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Pnldc1 poly(A)-specific ribonuclease (PARN)-like domain containing 1 [ Mus musculus (house mouse) ]

Gene ID: 240023, updated on 11-Apr-2024

Summary

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Official Symbol
Pnldc1provided by MGI
Official Full Name
poly(A)-specific ribonuclease (PARN)-like domain containing 1provided by MGI
Primary source
MGI:MGI:2685159
See related
Ensembl:ENSMUSG00000073460 AllianceGenome:MGI:2685159
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Gm313
Summary
Enables poly(A)-specific ribonuclease activity. Involved in nuclear-transcribed mRNA poly(A) tail shortening. Acts upstream of or within blastocyst formation. Located in endoplasmic reticulum. Is expressed in several structures, including early conceptus; gonad; and skin. Human ortholog(s) of this gene implicated in spermatogenic failure. Orthologous to human PNLDC1 (PARN like ribonuclease domain containing exonuclease 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis adult (RPKM 2.5), subcutaneous fat pad adult (RPKM 1.5) and 24 other tissues See more
Orthologs
human all
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Genomic context

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See Pnldc1 in Genome Data Viewer
Location:
17 A1; 17 8.71 cM
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (13107610..13129489, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (12888723..12910580, complement)

Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene MAS1 oncogene Neighboring gene predicted gene, 53988 Neighboring gene MAS-related GPR, member H Neighboring gene STARR-positive B cell enhancer ABC_E2471 Neighboring gene mitochondrial ribosomal protein L18 Neighboring gene predicted gene, 26130 Neighboring gene t-complex protein 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. An essential role for PNLDC1 in piRNA 3' end trimming and male fertility in mice. Zhang Y, et al. Cell Res, 2017 Nov. PMID 28994417, Free PMC Article
  2. PNLDC1, mouse pre-piRNA Trimmer, is required for meiotic and post-meiotic male germ cell development. Nishimura T, et al. EMBO Rep, 2018 Mar. PMID 29444933, Free PMC Article
  3. PNLDC1 is essential for piRNA 3' end trimming and transposon silencing during spermatogenesis in mice. Ding D, et al. Nat Commun, 2017 Oct 10. PMID 29018194, Free PMC Article
  4. Mammalian PNLDC1 is a novel poly(A) specific exonuclease with discrete expression during early development. Anastasakis D, et al. Nucleic Acids Res, 2016 Oct 14. PMID 27515512, Free PMC Article
  5. Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors. Sun YH, et al. Nat Cell Biol, 2020 Feb. PMID 32015435, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PNLDC1/PARN-1 has a conserved role in 3' trimming during piRNA maturation.
    Title: An essential role for PNLDC1 in piRNA 3' end trimming and male fertility in mice.
  2. PNLDC1-mediated piRNA trimming is indispensable for the function of piRNAs throughout mouse spermatogenesis.
    Title: PNLDC1, mouse pre-piRNA Trimmer, is required for meiotic and post-meiotic male germ cell development.
  3. PNLDC1 is a regulator of piRNA biogenesis, transposon silencing and spermatogenesis, protecting the germline genome in mice.
    Title: PNLDC1 is essential for piRNA 3' end trimming and transposon silencing during spermatogenesis in mice.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

General gene information

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Markers

Homology

Clone Names

  • FLJ35820

Gene Ontology Provided by MGI

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 exonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables poly(A)-specific ribonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables poly(A)-specific ribonuclease activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within blastocyst formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within 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 nuclear-transcribed mRNA poly(A) tail shortening IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nuclear-transcribed mRNA poly(A) tail shortening ISO
Inferred from Sequence Orthology
more info
  
involved_in piRNA processing ISO
Inferred from Sequence Orthology
more info
  
involved_in priRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in siRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spermatogenesis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
poly(A)-specific ribonuclease PNLDC1
Names
PARN-like domain-containing protein 1
poly(A)-specific ribonuclease PARN-like domain-containing protein 1
poly(A)-specific ribonuclease domain-containing protein 1
NP_001030038.1
XP_006523388.1
XP_006523389.1
XP_011244512.1
XP_017172953.1

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_001034866.1 → NP_001030038.1  poly(A)-specific ribonuclease PNLDC1

    See identical proteins and their annotated locations for NP_001030038.1

    Status: PROVISIONAL

    Source sequence(s)
    BC158033
    Consensus CDS
    CCDS49948.1
    UniProtKB/Swiss-Prot
    B2RXZ1
    Related
    ENSMUSP00000129377.2, ENSMUST00000163394.3
    Conserved Domains (1) summary
    pfam04857
    Location:3 → 373
    CAF1; CAF1 family ribonuclease

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000083.7 Reference GRCm39 C57BL/6J

    Range
    13107610..13129489 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006523325.4 → XP_006523388.1  poly(A)-specific ribonuclease PNLDC1 isoform X1

    Conserved Domains (1) summary
    pfam04857
    Location:3 → 368
    CAF1; CAF1 family ribonuclease

  2. XM_017317464.3 → XP_017172953.1  poly(A)-specific ribonuclease PNLDC1 isoform X4

    Conserved Domains (1) summary
    pfam04857
    Location:113 → 241
    CAF1; CAF1 family ribonuclease

  3. XM_006523326.3 → XP_006523389.1  poly(A)-specific ribonuclease PNLDC1 isoform X2

    Conserved Domains (1) summary
    pfam04857
    Location:199 → 327
    CAF1; CAF1 family ribonuclease

  4. XM_011246210.1 → XP_011244512.1  poly(A)-specific ribonuclease PNLDC1 isoform X3

    Conserved Domains (1) summary
    pfam04857
    Location:199 → 327
    CAF1; CAF1 family ribonuclease
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
B2RXZ1.1 GenPept UniProtKB/Swiss-Prot:B2RXZ1

Gene LinkOut

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