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PARN poly(A)-specific ribonuclease [ Homo sapiens (human) ]

Gene ID: 5073, updated on 11-Apr-2024

Summary

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Official Symbol
PARNprovided by HGNC
Official Full Name
poly(A)-specific ribonucleaseprovided by HGNC
Primary source
HGNC:HGNC:8609
See related
Ensembl:ENSG00000140694 MIM:604212; AllianceGenome:HGNC:8609
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
DAN; DKCB6; PFBMFT4
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 11.4), testis (RPKM 9.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16p13.12
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (14435701..14630260, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (14473312..14667845, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (14529558..14724117, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:14458211-14458712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:14466520-14467096 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:14468174-14468349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:14469696-14470196 Neighboring gene long intergenic non-protein coding RNA 2130 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:14487195-14487694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:14499557-14500058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10498 Neighboring gene Sharpr-MPRA regulatory region 5329 Neighboring gene Sharpr-MPRA regulatory region 2182 Neighboring gene long intergenic non-protein coding RNA 3107 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:14539490-14539990 Neighboring gene Sharpr-MPRA regulatory region 750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:14579525-14580460 Neighboring gene uncharacterized LOC105371094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:14589500-14590022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:14590023-14590545 Neighboring gene NFE2L2 motif-containing MPRA enhancer 233 Neighboring gene Sharpr-MPRA regulatory regions 10217 and 14533 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:14616510-14617247 Neighboring gene uncharacterized LOC107984865 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:14626034-14626783 Neighboring gene RNA, 7SL, cytoplasmic 274, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:14723085-14723608 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:14723609-14724130 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:14724131-14724653 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:14726253-14726820 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:14726821-14727390 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:14730046-14730899 Neighboring gene RNA, U7 small nuclear 125 pseudogene Neighboring gene bifunctional apoptosis regulator Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:14781374-14781874 Neighboring gene phospholipase A2 group X

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Regulation of poly(a)-specific ribonuclease activity by reversible lysine acetylation. Dejene EA, et al. J Biol Chem, 2020 Jul 24. PMID 32457045, Free PMC Article
  2. Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN). Duan TL, et al. Cells, 2020 Jan 9. PMID 31936572, Free PMC Article
  3. The Intrinsically Disordered C-Terminal Domain Triggers Nucleolar Localization and Function Switch of PARN in Response to DNA Damage. Duan TL, et al. Cells, 2019 Aug 5. PMID 31387300, Free PMC Article
  4. Poly(A)-specific ribonuclease sculpts the 3' ends of microRNAs. Lee D, et al. RNA, 2019 Mar. PMID 30591540, Free PMC Article
  5. PARN Modulates Y RNA Stability and Its 3'-End Formation. Shukla S, et al. Mol Cell Biol, 2017 Oct 15. PMID 28760775, Free PMC Article

