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PNPT1 polyribonucleotide nucleotidyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 87178, updated on 13-Feb-2019

Summary

Official Symbol
PNPT1provided by HGNC
Official Full Name
polyribonucleotide nucleotidyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:23166
See related
Ensembl:ENSG00000138035 MIM:610316
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
OLD35; DFNB70; PNPASE; old-35; COXPD13
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 6.2), testis (RPKM 5.9) and 25 other tissues See more
Orthologs

Genomic context

See PNPT1 in Genome Data Viewer
Location:
2p16.1
Exon count:
29
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (55634063..55693910, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (55861198..55921045, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene protein phosphatase 4 regulatory subunit 3B Neighboring gene uncharacterized LOC107985885 Neighboring gene uncharacterized LOC107985811 Neighboring gene uncharacterized LOC112268416 Neighboring gene EGF containing fibulin extracellular matrix protein 1

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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Combined oxidative phosphorylation deficiency 13
MedGen: C3554129 OMIM: 614932 GeneReviews: Not available
Compare labs
Deafness, autosomal recessive 70
MedGen: C1824925 OMIM: 614934 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp762K1914

Gene Ontology Provided by GOA

Function Evidence Code Pubs
3'-5'-exoribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
3'-5'-exoribonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding HDA PubMed 
miRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
poly(G) binding IDA
Inferred from Direct Assay
more info
PubMed 
poly(U) RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
polyribonucleotide nucleotidyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
polyribonucleotide nucleotidyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
RNA import into mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
RNA phosphodiester bond hydrolysis, exonucleolytic IEA
Inferred from Electronic Annotation
more info
 
RNA polyadenylation IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to interferon-beta IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to oxidative stress IDA
Inferred from Direct Assay
more info
PubMed 
liver regeneration IEA
Inferred from Electronic Annotation
more info
 
mRNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial RNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial RNA 3'-end processing IMP
Inferred from Mutant Phenotype
more info
PubMed 
mitochondrial RNA 5'-end processing IMP
Inferred from Mutant Phenotype
more info
PubMed 
mitochondrial RNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial RNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial RNA processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial mRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial mRNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial mRNA polyadenylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
mitochondrion morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
mitotic cell cycle arrest IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of growth IDA
Inferred from Direct Assay
more info
PubMed 
nuclear polyadenylation-dependent mRNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of miRNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of mitochondrial RNA catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
protein homooligomerization IDA
Inferred from Direct Assay
more info
PubMed 
protein homotrimerization IDA
Inferred from Direct Assay
more info
PubMed 
rRNA import into mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cellular respiration ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cellular senescence IDA
Inferred from Direct Assay
more info
PubMed 
response to cAMP IEA
Inferred from Electronic Annotation
more info
 
response to growth hormone IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
mitochondrial degradosome IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial intermembrane space IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
polysomal ribosome IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
polyribonucleotide nucleotidyltransferase 1, mitochondrial
Names
3'-5' RNA exonuclease OLD35
PNPase 1
PNPase old-35
polynucleotide phosphorylase 1
polynucleotide phosphorylase-like protein
NP_149100.2
XP_005264686.1
XP_016860661.1

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.

Genomic

  1. NG_033012.1 RefSeqGene

    Range
    5001..64848
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_033109.5NP_149100.2  polyribonucleotide nucleotidyltransferase 1, mitochondrial precursor

    See identical proteins and their annotated locations for NP_149100.2

    Status: REVIEWED

    Source sequence(s)
    AC015982, AJ458465, AW731791, BC009057, BU943827, CR749867, DB461021
    Consensus CDS
    CCDS1856.1
    UniProtKB/Swiss-Prot
    Q8TCS8
    Related
    ENSP00000400646.2, ENST00000447944.6
    Conserved Domains (6) summary
    smart00316
    Location:679750
    S1; Ribosomal protein S1-like RNA-binding domain
    cd11363
    Location:49273
    RNase_PH_PNPase_1; Polyribonucleotide nucleotidyltransferase, repeat 1
    cd11364
    Location:366596
    RNase_PH_PNPase_2; Polyribonucleotide nucleotidyltransferase, repeat 2
    PRK11824
    Location:49752
    PRK11824; polynucleotide phosphorylase/polyadenylase; Provisional
    pfam03726
    Location:282363
    PNPase; Polyribonucleotide nucleotidyltransferase, RNA binding domain
    cl00098
    Location:605664
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    55634063..55693910 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005172.1XP_016860661.1  polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1

    Conserved Domains (6) summary
    smart00316
    Location:599670
    S1; Ribosomal protein S1-like RNA-binding domain
    cd11364
    Location:286516
    RNase_PH_PNPase_2; Polyribonucleotide nucleotidyltransferase, repeat 2
    PRK11824
    Location:1672
    PRK11824; polynucleotide phosphorylase/polyadenylase; Provisional
    pfam03726
    Location:202283
    PNPase; Polyribonucleotide nucleotidyltransferase, RNA binding domain
    cl00098
    Location:525584
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    cl03114
    Location:1193
    RNase_PH; RNase PH-like 3'-5' exoribonucleases
  2. XM_005264629.2XP_005264686.1  polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1

    Conserved Domains (6) summary
    smart00316
    Location:599670
    S1; Ribosomal protein S1-like RNA-binding domain
    cd11364
    Location:286516
    RNase_PH_PNPase_2; Polyribonucleotide nucleotidyltransferase, repeat 2
    PRK11824
    Location:1672
    PRK11824; polynucleotide phosphorylase/polyadenylase; Provisional
    pfam03726
    Location:202283
    PNPase; Polyribonucleotide nucleotidyltransferase, RNA binding domain
    cl00098
    Location:525584
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    cl03114
    Location:1193
    RNase_PH; RNase PH-like 3'-5' exoribonucleases

RNA

  1. XR_001739010.1 RNA Sequence

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