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Aliases for PNPT1 Gene

Aliases for PNPT1 Gene

  • Polyribonucleotide Nucleotidyltransferase 1 2 3 5
  • Polynucleotide Phosphorylase-Like Protein 3 4
  • Polynucleotide Phosphorylase 1 3 4
  • 3-5 RNA Exonuclease OLD35 3 4
  • PNPase Old-35 3 4
  • EC 2.7.7.8 4 63
  • PNPase 1 3 4
  • PNPASE 3 4
  • Deafness, Autosomal Recessive 70 2
  • Polynucleotide Phosphorylase 2
  • 3-5 RNA Exonuclease 2
  • EC 2.7.7 63
  • COXPD13 3
  • Old-35 3
  • DFNB70 3
  • OLD35 3

External Ids for PNPT1 Gene

Previous HGNC Symbols for PNPT1 Gene

  • DFNB70

Previous GeneCards Identifiers for PNPT1 Gene

  • GC02M055820
  • GC02M055837
  • GC02M055836
  • GC02M055774
  • GC02M055715
  • GC02M055861

Summaries for PNPT1 Gene

Entrez Gene Summary for PNPT1 Gene

  • The protein encoded by this gene belongs to the evolutionary conserved polynucleotide phosphorylase family comprised of phosphate dependent 3'-to-5' exoribonucleases implicated in RNA processing and degradation. This enzyme is predominantly localized in the mitochondrial intermembrane space and is involved in import of RNA to mitochondria. Mutations in this gene have been associated with combined oxidative phosphorylation deficiency-13 and autosomal recessive nonsyndromic deafness-70. Related pseudogenes are found on chromosomes 3 and 7. [provided by RefSeq, Dec 2012]

GeneCards Summary for PNPT1 Gene

PNPT1 (Polyribonucleotide Nucleotidyltransferase 1) is a Protein Coding gene. Diseases associated with PNPT1 include combined oxidative phosphorylation deficiency 13 and deafness, autosomal recessive 70. Among its related pathways are Pyrimidine metabolism (KEGG) and Deadenylation-dependent mRNA decay. GO annotations related to this gene include nucleic acid binding and RNA binding.

UniProtKB/Swiss-Prot for PNPT1 Gene

  • RNA-binding protein implicated in numerous RNA metabolic processes. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3-to-5 direction. Mitochondrial intermembrane factor with RNA-processing exoribonulease activity. Component of the mitochondrial degradosome (mtEXO) complex, that degrades 3 overhang double-stranded RNA with a 3-to-5 directionality in an ATP-dependent manner. Required for correct processing and polyadenylation of mitochondrial mRNAs. Plays a role as a cytoplasmic RNA import factor that mediates the translocation of small RNA components, like the 5S RNA, the RNA subunit of ribonuclease P and the mitochondrial RNA-processing (MRP) RNA, into the mitochondrial matrix. Plays a role in mitochondrial morphogenesis and respiration; regulates the expression of the electron transport chain (ETC) components at the mRNA and protein levels. In the cytoplasm, shows a 3-to-5 exoribonuclease mediating mRNA degradation activity; degrades c-myc mRNA upon treatment with IFNB1/IFN-beta, resulting in a growth arrest in melanoma cells. Regulates the stability of specific mature miRNAs in melanoma cells; specifically and selectively degrades miR-221, preferentially. Plays also a role in RNA cell surveillance by cleaning up oxidized RNAs. Binds to the RNA subunit of ribonuclease P, MRP RNA and miR-221 microRNA.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PNPT1 Gene

Genomics for PNPT1 Gene

Regulatory Elements for PNPT1 Gene

Enhancers for PNPT1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PNPT1 on UCSC Golden Path with GeneCards custom track

Promoters for PNPT1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PNPT1 on UCSC Golden Path with GeneCards custom track

Genomic Location for PNPT1 Gene

Chromosome:
2
Start:
55,634,063 bp from pter
End:
55,693,910 bp from pter
Size:
59,848 bases
Orientation:
Minus strand

Genomic View for PNPT1 Gene

Genes around PNPT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PNPT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PNPT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PNPT1 Gene

