NT5M Gene
protein-coding GIFtS: 56
GCID: GC17P017206
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5',3'-nucleotidase, mitochondrial(Previous names: 5' nucleotidase, mitochondrial )
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Aliases
for NT5M gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| 5',3'-Nucleotidase, Mitochondrial1 2 3 | | DNT23 5 | | DNT-21 | | 5'(3')-Deoxyribonucleotidase, Mitochondrial2 | | 5' Nucleotidase, Mitochondrial1 2 | | 5(3)-Deoxyribonucleotidase1 | | DNT23 5 | | Mitochondrial 5' Nucleotidase2 | | MdN1 | | EC 3.1.3.-3 | | Deoxy-5'-Nucleotidase 22 3 | | EC 3.1.38 |
Export aliases for NT5M gene to outside databasesPrevious GC identifers: GC17P017521 GC17P018565 GC17P017149 GC17P017407 GC17P017147 GC17P016959 |
Summaries
for NT5M gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for NT5M:
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-Magenissyndrome region on chromosome 17. (provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: NT5M_HUMAN, Q9NPB1Function: Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and soprotects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP
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Genomic Views
for NT5M gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000017.10 NC_018928.1 NT_010718.16
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the NT5M gene promoter:
E2F-4 E2F-3a E2F-5 p53 POU3F1 E2F-2 CUTL1 E2F E2F-1 GCNF-2
Other transcription factors
Search SABiosciences Chromatin IP Primers for NT5M
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NT5M |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 17p11.2 Ensembl cytogenetic band: 17p11.2 HGNC cytogenetic band: 17p11.2NT5M Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 17 GeneLoc Exon Structure GeneLoc location for GC17P017206: view genomic region
(about GC identifiers)
Start:
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17,206,649 bp from pter |
End:
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17,250,977 bp from pter |
Size:
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44,329 bases |
Orientation:
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plus strand |
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Proteins
for NT5M gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: NT5M_HUMAN, Q9NPB1 (See
protein sequence)Recommended Name: 5'(3')-deoxyribonucleotidase, mitochondrial precursor Size: 228 amino acids; 25862 Da
Cofactor: Magnesium
Subunit: Homodimer (Probable)
Subcellular location: Mitochondrion
6/12 PDB 3D structures from  and Proteopedia  for NT5M (see all 12):1MH9 (3D)
1Q91 (3D)
1Q92 (3D)
1Z4I (3D)
1Z4J (3D)
1Z4K (3D)
Explore the universe of human proteins at neXtProt for NT5M: NX_Q9NPB1
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9NPB1
2 DME Specific Peptides for NT5M (Q9NPB1)
NT5M Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_064586.1
ENSEMBL proteins: ENSP00000373674 ENSP00000390695 ENSP00000464303 ENSP00000463674 ENSP00000467567 Reactome Protein details: Q9NPB1
Human Recombinant Protein Products:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
NT5M for ontologies About GeneDecksing
NT5M Antibody Products:
Assay Products for NT5M: |
Protein
Domains /
Families
for NT5M gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
NT5M for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9NPB1ProtoNet protein and cluster: Q9NPB1 1 Blocks protein family: IPB010708 5 nucleotidase
UniProtKB/Swiss-Prot: NT5M_HUMAN, Q9NPB1Similarity: Belongs to the 5'(3')-deoxyribonucleotidase family |
Function
for NT5M gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Function Summary:
UniProtKB/Swiss-Prot: NT5M_HUMAN, Q9NPB1Function: Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and soprotects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMPEnzyme Numbers (IUBMB): EC 3.1.32 EC 3.1.3.-1
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for NT5M (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for NT5M
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
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Synthesis Service for NT5M | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NT5M |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NT5M |
Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view): About this table
NT5M for ontologies About GeneDecksing
|
Pathways & Interactions
for NT5M gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Unified GeneCards pathways About this table
See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | NAD metabolism | | | 2 | Pyrimidine metabolism | | | 3 | Purine metabolism | | | 4 | Metabolism | | | 5 | Purine metabolism | |
Pathway sources
See GeneCards unified pathways
Show all pathways
1 EMD Millipore Pathway for NT5M
1  GeneGo (Thomson Reuters) Pathway for NT5M
4 
Reactome Pathways for NT5M
4 
Kegg Pathways (Kegg details for NT5M):
NT5M for pathways About GeneDecksing
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NT5M
STRING Interaction
Network Preview (showing 5 interactants - click image to see 25)
5/76 Interacting proteins for NT5M (ENSP000003736744) via UniProtKB, MINT, STRING, and/or I2D (see all 76)About this table
Gene Ontology (GO): 5/7 biological process terms (GO ID links to tree view) (see all 7): About this table
NT5M for ontologies About GeneDecksing
|
Drugs & Compounds
for NT5M gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
NT5M for compounds About GeneDecksing
 Browse Tocris compounds for NT5M
10/29 HMDB Compounds for NT5M (see all 29) About this table
2 DrugBank Compounds for NT5M About this table
1 Novoseek chemical compound relationship for NT5M gene About this table
| Compound |
-log (P-Val) |
Hits |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| thymidine |
46 |
7 |
14747464 (3), 12352955 (1), 15044615 (1) |
Search CenterWatch for drugs/clinical trials and news about NT5M
|
Transcripts
for NT5M gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for NT5M gene: NM_020201.3 Unigene Cluster for NT5M: 5',3'-nucleotidase, mitochondrial Hs.513977 [show with all ESTs]Unigene Representative Sequence: NM_0202017 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000389022(uc002grf.3 uc002grg.3) ENST00000446264 ENST00000478373
