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    Patl1 PAT1 homolog 1, processing body mRNA decay factor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361736, updated on 10-Jul-2024

    Summary

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    Official Symbol
    Patl1provided by RGD
    Official Full Name
    PAT1 homolog 1, processing body mRNA decay factorprovided by RGD
    Primary source
    RGD:1305514
    See related
    EnsemblRapid:ENSRNOG00000021052 AllianceGenome:RGD:1305514
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Pat1b; RGD1305514
    Summary
    Predicted to enable poly(G) binding activity and poly(U) RNA binding activity. Predicted to be involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Predicted to be located in cytoplasmic ribonucleoprotein granule and cytosol. Predicted to be active in P-body. Orthologous to human PATL1 (PAT1 homolog 1, processing body mRNA decay factor). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 60.6), Kidney (RPKM 58.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Patl1 in Genome Data Viewer
    Location:
    1q43
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (218255801..218287662)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (208831115..208862904)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (228337756..228369719)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene U4 spliceosomal RNA Neighboring gene olfactory receptor family 10 subfamily V member 9B Neighboring gene olfactory receptor family 10 subfamily V member 1 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene small nucleolar RNA SNORA32 Neighboring gene small Cajal body-specific RNA 23 like 1 Neighboring gene ribosomal protein L27A like 8 Neighboring gene oxysterol binding protein

    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. The human Pat1b protein: a novel mRNA deadenylation factor identified by a new immunoprecipitation technique. Totaro A, et al. Nucleic Acids Res, 2011 Jan. PMID 20852261, Free PMC Article
    2. The role of disordered protein regions in the assembly of decapping complexes and RNP granules. Jonas S, et al. Genes Dev, 2013 Dec 15. PMID 24352420, Free PMC Article
    3. The C-terminal alpha-alpha superhelix of Pat is required for mRNA decapping in metazoa. Braun JE, et al. EMBO J, 2010 Jul 21. PMID 20543818, Free PMC Article
    4. Distinct functions of maternal and somatic Pat1 protein paralogs. Marnef A, et al. RNA, 2010 Nov. PMID 20826699, Free PMC Article
    5. Human Pat1b connects deadenylation with mRNA decapping and controls the assembly of processing bodies. Ozgur S, et al. Mol Cell Biol, 2010 Sep. PMID 20584987, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables poly(G) binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables poly(U) RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in P-body assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in P-body assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in P-body assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in deadenylation-dependent decapping of nuclear-transcribed mRNA IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in deadenylation-dependent decapping of nuclear-transcribed mRNA IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in deadenylation-dependent decapping of nuclear-transcribed mRNA ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in deadenylation-dependent decapping of nuclear-transcribed mRNA ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of CCR4-NOT complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of CCR4-NOT complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in P-body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in P-body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in P-body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in PML body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasmic ribonucleoprotein granule ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein PAT1 homolog 1
    Names
    PAT1-like protein 1
    protein PAT1 homolog b
    protein associated with topoisomerase II homolog 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_001108520.2 → NP_001101990.1  protein PAT1 homolog 1

      See identical proteins and their annotated locations for NP_001101990.1

      Status: PROVISIONAL

      Source sequence(s)
      BC168974
      UniProtKB/Swiss-Prot
      B5DF93
      UniProtKB/TrEMBL
      A0A8I5ZRW2
      Related
      ENSRNOP00000059542.2, ENSRNOT00000066247.5
      Conserved Domains (1) summary
      cl22451
      Location:8 → 104
      ASF1_hist_chap; ASF1 like histone chaperone

    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_086019.1 Reference GRCr8

      Range
      218255801..218287662
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063268467.1 → XP_063124537.1  protein PAT1 homolog 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZRW2

    2. XM_063268466.1 → XP_063124536.1  protein PAT1 homolog 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZRW2

    3. XM_039084308.2 → XP_038940236.1  protein PAT1 homolog 1 isoform X3

      Conserved Domains (1) summary
      pfam09770
      Location:12 → 394
      PAT1; Topoisomerase II-associated protein PAT1
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B5DF93.1 GenPept UniProtKB/Swiss-Prot:B5DF93

    Gene LinkOut

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

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