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    Xrn1 5'-3' exoribonuclease 1 [ Mus musculus (house mouse) ]

    Gene ID: 24127, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Xrn1provided by MGI
    Official Full Name
    5'-3' exoribonuclease 1provided by MGI
    Primary source
    MGI:MGI:891964
    See related
    Ensembl:ENSMUSG00000032410 AllianceGenome:MGI:891964
    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
    exo; Dhm2; mXrn1
    Summary
    Enables 5'-3' RNA exonuclease activity; G-quadruplex DNA binding activity; and G-quadruplex RNA binding activity. Predicted to be involved in RNA catabolic process and negative regulation of translation. Located in P-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, Dec 2024]
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 4.0), whole brain E14.5 (RPKM 4.0) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Xrn1 in Genome Data Viewer
    Location:
    9; 9 E3.3
    Exon count:
    44
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (95836803..95939859)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (95954750..96057806)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene ataxia telangiectasia and Rad3 related Neighboring gene STARR-positive B cell enhancer ABC_E3852 Neighboring gene predicted gene, 24004 Neighboring gene predicted gene, 16794 Neighboring gene STARR-positive B cell enhancer ABC_E8307 Neighboring gene STARR-seq mESC enhancer starr_24940 Neighboring gene STARR-seq mESC enhancer starr_24941 Neighboring gene STARR-seq mESC enhancer starr_24942 Neighboring gene STARR-positive B cell enhancer ABC_E8308 Neighboring gene glycerol kinase 5 Neighboring gene STARR-seq mESC enhancer starr_24949 Neighboring gene transcription factor Dp 2 Neighboring gene predicted gene, 39408

    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. Neuronal XRN1 is required for maintenance of whole-body metabolic homeostasis. Takaoka S, et al. iScience, 2021 Oct 22. PMID 34646989, Free PMC Article
    2. Cloning and characterization of mouse Dhm2 cDNA, a functional homolog of budding yeast SEP1. Shobuike T, et al. Gene, 1997 Jun 3. PMID 9218715
    3. Identification of human SEP1 as a glial cell line-derived neurotrophic factor-inducible protein and its expression in the nervous system. Shimoyama Y, et al. Neuroscience, 2003. PMID 14580940
    4. Synaptic control of mRNA translation by reversible assembly of XRN1 bodies. Luchelli L, et al. J Cell Sci, 2015 Apr 15. PMID 25736288
    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 (32) 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)
    • Endonuclease-mediated (4)  1 citation
    • Gene trapped (1) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 5'-3' RNA exonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables 5'-3' RNA exonuclease activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables G-quadruplex DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables G-quadruplex RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables telomerase RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA processing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in histone mRNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in histone mRNA catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in meiotic cell cycle NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 telomere maintenance IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in telomere maintenance NAS
    Non-traceable Author Statement
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in neuronal cell body ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    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
    Names
    protein Dhm2
    strand-exchange protein 1 homolog
    NP_001298059.1
    NP_036046.2
    XP_006511217.1
    XP_006511218.1
    XP_006511219.1
    XP_011241045.1
    XP_036010829.1
    XP_036010830.1

    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_001311130.1 → NP_001298059.1  5'-3' exoribonuclease 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AC121499, AK052194, AK143400, AK162932, BB202930, BC054108
      Consensus CDS
      CCDS81053.1
      UniProtKB/Swiss-Prot
      O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5
      UniProtKB/TrEMBL
      A0A087WQN7
      Related
      ENSMUSP00000140278.2, ENSMUST00000185633.7
      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. NM_011916.3 → NP_036046.2  5'-3' exoribonuclease 1 isoform 1

      See identical proteins and their annotated locations for NP_036046.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC121499, AK052194, AK143400, AK162932, BB202930, BC054108
      Consensus CDS
      CCDS40728.1
      UniProtKB/Swiss-Prot
      O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5
      UniProtKB/TrEMBL
      F8VQ87
      Related
      ENSMUSP00000034981.8, ENSMUST00000034981.14
      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_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_000075.7 Reference GRCm39 C57BL/6J

      Range
      95836803..95939859
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006511154.4 → XP_006511217.1  5'-3' exoribonuclease 1 isoform X1

      UniProtKB/Swiss-Prot
      O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5
      Conserved Domains (5) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam18332
      Location:658 → 843
      XRN1_D1; Exoribonuclease Xrn1 D1 domain
      pfam18334
      Location:853 → 934
      XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
      pfam18129
      Location:1101 → 1171
      SH3_12; Xrn1 SH3-like domain
      cl00054
      Location:1473 → 1538
      DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

    2. XM_006511155.4 → XP_006511218.1  5'-3' exoribonuclease 1 isoform X2

      UniProtKB/Swiss-Prot
      O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5
      Conserved Domains (5) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam18332
      Location:658 → 843
      XRN1_D1; Exoribonuclease Xrn1 D1 domain
      pfam18334
      Location:853 → 934
      XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
      pfam18129
      Location:1101 → 1171
      SH3_12; Xrn1 SH3-like domain
      cl00054
      Location:1469 → 1534
      DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

    3. XM_036154936.1 → XP_036010829.1  5'-3' exoribonuclease 1 isoform X3

      UniProtKB/Swiss-Prot
      O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5
      Conserved Domains (5) summary
      COG5049
      Location:1 → 659
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam18129
      Location:1025 → 1095
      SH3_12; Xrn1 SH3-like domain
      pfam18332
      Location:582 → 767
      XRN1_D1; Exoribonuclease Xrn1 D1 domain
      pfam18334
      Location:777 → 858
      XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
      cl00054
      Location:1397 → 1462
      DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

    4. XM_011242743.4 → XP_011241045.1  5'-3' exoribonuclease 1 isoform X5

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

    5. XM_006511156.2 → XP_006511219.1  5'-3' exoribonuclease 1 isoform X4

      UniProtKB/Swiss-Prot
      O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5
      Conserved Domains (5) summary
      COG5049
      Location:1 → 653
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam18332
      Location:576 → 761
      XRN1_D1; Exoribonuclease Xrn1 D1 domain
      pfam18334
      Location:771 → 852
      XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
      pfam18129
      Location:1019 → 1089
      SH3_12; Xrn1 SH3-like domain
      cl00054
      Location:1391 → 1456
      DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

    6. XM_036154937.1 → XP_036010830.1  5'-3' exoribonuclease 1 isoform X6

      Conserved Domains (2) summary
      pfam18129
      Location:244 → 314
      SH3_12; Xrn1 SH3-like domain
      cl00054
      Location:616 → 681
      DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

    RNA

    1. XR_001778898.2 RNA Sequence

    2. XR_004935435.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P97789.1 GenPept UniProtKB/Swiss-Prot:P97789

    Gene LinkOut

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

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