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xrn2 5'-3' exoribonuclease 2 [ Danio rerio (zebrafish) ]

Gene ID: 321940, updated on 27-Mar-2024

Summary

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Official Symbol
xrn2provided by ZNC
Official Full Name
5'-3' exoribonuclease 2provided by ZNC
Primary source
ZFIN:ZDB-GENE-040426-2874
See related
Ensembl:ENSDARG00000101900 AllianceGenome:ZFIN:ZDB-GENE-040426-2874
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
zgc:55717; wu:fb38g12; wu:fj53d06
Summary
Predicted to enable 5'-3' exoribonuclease activity and RNA binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process. Predicted to act upstream of or within nucleobase-containing compound metabolic process. Predicted to be active in nucleus. 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]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 20
Exon count:
31
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 20 NC_007131.7 (48810491..48898560, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 20 NC_007131.6 (48979274..49067343, complement)

Chromosome 20 - NC_007131.7Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 61 Neighboring gene uncharacterized LOC110438203 Neighboring gene NK2 homeobox 4b Neighboring gene uncharacterized LOC110438201 Neighboring gene uncharacterized LOC110438204 Neighboring gene microRNA mir-2193 Neighboring gene crooked neck pre-mRNA splicing factor 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation. Rösel TD, et al. EMBO J, 2011 May 18. PMID 21468032, Free PMC Article
  2. A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos. Rosenthal SM, et al. Mol Cell Proteomics, 2021. PMID 34332124, Free PMC Article
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
  5. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

GeneRIFs: Gene References Into Functions

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 ZFIN

Function Evidence Code Pubs
enables 3'-5'-RNA exonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables 5'-3' RNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5'-3' RNA exonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA exonuclease activity, producing 5'-phosphomonoesters IEA
Inferred from Electronic Annotation
more info
  
enables exonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity 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
  
Process Evidence Code Pubs
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in nuclear-transcribed mRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within nucleobase-containing compound metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
5'-3' exoribonuclease 2
NP_001001944.2
XP_005160932.1

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_001001944.2 → NP_001001944.2  5'-3' exoribonuclease 2

    Status: VALIDATED

    Source sequence(s)
    BX005124, CT573061
    UniProtKB/TrEMBL
    A0A0R4ISJ3, A0A8M1MZQ7
    Related
    ENSDARP00000138850.1, ENSDART00000163071.2
    Conserved Domains (2) summary
    COG5049
    Location:1 → 796
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:1 → 253
    XRN_N; XRN 5'-3' exonuclease N-terminus

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007131.7 Reference GRCz11 Primary Assembly

    Range
    48810491..48898560 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005160875.4 → XP_005160932.1  5'-3' exoribonuclease 2 isoform X1

    UniProtKB/TrEMBL
    A0A8M2B7S3
    Conserved Domains (2) summary
    COG5049
    Location:1 → 782
    XRN1; 5'-3' exonuclease [Replication, recombination and repair]
    pfam03159
    Location:1 → 253
    XRN_N; XRN 5'-3' exonuclease N-terminus
Nucleotide Protein Strain
Heading Accession and Version

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