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

Gene ID: 22803, updated on 19-Jul-2021

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
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

See XRN2 in Genome Data Viewer
Location:
20p11.22
Exon count:
32
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (21303313..21389825)
105.20201022 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 VISTA enhancer hs914 Neighboring gene zinc finger protein 877, pseudogene 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?

Phenotypes

Associated conditions

Description Tests
Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus.
GeneReviews: Not available

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-5'-exoribonuclease activity EXP
Inferred from Experiment
more info
PubMed 
enables 5'-3' exonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
enables 5'-3' exoribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables 5'-3' exoribonuclease activity TAS
Traceable Author Statement
more info
PubMed 
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 DNA catabolic process, exonucleolytic IDA
Inferred from Direct Assay
more info
PubMed 
involved_in DNA-templated transcription, termination IEA
Inferred from Electronic Annotation
more info
 
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 phosphodiester bond hydrolysis, exonucleolytic IEA
Inferred from Electronic Annotation
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
PubMed 
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 
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
PubMed 

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_016883213.1

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_001317960.1NP_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/Swiss-Prot
    Q9H0D6
    UniProtKB/TrEMBL
    B4DZC3
    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
    Q9H0D6
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    21303313..21389825
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

  3. XM_017027724.1XP_016883213.1  5'-3' exoribonuclease 2 isoform X3

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