Proteins for PNPT1 Gene

  • Protein details for PNPT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TCS8-PNPT1_HUMAN
    Recommended name:
    Polyribonucleotide nucleotidyltransferase 1, mitochondrial
    Protein Accession:
    Q8TCS8
    Secondary Accessions:
    • Q53SU0
    • Q68CN1
    • Q7Z7D1
    • Q8IWX1
    • Q96T05
    • Q9BRU3
    • Q9BVX0

    Protein attributes for PNPT1 Gene

    Size:
    783 amino acids
    Molecular mass:
    85951 Da
    Quaternary structure:
    • Homotrimer; in free form. Homooligomer. Component of the mitochondrial degradosome (mtEXO) complex which is a heteropentamer containing 2 copies of SUPV3L1 and 3 copies of PNPT1. Interacts with TCL1A; the interaction has no effect on PNPT1 exonuclease activity.

    Three dimensional structures from OCA and Proteopedia for PNPT1 Gene

neXtProt entry for PNPT1 Gene

Proteomics data for PNPT1 Gene at MOPED

Selected DME Specific Peptides for PNPT1 Gene

Post-translational modifications for PNPT1 Gene

  • Ubiquitination at Lys 591
  • Modification sites at PhosphoSitePlus

Other Protein References for PNPT1 Gene

Antibody Products

Domains & Families for PNPT1 Gene

Suggested Antigen Peptide Sequences for PNPT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TCS8

UniProtKB/Swiss-Prot:

PNPT1_HUMAN :
  • Contains 1 KH domain.
  • Belongs to the polyribonucleotide nucleotidyltransferase family.
Domain:
  • Contains 1 KH domain.
  • Contains 1 S1 motif domain.
Family:
  • Belongs to the polyribonucleotide nucleotidyltransferase family.
genes like me logo Genes that share domains with PNPT1: view

No data available for Gene Families for PNPT1 Gene

Function for PNPT1 Gene

Molecular function for PNPT1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate.
UniProtKB/Swiss-Prot Function:
RNA-binding protein implicated in numerous RNA metabolic processes. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3-to-5 direction. Mitochondrial intermembrane factor with RNA-processing exoribonulease activity. Component of the mitochondrial degradosome (mtEXO) complex, that degrades 3 overhang double-stranded RNA with a 3-to-5 directionality in an ATP-dependent manner. Required for correct processing and polyadenylation of mitochondrial mRNAs. Plays a role as a cytoplasmic RNA import factor that mediates the translocation of small RNA components, like the 5S RNA, the RNA subunit of ribonuclease P and the mitochondrial RNA-processing (MRP) RNA, into the mitochondrial matrix. Plays a role in mitochondrial morphogenesis and respiration; regulates the expression of the electron transport chain (ETC) components at the mRNA and protein levels. In the cytoplasm, shows a 3-to-5 exoribonuclease mediating mRNA degradation activity; degrades c-myc mRNA upon treatment with IFNB1/IFN-beta, resulting in a growth arrest in melanoma cells. Regulates the stability of specific mature miRNAs in melanoma cells; specifically and selectively degrades miR-221, preferentially. Plays also a role in RNA cell surveillance by cleaning up oxidized RNAs. Binds to the RNA subunit of ribonuclease P, MRP RNA and miR-221 microRNA.
UniProtKB/Swiss-Prot Induction:
Up-regulated in cells upon senescence and terminal differentiation. Up-regulated after treatment with IFNB1/IFN-beta.

Enzyme Numbers (IUBMB) for PNPT1 Gene

Gene Ontology (GO) - Molecular Function for PNPT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0008266 poly(U) RNA binding IDA 18083836
GO:0035198 miRNA binding IDA 20547861
GO:0044822 poly(A) RNA binding IDA 22681889
genes like me logo Genes that share ontologies with PNPT1: view
genes like me logo Genes that share phenotypes with PNPT1: view

Human Phenotype Ontology for PNPT1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PNPT1 Gene

MGI Knock Outs for PNPT1:

Animal Model Products

No data available for Transcription Factor Targets and HOMER Transcription for PNPT1 Gene

Localization for PNPT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PNPT1 Gene

Cytoplasm. Mitochondrion. Mitochondrion intermembrane space; Peripheral membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PNPT1 Gene COMPARTMENTS Subcellular localization image for PNPT1 gene
Compartment Confidence
mitochondrion 5
cytosol 3
chloroplast 2
nucleus 2
extracellular 1

