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NT5C 5', 3'-nucleotidase, cytosolic [ Homo sapiens (human) ]

Gene ID: 30833, updated on 27-Nov-2024

Summary

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Official Symbol
NT5Cprovided by HGNC
Official Full Name
5', 3'-nucleotidase, cytosolicprovided by HGNC
Primary source
HGNC:HGNC:17144
See related
Ensembl:ENSG00000125458 MIM:191720; AllianceGenome:HGNC:17144
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DNT; cdN; DNT1; P5N2; PN-I; HEL74; PN-II; UMPH2; dNT-1
Summary
This gene encodes a nucleotidase that catalyzes the dephosphorylation of the 5' deoxyribonucleotides (dNTP) and 2'(3')-dNTP and ribonucleotides, but not 5' ribonucleotides. Of the different forms of nucleotidases characterized, this enzyme is unique in its preference for 5'-dNTP. It may be one of the enzymes involved in regulating the size of dNTP pools in cells. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2011]
Expression
Ubiquitous expression in colon (RPKM 12.8), spleen (RPKM 11.1) and 25 other tissues See more
Orthologs
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Genomic context

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See NT5C in Genome Data Viewer
Location:
17q25.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (75130228..75131742, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (76021691..76023204, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73126323..73127837, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73074528-73075727 Neighboring gene tripartite motif containing 80, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73089299-73089872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73089873-73090445 Neighboring gene solute carrier family 16 member 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73100784-73101284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73101285-73101785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8955 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73110035-73110574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12735 Neighboring gene armadillo repeat containing 7 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:73120068-73121267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12736 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:73126856-73127060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8956 Neighboring gene uncharacterized LOC107985034 Neighboring gene Jupiter microtubule associated homolog 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73143638-73144837 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8957 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73151095-73151690 Neighboring gene small ubiquitin like modifier 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73178362-73179012

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Assignment of the human gene for uridine 5'-monophosphate phosphohydrolase (UMPH2) to the long arm of chromosome 17. Wilson DE, et al. Ann Hum Genet, 1986 Jul. PMID 2833155
  2. 5'-(3')-nucleotidase mRNA levels in blast cells are a prognostic factor in acute myeloid leukemia patients treated with cytarabine. Galmarini CM, et al. Haematologica, 2004 May. PMID 15136231
  3. Cytoplasmic 5'(3')-nucleotidase from human placenta. Höglund L, et al. J Biol Chem, 1990 Apr 25. PMID 2157703
  4. Construction of a genetic map of human chromosome 17 by use of chromosome-mediated gene transfer. Xu WM, et al. Proc Natl Acad Sci U S A, 1988 Nov. PMID 3186746, Free PMC Article
  5. Kinetic evidence for covalent phosphoryl-enzyme intermediate in phosphotransferase activity of human red cell pyrimidine nucleotidases. Amici A, et al. Methods Enzymol, 2002. PMID 12418222

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  2. Data show that PN-I shows a higher affinity for oxynucleosides rather than deoxynucleosides, while the opposite is true for PN-II.
    Title: Kinetic evidence for covalent phosphoryl-enzyme intermediate in phosphotransferase activity of human red cell pyrimidine nucleotidases.
  3. Mutation analysis in the P5N-I gene led to the identification of 3 novel mutations
    Title: Molecular characterization of Turkish patients with pyrimidine 5' nucleotidase-I deficiency.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-nucleotidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables IMP 5'-nucleotidase activity IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleotidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables pyrimidine nucleotide binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in IMP catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in UMP catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in allantoin metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in amide catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in dCMP catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in dGMP catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in dTMP catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in dUMP catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in dephosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in pyrimidine deoxyribonucleotide catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in pyrimidine deoxyribonucleotide catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in mitochondrion HTP PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
5'(3')-deoxyribonucleotidase, cytosolic type
Names
5' nucleotidase, deoxy (pyrimidine), cytosolic type C
cytosolic 5',3'-pyrimidine nucleotidase
deoxy-5'-nucleotidase 1
epididymis luminal protein 74
epididymis secretory sperm binding protein
uridine 5'-monophosphate phosphohydrolase 2
uridine 5-prime monophosphate hydrolase 2
NP_001239306.1
NP_055410.1
XP_011523002.3
XP_054171866.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001252377.2 → NP_001239306.1  5'(3')-deoxyribonucleotidase, cytosolic type isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame coding exon, and uses an alternate in-frame acceptor splice site at the 3' terminal exon compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
    Source sequence(s)
    AF154829, BG034032, BQ431723
    UniProtKB/TrEMBL
    J3KSX6
    Related
    ENSP00000462697.1, ENST00000578407.5
    Conserved Domains (1) summary
    cl21460
    Location:7 → 132
    HAD_like; Haloacid Dehalogenase-like Hydrolases

  2. NM_014595.3 → NP_055410.1  5'(3')-deoxyribonucleotidase, cytosolic type isoform 1

    See identical proteins and their annotated locations for NP_055410.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript, and encodes the longer isoform (1).
    Source sequence(s)
    AF154829
    Consensus CDS
    CCDS11715.1
    UniProtKB/Swiss-Prot
    Q8TCD5, Q96HS6, Q9NP82
    UniProtKB/TrEMBL
    A0A384NYP3, V9HWF3
    Related
    ENSP00000245552.2, ENST00000245552.7
    Conserved Domains (1) summary
    cd02587
    Location:5 → 168
    HAD_5-3dNT; 5'(3')-deoxyribonucleotidase

RNA

  1. NR_045513.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses alternate acceptor and donor splice sites at an internal exon compared to variant 1. It is represented as non-coding because the use of the 5'-most supported translational start codon as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF154829, BC008183, BQ431723
    Related
    ENST00000580758.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    75130228..75131742 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011524700.3 → XP_011523002.3  5'(3')-deoxyribonucleotidase, cytosolic type isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    76021691..76023204 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054315891.1 → XP_054171866.1  5'(3')-deoxyribonucleotidase, cytosolic type isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TCD5.2 GenPept UniProtKB/Swiss-Prot:Q8TCD5

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