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    XRN2 5'-3' exoribonuclease 2 [ Homo sapiens (human) ]

    Gene ID: 22803, updated on 3-Dec-2024

    Summary

    Official Symbol
    XRN2provided by HGNC
    Official Full Name
    5'-3' exoribonuclease 2provided by HGNC
    Primary source
    HGNC:HGNC:12836
    See related
    Ensembl:ENSG00000088930 MIM:608851; AllianceGenome:HGNC:12836
    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
    Summary
    This gene encodes a 5'-3' exonuclease that promotes transcription termination at cotranscriptional cleavage sites. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
    Expression
    Ubiquitous expression in appendix (RPKM 21.1), thyroid (RPKM 20.8) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See XRN2 in Genome Data Viewer
    Location:
    20p11.22
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (21303331..21389825)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (21362698..21446483)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (21283969..21370463)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene kizuna centrosomal protein Neighboring gene KIZ antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:21204767-21205280 Neighboring gene VISTA enhancer hs914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17621 Neighboring gene zinc finger protein 877, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:21272495-21272995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17624 Neighboring gene uncharacterized LOC105372558 Neighboring gene NK2 homeobox 4 Neighboring gene RN7SK pseudogene 140

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag Interaction of HIV-1 Gag with 5'-3' exoribonuclease 2 (XRN2) is identified in a series of six affinity purification/mass spectrometry screens 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'-5'-RNA exonuclease activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables 5'-3' RNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables 5'-3' RNA exonuclease activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables 5'-3' exonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nuclease activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription termination site sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in RNA catabolic process TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in RNA metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in RNA processing TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in hippocampus development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nuclear-transcribed mRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in rRNA processing TAS
    Traceable Author Statement
    more info
     
    involved_in retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spermatogenesis IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in termination of RNA polymerase II transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in aggresome IDA
    Inferred from Direct Assay
    more info
     
    located_in membrane HDA PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    5'-3' exoribonuclease 2
    Names
    DHM1-like protein
    DHP protein
    NP_001304889.1
    NP_036387.2
    XP_016883211.1
    XP_016883212.1
    XP_054179168.1
    XP_054179169.1

    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_001317960.1NP_001304889.1  5'-3' exoribonuclease 2 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AF152169, AK302846, AL117332, DC403143
      UniProtKB/TrEMBL
      B3KMC9
      Conserved Domains (2) summary
      COG5049
      Location:118865
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:113331
      XRN_N; XRN 5'-3' exonuclease N-terminus
    2. NM_012255.5NP_036387.2  5'-3' exoribonuclease 2 isoform 2

      See identical proteins and their annotated locations for NP_036387.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon, resulting in a distinct 5' UTR and the use of an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus , and is shorter, compared to isoform 1.
      Source sequence(s)
      AF152169, AL136841, BC142960
      Consensus CDS
      CCDS13144.1
      UniProtKB/Swiss-Prot
      Q3L8N4, Q6KGZ9, Q9BQL1, Q9H0D6, Q9NTW0, Q9NXS6, Q9UL53
      UniProtKB/TrEMBL
      B3KMC9
      Related
      ENSP00000366396.3, ENST00000377191.5
      Conserved Domains (2) summary
      COG5049
      Location:1787
      XRN1; 5'-3' exonuclease [Replication, recombination and repair]
      pfam03159
      Location:1253
      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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      21303331..21389825
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027722.2XP_016883211.1  5'-3' exoribonuclease 2 isoform X1

    2. XM_017027723.3XP_016883212.1  5'-3' exoribonuclease 2 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      21362698..21446483
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323194.1XP_054179169.1  5'-3' exoribonuclease 2 isoform X1

    2. XM_054323193.1XP_054179168.1  5'-3' exoribonuclease 2 isoform X3

      UniProtKB/TrEMBL
      B4DZC3, B4E0B9