Gene Ontology (GO) - Cellular Components for PNPT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA 16055741
genes like me logo Genes that share ontologies with PNPT1: view

Pathways & Interactions for PNPT1 Gene

genes like me logo Genes that share pathways with PNPT1: view

Pathways by source for PNPT1 Gene

Gene Ontology (GO) - Biological Process for PNPT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000957 mitochondrial RNA catabolic process IDA 18501193
GO:0000958 mitochondrial mRNA catabolic process IDA 20691904
GO:0000964 mitochondrial RNA 5-end processing IMP 18083837
GO:0006401 RNA catabolic process IDA 18083836
GO:0006402 mRNA catabolic process IEA,IDA 12721301
genes like me logo Genes that share ontologies with PNPT1: view

No data available for SIGNOR curated interactions for PNPT1 Gene

Drugs & Compounds for PNPT1 Gene

(6) Drugs for PNPT1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
CDP Experimental Pharma 0
Guanosine diphosphate Experimental Pharma 0
Uridine-5'-Diphosphate Experimental Pharma 0

(10) Additional Compounds for PNPT1 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
dTDP
  • Deoxy-TDP
  • Deoxythymidine 5'-diphosphate
  • dTDP
  • TDP
  • Thymidine 5'-diphosphate
491-97-4
Phosphate
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
14265-44-2
phosphoric acid
  • Acide phosphorique (FRENCH)
  • Acido fosforico [Italian]
  • Acidum phosphoricum
  • Diphosphate tetrasodium
  • Fosforzuuroplossingen [Dutch]
7664-38-2
genes like me logo Genes that share compounds with PNPT1: view

Transcripts for PNPT1 Gene

Unigene Clusters for PNPT1 Gene

Polyribonucleotide nucleotidyltransferase 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PNPT1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a ·
SP1: -
SP2: - -
SP3: - -
SP4:

ExUns: 23b ^ 24 ^ 25 ^ 26 ^ 27 ^ 28
SP1:
SP2:
SP3:
SP4:

Relevant External Links for PNPT1 Gene

GeneLoc Exon Structure for
PNPT1
ECgene alternative splicing isoforms for
PNPT1

Expression for PNPT1 Gene

mRNA expression in normal human tissues for PNPT1 Gene

Protein differential expression in normal tissues from HIPED for PNPT1 Gene

This gene is overexpressed in Lymph node (15.4) and Adrenal (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PNPT1 Gene



SOURCE GeneReport for Unigene cluster for PNPT1 Gene Hs.388733

genes like me logo Genes that share expression patterns with PNPT1: view

Protein tissue co-expression partners for PNPT1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PNPT1 Gene

Orthologs for PNPT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PNPT1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PNPT1 35
  • 91.25 (n)
  • 91.98 (a)
PNPT1 36
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PNPT1 35
  • 90.04 (n)
  • 91.85 (a)
PNPT1 36
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pnpt1 35
  • 87.13 (n)
  • 91.05 (a)
Pnpt1 16
Pnpt1 36
  • 91 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PNPT1 35
  • 99.62 (n)
  • 99.74 (a)
PNPT1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pnpt1 35
  • 88.45 (n)
  • 91.82 (a)
oppossum
(Monodelphis domestica)
Mammalia PNPT1 36
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PNPT1 36
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves PNPT1 35
  • 77.62 (n)
  • 80.29 (a)
PNPT1 36
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PNPT1 36
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pnpt1 35
  • 74.88 (n)
  • 79.68 (a)
Str.3686 35
zebrafish
(Danio rerio)
Actinopterygii pnpt1 35
  • 64.2 (n)
  • 71.33 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010791 35
  • 55.37 (n)
  • 58.37 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG11337 35
  • 55.22 (n)
  • 57.97 (a)
CG11337 36
  • 55 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea BE0003N10.1 35
  • 49.31 (n)
  • 43.51 (a)
BE0003N10.1 36
  • 41 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G14580 35
  • 50.75 (n)
  • 41.65 (a)
Species with no ortholog for PNPT1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PNPT1 Gene

ENSEMBL:
Gene Tree for PNPT1 (if available)
TreeFam:
Gene Tree for PNPT1 (if available)

