smg-2 Regulator of nonsense transcripts 1 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: smg-2
Official Full Name: Regulator of nonsense transcripts 1
Primary source: WormBase:WBGene00004880
Locus tag: CELE_Y48G8AL.6
See related: AllianceGenome:WB:WBGene00004880
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 protein phosphatase 2A binding activity. Involved in embryonic genitalia morphogenesis and negative regulation of gene expression. Located in cytoplasm and nucleus. Is expressed in intestinal cell; muscle cell; and nervous system. Orthologous to human UPF1 (UPF1 RNA helicase and ATPase). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See smg-2 in Genome Data Viewer

Location:: chromosome: I

Exon count:: 9

Sequence:: Chromosome: I; NC_003279.8 (1176473..1190829)

Chromosome I - NC_003279.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003279.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SMG-2 interacts with SMG-3, SMG-3 interacts with SMG-4, and SMG-2 interacts indirectly with SMG-4 via shared interactions with SMG-3. SMG-2 preferentially associates with PTC-containing mRNAs.
Title: Caenorhabditis elegans SMG-2 selectively marks mRNAs containing premature translation termination codons.
results suggest that the role of SMG-5 is to direct protein phosphatase 2A to its SMG-2 substrate
Title: SMG-5, required for C.elegans nonsense-mediated mRNA decay, associates with SMG-2 and protein phosphatase 2A.

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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

Y48G8A_3304.a (e-PCR)
- UniSTS:322984

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables double-stranded DNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables helicase 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 protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein phosphatase 2A binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic genitalia morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in regulatory ncRNA-mediated post-transcriptional gene silencing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in siRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: Regulator of nonsense transcripts 1

NP_490829.1

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_003279.8 Reference assembly

Range

1176473..1190829

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_058428.6 → NP_490829.1 Regulator of nonsense transcripts 1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_490829.1

Status: REVIEWED

UniProtKB/Swiss-Prot

O76512, Q9BL16

Conserved Domains (4) summary

COG1112
Location:117 → 874

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

pfam09416
Location:93 → 243

UPF1_Zn_bind; RNA helicase (UPF2 interacting domain)

pfam13087
Location:654 → 851

AAA_12; AAA domain

pfam13245
Location:452 → 509

AAA_19; Part of AAA domain