17M017313
GH17G017231 0.6 dbSUPER 28.4 -71.1 -71099 2.1 POLR2A SMARCA4 ZNF600 HNF4A NR2F6 ZIC2 FLCN NT5M ENSG00000266498 PLD6
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NT5M on UCSC Golden Path with GeneCards custom track

Promoters for NT5M Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000091883 165 1401 HDGF PKNOX1 CREB3L1 ARNT MLX ARID4B SIN3A DMAP1 FEZF1 ZNF2

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

Selected DME Specific Peptides for NT5M Gene

Q9NPB1:
  • GVLADFE
  • DLLIDDRP

Post-translational modifications for NT5M Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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:0000166 nucleotide binding IEA --
GO:0008252 nucleotidase activity TAS 10899995
GO:0008253 5-nucleotidase activity IEA,EXP 10899995
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
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

Inhibitory RNA Products

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
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 NT5M gene
Compartment Confidence
mitochondrion 5
plasma membrane 2
cytoskeleton 2
peroxisome 2
nucleus 2
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for NT5M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion TAS 10899995
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with NT5M: view

Pathways & Interactions for NT5M Gene

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

Pathways by source for NT5M Gene

Gene Ontology (GO) - Biological Process for NT5M Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006260 DNA replication TAS 10899995
GO:0009117 nucleotide metabolic process IEA --
GO:0009223 pyrimidine deoxyribonucleotide catabolic process TAS 10899995
GO:0009264 deoxyribonucleotide catabolic process IEA --
GO:0016311 dephosphorylation IEA --
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine Approved, Investigational Pharma Agonist 419
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
thymidine Experimental Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
beta-nicotinamide D-ribonucleotide
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
dIMP
  • 2'-Deoxy-5'-inosinic acid
  • 2'-Deoxyinosine 5'-monophosphate
  • 2'-Deoxyinosine 5'-phosphate
  • 9-(2-Deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purin-6-ol
  • 9-(2-Deoxy-5-O-phosphono-beta-delta-erythro-pentofuranosyl)-9H-purin-6-ol
3393-18-8
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:

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for NT5M Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of NT5M Gene:

NT5M

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.

Evidence on tissue expression from TISSUES for NT5M Gene

  • Muscle(4.3)
  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with NT5M: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34 35
  • 99.56 (n)
mouse
(Mus musculus)
Mammalia Nt5m 34 16 35
  • 90.83 (n)
dog
(Canis familiaris)
Mammalia NT5M 35 34
  • 90.01 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NT5M 34 35
  • 88.69 (n)
rat
(Rattus norvegicus)
Mammalia Nt5m 34
  • 85.25 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NT5M 35
  • 63 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NT5M 35
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves NT5M 35 34
  • 80.95 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NT5M 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nt5m 34
  • 74.96 (n)
Species where no ortholog for NT5M 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)
  • 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
rs1000031266 -- 17,322,619(+) GTAGC(A/G)AACGC intron-variant
rs1000044415 -- 17,306,194(+) TGGTC(C/T)AGCCT intron-variant
rs1000046179 -- 17,328,359(+) CACCA(C/T)CTTTA intron-variant
rs1000069304 -- 17,311,561(+) TTTAT(A/T)TCTAG intron-variant
rs1000101140 -- 17,323,755(+) GTTGG(-/AGC)AGCTC intron-variant

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

Variant ID Type Subtype PubMed ID
esv1198553 CNV deletion 17803354
esv26411 CNV loss 19812545
esv2659771 CNV deletion 23128226
esv2673352 CNV deletion 23128226
esv2813 CNV loss 18987735
esv3161567 CNV deletion 24192839
esv33859 CNV loss 17666407
esv3554215 CNV deletion 23714750
esv3640127 CNV loss 21293372
esv3640128 CNV loss 21293372
esv5295 CNV loss 18987735
esv6568 CNV loss 19470904
nsv1061186 CNV gain 25217958
nsv112007 CNV deletion 16902084
nsv1125206 CNV deletion 24896259
nsv1146229 CNV deletion 26484159
nsv155 OTHER inversion 15895083
nsv469777 CNV gain 16826518
nsv499114 OTHER inversion 21111241
nsv833380 CNV loss 17160897
nsv833382 CNV loss 17160897
nsv9500 CNV loss 18304495
nsv954571 CNV deletion 24416366
nsv955407 CNV deletion 24416366

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

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NT5M

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

Disorders for NT5M Gene

MalaCards: The human disease database

(4) MalaCards diseases for NT5M Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
adiaspiromycosis
ametropic amblyopia
  • refractive amblyopia
dentin sensitivity
  • sensitive dentin
byssinosis
  • cotton mill fever
- 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. Crystal structure of a human mitochondrial deoxyribonucleotidase. (PMID: 12352955) Rinaldo-Matthis A. … Nordlund P. (Nat. Struct. Biol. 2002) 3 4 22 64
  2. 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 64
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3 46 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Human mitochondrial 5'-deoxyribonucleotidase. Overproduction in cultured cells and functional aspects. (PMID: 12124385) Gallinaro L. … Bianchi V. (J. Biol. Chem. 2002) 3 22 64

Products for NT5M Gene

Sources for NT5M Gene

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