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Xrn2 5'-3' exoribonuclease 2 [ Mus musculus (house mouse) ]

Gene ID: 24128, updated on 27-Nov-2024

Summary

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Official Symbol
Xrn2provided by MGI
Official Full Name
5'-3' exoribonuclease 2provided by MGI
Primary source
MGI:MGI:894687
See related
Ensembl:ENSMUSG00000027433 AllianceGenome:MGI:894687
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
Summary
Predicted to enable RNA exonuclease activity, producing 5'-phosphomonoesters; identical protein binding activity; and nucleic acid binding activity. Involved in RNA metabolic process and spermatogenesis. Predicted to be located in aggresome; nucleolus; and nucleoplasm. 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]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 11.8), CNS E14 (RPKM 11.3) and 24 other tissues See more
Orthologs
human all
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Genomic context

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See Xrn2 in Genome Data Viewer
Location:
2 G2; 2 72.63 cM
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (146854672..146919922)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (147012755..147078000)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene kizuna centrosomal protein Neighboring gene translocase of inner mitochondrial membrane 23 homolog pseudogene Neighboring gene Mki67 (FHA domain) interacting nucleolar phosphoprotein pseudogene Neighboring gene STARR-seq mESC enhancer starr_05954 Neighboring gene STARR-seq mESC enhancer starr_05956 Neighboring gene STARR-seq mESC enhancer starr_05957 Neighboring gene predicted gene, 34889 Neighboring gene NK2 homeobox 4 Neighboring gene NK2 homeobox 2

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. 5'-end surveillance by Xrn2 acts as a shared mechanism for mammalian pre-rRNA maturation and decay. Wang M, et al. Nucleic Acids Res, 2011 Mar. PMID 21036871, Free PMC Article
  2. RNA degradation eliminates developmental transcripts during murine embryonic stem cell differentiation via CAPRIN1-XRN2. Viegas JO, et al. Dev Cell, 2022 Dec 19. PMID 36495875, Free PMC Article
  3. Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development. Nimura K, et al. Elife, 2016 Jun 22. PMID 27331609, Free PMC Article
  4. RNF8 ubiquitylation of XRN2 facilitates R-loop resolution and restrains genomic instability in BRCA1 mutant cells. Krishnan R, et al. Nucleic Acids Res, 2023 Oct 27. PMID 37697435, Free PMC Article
  5. Characterization of cDNA encoding mouse homolog of fission yeast dhp1+ gene: structural and functional conservation. Shobuike T, et al. Nucleic Acids Res, 1995 Feb 11. PMID 7885830, Free PMC Article

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RNF8 ubiquitylation of XRN2 facilitates R-loop resolution and restrains genomic instability in BRCA1 mutant cells.
    Title: RNF8 ubiquitylation of XRN2 facilitates R-loop resolution and restrains genomic instability in BRCA1 mutant cells.
  2. RNA degradation eliminates developmental transcripts during murine embryonic stem cell differentiation via CAPRIN1-XRN2.
    Title: RNA degradation eliminates developmental transcripts during murine embryonic stem cell differentiation via CAPRIN1-XRN2.
  3. Nkx2-5 genetically interacts with Xrn2 because Nkx2-5(+/-)Xrn2(+/-), but neither Nkx2-5(+/-)nor Xrn2(+/-), newborns exhibited a defect in ventricular septum formation, suggesting that the association between Nkx2-5 and Xrn2 is essential for heart development.
    Title: Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development.
  4. Genetic variants regulating Xrn2 expression in cis are determinants of spontaneous lung tumor susceptibility in mice and have genetic equivalents in lung cancer susceptibility in human beings.
    Title: Genetic variants cis-regulating Xrn2 expression contribute to the risk of spontaneous lung tumor.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3)  1 citation
  • Gene trapped (1) 

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 MGI

Function Evidence Code Pubs
enables 3'-5'-RNA exonuclease activity ISO
Inferred from Sequence Orthology
more info
  
enables 5'-3' RNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5'-3' RNA exonuclease activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables 5'-3' exonuclease activity ISO
Inferred from Sequence Orthology
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 identical protein binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription termination site sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables transcription termination site sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in DNA recombination NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in DNA repair NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in RNA metabolic process IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in hippocampus development IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in microtubule-based process TAS
Traceable Author Statement
more info
 PubMed 
involved_in neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in nuclear-transcribed mRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retina development in camera-type eye IEA
Inferred from Electronic Annotation
more info
  
involved_in spermatogenesis IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in termination of RNA polymerase II transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in termination of RNA polymerase II transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in aggresome IEA
Inferred from Electronic Annotation
more info
  
located_in aggresome ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
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 2
Names
protein Dhm1
NP_001343331.1
NP_001343332.1
NP_036047.2
XP_011237821.1
XP_030106843.1

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_001356402.1 → NP_001343331.1  5'-3' exoribonuclease 2 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AL928876
    Conserved Domains (1) summary
    cl27292
    Location:1 → 621
    XRN_N; XRN 5'-3' exonuclease N-terminus

  2. NM_001356403.1 → NP_001343332.1  5'-3' exoribonuclease 2 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AL928876
    Conserved Domains (1) summary
    cl27292
    Location:53 → 556
    XRN_N; XRN 5'-3' exonuclease N-terminus

  3. NM_011917.3 → NP_036047.2  5'-3' exoribonuclease 2 isoform 1

    See identical proteins and their annotated locations for NP_036047.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL928876
    Consensus CDS
    CCDS38258.1
    UniProtKB/Swiss-Prot
    Q3TI26, Q3TKF2, Q3UZT9, Q61489, Q99KS7, Q9DBR1
    Related
    ENSMUSP00000028921.6, ENSMUST00000028921.6
    Conserved Domains (2) summary
    COG5049
    Location:1 → 787
    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_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_000068.8 Reference GRCm39 C57BL/6J

    Range
    146854672..146919922
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011239519.4 → XP_011237821.1  5'-3' exoribonuclease 2 isoform X1

    Conserved Domains (1) summary
    COG5049
    Location:1 → 739
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]

  2. XM_030250983.2 → XP_030106843.1  5'-3' exoribonuclease 2 isoform X2

    Conserved Domains (1) summary
    pfam17846
    Location:72 → 362
    XRN_M; Xrn1 helical domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9DBR1.1 GenPept UniProtKB/Swiss-Prot:Q9DBR1

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