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NT5M 5',3'-nucleotidase, mitochondrial [ Homo sapiens (human) ]

Gene ID: 56953, updated on 4-May-2020

Summary

Official Symbol
NT5Mprovided by HGNC
Official Full Name
5',3'-nucleotidase, mitochondrialprovided by HGNC
Primary source
HGNC:HGNC:15769
See related
Ensembl:ENSG00000205309 MIM:605292
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
mdN; dNT2; dNT-2
Summary
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]
Expression
Broad expression in testis (RPKM 2.8), bone marrow (RPKM 2.2) and 23 other tissues See more
Orthologs

Genomic context

See NT5M in Genome Data Viewer
Location:
17p11.2
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (17303373..17347663)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (17206680..17250977)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene actin gamma 1 pseudogene 24 Neighboring gene COP9 signalosome subunit 3 Neighboring gene Sharpr-MPRA regulatory region 4579 Neighboring gene ribosomal protein L13 pseudogene 12

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
5'-nucleotidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
5'-nucleotidase activity IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
nucleotidase activity TAS
Traceable Author Statement
more info
PubMed 
nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA replication TAS
Traceable Author Statement
more info
PubMed 
dUMP catabolic process IEA
Inferred from Electronic Annotation
more info
 
dephosphorylation IEA
Inferred from Electronic Annotation
more info
 
pyrimidine deoxyribonucleotide catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pyrimidine deoxyribonucleotide catabolic process TAS
Traceable Author Statement
more info
PubMed 
pyrimidine nucleoside catabolic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
mitochondrial matrix TAS
Traceable Author Statement
more info
 
mitochondrion TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
5'(3')-deoxyribonucleotidase, mitochondrial
Names
5' nucleotidase, mitochondrial
5(3)-deoxyribonucleotidase
deoxy-5'-nucleotidase 2
mitochondrial 5' nucleotidase
NP_064586.1
XP_005256788.1
XP_005256789.1
XP_005256790.1
XP_005256791.1
XP_005256794.1
XP_011522264.1
XP_011522265.1
XP_011522266.1
XP_011522267.1
XP_011522268.1
XP_011522269.1
XP_016880368.1

NCBI Reference Sequences (RefSeq)

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_020201.4NP_064586.1  5'(3')-deoxyribonucleotidase, mitochondrial precursor

    See identical proteins and their annotated locations for NP_064586.1

    Status: REVIEWED

    Source sequence(s)
    AF210652, AL526346, BC035838
    Consensus CDS
    CCDS32581.1
    UniProtKB/Swiss-Prot
    Q9NPB1
    Related
    ENSP00000373674.4, ENST00000389022.9
    Conserved Domains (2) summary
    pfam00702
    Location:38168
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:38225
    HAD_like; Haloacid Dehalogenase-like Hydrolases

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    17303373..17347663
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017024879.1XP_016880368.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X7

    Conserved Domains (1) summary
    cl21460
    Location:51145
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  2. XM_011523967.2XP_011522269.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X1

    Conserved Domains (2) summary
    pfam00702
    Location:38131
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:38262
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  3. XM_005256731.3XP_005256788.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X2

    Conserved Domains (2) summary
    pfam00702
    Location:38168
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:38250
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  4. XM_005256732.3XP_005256789.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X3

    See identical proteins and their annotated locations for XP_005256789.1

    UniProtKB/TrEMBL
    Q2I378
    Related
    ENSP00000481269.1, ENST00000616989.1
    Conserved Domains (2) summary
    pfam00702
    Location:38168
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:38231
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  5. XM_005256733.3XP_005256790.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X4

    Conserved Domains (2) summary
    pfam00702
    Location:38168
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:38186
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  6. XM_005256734.3XP_005256791.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X5

    Conserved Domains (2) summary
    pfam00702
    Location:38168
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:38178
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  7. XM_011523966.1XP_011522268.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X8

    Conserved Domains (2) summary
    pfam00702
    Location:38131
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:38120
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  8. XM_011523962.2XP_011522264.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X6

    Conserved Domains (2) summary
    pfam00702
    Location:38131
    Hydrolase; haloacid dehalogenase-like hydrolase
    cl21460
    Location:38120
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  9. XM_005256737.1XP_005256794.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X9

    Conserved Domains (1) summary
    cl21460
    Location:11114
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  10. XM_011523963.1XP_011522265.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X7

    See identical proteins and their annotated locations for XP_011522265.1

    Conserved Domains (1) summary
    cl21460
    Location:51145
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  11. XM_011523965.2XP_011522267.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X7

    See identical proteins and their annotated locations for XP_011522267.1

    Conserved Domains (1) summary
    cl21460
    Location:51145
    HAD_like; Haloacid Dehalogenase-like Hydrolases
  12. XM_011523964.2XP_011522266.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X7

    See identical proteins and their annotated locations for XP_011522266.1

    Conserved Domains (1) summary
    cl21460
    Location:51145
    HAD_like; Haloacid Dehalogenase-like Hydrolases
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