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    Pan3 poly(A) specific ribonuclease subunit PAN3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 360760, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Pan3provided by RGD
    Official Full Name
    poly(A) specific ribonuclease subunit PAN3provided by RGD
    Primary source
    RGD:1590880
    See related
    EnsemblRapid:ENSRNOG00000000942 AllianceGenome:RGD:1590880
    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
    Summary
    Predicted to enable poly(A) binding activity. Predicted to contribute to poly(A)-specific ribonuclease activity. Predicted to be involved in nuclear-transcribed mRNA poly(A) tail shortening. Predicted to act upstream of or within deadenylation-dependent decapping of nuclear-transcribed mRNA; positive regulation of cytoplasmic mRNA processing body assembly; and protein targeting. Predicted to be part of PAN complex. Predicted to be active in P-body. Orthologous to human PAN3 (poly(A) specific ribonuclease subunit PAN3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 481.5), Spleen (RPKM 206.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pan3 in Genome Data Viewer
    Location:
    12p11
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (12512835..12637066, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (7476707..7595384, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (9214116..9331901, complement)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene Fms related receptor tyrosine kinase 1 Neighboring gene uncharacterized LOC102547586 Neighboring gene uncharacterized LOC120095883 Neighboring gene uncharacterized LOC134481261 Neighboring gene uncharacterized LOC134481260 Neighboring gene ribosomal protein L18A, pseudogene 2 Neighboring gene Fms related receptor tyrosine kinase 3

    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
    • 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. Identification of a human cytoplasmic poly(A) nuclease complex stimulated by poly(A)-binding protein. Uchida N, et al. J Biol Chem, 2004 Jan 9. PMID 14583602
    2. RNA decay machines: deadenylation by the Ccr4-not and Pan2-Pan3 complexes. Wahle E, et al. Biochim Biophys Acta, 2013 Jun-Jul. PMID 23337855
    3. Deadenylation is prerequisite for P-body formation and mRNA decay in mammalian cells. Zheng D, et al. J Cell Biol, 2008 Jul 14. PMID 18625844, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(A) binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to poly(A)-specific ribonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within deadenylation-dependent decapping of nuclear-transcribed mRNA ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA processing 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
    		  
    acts_upstream_of_or_within positive regulation of cytoplasmic mRNA processing body assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein targeting ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in P-body ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of PAN complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of PAN complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    PAN2-PAN3 deadenylation complex subunit PAN3
    Names
    PAB-dependent poly(A)-specific ribonuclease subunit PAN3
    PAN3 poly(A) specific ribonuclease subunit
    PAN3 polyA specific ribonuclease subunit homolog
    NP_001406717.1
    XP_006248904.1
    XP_038945852.1
    XP_038945853.1
    XP_038945854.1
    XP_038945855.1
    XP_038945856.1
    XP_038945857.1
    XP_038945858.1
    XP_063127509.1
    XP_063127511.1
    XP_346915.4

    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_001419788.1 → NP_001406717.1  PAN2-PAN3 deadenylation complex subunit PAN3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012
      Related
      ENSRNOP00000040388.7, ENSRNOT00000044134.8

    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_086030.1 Reference GRCr8

      Range
      12512835..12637066 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063271439.1 → XP_063127509.1  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X5

    2. XM_346914.10 → XP_346915.4  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X4

      UniProtKB/TrEMBL
      A0A8I5Y6J5
      Conserved Domains (2) summary
      pfam00642
      Location:51 → 70
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
      cl21453
      Location:435 → 603
      PKc_like; Protein Kinases, catalytic domain

    3. XM_039089924.2 → XP_038945852.1  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X2

      Conserved Domains (4) summary
      PRK11901
      Location:315 → 389
      PRK11901; hypothetical protein; Reviewed
      pfam00642
      Location:51 → 70
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
      pfam18101
      Location:737 → 874
      Pan3_PK; Pan3 Pseudokinase domain
      cl21453
      Location:488 → 656
      PKc_like; Protein Kinases, catalytic domain

    4. XM_006248842.5 → XP_006248904.1  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1

      UniProtKB/TrEMBL
      D4ADM2
      Related
      ENSRNOP00000106896.1, ENSRNOT00000125544.1
      Conserved Domains (2) summary
      pfam00642
      Location:51 → 70
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
      cl21453
      Location:489 → 657
      PKc_like; Protein Kinases, catalytic domain

    5. XM_039089925.2 → XP_038945853.1  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X3

      Conserved Domains (4) summary
      PRK11901
      Location:315 → 389
      PRK11901; hypothetical protein; Reviewed
      pfam00642
      Location:51 → 70
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
      pfam18101
      Location:738 → 875
      Pan3_PK; Pan3 Pseudokinase domain
      cl21453
      Location:489 → 657
      PKc_like; Protein Kinases, catalytic domain

    6. XM_039089926.2 → XP_038945854.1  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X6

      Conserved Domains (3) summary
      pfam05109
      Location:110 → 304
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam18101
      Location:607 → 744
      Pan3_PK; Pan3 Pseudokinase domain
      cl21453
      Location:358 → 526
      PKc_like; Protein Kinases, catalytic domain

    7. XM_039089927.2 → XP_038945855.1  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X7

      Conserved Domains (3) summary
      pfam05109
      Location:99 → 293
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam18101
      Location:596 → 733
      Pan3_PK; Pan3 Pseudokinase domain
      cl21453
      Location:347 → 515
      PKc_like; Protein Kinases, catalytic domain

    8. XM_039089930.2 → XP_038945858.1  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X9

      Conserved Domains (2) summary
      pfam18101
      Location:408 → 545
      Pan3_PK; Pan3 Pseudokinase domain
      cl21453
      Location:159 → 327
      PKc_like; Protein Kinases, catalytic domain

    9. XM_039089928.2 → XP_038945856.1  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X8

      Conserved Domains (3) summary
      PRK11901
      Location:2 → 62
      PRK11901; hypothetical protein; Reviewed
      pfam18101
      Location:411 → 548
      Pan3_PK; Pan3 Pseudokinase domain
      cl21453
      Location:162 → 330
      PKc_like; Protein Kinases, catalytic domain

    10. XM_063271441.1 → XP_063127511.1  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X9

    11. XM_039089929.2 → XP_038945857.1  PAN2-PAN3 deadenylation complex subunit PAN3 isoform X9

      Conserved Domains (2) summary
      pfam18101
      Location:408 → 545
      Pan3_PK; Pan3 Pseudokinase domain
      cl21453
      Location:159 → 327
      PKc_like; Protein Kinases, catalytic domain

    RNA

    1. XR_010056399.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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