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WormBase Tree Display for Variation: WBVar00601579

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Name Class

WBVar00601579EvidencePaper_evidenceWBPaper00040453
NamePublic_nameqd101
Other_nameCE28367:p.Arg397Ter
Y48G8AL.6.1:c.1189C>T
HGVSgCHROMOSOME_I:g.1180357C>T
Sequence_detailsSMapS_parentSequenceY48G8AL
Flanking_sequencesGACGTCGTCTGGAACGCCACCACCTTCGAGGACAGTACAAGGCTCTTGCGGCGCTGCTCA
Mapping_targetY48G8AL
Type_of_mutationSubstitutionctPaper_evidenceWBPaper00040453
Curator_confirmedWBPerson51134
RemarkResequenced and confirmed by WBPerson56105
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
LaboratoryZD
StatusLive
AffectsGeneWBGene00004880
TranscriptY48G8AL.6.1VEP_consequencestop_gained
VEP_impactHIGH
HGVScY48G8AL.6.1:c.1189C>T
HGVSpCE28367:p.Arg397Ter
cDNA_position1191
CDS_position1189
Protein_position397
Exon_number5/11
Codon_changeCga/Tga
Amino_acid_changeR/*
InteractorWBInteraction000534934
WBInteraction000536437
GeneticsInterpolated_map_positionI-16.9145
DescriptionPhenotypeWBPhenotype:0000136Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
Remark"We next examined the level of WT xbp-1 mRNA in the smg-2(qd101) mutant, and we observed that NMD inhibition increased the level of xbp-1 mRNA 2-fold relative to WT C. elegans (Figure 1C), which suggests that the NMD complex may function to decrease the level of WT xbp-1 mRNA."Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
WBPhenotype:0000508Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
Remarksmg-2(qd101) resulted in accumulation of early stop codon-containing xbp-1 transcripts in the xbp-1(zc12) mutant background (Figure 1B)Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
WBPhenotype:0001012Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
Remark"Whereas a 4 h exposure of the WT strain to P. aeruginosa PA14 causes a two-fold increase in spliced xbp-1 mRNA relative to exposure to the relatively non-pathogenic bacterial food Escherichia coli OP50 (Figure 3A and [21]), we observe a blunted response to P. aeruginosa infection in the smg-2(qd101) mutant (Figure 3A)."Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
Phenotype_not_observedWBPhenotype:0000359Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
Remark"... the loss of NMD did not increase the lethality of either the WT strain or xbp-1(zc12) mutant when grown in the presence of tunicamycin (Figure 1D)."Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
Affected_byMoleculeWBMol:00004565Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
Phenotype_assayGenotypexbp-1(zc12)Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
WBPhenotype:0001807Paper_evidenceWBPaper00049407
Curator_confirmedWBPerson712
Remarkthis smg-2 mutation did not result in the amplification of additional products not present in the wild-type sample, suggesting that this region of the daf-12 pre-mRNA is not subject to alternative splicing.Paper_evidenceWBPaper00049407
Curator_confirmedWBPerson712
WBPhenotype:0001834Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
Remark"... after exposing both the WT and smg-2(qd101) strains to tunicamycin for 4 h, the level of IRE-1-spliced xbp-1 mRNA was similar between the two strains (Figure 1C)."Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
Affected_byMoleculeWBMol:00004565Paper_evidenceWBPaper00040453
Curator_confirmedWBPerson2987
ReferenceWBPaper00040453
WBPaper00049407
MethodSubstitution_allele