Xrn1 5'-3' exoribonuclease 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Xrn1provided by MGI
Official Full Name: 5'-3' exoribonuclease 1provided by MGI
Primary source: MGI:MGI:891964
See related: Ensembl:ENSMUSG00000032410 AllianceGenome:MGI:891964
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
Also known as: exo; Dhm2; mXrn1
Summary: Enables 5'-3' exoribonuclease activity; G-quadruplex DNA binding activity; and G-quadruplex RNA binding activity. Involved in RNA phosphodiester bond hydrolysis, exonucleolytic. Located in P-body. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human XRN1 (5'-3' exoribonuclease 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in limb E14.5 (RPKM 4.0), whole brain E14.5 (RPKM 4.0) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9; 9 E3.3

Exon count:: 44

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (95836803..95939859)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (95954750..96057806)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m(6)A recognition.
Title: The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m(6)A recognition.
XRN1 knockdown impairs the translational repression triggered by NMDA. Collectively, these observations support a role for the SX-bodies in the reversible masking and silencing of mRNAs at the synapse.
Title: Synaptic control of mRNA translation by reversible assembly of XRN1 bodies.

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Variation

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Alleles

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

Endonuclease-mediated (4) 1 citation
Gene trapped (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

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	ISO Inferred from Sequence Orthology more info
enables 5'-3' RNA exonuclease activity	TAS Traceable Author Statement more info	PubMed
enables 5'-3' exonuclease activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables G-quadruplex DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables G-quadruplex RNA binding	IDA Inferred from Direct Assay more info	PubMed
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 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

Process	Evidence Code	Pubs
involved_in RNA processing	TAS Traceable Author Statement more info	PubMed
involved_in histone mRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in meiotic cell cycle	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of translation	ISO Inferred from Sequence Orthology more info
involved_in nuclear mRNA surveillance	ISO Inferred from Sequence Orthology more info
involved_in nuclear-transcribed mRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in rRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in rRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance	IC Inferred by Curator more info	PubMed
involved_in telomere maintenance	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in P-body	IDA Inferred from Direct Assay more info	PubMed
located_in P-body	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: 5'-3' exoribonuclease 1

Names: protein Dhm2; strand-exchange protein 1 homolog

NP_001298059.1

EC 3.1.13.-

NP_036046.2

EC 3.1.13.-

XP_006511217.1

EC 3.1.13.-

XP_006511218.1

EC 3.1.13.-

XP_006511219.1

EC 3.1.13.-

XP_011241045.1

EC 3.1.13.-

XP_036010829.1

EC 3.1.13.-

XP_036010830.1

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_001311130.1 → NP_001298059.1 5'-3' exoribonuclease 1 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.

Source sequence(s)

AC121499, AK052194, AK143400, AK162932, BB202930, BC054108

Consensus CDS

CCDS81053.1

UniProtKB/Swiss-Prot

O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5

UniProtKB/TrEMBL

A0A087WQN7

Related

ENSMUSP00000140278.2, ENSMUST00000185633.7

Conserved Domains (2) summary

COG5049
Location:1 → 735

XRN1; 5'-3' exonuclease [Replication, recombination and repair]

pfam03159
Location:1 → 226

XRN_N; XRN 5'-3' exonuclease N-terminus
NM_011916.3 → NP_036046.2 5'-3' exoribonuclease 1 isoform 1

See identical proteins and their annotated locations for NP_036046.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC121499, AK052194, AK143400, AK162932, BB202930, BC054108

Consensus CDS

CCDS40728.1

UniProtKB/Swiss-Prot

O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5

UniProtKB/TrEMBL

F8VQ87

Related

ENSMUSP00000034981.8, ENSMUST00000034981.14

Conserved Domains (2) summary

COG5049
Location:1 → 735

XRN1; 5'-3' exonuclease [Replication, recombination and repair]

pfam03159
Location:1 → 226

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_000075.7 Reference GRCm39 C57BL/6J

Range

95836803..95939859

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006511154.4 → XP_006511217.1 5'-3' exoribonuclease 1 isoform X1

UniProtKB/Swiss-Prot

O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5

Conserved Domains (5) summary

COG5049
Location:1 → 735

XRN1; 5'-3' exonuclease [Replication, recombination and repair]

pfam18332
Location:658 → 843

XRN1_D1; Exoribonuclease Xrn1 D1 domain

pfam18334
Location:853 → 934

XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain

pfam18129
Location:1101 → 1171

SH3_12; Xrn1 SH3-like domain

cl00054
Location:1473 → 1538

DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily
XM_006511155.4 → XP_006511218.1 5'-3' exoribonuclease 1 isoform X2

UniProtKB/Swiss-Prot

O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5

Conserved Domains (5) summary

COG5049
Location:1 → 735

XRN1; 5'-3' exonuclease [Replication, recombination and repair]

pfam18332
Location:658 → 843

XRN1_D1; Exoribonuclease Xrn1 D1 domain

pfam18334
Location:853 → 934

XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain

pfam18129
Location:1101 → 1171

SH3_12; Xrn1 SH3-like domain

cl00054
Location:1469 → 1534

DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily
XM_036154936.1 → XP_036010829.1 5'-3' exoribonuclease 1 isoform X3

UniProtKB/Swiss-Prot

O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5

Conserved Domains (5) summary

COG5049
Location:1 → 659

XRN1; 5'-3' exonuclease [Replication, recombination and repair]

pfam18129
Location:1025 → 1095

SH3_12; Xrn1 SH3-like domain

pfam18332
Location:582 → 767

XRN1_D1; Exoribonuclease Xrn1 D1 domain

pfam18334
Location:777 → 858

XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain

cl00054
Location:1397 → 1462

DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily
XM_011242743.4 → XP_011241045.1 5'-3' exoribonuclease 1 isoform X5

Conserved Domains (4) summary

COG5049
Location:1 → 735

XRN1; 5'-3' exonuclease [Replication, recombination and repair]

pfam18332
Location:658 → 843

XRN1_D1; Exoribonuclease Xrn1 D1 domain

pfam18334
Location:853 → 934

XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain

pfam18129
Location:1101 → 1171

SH3_12; Xrn1 SH3-like domain
XM_006511156.2 → XP_006511219.1 5'-3' exoribonuclease 1 isoform X4

UniProtKB/Swiss-Prot

O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5

Conserved Domains (5) summary

COG5049
Location:1 → 653

XRN1; 5'-3' exonuclease [Replication, recombination and repair]

pfam18332
Location:576 → 761

XRN1_D1; Exoribonuclease Xrn1 D1 domain

pfam18334
Location:771 → 852

XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain

pfam18129
Location:1019 → 1089

SH3_12; Xrn1 SH3-like domain

cl00054
Location:1391 → 1456

DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily
XM_036154937.1 → XP_036010830.1 5'-3' exoribonuclease 1 isoform X6

Conserved Domains (2) summary

pfam18129
Location:244 → 314

SH3_12; Xrn1 SH3-like domain

cl00054
Location:616 → 681

DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily