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    Patl1 protein associated with topoisomerase II homolog 1 (yeast) [ Mus musculus (house mouse) ]

    Gene ID: 225929, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Patl1provided by MGI
    Official Full Name
    protein associated with topoisomerase II homolog 1 (yeast)provided by MGI
    Primary source
    MGI:MGI:2147679
    See related
    Ensembl:ENSMUSG00000046139 AllianceGenome:MGI:2147679
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Pat1b
    Summary
    Predicted to enable RNA binding activity and translation repressor activity. Predicted to be involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Predicted to act upstream of or within negative regulation of translation. Predicted to be located in cytoplasmic ribonucleoprotein granule and cytosol. Predicted to be part of CCR4-NOT complex. Predicted to be active in P-body. Is expressed in heart; male reproductive gland or organ; metanephros; and pancreas. Orthologous to human PATL1 (PAT1 homolog 1, processing body mRNA decay factor). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 13.6), whole brain E14.5 (RPKM 11.1) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Patl1 in Genome Data Viewer
    Location:
    19 A; 19 8.57 cM
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (11889728..11922462)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (11912399..11945096)

    Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene predicted pseudogene 6365 Neighboring gene predicted gene, 31092 Neighboring gene olfactory receptor family 10 subfamily V member 1 Neighboring gene STARR-positive B cell enhancer ABC_E9000 Neighboring gene STARR-positive B cell enhancer ABC_E3244 Neighboring gene microRNA 6994 Neighboring gene predicted gene, 22272 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:12039881-12040064 Neighboring gene uncharacterized protein C11orf98 homolog pseudogene 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: Mouse ENCODE transcriptome data 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. Distinct functions of maternal and somatic Pat1 protein paralogs. Marnef A, et al. RNA, 2010 Nov. PMID 20826699, Free PMC Article
    2. Identification and developmental analysis of genes expressed by dopaminergic neurons of the substantia nigra pars compacta. Thuret S, et al. Mol Cell Neurosci, 2004 Mar. PMID 15033168
    3. Proteomic and yeast 2-hybrid screens to identify PTEN binding partners. Tibarewal P, et al. Adv Biol Regul, 2024 Jan. PMID 37839992
    4. New roles for the de-ubiquitylating enzyme OTUD4 in an RNA-protein network and RNA granules. Das R, et al. J Cell Sci, 2019 Jun 17. PMID 31138677, Free PMC Article
    5. Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method. Piao Y, et al. Genome Res, 2001 Sep. PMID 11544199, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2) 

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • D430024J04

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables G-quadruplex RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    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
    		 PubMed 
    enables poly(U) RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    enables translation repressor activity ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    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 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 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
    		  
    acts_upstream_of_or_within negative regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    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 ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    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 cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    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

    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_001426305.1 → NP_001413234.1  protein PAT1 homolog 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC124464, AC126266

    2. NM_172635.4 → NP_766223.2  protein PAT1 homolog 1 isoform 1

      See identical proteins and their annotated locations for NP_766223.2

      Status: VALIDATED

      Source sequence(s)
      AC124464, AC126266
      Consensus CDS
      CCDS37924.1
      UniProtKB/Swiss-Prot
      Q3TC46, Q3TD30, Q3U4Q3, Q3UD09, Q6PD49, Q8BN50, Q8C3S7
      Related
      ENSMUSP00000060398.8, ENSMUST00000061618.9
      Conserved Domains (1) summary
      cl22451
      Location:8 → 104
      ASF1_hist_chap; ASF1 like histone chaperone

    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_000085.7 Reference GRCm39 C57BL/6J

      Range
      11889728..11922462
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036161548.1 → XP_036017441.1  protein PAT1 homolog 1 isoform X3

      Conserved Domains (2) summary
      pfam09770
      Location:241 → 436
      PAT1; Topoisomerase II-associated protein PAT1
      cl22451
      Location:8 → 104
      ASF1_hist_chap; ASF1 like histone chaperone

    2. XM_036161547.1 → XP_036017440.1  protein PAT1 homolog 1 isoform X1

      Conserved Domains (1) summary
      pfam09770
      Location:166 → 538
      PAT1; Topoisomerase II-associated protein PAT1

    RNA

    1. XR_004940138.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3TC46.2 GenPept UniProtKB/Swiss-Prot:Q3TC46

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