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Parn poly(A)-specific ribonuclease [ Rattus norvegicus (Norway rat) ]

Gene ID: 360464, updated on 2-Nov-2024

Summary

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Official Symbol
Parnprovided by RGD
Official Full Name
poly(A)-specific ribonucleaseprovided by RGD
Primary source
RGD:1565449
See related
EnsemblRapid:ENSRNOG00000002912 AllianceGenome:RGD:1565449
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
RGD1565449
Summary
Predicted to enable several functions, including poly(A)-specific ribonuclease activity; protein kinase binding activity; and telomerase RNA binding activity. Predicted to be involved in RNA metabolic process; regulation of nucleobase-containing compound metabolic process; and regulation of telomerase RNA localization to Cajal body. Is active in glutamatergic synapse and postsynapse. Human ortholog(s) of this gene implicated in autosomal recessive dyskeratosis congenita 6. Orthologous to human PARN (poly(A)-specific ribonuclease). [provided by Alliance of Genome Resources, Nov 2024]
Annotation information
Note: This gene aligns across a gap in the Rnor_6.0 reference genome assembly, and therefore, annotation of this gene is split across NW_007905911.1 and NW_007905912.1 in NCBI's Rattus norvegicus Annotation Release 105. [18 Jun 2015]
Expression
Biased expression in Spleen (RPKM 83.1), Thymus (RPKM 78.5) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Parn in Genome Data Viewer
Location:
10q11
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (1917830..2055749, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (1410636..1548573, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (1309724..1461123, complement)

Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102547286 Neighboring gene uncharacterized LOC134480737 Neighboring gene uncharacterized LOC120095007 Neighboring gene dynein light chain LC8-type 1 like Neighboring gene bifunctional apoptosis regulator 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Coordination of divalent metal ions in the active site of poly(A)-specific ribonuclease. Ren YG, et al. J Biol Chem, 2004 Nov 19. PMID 15358788
  2. Poly(A)-specific ribonuclease (PARN) mediates 3'-end maturation of the telomerase RNA component. Moon DH, et al. Nat Genet, 2015 Dec. PMID 26482878, Free PMC Article
  3. Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming. Berndt H, et al. RNA, 2012 May. PMID 22442037, Free PMC Article
  4. The BTG2 protein is a general activator of mRNA deadenylation. Mauxion F, et al. EMBO J, 2008 Apr 9. PMID 18337750, Free PMC Article
  5. PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. Boele J, et al. Proc Natl Acad Sci U S A, 2014 Aug 5. PMID 25049417, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables 3'-5'-RNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cation binding ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables poly(A)-specific ribonuclease activity ISO
Inferred from Sequence Orthology
more info
  
enables protein kinase binding ISO
Inferred from Sequence Orthology
more info
  
enables telomerase RNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in box H/ACA sno(s)RNA 3'-end processing ISO
Inferred from Sequence Orthology
more info
  
involved_in lncRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in lncRNA processing ISO
Inferred from Sequence Orthology
more info
  
involved_in miRNA catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in nuclear-transcribed mRNA poly(A) tail shortening IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within nuclear-transcribed mRNA poly(A) tail shortening ISO
Inferred from Sequence Orthology
more info
  
involved_in poly(A)-dependent snoRNA 3'-end processing ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of telomere maintenance via telomerase ISO
Inferred from Sequence Orthology
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
involved_in siRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in telomerase RNA stabilization ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in postsynapse IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
poly(A)-specific ribonuclease PARN
Names
poly(A)-specific ribonuclease (deadenylation nuclease)
NP_001257344.1
XP_038942176.1
XP_038942177.1
XP_038942178.1
XP_038942179.1
XP_038942181.1
XP_038942182.1
XP_038942183.1
XP_038942184.1
XP_063125341.1
XP_063125342.1
XP_063125343.1
XP_063125344.1
XP_063125345.1
XP_063125347.1
XP_063125348.1

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.

mRNA and Protein(s)

  1. NM_001270415.3 → NP_001257344.1  poly(A)-specific ribonuclease PARN

    See identical proteins and their annotated locations for NP_001257344.1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000010
    UniProtKB/TrEMBL
    A0A0G2QC45, A6K4E3
    Related
    ENSRNOP00000073884.4, ENSRNOT00000078421.4
    Conserved Domains (2) summary
    pfam04857
    Location:3 → 383
    CAF1; CAF1 family ribonuclease
    pfam08675
    Location:431 → 505
    RNA_bind; RNA binding domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086028.1 Reference GRCr8

