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Aliases for PARN Gene

Aliases for PARN Gene

  • Poly(A)-Specific Ribonuclease 2 3
  • Deadenylation Nuclease 2 3 4
  • DAN 3 4 6
  • Poly(A)-Specific Ribonuclease (Deadenylation Nuclease) 2 3
  • Polyadenylate-Specific Ribonuclease 3 4
  • Deadenylating Nuclease 3 4
  • EC 3.1.13.4 4 64
  • Poly(A)-Specific Ribonuclease PARN 3

External Ids for PARN Gene

Summaries for PARN Gene

Entrez Gene Summary for PARN Gene

  • The protein encoded by this gene is a 3'-exoribonuclease, with similarity to the RNase D family of 3'-exonucleases. It prefers poly(A) as the substrate, hence, efficiently degrades poly(A) tails of mRNAs. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs. This protein is also involved in silencing of certain maternal mRNAs during oocyte maturation and early embryonic development, as well as in nonsense-mediated decay (NMD) of mRNAs that contain premature stop codons. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

GeneCards Summary for PARN Gene

PARN (Poly(A)-Specific Ribonuclease) is a Protein Coding gene. Among its related pathways are Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein and Translational Control. GO annotations related to this gene include nucleotide binding and mRNA 3-UTR binding. An important paralog of this gene is PNLDC1.

UniProtKB/Swiss-Prot for PARN Gene

  • 3-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3-end poly(A) tail and the 5-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization.

Gene Wiki entry for PARN Gene

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

Genomics for PARN Gene

Genomic Location for PARN Gene

Start:
14,435,700 bp from pter
End:
14,632,728 bp from pter
Size:
197,029 bases
Orientation:
Minus strand

Genomic View for PARN Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PARN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PARN Gene

Regulatory Elements for PARN Gene

Proteins for PARN Gene

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

    Protein Symbol:
    O95453-PARN_HUMAN
    Recommended name:
    Poly(A)-specific ribonuclease PARN
    Protein Accession:
    O95453
    Secondary Accessions:
    • B2RCB3
    • B4DDG8
    • B4DSB0
    • B4DWR4
    • B4E1H6

    Protein attributes for PARN Gene

    Size:
    639 amino acids
    Molecular mass:
    73451 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Note=Divalent metal cations. Mg(2+) is the most probable.;
    Quaternary structure:
    • Homodimer. Interacts with KHSRP and CELF1/CUGBP1. Found in a mRNA decay complex with RENT1, RENT2 and RENT3B. Interacts with ZC3HAV1 in an RNA-independent manner.

    Three dimensional structures from OCA and Proteopedia for PARN Gene

    Alternative splice isoforms for PARN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PARN Gene

Proteomics data for PARN Gene at MOPED

Post-translational modifications for PARN Gene

  • Phosphorylation by MAPKAPK2, preventing GADD45A mRNA degradation after genotoxic stress.
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys326

Other Protein References for PARN Gene

Domains for PARN Gene

UniProtKB/Swiss-Prot:

PARN_HUMAN
Domain:
  • Contains 1 R3H domain.:
    • O95453
Family:
  • Belongs to the CAF1 family.:
    • O95453
genes like me logo Genes that share domains with PARN: view

No data available for Gene Families for PARN Gene

Function for PARN Gene

Molecular function for PARN Gene

GENATLAS Biochemistry: poly A specific ribonuclease,deadenylation nuclease,ubiquitously expressed,degrading poly A tail of mRNA molecules
UniProtKB/Swiss-Prot CatalyticActivity: Exonucleolytic cleavage of poly(A) to 5-AMP.
UniProtKB/Swiss-Prot Function: 3-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3-end poly(A) tail and the 5-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization.

Enzyme Numbers (IUBMB) for PARN Gene

Gene Ontology (GO) - Molecular Function for PARN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding --
GO:0003723 RNA binding --
GO:0003730 mRNA 3-UTR binding TAS 9736620
GO:0004518 nuclease activity TAS 9736620
genes like me logo Genes that share ontologies with PARN: view

miRNA for PARN Gene

miRTarBase miRNAs that target PARN

No data available for Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for PARN Gene

Localization for PARN Gene

Subcellular locations from UniProtKB/Swiss-Prot for PARN Gene

Nucleus. Cytoplasm. Nucleus, nucleolus. Note=Some nuclear fraction is nucleolar.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PARN Gene COMPARTMENTS Subcellular localization image for PARN gene
Compartment Confidence
nucleus 5
cytosol 4

Gene Ontology (GO) - Cellular Components for PARN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 9736620
GO:0005730 nucleolus IEA --
GO:0005737 cytoplasm TAS 9736620
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with PARN: view

Pathways for PARN Gene

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

Pathways by source for PARN Gene

1 KEGG pathway for PARN Gene

Gene Ontology (GO) - Biological Process for PARN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP 22890540
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay TAS --
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening TAS --
GO:0006402 mRNA catabolic process --
GO:0007292 female gamete generation TAS 9736620
genes like me logo Genes that share ontologies with PARN: view

