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    xrn2 5'-3' exoribonuclease 2 [ Danio rerio (zebrafish) ]

    Gene ID: 321940, updated on 2-Nov-2024

    Summary

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    Official Symbol
    xrn2provided by ZNC
    Official Full Name
    5'-3' exoribonuclease 2provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-2874
    See related
    Ensembl:ENSDARG00000101900 AllianceGenome:ZFIN:ZDB-GENE-040426-2874
    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:55717; wu:fb38g12; wu:fj53d06
    Summary
    Predicted to enable 5'-3' RNA exonuclease activity and RNA binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process. Predicted to act upstream of or within nucleobase-containing compound metabolic process. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in adenoid cystic carcinoma and lung cancer. Orthologous to human XRN2 (5'-3' exoribonuclease 2). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See xrn2 in Genome Data Viewer
    Location:
    chromosome: 20
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 20 NC_007131.7 (48810491..48898560, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 20 NC_007131.6 (48979274..49067343, complement)

    Chromosome 20 - NC_007131.7Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 61 Neighboring gene NK2 homeobox 2b Neighboring gene NK2 homeobox 4b Neighboring gene uncharacterized LOC110438201 Neighboring gene uncharacterized LOC137488701 Neighboring gene microRNA mir-2193 Neighboring gene uncharacterized LOC137488702

    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 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. RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation. Rösel TD, et al. EMBO J, 2011 May 18. PMID 21468032, Free PMC Article
    2. A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos. Rosenthal SM, et al. Mol Cell Proteomics, 2021. PMID 34332124, Free PMC Article
    3. 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
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
    5. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    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

    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' RNA exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    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 metal ion binding 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
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within nucleobase-containing compound metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    5'-3' exoribonuclease 2
    NP_001001944.2
    XP_005160932.1

    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_001001944.2 → NP_001001944.2  5'-3' exoribonuclease 2

      Status: VALIDATED

      Source sequence(s)
      BX005124, CT573061
      UniProtKB/TrEMBL
      A0A0R4ISJ3, A0A8M1MZQ7
      Related
      ENSDARP00000138850.1, ENSDART00000163071.2
      Conserved Domains (2) summary
      COG5049
      Location:1 → 796
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 253
      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_007131.7 Reference GRCz11 Primary Assembly

      Range
      48810491..48898560 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005160875.5 → XP_005160932.1  5'-3' exoribonuclease 2 isoform X1

      UniProtKB/TrEMBL
      A0A8M2B7S3
      Conserved Domains (2) summary
      COG5049
      Location:1 → 782
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 253
      XRN_N; XRN 5'-3' exonuclease N-terminus
    Nucleotide Protein Strain
    Heading Accession and Version

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