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

    Gene ID: 240023, updated on 12-May-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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    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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