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    Rat1 Rat1 5'-3' exoribonuclease [ Drosophila melanogaster (fruit fly) ]

    Gene ID: 33964, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Rat1provided by FlyBase
    Official Full Name
    Rat1 5'-3' exoribonucleaseprovided by FlyBase
    Primary source
    FLYBASE:FBgn0031868
    Locus tag
    Dmel_CG10354
    See related
    AllianceGenome:FB:FBgn0031868
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Drosophila melanogaster
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
    Also known as
    CG10354; dhp1; Dmel\CG10354; dRAT1; RAT1; Xrn2; XRN2
    Summary
    Enables 5'-3' RNA exonuclease activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process and termination of RNA polymerase II transcription. Located in nucleus. Is expressed in adult head and organism. 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, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See Rat1 in Genome Data Viewer
    Location:
    27C4-27C4; 2-23 cM
    Exon count:
    1
    Annotation release Status Assembly Chr Location
    Release 6.54 current Release 6 plus ISO1 MT (GCF_000001215.4) 2L NT_033779.5 (6908083..6911423)
    Release 5.57 previous assembly Release 5 (GCF_000001215.2) 2L NT_033779.4 (6908083..6911423)

    Chromosome 2L - NT_033779.5Genomic Context describing neighboring genes Neighboring gene Neuroligin 2 Neighboring gene mir-932 stem loop Neighboring gene RNA polymerase I subunit F Neighboring gene ncRNA Neighboring gene Wee1 kinase Neighboring gene uncharacterized protein Neighboring gene x16 splicing factor Neighboring gene nop5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Splice-site mutations cause Rrp6-mediated nuclear retention of the unspliced RNAs and transcriptional down-regulation of the splicing-defective genes. Eberle AB, et al. PLoS One, 2010 Jul 12. PMID 20634951, Free PMC Article
    2. The 5' → 3' exoribonuclease XRN1/Pacman and its functions in cellular processes and development. Jones CI, et al. Wiley Interdiscip Rev RNA, 2012 Jul-Aug. PMID 22383165
    3. Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila. Gatfield D, et al. Nature, 2004 Jun 3. PMID 15175755
    4. Antisense oligonucleotide technology can be used to investigate a circular but not linear RNA-mediated function for its encoded gene locus. Song Z, et al. Sci China Life Sci, 2021 May. PMID 32815066
    5. Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors. Chen YA, et al. Mol Cell, 2016 Jul 7. PMID 27292797, Free PMC Article

    See all (48) citations in PubMed

    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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    Homology

    Gene Ontology Provided by FlyBase

    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables 5'-3' exonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    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
    		  
    involved_in nucleobase-containing compound metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in termination of RNA polymerase II transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    Rat1 5'-3' exoribonuclease
    Names
    CG10354-PA
    CG10354-PB
    Rat1-PA
    Rat1-PB
    NP_001260166.1
    NP_609082.1

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NT_033779.5 Reference assembly

      Range
      6908083..6911423
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_135238.3 → NP_609082.1  Rat1 5'-3' exoribonuclease, isoform A [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_609082.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B8A3W7, M9PEY6, Q5BI90, Q9VM71
      Related
      FBpp0078973
      Conserved Domains (2) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 255
      XRN_N; XRN 5'-3' exonuclease N-terminus

    2. NM_001273237.1 → NP_001260166.1  Rat1 5'-3' exoribonuclease, isoform B [Drosophila melanogaster]

      See identical proteins and their annotated locations for NP_001260166.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B8A3W7, M9PEY6, Q5BI90, Q9VM71
      Conserved Domains (2) summary
      COG5049
      Location:1 → 735
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1 → 255
      XRN_N; XRN 5'-3' exonuclease N-terminus
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    M9PEY6 M9PEY6
    Q95RS5 Q95RS5
    Q9VM71.2 Q9VM71

    Gene LinkOut

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