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Aliases for PARN Gene

Aliases for PARN Gene

  • Poly(A)-Specific Ribonuclease 2 3 5
  • Deadenylation Nuclease 2 3 4
  • Polyadenylate-Specific Ribonuclease 3 4
  • Deadenylating Nuclease 3 4
  • EC 3.1.13.4 4 61
  • DAN 3 4
  • Poly(A)-Specific Ribonuclease (Deadenylation Nuclease) 2
  • Poly(A)-Specific Ribonuclease PARN 3
  • PFBMFT4 3
  • DKCB6 3

External Ids for PARN Gene

Previous GeneCards Identifiers for PARN Gene

  • GC16M014478
  • GC16P017836
  • GC16M014495
  • GC16M014437
  • GC16M014529

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. Diseases associated with PARN include Pulmonary Fibrosis And/Or Bone Marrow Failure, Telomere-Related, 4 and Dyskeratosis Congenita, Autosomal Recessive 6. Among its related pathways are Deadenylation-dependent mRNA decay and Wnt / Hedgehog / Notch. GO annotations related to this gene include nucleic acid binding and RNA 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

Regulatory Elements for PARN Gene

Enhancers for PARN Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16F014607 0.8 ENCODE 0.3 +24.2 24183 2.9 SOX13 TBL1XR1 ASH2L RBBP5 CEBPG RELA EED CREM MIXL1 GATAD2A RN7SL274P PARN
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PARN on UCSC Golden Path with GeneCards custom track

Promoters for PARN Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000664847 -572 2201 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF207

Genomic Location for PARN Gene

Chromosome:
16
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

Genes around PARN on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence 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;
    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

Selected DME Specific Peptides for PARN Gene

O95453:
  • TKSFNFYVFPKPF
  • IAVNTSKYAESYRIQTYA
  • EQEELNDAVGFSRVI
  • VTFPKEWKTSDLYQLFSAFGNIQ
  • GFDTPEERYQKLKKHSMDFLLFQFGLC
  • MDIPYLNLEGPDLQPKRD
  • PCTGFQRKLIYQTLSWKYPKGIHVETLET
  • PPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANY
  • LDTKLMAST
  • GIPYLNQEEE
  • NTSLAEL
  • LETEKKER
  • DDTSAFVSLSQ
  • TASEQLHEAGYDAYITGLCFISMANYLGSFLSPPK
  • EKKERYIVISKVDEEERKR

Post-translational modifications for PARN Gene

  • Phosphorylation by MAPKAPK2, preventing GADD45A mRNA degradation after genotoxic stress.
  • Ubiquitination at Lys 326
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PARN (PARN)

Domains & Families for PARN Gene

Graphical View of Domain Structure for InterPro Entry

O95453

UniProtKB/Swiss-Prot:

PARN_HUMAN :
  • Contains 1 R3H domain.
  • Belongs to the CAF1 family.
Domain:
  • Contains 1 R3H domain.
Family:
  • Belongs to the CAF1 family.
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 IEA --
GO:0003723 RNA binding IEA --
GO:0003730 mRNA 3-UTR binding TAS 9736620
GO:0004518 nuclease activity IEA,TAS 9736620
genes like me logo Genes that share ontologies with PARN: view
genes like me logo Genes that share phenotypes with PARN: view

Human Phenotype Ontology for PARN Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for PARN

Inhibitory RNA Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets 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
cytosol 5
nucleus 5
extracellular 1

Gene Ontology (GO) - Cellular Components for PARN Gene

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

Pathways & Interactions for PARN Gene

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

Pathways by source for PARN Gene

SIGNOR curated interactions for PARN Gene

Is inactivated by:

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:0000289 nuclear-transcribed mRNA poly(A) tail shortening TAS --
GO:0006402 mRNA catabolic process IEA --
GO:0007292 female gamete generation TAS 9736620
GO:0009451 RNA modification TAS 9736620
genes like me logo Genes that share ontologies with PARN: view

Drugs & Compounds for PARN Gene

(1) Additional Compounds for PARN Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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:

Inhibitory RNA Products

Flow Cytometry Products

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 from GTEx, Illumina, BioGPS, and SAGE for PARN Gene

Protein differential expression in normal tissues from HIPED for PARN Gene

This gene is overexpressed in Lavage (32.3).

