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

    Gene ID: 54464, updated on 10-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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

      UniProtKB/TrEMBL
      B3KW17

    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.