See all (105) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN).
    Title: Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN).
  2. Regulation of poly(a)-specific ribonuclease activity by reversible lysine acetylation.
    Title: Regulation of poly(a)-specific ribonuclease activity by reversible lysine acetylation.
  3. PARN regulates miRNA levels by stabilizing either mature or precursor miRNAs by removing oligo(A) tails added by the poly(A) polymerase PAPD5, which if remaining recruit the exonuclease DIS3L or DIS3L2 to degrade the miRNA. PARN knockdown destabilizes multiple miRNAs that repress p53 translation, leading to p53 accumulation.
    Title: The RNase PARN Controls the Levels of Specific miRNAs that Contribute to p53 Regulation.
  4. Study reports a family with idiopathic pulmonary fibrosis with a rare missense mutation, p.Y91C, and a novel insertion, p.(I274*) in PARN gene. PARN p.Y91C had reduced deadenylase activity and the p.(I274*) transcript was depleted.
    Title: From incomplete penetrance with normal telomere length to severe disease and telomere shortening in a family with monoallelic and biallelic PARN pathogenic variants.
  5. Impaired telomere integrity and rRNA biogenesis in PARN-deficient patients and knock-out models.
    Title: Impaired telomere integrity and rRNA biogenesis in PARN-deficient patients and knock-out models.
  6. Intrinsically disordered PARN C-terminal domain is required for PARN nuclear localization in response to DNA damage.
    Title: The Intrinsically Disordered C-Terminal Domain Triggers Nucleolar Localization and Function Switch of PARN in Response to DNA Damage.
  7. We find that mature hTR derives from extended precursors but that in PARN-mutant cells hTR maturation kinetically stalls and unprocessed precursors are degraded. Loss of poly(A)polymerase PAPD5 in PARN-mutant cells accelerates hTR maturation and restores hTR processing, indicating that oligoadenylation and deadenylation set rates of hTR maturation
    Title: Disruption of Telomerase RNA Maturation Kinetics Precipitates Disease.
  8. PARN and TOE1 do not modulate the length of mRNA poly(A) tails. Rather, they promote the maturation of nuclear small non-coding RNAs (ncRNAs). PARN and TOE1 act redundantly on some ncRNAs, most prominently small Cajal body-specific RNAs (scaRNAs).
    Title: PARN and TOE1 Constitute a 3' End Maturation Module for Nuclear Non-coding RNAs.
  9. PARN-mediated shortening is pervasive across most miRNAs and appears to be a conserved mechanism contributing to the 3' end formation of vertebrate miRNAs. Our findings add miRNAs to the expanding list of noncoding RNAs whose 3' end formation depends on PARN.
    Title: Poly(A)-specific ribonuclease sculpts the 3' ends of microRNAs.
  10. Processing of 3' telomerase RNA occurs in two steps with longer forms first being trimmed by RRP6 and shorter forms then being processed by PARN.
    Title: The H/ACA complex disrupts triplex in hTR precursor to permit processing by RRP6 and PARN.
Submit: New GeneRIF Correction See all GeneRIFs (45)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-5'-RNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cation binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables mRNA 3'-UTR binding TAS
Traceable Author Statement
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nuclease activity TAS
Traceable Author Statement
more info
 PubMed 
enables poly(A)-specific ribonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables poly(A)-specific ribonuclease activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables telomerase RNA binding IC
Inferred by Curator
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA modification TAS
Traceable Author Statement
more info
 PubMed 
involved_in box H/ACA sno(s)RNA 3'-end processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in female gamete generation TAS
Traceable Author Statement
more info
 PubMed 
involved_in miRNA catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in ncRNA deadenylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IEA
Inferred from Electronic Annotation
more info
  
involved_in nuclear-transcribed mRNA poly(A) tail shortening IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in poly(A)-dependent snoRNA 3'-end processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of telomerase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of telomere maintenance via telomerase IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in priRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of telomerase RNA localization to Cajal body IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in siRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in telomerase RNA stabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 
located_in postsynapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
poly(A)-specific ribonuclease PARN
Names
deadenylating nuclease
deadenylation nuclease
polyadenylate-specific ribonuclease
NP_001127949.1
NP_001229921.1
NP_002573.1
XP_011520816.1
XP_047290137.1
XP_047290138.1
XP_047290139.1
XP_047290140.1
XP_047290141.1
XP_054185071.1
XP_054185072.1
XP_054185073.1
XP_054185074.1
XP_054185075.1
XP_054185076.1
XP_054236386.1
XP_054236387.1
XP_054236388.1
XP_054236389.1
XP_054236390.1
XP_054236391.1
XP_054236392.1
XP_054236393.1
XP_054236394.1
XP_054236395.1
XP_054236396.1

NCBI Reference Sequences (RefSeq)

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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_042871.1 RefSeqGene

    Range
    5012..199571
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1286

mRNA and Protein(s)

  1. NM_001134477.3 → NP_001127949.1  poly(A)-specific ribonuclease PARN isoform 2

    See identical proteins and their annotated locations for NP_001127949.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate donor splice site in the 5' terminal exon compared to transcript variant 1, resulting in translation initiation from an alternate, in-frame downstream AUG and a shorter isoform (2) compared to isoform 1.
    Source sequence(s)
    AK023866, AK293189, BF435512
    Consensus CDS
    CCDS45420.1
    UniProtKB/TrEMBL
    A0A494C0W0
    Related
    ENSP00000345456.7, ENST00000341484.11
    Conserved Domains (2) summary
    pfam04857
    Location:1 → 329
    CAF1; CAF1 family ribonuclease
    pfam08675
    Location:377 → 451
    RNA_bind; RNA binding domain

  2. NM_001242992.2 → NP_001229921.1  poly(A)-specific ribonuclease PARN isoform 3

    See identical proteins and their annotated locations for NP_001229921.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses two alternate in-frame splice sites and lacks an alternate exon in the 5' coding region compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AK023866, AK301648, BF435512, DA308295
    Consensus CDS
    CCDS58425.1
    UniProtKB/TrEMBL
    A0A494C0K5
    Related
    ENSP00000410525.2, ENST00000420015.6
    Conserved Domains (2) summary
    pfam04857
    Location:3 → 344
    CAF1; CAF1 family ribonuclease
    pfam08675
    Location:392 → 466
    RNA_bind; RNA binding domain

