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    xrn1 5'-3' exoribonuclease 1 [ Danio rerio (zebrafish) ]

    Gene ID: 394008, updated on 9-Dec-2024

    Summary

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    Official Symbol
    xrn1provided by ZNC
    Official Full Name
    5'-3' exoribonuclease 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-1203
    See related
    Ensembl:ENSDARG00000091652 AllianceGenome:ZFIN:ZDB-GENE-040426-1203
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:63635; wu:fk92c07
    Summary
    Predicted to enable 5'-3' RNA exonuclease activity and RNA binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process and rRNA catabolic process. Predicted to be located in cytoplasm. Predicted to be active in nucleus. 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]
    Orthologs
    human mouse all
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    Genomic context

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    See xrn1 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 2 NC_007113.7 (16596984..16647263)
    105 previous assembly GRCz10 (GCF_000002035.5) 2 NC_007113.6 (16928290..16978673)

    Chromosome 2 - NC_007113.7Genomic Context describing neighboring genes Neighboring gene ATPase Na+/K+ transporting subunit beta 3a Neighboring gene major histocompatibility complex class I HAA Neighboring gene glycerol kinase 5 Neighboring gene protein phosphatase 1, regulatory (inhibitor) subunit 7

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Depletion of Tissue-Specific Ion Transporters Causes Differential Expression of PRL Targets in Response to Increased Levels of Endogenous PRL. Shu T, et al. Front Endocrinol (Lausanne), 2018. PMID 30515132, Free PMC Article
    2. Sequential, Divergent, and Cooperative Requirements of Foxl2a and Foxl2b in Ovary Development and Maintenance of Zebrafish. Yang YJ, et al. Genetics, 2017 Apr. PMID 28193729, Free PMC Article
    3. Contrasted innate responses to two viruses in zebrafish: insights into the ancestral repertoire of vertebrate IFN-stimulated genes. Briolat V, et al. J Immunol, 2014 May 1. PMID 24683187
    4. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    5. 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

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC63635

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables 5'-3' RNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 5'-3' exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA exonuclease activity, producing 5'-phosphomonoesters IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in nuclear-transcribed mRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    5'-3' exoribonuclease 1
    NP_957327.2
    XP_005163374.1
    XP_005163375.1

    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_201033.2 → NP_957327.2  5'-3' exoribonuclease 1

      Status: VALIDATED

      Source sequence(s)
      CU929319
      UniProtKB/TrEMBL
      A0A8M1PFH0, F1Q4U5
      Related
      ENSDARP00000105487.1, ENSDART00000125413.4
      Conserved Domains (2) summary
      COG5049
      Location:1 → 734
      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_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007113.7 Reference GRCz11 Primary Assembly

      Range
      16596984..16647263
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005163318.5 → XP_005163375.1  5'-3' exoribonuclease 1 isoform X2

      UniProtKB/TrEMBL
      A0A8M2BAC4
      Conserved Domains (2) summary
      COG5049
      Location:1 → 734
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 226
      XRN_N; XRN 5'-3' exonuclease N-terminus

    2. XM_005163317.5 → XP_005163374.1  5'-3' exoribonuclease 1 isoform X1

      UniProtKB/TrEMBL
      A0A8M2BAQ6
      Conserved Domains (2) summary
      COG5049
      Location:1 → 733
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 226
      XRN_N; XRN 5'-3' exonuclease N-terminus
    Nucleotide Protein Strain
    Heading Accession and Version

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