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

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: mouse all
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Genomic context

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_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
XRN2 Is Required for Cell Motility and Invasion in Glioblastomas.
Title: XRN2 Is Required for Cell Motility and Invasion in Glioblastomas.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

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	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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH65531 (e-PCR)
- UniSTS:60479

D20S190 (e-PCR), detects polymorphism
- UniSTS:69703

D20S190 (e-PCR), detects polymorphism
- UniSTS:36946

RH93448 (e-PCR)
- UniSTS:90258

SHGC-53620 (e-PCR)
- UniSTS:40364

SHGC-132862 (e-PCR)
- UniSTS:170930

WI-10427 (e-PCR)
- UniSTS:45013

G62873 (e-PCR)
- UniSTS:139998

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 more info	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 more info	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

EC 3.1.13.-

NP_036387.2

EC 3.1.13.-

XP_016883211.1

EC 3.1.13.-

XP_016883212.1

EC 3.1.13.-

XP_054179168.1

EC 3.1.13.-

XP_054179169.1

EC 3.1.13.-

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)

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
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

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

21303331..21389825

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017027722.2 → XP_016883211.1 5'-3' exoribonuclease 2 isoform X1
XM_017027723.3 → XP_016883212.1 5'-3' exoribonuclease 2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

21362698..21446483

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054323194.1 → XP_054179169.1 5'-3' exoribonuclease 2 isoform X1
XM_054323193.1 → XP_054179168.1 5'-3' exoribonuclease 2 isoform X3

UniProtKB/TrEMBL

B4DZC3