  3. NM_002582.4 → NP_002573.1  poly(A)-specific ribonuclease PARN isoform 1

    See identical proteins and their annotated locations for NP_002573.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK023866, AK315020, BF435512
    Consensus CDS
    CCDS45419.1
    UniProtKB/Swiss-Prot
    B2RCB3, B4DDG8, B4DSB0, B4DWR4, B4E1H6, O95453
    UniProtKB/TrEMBL
    A0A494C0W0
    Related
    ENSP00000387911.2, ENST00000437198.7
    Conserved Domains (2) summary
    pfam08675
    Location:438 → 512
    RNA_bind; RNA binding domain
    pfam04857
    Location:3 → 390
    CAF1; CAF1 family ribonuclease

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    14435701..14630260 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047434184.1 → XP_047290140.1  poly(A)-specific ribonuclease PARN isoform X4

  2. XM_047434183.1 → XP_047290139.1  poly(A)-specific ribonuclease PARN isoform X3

  3. XM_047434181.1 → XP_047290137.1  poly(A)-specific ribonuclease PARN isoform X1

    Related
    ENSP00000499078.1, ENST00000651634.1

  4. XM_047434182.1 → XP_047290138.1  poly(A)-specific ribonuclease PARN isoform X2

    UniProtKB/TrEMBL
    A0A494C1N1
    Related
    ENSP00000499110.1, ENST00000650960.1

  5. XM_011522514.3 → XP_011520816.1  poly(A)-specific ribonuclease PARN isoform X5

    See identical proteins and their annotated locations for XP_011520816.1

    UniProtKB/TrEMBL
    A0A494C156
    Related
    ENSP00000498898.1, ENST00000652051.1
    Conserved Domains (1) summary
    pfam04857
    Location:3 → 390
    CAF1; CAF1 family ribonuclease

  6. XM_047434185.1 → XP_047290141.1  poly(A)-specific ribonuclease PARN isoform X6

    Related
    ENSP00000498315.1, ENST00000651348.1

RNA

  1. XR_007064884.1 RNA Sequence

  2. XR_007064883.1 RNA Sequence

  3. XR_007064882.1 RNA Sequence

  4. XR_007064881.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187607.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    8558..203161 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329096.1 → XP_054185071.1  poly(A)-specific ribonuclease PARN isoform X1

  2. XM_054329097.1 → XP_054185072.1  poly(A)-specific ribonuclease PARN isoform X2

    UniProtKB/TrEMBL
    A0A494C1N1

  3. XM_054329099.1 → XP_054185074.1  poly(A)-specific ribonuclease PARN isoform X4

  4. XM_054329098.1 → XP_054185073.1  poly(A)-specific ribonuclease PARN isoform X3

  5. XM_054329100.1 → XP_054185075.1  poly(A)-specific ribonuclease PARN isoform X5

  6. XM_054329101.1 → XP_054185076.1  poly(A)-specific ribonuclease PARN isoform X6

RNA

  1. XR_008485621.1 RNA Sequence

  2. XR_008485620.1 RNA Sequence

  3. XR_008485619.1 RNA Sequence

  4. XR_008485622.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    14473312..14667845 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054380414.1 → XP_054236389.1  poly(A)-specific ribonuclease PARN isoform X8

    UniProtKB/TrEMBL
    A0A494C1K5

  2. XM_054380413.1 → XP_054236388.1  poly(A)-specific ribonuclease PARN isoform X7

    UniProtKB/TrEMBL
    A0A494C0Q2

  3. XM_054380417.1 → XP_054236392.1  poly(A)-specific ribonuclease PARN isoform X9

  4. XM_054380421.1 → XP_054236396.1  poly(A)-specific ribonuclease PARN isoform X11

  5. XM_054380420.1 → XP_054236395.1  poly(A)-specific ribonuclease PARN isoform X10

  6. XM_054380411.1 → XP_054236386.1  poly(A)-specific ribonuclease PARN isoform X1

  7. XM_054380412.1 → XP_054236387.1  poly(A)-specific ribonuclease PARN isoform X2

    UniProtKB/TrEMBL
    A0A494C1N1

  8. XM_054380416.1 → XP_054236391.1  poly(A)-specific ribonuclease PARN isoform X4

  9. XM_054380415.1 → XP_054236390.1  poly(A)-specific ribonuclease PARN isoform X3

  10. XM_054380418.1 → XP_054236393.1  poly(A)-specific ribonuclease PARN isoform X5

  11. XM_054380419.1 → XP_054236394.1  poly(A)-specific ribonuclease PARN isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95453.1 GenPept UniProtKB/Swiss-Prot:O95453

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