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    Xrn1 5'-3' exoribonuclease 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 300944, updated on 27-Nov-2024

    Summary

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    Symbol
    Xrn1provided by RGD
    Full Name
    5'-3' exoribonuclease 1provided by RGD
    Primary source
    RGD:1309713
    See related
    EnsemblRapid:ENSRNOG00000042951 AllianceGenome:RGD:1309713
    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
    Also known as
    RGD1309713
    Summary
    Predicted to enable 5'-3' RNA exonuclease activity and nucleic acid binding activity. Involved in several processes, including cellular response to cycloheximide; cellular response to puromycin; and response to testosterone. Located in P-body; dendrite; and neuronal cell body. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human XRN1 (5'-3' exoribonuclease 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 89.5), Thymus (RPKM 86.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Xrn1 in Genome Data Viewer
    Location:
    8q31
    Exon count:
    45
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (105407785..105516967)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (96527871..96637385)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (103774125..103883563)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene plastin 1 Neighboring gene uncharacterized LOC120094232 Neighboring gene BCL2 interacting protein 3, pseudogene 2 Neighboring gene ATR serine/threonine kinase Neighboring gene uncharacterized LOC120094234 Neighboring gene glycerol kinase 5 Neighboring gene uncharacterized LOC134480216 Neighboring gene transcription factor Dp-2

    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. A monoclonal antibody against p53 cross-reacts with processing bodies. Thomas MG, et al. PLoS One, 2012. PMID 22590546, Free PMC Article
    2. Synaptic control of mRNA translation by reversible assembly of XRN1 bodies. Luchelli L, et al. J Cell Sci, 2015 Apr 15. PMID 25736288
    3. Beta-amyloid toxicity modifier genes and the risk of Alzheimer's disease. Rosenthal SL, et al. Am J Neurodegener Dis, 2012. PMID 22984654, Free PMC Article
    4. A dual yet opposite growth-regulating function of miR-204 and its target XRN1 in prostate adenocarcinoma cells and neuroendocrine-like prostate cancer cells. Ding M, et al. Oncotarget, 2015 Apr 10. PMID 25797256, Free PMC Article
    5. A mouse cytoplasmic exoribonuclease (mXRN1p) with preference for G4 tetraplex substrates. Bashkirov VI, et al. J Cell Biol, 1997 Feb 24. PMID 9049243, Free PMC Article

    See all (15) 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 5'-3' RNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 5'-3' RNA exonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables G-quadruplex DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables G-quadruplex RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables telomerase RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cellular response to cycloheximide IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in cellular response to puromycin IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in histone mRNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of translation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear mRNA surveillance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in rRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in rRNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to testosterone IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in P-body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in P-body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm 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 dendrite IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in neuronal cell body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    5'-3' exoribonuclease 1
    NP_001292169.1
    XP_006243656.1
    XP_006243658.1
    XP_006243660.1
    XP_008764795.1
    XP_038937098.1
    XP_038937099.1
    XP_038937100.1
    XP_038937101.1
    XP_063121279.1
    XP_063121280.1
    XP_063121281.1
    XP_063121282.1
    XP_217233.5

    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_001305240.1 → NP_001292169.1  5'-3' exoribonuclease 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A6I270
      Related
      ENSRNOP00000014481.7, ENSRNOT00000014481.10
      Conserved Domains (2) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 226
      XRN_N; XRN 5'-3' exonuclease N-terminus

    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_086026.1 Reference GRCr8

      Range
      105407785..105516967
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006243594.5 → XP_006243656.1  5'-3' exoribonuclease 1 isoform X1

      See identical proteins and their annotated locations for XP_006243656.1

      UniProtKB/TrEMBL
      A6I270
      Conserved Domains (2) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 226
      XRN_N; XRN 5'-3' exonuclease N-terminus

    2. XM_006243596.5 → XP_006243658.1  5'-3' exoribonuclease 1 isoform X3

      See identical proteins and their annotated locations for XP_006243658.1

      UniProtKB/TrEMBL
      A6I270
      Conserved Domains (2) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 226
      XRN_N; XRN 5'-3' exonuclease N-terminus

    3. XM_217233.11 → XP_217233.5  5'-3' exoribonuclease 1 isoform X4

      See identical proteins and their annotated locations for XP_217233.5

      UniProtKB/TrEMBL
      A6I270, D4ABN8
      Conserved Domains (2) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 226
      XRN_N; XRN 5'-3' exonuclease N-terminus

    4. XM_006243598.5 → XP_006243660.1  5'-3' exoribonuclease 1 isoform X6

      See identical proteins and their annotated locations for XP_006243660.1

      UniProtKB/TrEMBL
      A6I270
      Conserved Domains (2) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 226
      XRN_N; XRN 5'-3' exonuclease N-terminus

    5. XM_039081171.2 → XP_038937099.1  5'-3' exoribonuclease 1 isoform X7

      UniProtKB/TrEMBL
      A6I270
      Conserved Domains (5) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam18129
      Location:1101 → 1171
      SH3_12; Xrn1 SH3-like domain
      pfam18332
      Location:658 → 843
      XRN1_D1; Exoribonuclease Xrn1 D1 domain
      pfam18334
      Location:853 → 934
      XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
      cl00054
      Location:1443 → 1508
      DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

    6. XM_063265210.1 → XP_063121280.1  5'-3' exoribonuclease 1 isoform X8

    7. XM_039081170.2 → XP_038937098.1  5'-3' exoribonuclease 1 isoform X2

      UniProtKB/TrEMBL
      A6I270
      Conserved Domains (5) summary
      COG5049
      Location:1 → 733
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam18129
      Location:1099 → 1169
      SH3_12; Xrn1 SH3-like domain
      pfam18332
      Location:656 → 841
      XRN1_D1; Exoribonuclease Xrn1 D1 domain
      pfam18334
      Location:851 → 932
      XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
      cl00054
      Location:1476 → 1541
      DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

    8. XM_063265209.1 → XP_063121279.1  5'-3' exoribonuclease 1 isoform X5

    9. XM_039081172.2 → XP_038937100.1  5'-3' exoribonuclease 1 isoform X10

      Conserved Domains (4) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam18129
      Location:1101 → 1171
      SH3_12; Xrn1 SH3-like domain
      pfam18332
      Location:658 → 843
      XRN1_D1; Exoribonuclease Xrn1 D1 domain
      pfam18334
      Location:853 → 934
      XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain

    10. XM_008766573.4 → XP_008764795.1  5'-3' exoribonuclease 1 isoform X12

      See identical proteins and their annotated locations for XP_008764795.1

      UniProtKB/TrEMBL
      A0A8I5XWP1
      Conserved Domains (2) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 226
      XRN_N; XRN 5'-3' exonuclease N-terminus

    11. XM_063265212.1 → XP_063121282.1  5'-3' exoribonuclease 1 isoform X13

    12. XM_063265211.1 → XP_063121281.1  5'-3' exoribonuclease 1 isoform X9

    13. XM_039081173.1 → XP_038937101.1  5'-3' exoribonuclease 1 isoform X11

      Conserved Domains (4) summary
      pfam18129
      Location:524 → 594
      SH3_12; Xrn1 SH3-like domain
      pfam18332
      Location:81 → 266
      XRN1_D1; Exoribonuclease Xrn1 D1 domain
      pfam18334
      Location:276 → 357
      XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
      cl00054
      Location:901 → 966
      DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

    RNA

    1. XR_010053953.1 RNA Sequence

      Related
      ENSRNOT00000102470.2
    Nucleotide Protein Strain
    Heading Accession and Version

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