ENST00000470418 ENST00000483704 ENST00000582909 ENST00000480529
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for NT5M (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for NT5M
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: NT5M (NM_020201) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for NT5M | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NT5M |
Additional cDNA sequence: AF210652.1 BC035838.1 DQ323995.1 4 DOTS entries: DT.442499 DT.100739089 DT.75117837 DT.99938163 24/49 AceView cDNA sequences (see all 49): AI085646 NM_020201 BQ943179 CR602400 BF431576 BI255109 BQ933896 BC035838 BM798008 AL514954 BX327438 BM547741 AW205623 BX116854 AI125461 CA436029 BU620529 AW272329 AA446187 AW137930 T95938 BM723748 AL526310 BG819613
GeneLoc Exon Structure
|
Expression
for NT5M gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| NT5M expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
See NT5M Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for NT5M
SOURCE GeneReport for Unigene cluster: Hs.513977
UniProtKB/Swiss-Prot: NT5M_HUMAN, Q9NPB1Tissue specificity: Highly expressed in heart, brain and skeletal muscle. Detected at very low levels in kidney andpancreas
SABiosciences Custom PCR Arrays for NT5M
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for NT5M
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat NT5M | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat NT5M | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat NT5M | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NT5M |
Orthologs
for NT5M gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of chordates.
Orthologs for NT5M gene from 2/9 species (see all 9) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
chicken
(Gallus gallus) |
Aves |
NT5M1 |
5',3'-nucleotidase, mitochondrial |
77.83(n)
82.08(a) |
|
416505 XM_414809.3 XP_414809.2 |
lizard
(Anolis carolinensis) |
Reptilia |
NT5C6 |
-- |
72(a) |
1 ↔ 1 |
GL343500.1(353662-359011) |
ENSEMBL Gene Tree for NT5M (if available)
TreeFam Gene Tree for NT5M (if available) |
Paralogs
for NT5M gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for NT5M gene
- NT5C2
1 SIMAP similar gene for NT5M using alignment to 5 protein entries: NT5M_HUMAN (see all proteins):NT5C
NT5M for paralogs About GeneDecksing
|
Genomic Variants
for NT5M gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 17 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for NT5M (17206649 - 17250977 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 9 variations for NT5M
4 CNVs: 67150 43258 7143 61561
4 Indels: 25787 11877 41857 33643
1 Inversion: 0495 | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing NT5M |
|
Disorders
/ Diseases
for NT5M gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
NT5M for disorders About GeneDecksing
OMIM gene information: 605292
OMIM disorders: --
8  diseases for NT5M: About MalaCardssmith-magenis syndrome nevoid basal cell carcinoma syndrome dentin sensitivity basal cell carcinoma
periodontal disease genetic disease periodontitis carcinoma
1 disease from the University of Copenhagen DISEASES database for NT5M:Dentin sensitivity Human Genome Epidemiology (HuGE) Navigator: NT5M (1 document)
Export disorders for NT5M gene to outside databases
|
Publications
for NT5M gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for NT5M gene, integrated from 9 sources (see all 15):
(articles sorted by number of sources associating them with NT5M) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- A deoxyribonucleotidase in mitochondria: involvement in regulation of dNTP pools and possible link to genetic disease. (PubMed id 10899995)1, 2, 3 Rampazzo C....Bianchi V. (2000)
- Crystal structure of a human mitochondrial deoxyribonucleotidase. (PubMed id 12352955)1, 2, 9 Rinaldo-Matthis A.... Nordlund P. (2002)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
- Human mitochondrial 5'-deoxyribonucleotidase. Overproduction in cultured cells and functional aspects. (PubMed id 12124385)1, 9 Gallinaro L....Bianchi V. (2002)
- Genetic variants in nuclear-encoded mitochondrial gen es influence AIDS progression. (PubMed id 20877624)1 Hendrickson S.L....O'Brien S.J. (2010)
- Drugs, their targets and the nature and number of dru g targets. (PubMed id 17016423)7 Imming P....Meyer A. (2006)
- How many drug targets are there? (PubMed id 17139284)7 Overington J.P....Hopkins A.L. (2006)
- Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase. (PubMed id 16004879)1 Wallden K....Nordlund P. (2005)
- Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
- The Protein Data Bank. (PubMed id 10592235)7 Berman H.M....Bourne P.E. (2000)
|
External Searches for NT5M gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing NT5M gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing NT5M gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing NT5M gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for NT5M | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for NT5M gene:
Search GeneIP for patents involving NT5M
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for NT5M gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
 | |
 | |
 |
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat NT5M | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing NT5M | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NT5M | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat NT5M | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat NT5M | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat NT5M |
| |
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|
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 |
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 | | | NT5M Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NT5M |
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| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NT5M |
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