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



Protein tissue co-expression partners for PARN Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PARN Gene:

PARN

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 expression patterns with PARN: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PARN Gene

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 34 35
  • 99.79 (n)
oppossum
(Monodelphis domestica)
Mammalia PARN 35
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PARN 34 35
  • 91.85 (n)
cow
(Bos Taurus)
Mammalia PARN 34 35
  • 91.64 (n)
mouse
(Mus musculus)
Mammalia Parn 34 16 35
  • 86.54 (n)
rat
(Rattus norvegicus)
Mammalia Parn 34
  • 85.74 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PARN 35
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves PARN 34 35
  • 79.18 (n)
lizard
(Anolis carolinensis)
Reptilia PARN 35
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia parn 34
  • 74.21 (n)
Str.15241 34
African clawed frog
(Xenopus laevis)
Amphibia parn-A 34
zebrafish
(Danio rerio)
Actinopterygii parn 34 35
  • 64.28 (n)
zgc56067 34
African malaria mosquito
(Anopheles gambiae)
Insecta PARN 34
  • 46.78 (n)
worm
(Caenorhabditis elegans)
Secernentea K10C8.1 34
  • 43.05 (n)
parn-1 35
  • 19 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AHG2 34
  • 43.63 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC29A10.09c 34
  • 42.7 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 31 (a)
OneToOne
Species where no ortholog for PARN was found in the sources mined by GeneCards:
  • 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

(1) 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
rs777090017 Pulmonary fibrosis, and/or bone marrow failure, telomere-related, 4 (PFBMFT4) [MIM:616371], Pathogenic 14,580,874(+) CTTAC(C/T)TGTTA nc-transcript-variant, reference, missense
rs786200999 Dyskeratosis congenita, autosomal recessive, 6 (DKCB6) [MIM:616353], Pathogenic 14,582,225(-) CGATG(C/T)CTACA nc-transcript-variant, reference, missense
rs751381953 Pathogenic 14,627,189(+) ATACC(C/T)GGGAT intron-variant, upstream-variant-2KB, splice-acceptor-variant
rs754368658 Pathogenic 14,584,383(+) TAACC(A/G)CTTTT nc-transcript-variant, reference, missense
rs756132866 Pathogenic 14,593,300(+) ACTTA(A/C)CGCAG intron-variant, splice-donor-variant

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

Variant ID Type Subtype PubMed ID
dgv2738n100 CNV gain 25217958
esv2662886 CNV deletion 23128226
esv2669004 CNV deletion 23128226
esv2714011 CNV deletion 23290073
esv2758632 CNV gain+loss 17122850
esv3397104 CNV insertion 20981092
esv3638008 CNV loss 21293372
esv3638009 CNV loss 21293372
esv3638010 CNV loss 21293372
nsv833144 CNV gain 17160897
nsv974759 CNV duplication 23825009

Variation tolerance for PARN Gene

Residual Variation Intolerance Score: 48.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.75; 33.19% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PARN Gene

Human Gene Mutation Database (HGMD)
PARN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PARN

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

Disorders for PARN Gene

MalaCards: The human disease database

(9) MalaCards diseases for PARN Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
pulmonary fibrosis and/or bone marrow failure, telomere-related, 4
  • pulmonary fibrosis and/or bone marrow failure, telomere-related 4
dyskeratosis congenita, autosomal recessive 6
  • dkcb6
dyskeratosis congenita
  • zinsser-cole-engman syndrome
parn-related dyskeratosis congenita
  • dyskeratosis congenita, autosomal recessive 6
dyskeratosis congenita, x-linked
  • dyskeratosis congenita x-linked
- elite association - COSMIC cancer census association via MalaCards
Search PARN in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PARN_HUMAN
  • Dyskeratosis congenita, autosomal recessive, 6 (DKCB6) [MIM:616353]: A form of dyskeratosis congenita, a rare multisystem disorder caused by defective telomere maintenance. It is characterized by progressive bone marrow failure, and the clinical triad of reticulated skin hyperpigmentation, nail dystrophy, and mucosal leukoplakia. Common but variable features include premature graying, aplastic anemia, low platelets, osteoporosis, pulmonary fibrosis, and liver fibrosis among others. Early mortality is often associated with bone marrow failure, infections, fatal pulmonary complications, or malignancy. {ECO:0000269 PubMed:25893599}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Pulmonary fibrosis, and/or bone marrow failure, telomere-related, 4 (PFBMFT4) [MIM:616371]: A disease associated with shortened telomeres. Pulmonary fibrosis is the most common manifestation. Other manifestations include aplastic anemia due to bone marrow failure, hepatic fibrosis, and increased cancer risk, particularly myelodysplastic syndrome and acute myeloid leukemia. Phenotype, age at onset, and severity are determined by telomere length. {ECO:0000269 PubMed:25848748}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PARN

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

No data available for Genatlas 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 22 64
  2. CUG-BP binds to RNA substrates and recruits PARN deadenylase. (PMID: 16601207) Moraes K.C. … Wilusz J. (RNA 2006) 3 4 22 64
  3. Structural insight into poly(A) binding and catalytic mechanism of human PARN. (PMID: 16281054) Wu M. … Song H. (EMBO J. 2005) 3 4 22 64
  4. A KH domain RNA binding protein, KSRP, promotes ARE-directed mRNA turnover by recruiting the degradation machinery. (PMID: 15175153) Gherzi R. … Chen C.-Y. (Mol. Cell 2004) 3 4 22 64
  5. Coordination of divalent metal ions in the active site of poly(A)- specific ribonuclease. (PMID: 15358788) Ren Y.-G. … Virtanen A. (J. Biol. Chem. 2004) 3 4 22 64

Products for PARN Gene

Sources for PARN Gene

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