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XRN1 5'-3' exoribonuclease 1 [ Homo sapiens (human) ]

Gene ID: 54464, updated on 3-Nov-2024

Summary

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Official Symbol
XRN1provided by HGNC
Official Full Name
5'-3' exoribonuclease 1provided by HGNC
Primary source
HGNC:HGNC:30654
See related
Ensembl:ENSG00000114127 MIM:607994; AllianceGenome:HGNC:30654
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SEP1
Summary
This gene encodes a member of the 5'-3' exonuclease family. The encoded protein may be involved in replication-dependent histone mRNA degradation, and interacts directly with the enhancer of mRNA-decapping protein 4. In addition to mRNA metabolism, a similar protein in yeast has been implicated in a variety of nuclear and cytoplasmic functions, including homologous recombination, meiosis, telomere maintenance, and microtubule assembly. Mutations in this gene are associated with osteosarcoma, suggesting that the encoded protein may also play a role in bone formation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
Expression
Ubiquitous expression in appendix (RPKM 6.9), lymph node (RPKM 6.5) and 25 other tissues See more
Orthologs
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Genomic context

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See XRN1 in Genome Data Viewer
Location:
3q23
Exon count:
43
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (142306610..142448037, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (145053903..145195321, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (142025452..142166879, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene transcription factor Dp-2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14784 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:141868031-141868531 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14787 Neighboring gene NANOG hESC enhancer GRCh37_chr3:141883131-141883866 Neighboring gene RNA, U6 small nuclear 425, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14788 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14789 Neighboring gene glycerol kinase 5 Neighboring gene NANOG hESC enhancer GRCh37_chr3:141961954-141962455 Neighboring gene Sharpr-MPRA regulatory region 12219 Neighboring gene RNA, U6 small nuclear 1294, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr3:142162923-142163129 Neighboring gene RNA, U1 small nuclear 100, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20642 Neighboring gene EIF2AK1 pseudogene 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:142203676-142204875 Neighboring gene ATR serine/threonine kinase Neighboring gene SUCLG2 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Cloning and characterization of human Sep1 (hSEP1) gene and cytoplasmic localization of its product. Sato Y, et al. DNA Res, 1998 Aug 31. PMID 9802570
  2. The human homolog of yeast SEP1 is a novel candidate tumor suppressor gene in osteogenic sarcoma. Zhang K, et al. Gene, 2002 Oct 2. PMID 12426100
  3. Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1. Charley PA, et al. J Biol Chem, 2018 Jan 5. PMID 29118186, Free PMC Article
  4. Degradation of initiator tRNAMet by Xrn1/2 via its accumulation in the nucleus of heat-treated HeLa cells. Watanabe K, et al. Nucleic Acids Res, 2013 Apr. PMID 23471000, Free PMC Article
  5. Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences. Boehm V, et al. Nat Commun, 2016 Dec 5. PMID 27917860, Free PMC Article

See all (137) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Host 5'-3' Exoribonuclease XRN1 Acts as a Proviral Factor for Measles Virus Replication by Downregulating the dsRNA-Activated Kinase PKR.
    Title: Host 5'-3' Exoribonuclease XRN1 Acts as a Proviral Factor for Measles Virus Replication by Downregulating the dsRNA-Activated Kinase PKR.
  2. Dysregulated non-coding telomerase RNA component and associated exonuclease XRN1 in leucocytes from women developing preeclampsia-possible link to enhanced senescence.
    Title: Dysregulated non-coding telomerase RNA component and associated exonuclease XRN1 in leucocytes from women developing preeclampsia-possible link to enhanced senescence.
  3. Cellular 5'-3' mRNA Exoribonuclease XRN1 Inhibits Interferon Beta Activation and Facilitates Influenza A Virus Replication.
    Title: Cellular 5'-3' mRNA Exoribonuclease XRN1 Inhibits Interferon Beta Activation and Facilitates Influenza A Virus Replication.
  4. Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs.
    Title: Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs.
  5. We show that knockdown of human XRN1, CNOT6 and ETF1 genes in HepG2 cells led to significant alteration in stability of specific mRNAs, alterations in half-life were inversely associated with transcription rates, mostly not resulting in changes in abundance
    Title: mRNA levels are buffered upon knockdown of RNA decay and translation factors via adjustment of transcription rates in human HepG2 cells.
  6. Another decapping activator PatL1 directly interacts with CIR and alleviates the CIR-mediated inhibition of CCR4-NOT activity in vitro. Ribosome profiling revealed that XRN1 loss impacts not only on mRNA levels but also on the translational efficiency of many cellular transcripts likely as a consequence of incomplete decay
    Title: A low-complexity region in human XRN1 directly recruits deadenylation and decapping factors in 5'-3' messenger RNA decay.
  7. This work provides insight into the role of the RNA decay factor Xrn1/XRN1 as a post-transcriptional regulator of autophagy.
    Title: The exoribonuclease Xrn1 is a post-transcriptional negative regulator of autophagy.
  8. Authors use a series of assays to demonstrate that the 3'-terminal portion of the nucleocapsid (N) mRNA of Rift Valley fever virus can effectively stall and repress XRN1. The region responsible for impeding XRN1 includes a G-rich portion that likely forms a G-quadruplex structure. The 3'-terminal portions of ambisense-derived transcripts of multiple arenaviruses also stalled XRN1.
    Title: Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1.
  9. Insertion of 5'-3' exoribonuclease 1 (XRN1)-resistant sequences (xrRNAs) into different reporter mRNAs allowed to monitor RNA decay activity by the nonsense-mediated mRNA decay pathway (NMD).
    Title: Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences.
  10. These findings suggest that sequestration of the exoribonucleases DIS3L2 and XRN1 to nuclear inclusions may be related to the pathogenesis of intranuclear inclusion body disease
    Title: Immunohistochemical localization of exoribonucleases (DIS3L2 and XRN1) in intranuclear inclusion body disease.
Submit: New GeneRIF Correction See all GeneRIFs (18)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag Cellular biotinylated 5'-3' exoribonuclease 1 protein (XRN1) is incorporated into HIV-1 Gag virus-like particles PubMed

