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WormBase Tree Display for Variation: WBVar00092993

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Name Class

WBVar00092993NamePublic_nameok1794
Other_nameY54F10AL.2c.1:c.3117+109_3239-137del
Y54F10AL.2a.1:c.3183+109_3305-137del
HGVSgCHROMOSOME_III:g.2484395_2485314del
Sequence_detailsSMapS_parentSequenceY54F10AL
Flanking_sequencescaattaaaaattttttttcttgattttctaaaaattgtgtctaggggtgaaaaattgcga
Mapping_targetY54F10AL
Type_of_mutationDeletion
PCR_productOK1794_external
OK1794_internal
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
StrainWBStrain00036497
LaboratoryRB
PersonWBPerson46
KO_consortium_allele
StatusLive
AffectsGeneWBGene00004884
TranscriptY54F10AL.2c.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScY54F10AL.2c.1:c.3117+109_3239-137del
Intron_number15-16/18
Exon_number16/19
Y54F10AL.2a.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScY54F10AL.2a.1:c.3183+109_3305-137del
Intron_number16-17/19
Exon_number17/20
InteractorWBInteraction000536768
WBInteraction000536771
WBInteraction000536775
IsolationMutagenEMS
DescriptionPhenotypeWBPhenotype:0000030Paper_evidenceWBPaper00041065
Curator_confirmedWBPerson2987
Remark"The smg-1, smg-4, and smg-6 mutants exhibited synthetic growth defects upon silencing of ire-1 (Fig. S7)."Paper_evidenceWBPaper00041065
Curator_confirmedWBPerson2987
Phenotype_assayGenotypeire-1(RNAi)Paper_evidenceWBPaper00041065
Curator_confirmedWBPerson2987
WBPhenotype:0000136Paper_evidenceWBPaper00041065
Curator_confirmedWBPerson2987
Remark"To assess whether ER protein-folding homeostasis requires NMD-mediated mRNA surveillance, we analyzed deletions of the NMD genes smg-1, smg-4, and smg-6 in the zcIs4 transgenic hsp-4 GFP reporter strain. All strains displayed greater GFP fluorescence compared the parental zcIs4 strain (Fig. 2A and Fig. S6), and qRT-PCR revealed that the expression of endogenous hsp-4 mRNA was constitutively elevated in the smg-1(tm849) and smg-6(ok1794) mutant strains compared the wild type N2 (Fig. 2B)."Paper_evidenceWBPaper00041065
Curator_confirmedWBPerson2987
WBPhenotype:0001236Paper_evidenceWBPaper00041065
Curator_confirmedWBPerson2987
Remark"To assess whether ER protein-folding homeostasis requires NMD-mediated mRNA surveillance, we analyzed deletions of the NMD genes smg-1, smg-4, and smg-6 in the zcIs4 transgenic hsp-4 GFP reporter strain. All strains displayed greater GFP fluorescence compared the parental zcIs4 strain (Fig. 2A and Fig. S6), and qRT-PCR revealed that the expression of endogenous hsp-4 mRNA was constitutively elevated in the smg-1(tm849) and smg-6(ok1794) mutant strains compared the wild type N2 (Fig. 2B)."Paper_evidenceWBPaper00041065
Curator_confirmedWBPerson2987
Phenotype_assayGenotypezcIs4 [Phsp-4::GFP]Paper_evidenceWBPaper00041065
Curator_confirmedWBPerson2987
WBPhenotype:0001485Paper_evidenceWBPaper00041065
Curator_confirmedWBPerson4260
ReferenceWBPaper00041065
RemarkSequenced by the C. elegans Gene Knockout ConsortiumPaper_evidenceWBPaper00041807
MethodKO_consortium_allele