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

Gene ID: 22803, updated on 7-Apr-2024

Summary

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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
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Genomic context

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Location:
20p11.22
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (21303331..21389825)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (21362698..21446483)
105.20220307 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. XRN2 Is Required for Cell Motility and Invasion in Glioblastomas. Dang TT, et al. Cells, 2022 Apr 28. PMID 35563787, Free PMC Article
  2. Upregulation of XRN2 acts as an oncogene in oral squamous cell carcinoma and correlates with poor prognosis. Liu JC, et al. Pathol Res Pract, 2021 Mar. PMID 33626405
  3. An end in sight? Xrn2 and transcriptional termination by RNA polymerase II. Eaton JD, et al. Transcription, 2018. PMID 30035655, Free PMC Article
  4. XRN2 Links Transcription Termination to DNA Damage and Replication Stress. Morales JC, et al. PLoS Genet, 2016 Jul. PMID 27437695, Free PMC Article
  5. P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates. Sansó M, et al. Genes Dev, 2016 Jan 1. PMID 26728557, Free PMC Article

See all (188) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The exoribonuclease XRN2 mediates degradation of the long non-coding telomeric RNA TERRA.
    Title: The exoribonuclease XRN2 mediates degradation of the long non-coding telomeric RNA TERRA.
  2. The transcriptional terminator XRN2 and the RNA-binding protein Sam68 link alternative polyadenylation to cell cycle progression in prostate cancer.
    Title: The transcriptional terminator XRN2 and the RNA-binding protein Sam68 link alternative polyadenylation to cell cycle progression in prostate cancer.
  3. XRN2 Is Required for Cell Motility and Invasion in Glioblastomas.
    Title: XRN2 Is Required for Cell Motility and Invasion in Glioblastomas.
  4. Upregulation of XRN2 acts as an oncogene in oral squamous cell carcinoma and correlates with poor prognosis.
    Title: Upregulation of XRN2 acts as an oncogene in oral squamous cell carcinoma and correlates with poor prognosis.
  5. Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution.
    Title: Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution.
  6. XRN2, a gene proximal to an autism spectrum disorder (ASD) genome-wide association study (GWAS) locus, was inferred to be significantly upregulated in ASD, providing insight into the functional consequence of this associated locus.
    Title: Novel Insight Into the Etiology of Autism Spectrum Disorder Gained by Integrating Expression Data With Genome-wide Association Statistics.
  7. Authors engineered cells in which the 3'-->5' exoribonucleases of the exosome complex, DIS3 and EXOSC10, can be rapidly eliminated to assess their immediate roles in nuclear RNA biology. The 5'-->3' exoribonuclease, XRN2, has little activity on exosome substrates, but its elimination uncovers different mechanisms for the early termination of transcription from protein-coding gene promoters.
    Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control.
  8. Xrn2 depletion induces a transcriptional termination defect at the majority of protein-coding genes.
    Title: An end in sight? Xrn2 and transcriptional termination by RNA polymerase II.
  9. depletion of NKRF, XRN2 or DHX15 impairs an early pre-rRNA cleavage step.
    Title: The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis.
  10. XRN2 is a novel regulator of EMT that contributes to the metastatic processes in lung cancer through a novel miRNA regulatory mechanism.
    Title: XRN2 promotes EMT and metastasis through regulating maturation of miR-10a.
Submit: New GeneRIF Correction See all GeneRIFs (29)

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

EBI GWAS Catalog

Description
Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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

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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

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

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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)

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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_001317960.1 → NP_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:118 → 865
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:113 → 331
    XRN_N; XRN 5'-3' exonuclease N-terminus

  2. NM_012255.5 → NP_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:1 → 787
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:1 → 253
    XRN_N; XRN 5'-3' exonuclease N-terminus

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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_017027722.2 → XP_016883211.1  5'-3' exoribonuclease 2 isoform X1

  2. XM_017027723.3 → XP_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_054323194.1 → XP_054179169.1  5'-3' exoribonuclease 2 isoform X1

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

    UniProtKB/TrEMBL
    B4DZC3
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H0D6.1 GenPept UniProtKB/Swiss-Prot:Q9H0D6

Gene LinkOut

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Chemical Information
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