    Range
    1917830..2055749 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039086248.2 → XP_038942176.1  poly(A)-specific ribonuclease PARN isoform X1

    UniProtKB/TrEMBL
    A6K4E3
    Conserved Domains (2) summary
    pfam04857
    Location:5 → 383
    CAF1; CAF1 family ribonuclease
    pfam08675
    Location:431 → 505
    RNA_bind; RNA binding domain

  2. XM_039086249.2 → XP_038942177.1  poly(A)-specific ribonuclease PARN isoform X2

    UniProtKB/TrEMBL
    A6K4E3
    Conserved Domains (2) summary
    pfam04857
    Location:5 → 382
    CAF1; CAF1 family ribonuclease
    pfam08675
    Location:430 → 504
    RNA_bind; RNA binding domain

  3. XM_039086251.2 → XP_038942179.1  poly(A)-specific ribonuclease PARN isoform X4

    UniProtKB/TrEMBL
    A6K4E3
    Conserved Domains (2) summary
    pfam04857
    Location:5 → 357
    CAF1; CAF1 family ribonuclease
    pfam08675
    Location:405 → 479
    RNA_bind; RNA binding domain

  4. XM_039086250.2 → XP_038942178.1  poly(A)-specific ribonuclease PARN isoform X3

    UniProtKB/TrEMBL
    A6K4E3
    Conserved Domains (2) summary
    pfam04857
    Location:5 → 383
    CAF1; CAF1 family ribonuclease
    cl17169
    Location:431 → 480
    RRM_SF; RNA recognition motif (RRM) superfamily

  5. XM_063269275.1 → XP_063125345.1  poly(A)-specific ribonuclease PARN isoform X9

  6. XM_063269274.1 → XP_063125344.1  poly(A)-specific ribonuclease PARN isoform X8

  7. XM_063269272.1 → XP_063125342.1  poly(A)-specific ribonuclease PARN isoform X6

    Related
    ENSRNOP00000100699.1, ENSRNOT00000163464.1

  8. XM_063269271.1 → XP_063125341.1  poly(A)-specific ribonuclease PARN isoform X5

  9. XM_063269273.1 → XP_063125343.1  poly(A)-specific ribonuclease PARN isoform X7

    Related
    ENSRNOP00000100067.1, ENSRNOT00000140097.1

  10. XM_063269278.1 → XP_063125348.1  poly(A)-specific ribonuclease PARN isoform X12

  11. XM_039086254.2 → XP_038942182.1  poly(A)-specific ribonuclease PARN isoform X12

    Conserved Domains (2) summary
    pfam04857
    Location:1 → 102
    CAF1; CAF1 family ribonuclease
    pfam08675
    Location:150 → 224
    RNA_bind; RNA binding domain

  12. XM_039086255.2 → XP_038942183.1  poly(A)-specific ribonuclease PARN isoform X13

    Conserved Domains (2) summary
    pfam04857
    Location:1 → 77
    CAF1; CAF1 family ribonuclease
    pfam08675
    Location:125 → 199
    RNA_bind; RNA binding domain

  13. XM_063269277.1 → XP_063125347.1  poly(A)-specific ribonuclease PARN isoform X10

    UniProtKB/TrEMBL
    A0A0G2K386, A0A0G2K6N8
    Related
    ENSRNOP00000070962.4, ENSRNOT00000083125.4

  14. XM_039086253.2 → XP_038942181.1  poly(A)-specific ribonuclease PARN isoform X11

    Conserved Domains (2) summary
    pfam04857
    Location:5 → 383
    CAF1; CAF1 family ribonuclease
    cl17169
    Location:431 → 463
    RRM_SF; RNA recognition motif (RRM) superfamily

  15. XM_039086256.2 → XP_038942184.1  poly(A)-specific ribonuclease PARN isoform X14

    Conserved Domains (1) summary
    pfam04857
    Location:5 → 353
    CAF1; CAF1 family ribonuclease

RNA

  1. XR_005489883.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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