Go to the HIV-1, Human Interaction Database

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

Clone Names

  • FLJ41903, DKFZp434P0721, DKFZp686B22225, DKFZp686F19113

Gene Ontology Provided by GOA

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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables 5'-3' RNA exonuclease activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables G-quadruplex DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables G-quadruplex RNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables RNA binding HDA 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 IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to cycloheximide IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to puromycin IEA
Inferred from Electronic Annotation
more info
  
involved_in histone mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of telomere maintenance via telomerase IC
Inferred by Curator
more info
 PubMed 
involved_in negative regulation of translation IEA
Inferred from Electronic Annotation
more info
  
involved_in nuclear mRNA surveillance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nuclear-transcribed mRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nuclear-transcribed mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in rRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in rRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to testosterone IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in P-body IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
located_in neuronal cell body IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
5'-3' exoribonuclease 1
Names
strand-exchange protein 1 homolog
NP_001269786.1
NP_001269788.1
NP_061874.3
XP_006713736.1
XP_011511221.1
XP_011511222.1
XP_016862129.1
XP_016862130.1
XP_016862131.1
XP_047304312.1
XP_047304313.1
XP_047304314.1
XP_047304315.1
XP_054202903.1
XP_054202904.1
XP_054202905.1
XP_054202906.1
XP_054202907.1
XP_054202908.1
XP_054202909.1
XP_054202910.1
XP_054202911.1
XP_054202912.1

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_001282857.2 → NP_001269786.1  5'-3' exoribonuclease 1 isoform c

    See identical proteins and their annotated locations for NP_001269786.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (c) is shorter, compared to isoform a.
    Source sequence(s)
    AC023508, AC109992, AK096177
    Consensus CDS
    CCDS63801.1
    UniProtKB/Swiss-Prot
    Q8IZH2
    Related
    ENSP00000376707.2, ENST00000392981.7
    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

  2. NM_001282859.2 → NP_001269788.1  5'-3' exoribonuclease 1 isoform d

    See identical proteins and their annotated locations for NP_001269788.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (d) has a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AK096177, BC039314
    Consensus CDS
    CCDS75028.1
    UniProtKB/Swiss-Prot
    Q8IZH2
    Related
    ENSP00000418404.1, ENST00000463916.5
    Conserved Domains (1) summary
    pfam03159
    Location:1 → 226
    XRN_N; XRN 5'-3' exonuclease N-terminus

  3. NM_019001.5 → NP_061874.3  5'-3' exoribonuclease 1 isoform a

    See identical proteins and their annotated locations for NP_061874.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC023508, AK096177, AL133623, AY137776
    Consensus CDS
    CCDS3123.1
    UniProtKB/Swiss-Prot
    Q4G0S3, Q68D88, Q6AI24, Q6MZS8, Q86WS7, Q8IZH2, Q8N8U4, Q9UF39
    Related
    ENSP00000264951.4, ENST00000264951.8
    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_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    142306610..142448037 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047448357.1 → XP_047304313.1  5'-3' exoribonuclease 1 isoform X6

  2. XM_047448356.1 → XP_047304312.1  5'-3' exoribonuclease 1 isoform X4

  3. XM_017006640.2 → XP_016862129.1  5'-3' exoribonuclease 1 isoform X2

  4. XM_017006641.2 → XP_016862130.1  5'-3' exoribonuclease 1 isoform X5

  5. XM_011512920.3 → XP_011511222.1  5'-3' exoribonuclease 1 isoform X3

    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

  6. XM_011512919.3 → XP_011511221.1  5'-3' exoribonuclease 1 isoform X1

    Conserved Domains (1) summary
    COG5049
    Location:1 → 735
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]

  7. XM_047448358.1 → XP_047304314.1  5'-3' exoribonuclease 1 isoform X7

  8. XM_047448359.1 → XP_047304315.1  5'-3' exoribonuclease 1 isoform X8

  9. XM_017006642.2 → XP_016862131.1  5'-3' exoribonuclease 1 isoform X9

  10. XM_006713673.3 → XP_006713736.1  5'-3' exoribonuclease 1 isoform X10

    UniProtKB/TrEMBL
    B3KW17
    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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    145053903..145195321 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346933.1 → XP_054202908.1  5'-3' exoribonuclease 1 isoform X6

  2. XM_054346931.1 → XP_054202906.1  5'-3' exoribonuclease 1 isoform X4

  3. XM_054346929.1 → XP_054202904.1  5'-3' exoribonuclease 1 isoform X2

  4. XM_054346932.1 → XP_054202907.1  5'-3' exoribonuclease 1 isoform X5

  5. XM_054346930.1 → XP_054202905.1  5'-3' exoribonuclease 1 isoform X3

  6. XM_054346928.1 → XP_054202903.1  5'-3' exoribonuclease 1 isoform X1

  7. XM_054346934.1 → XP_054202909.1  5'-3' exoribonuclease 1 isoform X7

  8. XM_054346935.1 → XP_054202910.1  5'-3' exoribonuclease 1 isoform X8

  9. XM_054346936.1 → XP_054202911.1  5'-3' exoribonuclease 1 isoform X9

  10. XM_054346937.1 → XP_054202912.1  5'-3' exoribonuclease 1 isoform X10

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001042604.1: Suppressed sequence

    Description
    NM_001042604.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IZH2.1 GenPept UniProtKB/Swiss-Prot:Q8IZH2

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