Paralogs for PNPT1 Gene

Pseudogenes.org Pseudogenes for PNPT1 Gene

genes like me logo Genes that share paralogs with PNPT1: view

No data available for Paralogs for PNPT1 Gene

Variants for PNPT1 Gene

Sequence variations from dbSNP and Humsavar for PNPT1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs782572 - 55,684,985(+) ACCAA(C/T)CTCTC reference, missense
rs7594497 - 55,645,403(+) TTTGT(C/T)CATGA reference, missense
rs34928857 - 55,673,071(-) TGTTG(C/G)AAGCC reference, missense
VAR_069248 Combined oxidative phosphorylation deficiency 13 (COXPD13)
VAR_069249 Deafness, autosomal recessive, 70 (DFNB70)

Structural Variations from Database of Genomic Variants (DGV) for PNPT1 Gene

Variant ID Type Subtype PubMed ID
nsv520581 CNV Loss 19592680
nsv834080 CNV Loss 17160897
dgv1185e1 CNV Complex 17122850
nsv9791 CNV Gain 18304495
nsv9802 CNV Gain 18304495
esv22582 CNV Gain 19812545
nsv442740 CNV CNV 18776908
nsv514069 CNV Gain 21397061

Variation tolerance for PNPT1 Gene

Residual Variation Intolerance Score: 40.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.01; 93.71% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PNPT1 Gene

HapMap Linkage Disequilibrium report
PNPT1
Human Gene Mutation Database (HGMD)
PNPT1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PNPT1 Gene

Disorders for PNPT1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for PNPT1 Gene - From: OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
combined oxidative phosphorylation deficiency 13
  • combined oxidative phosphorylation defect type 13
deafness, autosomal recessive 70
  • deafness, autosomal recessive, 70
autosomal recessive non-syndromic sensorineural deafness type dfnb
  • autosomal recessive isolated neurosensory deafness type dfnb
ovary serous adenocarcinoma
  • malignant ovarian serous tumor
autosomal recessive nonsyndromic deafness
  • autosomal recessive deafness
- elite association - COSMIC cancer census association via MalaCards
Search PNPT1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PNPT1_HUMAN
  • Combined oxidative phosphorylation deficiency 13 (COXPD13) [MIM:614932]: A mitochondrial disorder characterized by early onset severe encephalomyopathy, dystonia, choreoathetosis, bucofacial dyskinesias and combined mitochondrial respiratory chain deficiency. Nerve conductions velocities are decreased. Levels of plasma and cerebrospinal fluid lactate are increased. {ECO:0000269 PubMed:23084291}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Deafness, autosomal recessive, 70 (DFNB70) [MIM:614934]: A form of non-syndromic deafness characterized by severe, bilateral hearing impairment with prelingual onset, resulting in inability to acquire normal speech. {ECO:0000269 PubMed:23084290}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PNPT1

Genetic Association Database (GAD)
PNPT1
Human Genome Epidemiology (HuGE) Navigator
PNPT1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PNPT1
genes like me logo Genes that share disorders with PNPT1: view

No data available for Genatlas for PNPT1 Gene

Publications for PNPT1 Gene

  1. Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring. (PMID: 12419256) Raijmakers R. … Pruijn G.J.M. (J. Mol. Biol. 2002) 2 3 4 67
  2. Human mitochondrial RNA turnover caught in flagranti: involvement of hSuv3p helicase in RNA surveillance. (PMID: 19864255) Szczesny R.J. … Stepien P.P. (Nucleic Acids Res. 2010) 3 23
  3. Human mitochondrial SUV3 and polynucleotide phosphorylase form a 330- kDa heteropentamer to cooperatively degrade double-stranded RNA with a 3'-to-5' directionality. (PMID: 19509288) Wang D.D. … Lee W.H. (J. Biol. Chem. 2009) 3 23
  4. Analysis of the human polynucleotide phosphorylase (PNPase) reveals differences in RNA binding and response to phosphate compared to its bacterial and chloroplast counterparts. (PMID: 18083836) Portnoy V. … Schuster G. (RNA 2008) 3 23
  5. Stable PNPase RNAi silencing: its effect on the processing and adenylation of human mitochondrial RNA. (PMID: 18083837) Slomovic S. … Schuster G. (RNA 2008) 3 23

Products for PNPT1 Gene

Sources for PNPT1 Gene

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