xrn-2 5'-3' exoribonuclease 2 homolog [Caenorhabditis elegans] - Gene

Summary

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Gene symbol: xrn-2
Gene description: 5'-3' exoribonuclease 2 homolog
Primary source: WormBase:WBGene00006964
Locus tag: CELE_Y48B6A.3
See related: AllianceGenome:WB:WBGene00006964
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Enables 5'-3' exoribonuclease activity. Involved in several processes, including miRNA catabolic process; negative regulation of gene silencing by miRNA; and regulation of vulval development. Located in nucleus. Is expressed in M5 neuron; PVT; intestine; and pharyngeal epithelial cell. Human ortholog(s) of this gene implicated in adenoid cystic carcinoma and lung cancer. Orthologous to human XRN2 (5'-3' exoribonuclease 2). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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Location:: chromosome: II

Exon count:: 7

Sequence:: Chromosome: II; NC_003280.10 (14155768..14166030)

Chromosome II - NC_003280.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003280.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

De-repression appears to be triggered such that more robust XRN2 perturbation, by elimination of both PAXT-1 and BPNT1, is less detrimental to worm viability than absence of PAXT-1 alone. Indeed, we find that two distinct XRN2 repression mechanisms are alleviated at different thresholds of XRN2 inactivation. Like more than 15% of C. elegans genes, xrn-2 occurs in an operon, and we identify additional
Title: XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans.
In Caenorhabditis elegans, XRN-2 functions with PAXT-1, which shares a putative XRN-2-binding domain (XTBD) with otherwise unrelated mammalian proteins. The study characterizes the structure and function of an XTBD-XRN2 complex.
Title: Structural basis and function of XRN2 binding by XTB domains.
XRN2 has unanticipated miRNA specificity in vivo, and its diverse developmental functions may relate to distinct substrates.
Title: Engineering of a conditional allele reveals multiple roles of XRN2 in Caenorhabditis elegans development and substrate specificity in microRNA turnover.
degradation of mature miRNAs in the nematode Caenorhabditis elegans, mediated by the 5'-->3' exoribonuclease XRN-2, affects functional miRNA homeostasis in vivo
Title: Active turnover modulates mature microRNA activity in Caenorhabditis elegans.

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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

Y48B6A.2 (e-PCR)
- UniSTS:321872

Y48B6A.3 (e-PCR)
- UniSTS:321739

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

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	IDA Inferred from Direct Assay more info	PubMed
enables 5'-3' RNA exonuclease activity	IEA Inferred from Electronic Annotation more info
enables 5'-3' exonuclease activity	ISS Inferred from Sequence or Structural Similarity more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables exonuclease activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nuclease activity	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA-templated transcription termination	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in miRNA catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in miRNA catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of miRNA-mediated gene silencing	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 nucleobase-containing compound metabolic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of development, heterochronic	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of vulval development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in termination of RNA polymerase II transcription	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: 5'-3' exoribonuclease 2 homolog

NP_496958.2

Confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_003280.10 Reference assembly

Range

14155768..14166030

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_064557.7 → NP_496958.2 5'-3' exoribonuclease 2 homolog [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_496958.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9U299

Conserved Domains (2) summary

COG5049
Location:1 → 848

XRN1; 5'-3' exonuclease [Replication, recombination and repair]

pfam03159
Location:1 → 254

XRN_N; XRN 5'-3' exonuclease N-terminus