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Xrn1 5'-3' exoribonuclease 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 300944, updated on 13-Apr-2024

Summary

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Symbol
Xrn1provided by RGD
Full Name
5'-3' exoribonuclease 1provided by RGD
Primary source
RGD:1309713
See related
Ensembl:ENSRNOG00000042951 AllianceGenome:RGD:1309713
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
RGD1309713
Summary
Predicted to enable 5'-3' exoribonuclease activity; G-quadruplex DNA binding activity; and G-quadruplex RNA binding activity. Involved in cellular response to organonitrogen compound; negative regulation of translation; and response to testosterone. Located in several cellular components, including P-body; dendrite; and neuronal cell 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
Biased expression in Spleen (RPKM 89.5), Thymus (RPKM 86.0) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
8q31
Exon count:
45
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (105407785..105516967)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (96527871..96637385)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (103774125..103883563)

Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene plastin 1 Neighboring gene uncharacterized LOC120094232 Neighboring gene BCL2 interacting protein 3, pseudogene 2 Neighboring gene ATR serine/threonine kinase Neighboring gene uncharacterized LOC120094234 Neighboring gene glycerol kinase 5 Neighboring gene uncharacterized LOC134480216 Neighboring gene transcription factor Dp-2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. A monoclonal antibody against p53 cross-reacts with processing bodies. Thomas MG, et al. PLoS One, 2012. PMID 22590546, Free PMC Article
  2. Synaptic control of mRNA translation by reversible assembly of XRN1 bodies. Luchelli L, et al. J Cell Sci, 2015 Apr 15. PMID 25736288
  3. Beta-amyloid toxicity modifier genes and the risk of Alzheimer's disease. Rosenthal SL, et al. Am J Neurodegener Dis, 2012. PMID 22984654, Free PMC Article
  4. A dual yet opposite growth-regulating function of miR-204 and its target XRN1 in prostate adenocarcinoma cells and neuroendocrine-like prostate cancer cells. Ding M, et al. Oncotarget, 2015 Apr 10. PMID 25797256, Free PMC Article
  5. A mouse cytoplasmic exoribonuclease (mXRN1p) with preference for G4 tetraplex substrates. Bashkirov VI, et al. J Cell Biol, 1997 Feb 24. PMID 9049243, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by RGD

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 ISO
Inferred from Sequence Orthology
more info
  
enables G-quadruplex DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables G-quadruplex RNA binding ISO
Inferred from Sequence Orthology
more info
  
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cellular response to cycloheximide IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in cellular response to puromycin IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in histone mRNA catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of translation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 response to testosterone IEP
Inferred from Expression Pattern
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 ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in dendrite IDA
Inferred from Direct Assay
more info
 PubMed 
located_in neuronal cell body IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
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
NP_001292169.1
XP_006243656.1
XP_006243658.1
XP_006243660.1
XP_008764795.1
XP_038937098.1
XP_038937099.1
XP_038937100.1
XP_038937101.1
XP_063121279.1
XP_063121280.1
XP_063121281.1
XP_063121282.1
XP_217233.5

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_001305240.1 → NP_001292169.1  5'-3' exoribonuclease 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000008
    UniProtKB/TrEMBL
    A6I270
    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_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086026.1 Reference GRCr8

    Range
    105407785..105516967
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006243594.5 → XP_006243656.1  5'-3' exoribonuclease 1 isoform X1

    See identical proteins and their annotated locations for XP_006243656.1

    UniProtKB/TrEMBL
    A6I270
    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

  2. XM_006243596.5 → XP_006243658.1  5'-3' exoribonuclease 1 isoform X3

    See identical proteins and their annotated locations for XP_006243658.1

    UniProtKB/TrEMBL
    A6I270
    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

  3. XM_217233.11 → XP_217233.5  5'-3' exoribonuclease 1 isoform X4

    See identical proteins and their annotated locations for XP_217233.5

    UniProtKB/TrEMBL
    A6I270, D4ABN8
    Related
    ENSRNOP00000014481.6
    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

  4. XM_006243598.5 → XP_006243660.1  5'-3' exoribonuclease 1 isoform X6

    See identical proteins and their annotated locations for XP_006243660.1

    UniProtKB/TrEMBL
    A6I270
    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

  5. XM_039081171.2 → XP_038937099.1  5'-3' exoribonuclease 1 isoform X7

    UniProtKB/TrEMBL
    A6I270
    Conserved Domains (5) summary
    COG5049
    Location:1 → 735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam18129
    Location:1101 → 1171
    SH3_12; Xrn1 SH3-like domain
    pfam18332
    Location:658 → 843
    XRN1_D1; Exoribonuclease Xrn1 D1 domain
    pfam18334
    Location:853 → 934
    XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
    cl00054
    Location:1443 → 1508
    DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

  6. XM_063265210.1 → XP_063121280.1  5'-3' exoribonuclease 1 isoform X8

  7. XM_039081170.2 → XP_038937098.1  5'-3' exoribonuclease 1 isoform X2

    UniProtKB/TrEMBL
    A6I270
    Conserved Domains (5) summary
    COG5049
    Location:1 → 733
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam18129
    Location:1099 → 1169
    SH3_12; Xrn1 SH3-like domain
    pfam18332
    Location:656 → 841
    XRN1_D1; Exoribonuclease Xrn1 D1 domain
    pfam18334
    Location:851 → 932
    XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
    cl00054
    Location:1476 → 1541
    DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

  8. XM_063265209.1 → XP_063121279.1  5'-3' exoribonuclease 1 isoform X5

  9. XM_039081172.2 → XP_038937100.1  5'-3' exoribonuclease 1 isoform X10

    Conserved Domains (4) summary
    COG5049
    Location:1 → 735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam18129
    Location:1101 → 1171
    SH3_12; Xrn1 SH3-like domain
    pfam18332
    Location:658 → 843
    XRN1_D1; Exoribonuclease Xrn1 D1 domain
    pfam18334
    Location:853 → 934
    XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain

  10. XM_008766573.4 → XP_008764795.1  5'-3' exoribonuclease 1 isoform X12

    See identical proteins and their annotated locations for XP_008764795.1

    UniProtKB/TrEMBL
    A0A8I5XWP1
    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

  11. XM_063265212.1 → XP_063121282.1  5'-3' exoribonuclease 1 isoform X13

  12. XM_063265211.1 → XP_063121281.1  5'-3' exoribonuclease 1 isoform X9

  13. XM_039081173.1 → XP_038937101.1  5'-3' exoribonuclease 1 isoform X11

    Conserved Domains (4) summary
    pfam18129
    Location:524 → 594
    SH3_12; Xrn1 SH3-like domain
    pfam18332
    Location:81 → 266
    XRN1_D1; Exoribonuclease Xrn1 D1 domain
    pfam18334
    Location:276 → 357
    XRN1_D2_D3; Exoribonuclease Xrn1 D2/D3 domain
    cl00054
    Location:901 → 966
    DSRM_SF; double-stranded RNA binding motif (DSRM) superfamily

RNA

  1. XR_010053953.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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