Compounds for PARN Gene

(1) Novoseek inferred chemical compound relationships for PARN Gene

Compound -log(P) Hits PubMed IDs
adenylate 72.3 22
genes like me logo Genes that share compounds with PARN: view

Transcripts for PARN Gene

Unigene Clusters for PARN Gene

Poly(A)-specific ribonuclease:
Representative Sequences:

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

No ASD Table

Relevant External Links for PARN Gene

GeneLoc Exon Structure for
PARN
ECgene alternative splicing isoforms for
PARN

Expression for PARN Gene

mRNA expression in normal human tissues for PARN Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for PARN Gene

SOURCE GeneReport for Unigene cluster for PARN Gene Hs.253197

mRNA Expression by UniProt/SwissProt for PARN Gene

O95453-PARN_HUMAN
Tissue specificity: Ubiquitous.
genes like me logo Genes that share expressions with PARN: view

Orthologs for PARN Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PARN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PARN 36
  • 99.79 (n)
  • 99.84 (a)
PARN 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PARN 36
  • 91.64 (n)
  • 94.51 (a)
PARN 37
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PARN 36
  • 91.85 (n)
  • 93.1 (a)
PARN 37
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Parn 36
  • 86.54 (n)
  • 88.62 (a)
Parn 16
Parn 37
  • 88 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PARN 37
  • 94 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PARN 37
  • 84 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Parn 36
  • 85.74 (n)
  • 88.3 (a)
chicken
(Gallus gallus)
Aves PARN 36
  • 79.18 (n)
  • 83.33 (a)
PARN 37
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PARN 37
  • 80 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia parn-A 36
tropical clawed frog
(Silurana tropicalis)
Amphibia parn 36
  • 74.21 (n)
  • 75.32 (a)
Str.15241 36
zebrafish
(Danio rerio)
Actinopterygii parn 36
  • 64.28 (n)
  • 67.52 (a)
parn 37
  • 62 (a)
OneToOne
zgc56067 36
African malaria mosquito
(Anopheles gambiae)
Insecta PARN 36
  • 46.78 (n)
  • 34.84 (a)
worm
(Caenorhabditis elegans)
Secernentea K10C8.1 36
  • 43.05 (n)
  • 29.16 (a)
parn-1 37
  • 19 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AHG2 36
  • 43.63 (n)
  • 30.04 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC29A10.09c 36
  • 42.7 (n)
  • 30 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 31 (a)
OneToOne
Species with no ortholog for PARN:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 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 PARN Gene

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

Paralogs for PARN Gene

Paralogs for PARN Gene

Selected SIMAP similar genes for PARN Gene using alignment to 6 proteins:

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

Variants for PARN Gene

Sequence variations from dbSNP and Humsavar for PARN Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type MAF
rs717262 -- 14,576,214(-) CTACC(A/G)ATGAG intron-variant
rs732459 -- 14,533,837(+) ACCTG(C/T)CTGCA intron-variant
rs753951 -- 14,534,019(+) gtgtt(C/T)gagac intron-variant
rs873781 -- 14,609,816(-) ATCCA(G/T)CCTGT intron-variant
rs956690 -- 14,528,243(-) GCTTT(C/T)TGTTA intron-variant

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

Variant ID Type Subtype PubMed ID
esv2662886 CNV Deletion 23128226
esv2714011 CNV Deletion 23290073
dgv810e1 CNV Complex 17122850
dgv811e1 CNV Complex 17122850
esv2669004 CNV Deletion 23128226
esv271073 CNV Insertion 20981092
nsv833144 CNV Gain 17160897
nsv905356 CNV Gain 21882294

Relevant External Links for PARN Gene

HapMap Linkage Disequilibrium report
PARN

Disorders for PARN Gene

Relevant External Links for PARN

Genetic Association Database (GAD)
PARN
Human Genome Epidemiology (HuGE) Navigator
PARN
genes like me logo Genes that share disorders with PARN: view

No data available for UniProtKB/Swiss-Prot for PARN Gene

Publications for PARN Gene

  1. The human gene for the poly(A)-specific ribonuclease (PARN) maps to 16p13 and has a truncated copy in the Prader-Willi/Angelman syndrome region on 15q11-->q13. (PMID: 10640832) Buiting K. … Horsthemke B. (Cytogenet. Cell Genet. 1999) 2 3 4 23
  2. The deadenylating nuclease (DAN) is involved in poly(A) tail removal during the meiotic maturation of Xenopus oocytes. (PMID: 9736620) Koerner C.G. … Wahle E. (EMBO J. 1998) 3 4 23
  3. Identification of the active site of poly(A)-specific ribonuclease by site-directed mutagenesis and Fe(2+)-mediated cleavage. (PMID: 11742007) Ren Y.-G. … Virtanen A. (J. Biol. Chem. 2002) 3 4 23
  4. Tristetraprolin and its family members can promote the cell-free deadenylation of AU-rich element-containing mRNAs by poly(A) ribonuclease. (PMID: 12748283) Lai W.S. … Blackshear P.J. (Mol. Cell. Biol. 2003) 3 4 23
  5. Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. (PMID: 14527413) Lejeune F. … Maquat L.E. (Mol. Cell 2003) 3 4 23

Products for PARN Gene

Sources for PARN Gene

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