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

Gene ID: 24127, updated on 18-Sep-2024

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
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Genomic context

See Xrn1 in Genome Data Viewer
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_000075.7Genomic Context describing neighboring genes Neighboring gene ataxia telangiectasia and Rad3 related Neighboring gene STARR-positive B cell enhancer ABC_E3852 Neighboring gene predicted gene, 24004 Neighboring gene predicted gene, 16794 Neighboring gene STARR-positive B cell enhancer ABC_E8307 Neighboring gene STARR-seq mESC enhancer starr_24940 Neighboring gene STARR-seq mESC enhancer starr_24941 Neighboring gene STARR-seq mESC enhancer starr_24942 Neighboring gene STARR-positive B cell enhancer ABC_E8308 Neighboring gene glycerol kinase 5 Neighboring gene STARR-seq mESC enhancer starr_24949 Neighboring gene transcription factor Dp 2 Neighboring gene predicted gene, 39408

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data 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

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4)  1 citation
  • Gene trapped (1) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 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 protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables telomerase RNA binding ISO
Inferred from Sequence Orthology
more info
 
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 histone mRNA catabolic process ISS
Inferred from Sequence or Structural Similarity
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

Preferred Names
5'-3' exoribonuclease 1
Names
protein Dhm2
strand-exchange protein 1 homolog
NP_001298059.1
NP_036046.2
XP_006511217.1
XP_006511218.1
XP_006511219.1
XP_011241045.1
XP_036010829.1
XP_036010830.1

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_001311130.1NP_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:1735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:1226
    XRN_N; XRN 5'-3' exonuclease N-terminus
  2. NM_011916.3NP_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:1735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:1226
    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_000075.7 Reference GRCm39 C57BL/6J

    Range
    95836803..95939859
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5
    Conserved Domains (5) summary
    COG5049
    Location:1735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam18332
    Location:658843
    XRN1_D1; Exoribonuclease Xrn1 D1 domain
    pfam18334
    Location:853934
    XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
    pfam18129
    Location:11011171
    SH3_12; Xrn1 SH3-like domain
    cl00054
    Location:14731538
    DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily
  2. XM_006511155.4XP_006511218.1  5'-3' exoribonuclease 1 isoform X2

    UniProtKB/Swiss-Prot
    O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5
    Conserved Domains (5) summary
    COG5049
    Location:1735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam18332
    Location:658843
    XRN1_D1; Exoribonuclease Xrn1 D1 domain
    pfam18334
    Location:853934
    XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
    pfam18129
    Location:11011171
    SH3_12; Xrn1 SH3-like domain
    cl00054
    Location:14691534
    DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily
  3. XM_036154936.1XP_036010829.1  5'-3' exoribonuclease 1 isoform X3

    UniProtKB/Swiss-Prot
    O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5
    Conserved Domains (5) summary
    COG5049
    Location:1659
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam18129
    Location:10251095
    SH3_12; Xrn1 SH3-like domain
    pfam18332
    Location:582767
    XRN1_D1; Exoribonuclease Xrn1 D1 domain
    pfam18334
    Location:777858
    XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
    cl00054
    Location:13971462
    DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily
  4. XM_011242743.4XP_011241045.1  5'-3' exoribonuclease 1 isoform X5

    Conserved Domains (4) summary
    COG5049
    Location:1735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam18332
    Location:658843
    XRN1_D1; Exoribonuclease Xrn1 D1 domain
    pfam18334
    Location:853934
    XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
    pfam18129
    Location:11011171
    SH3_12; Xrn1 SH3-like domain
  5. XM_006511156.2XP_006511219.1  5'-3' exoribonuclease 1 isoform X4

    UniProtKB/Swiss-Prot
    O35651, P97789, P97790, Q3TE44, Q3TRE9, Q3UQL5
    Conserved Domains (5) summary
    COG5049
    Location:1653
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam18332
    Location:576761
    XRN1_D1; Exoribonuclease Xrn1 D1 domain
    pfam18334
    Location:771852
    XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
    pfam18129
    Location:10191089
    SH3_12; Xrn1 SH3-like domain
    cl00054
    Location:13911456
    DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily
  6. XM_036154937.1XP_036010830.1  5'-3' exoribonuclease 1 isoform X6

    Conserved Domains (2) summary
    pfam18129
    Location:244314
    SH3_12; Xrn1 SH3-like domain
    cl00054
    Location:616681
    DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

RNA

  1. XR_001778898.2 RNA Sequence

  2. XR_004935435.1 RNA Sequence