U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 33964, updated on 10-May-2024

Summary

Go to the top of the page Help
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' exoribonuclease activity. Predicted to be involved in DNA catabolic process, exonucleolytic and nuclear-transcribed mRNA catabolic process. 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, Apr 2022]
Orthologs
all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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 (46) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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 exonuclease 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
  
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

Go to the top of the page Help
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)

Go to the top of the page Help

NEW Try the new Transcript table

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, Q5BI90, Q9VM71
    UniProtKB/TrEMBL
    M9PEY6
    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, Q5BI90, Q9VM71
    UniProtKB/TrEMBL
    M9PEY6
    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

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

Other Literature Sources
Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous