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

Summary

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 exoribonuclease activity, producing 5'-phosphomonoesters; identical protein binding activity; and nucleic acid binding activity. Involved in RNA metabolic process. Acts upstream of or within 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, Apr 2022]
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

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_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Endonuclease-mediated (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH125855 (e-PCR)
- UniSTS:162593

NoName (e-PCR)
- UniSTS:234548

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 DNA binding	IEA Inferred from Electronic Annotation 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 hydrolase activity	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 nuclease activity	IEA Inferred from Electronic Annotation more info
enables nucleic acid 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

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
acts_upstream_of_or_within DNA-templated transcription termination	IEA Inferred from Electronic Annotation more info
involved_in RNA metabolic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in microtubule-based process	TAS Traceable Author Statement more info	PubMed
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 spermatogenesis	IEP Inferred from Expression Pattern more info	PubMed
involved_in termination of RNA polymerase II transcription	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in aggresome	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology 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

EC 3.1.13.-

NP_001343332.1

EC 3.1.13.-

NP_036047.2

EC 3.1.13.-

XP_011237821.1

EC 3.1.13.-

XP_030106843.1

EC 3.1.13.-

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)

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
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
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

NC_000068.8 Reference GRCm39 C57BL/6J

Range

146854672..146919922

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
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