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WormBase Tree Display for Variation: WBVar00251819

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Name Class

WBVar00251819NamePublic_nametm3036
Other_name (21)
HGVSgCHROMOSOME_III:g.3870942_3871210del
Sequence_detailsSMapS_parentSequenceF13B10
Flanking_sequencesgttcttgagcaatgagctgtcgaattttcccatttgtgagcatttggtaggtgtaaacag
Mapping_targetF13B10
Source_location7CHROMOSOME_III38709413871211Inferred_automaticallyNational_Bioresource_Project
Type_of_mutationDeletion
PCR_producttm3036_external
tm3036_internal
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
StrainWBStrain00021983
WBStrain00021984
WBStrain00055930
LaboratoryFX
IG
JN
AuthorMitani S
DB_infoDatabaseNational_Bioresource_Projectseq3036
NBP_allele
StatusLive
AffectsGeneWBGene00171984
WBGene00006575
Transcript (14)
InteractorWBInteraction000503569
WBInteraction000504797
IsolationMutagenTMP/UV
GeneticsMapIII
DescriptionPhenotypeWBPhenotype:0000039Paper_evidenceWBPaper00032031
WBPaper00031666
Curator_confirmedWBPerson712
RemarkAnimals had substantially reduced lifespans in the absence of infection.Paper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
Life span is decreased compared to wild type animals.Paper_evidenceWBPaper00031666
Curator_confirmedWBPerson712
Variation_effectNullPaper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
Phenotype_assayTreatmentAssayed on E. coli.Paper_evidenceWBPaper00031666
Curator_confirmedWBPerson712
WBPhenotype:0000142Paper_evidenceWBPaper00032031
WBPaper00031666
Curator_confirmedWBPerson712
RemarkConstitutive expression of pnlp-29::GFP as well as induction, by infection or high salt, was reduced. GFP expression was knocked down by half in untreated worms as well as worms treated with high osmotic stress or infection by D. coniospora.Paper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
D. coniospora pathogen induced upregulation of pnlp-29::GFP was blocked.Paper_evidenceWBPaper00031666
Curator_confirmedWBPerson712
Variation_effectNullPaper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
Phenotype_assayTreatmentInfections with a freshly harvested solution of D. coniospora spores were done as described [65]; worms were analyzed after 24 h at 25C. Worms were pricked in the tail region using a microinjection needle under a dissecting microscope and analyzed 6 h later for GFP induction or 2 hours later for qRT-PCR.Paper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
Animals were infected with D. coniospora at the L4 stage and maintained on OP50 at 20C.Paper_evidenceWBPaper00031666
Curator_confirmedWBPerson712
GenotypefrIs7Paper_evidenceWBPaper00031666
Curator_confirmedWBPerson712
WBPhenotype:0000384Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
Variation_effectProbable_null_via_phenotypePaper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
EQ_annotationsAnatomy_termWBbt:0005672PATO:0000460Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
Phenotype_assayGenotype[str-2p::GFP]Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
WBPhenotype:0000961Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
RemarkThe localization pattern and level of UNC-43::GFP in the AWC axons is similar in wild type and tir-1(tm3036lf) mutants.Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
Variation_effectProbable_null_via_phenotypePaper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
EQ_annotationsAnatomy_termWBbt:0005672PATO:0000460Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
Phenotype_assayGenotype[str-2p::GFP]Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
WBPhenotype:0001013Paper_evidenceWBPaper00032031
WBPaper00031666
Curator_confirmedWBPerson712
RemarkAnimals had marked reductions in resistance to D. coniospora infection.Paper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
Animals exhibit a significant reduction in survival when infected with D. coniospora.Paper_evidenceWBPaper00031666
Curator_confirmedWBPerson712
Variation_effectNullPaper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
Phenotype_assayTreatmentInfections with a freshly harvested solution of D. coniospora spores were done as described [65]; worms were analyzed after 24 h at 25C. Worms were pricked in the tail region using a microinjection needle under a dissecting microscope and analyzed 6 h later for GFP induction or 2 hours later for qRT-PCR.Paper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
Animals were infected with D. coniospora at the L4 stage and maintained on OP50 at 20C.Paper_evidenceWBPaper00031666
Curator_confirmedWBPerson712
WBPhenotype:0001351Paper_evidenceWBPaper00037959
Curator_confirmedWBPerson712
RemarkPMK-1 activation in response to anoxia was suppressed in the tir-1(tm3036) mutant.Paper_evidenceWBPaper00037959
Curator_confirmedWBPerson712
Affected_byMoleculeWBMol:00005312Paper_evidenceWBPaper00037959
Curator_confirmedWBPerson712
WBPhenotype:0001381Paper_evidenceWBPaper00037959
Curator_confirmedWBPerson712
RemarkA mutation in the TIR domain-containing adaptor protein TIR-1 increased the survival rate in anoxia.Paper_evidenceWBPaper00037959
Curator_confirmedWBPerson712
WBPhenotype:0001661Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
RemarkLoss-of-function mutants showed a 2AWC-ON phenotype resembling that caused by nocodazole treatment.Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
Variation_effectProbable_null_via_phenotypePaper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
EQ_annotationsAnatomy_termWBbt:0005672PATO:0000460Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
Phenotype_assayGenotype[str-2p::GFP]Paper_evidenceWBPaper00039901
Curator_confirmedWBPerson712
WBPhenotype:0001687Paper_evidenceWBPaper00056945
Curator_confirmedWBPerson712
Remarktir-1(tm3036) animals showed positive staining of L2-L4 stages. mAb M37 stains only the L1 stage in wild type C. elegans under normal growth conditions.Paper_evidenceWBPaper00056945
Curator_confirmedWBPerson712
ImageWBPicture0000014905Paper_evidenceWBPaper00056945
Curator_confirmedWBPerson712
WBPhenotype:0001838Paper_evidenceWBPaper00033094
Curator_confirmedWBPerson2021
RemarkThe PMA-induced upregulation of pnlp-29::GFP expression was blocked in tir-1(tm3036) mutantPaper_evidenceWBPaper00033094
Curator_confirmedWBPerson2021
Phenotype_assayGenotypefrIs7 [pnlp-29::GFP]Paper_evidenceWBPaper00033094
Curator_confirmedWBPerson2021
Phenotype_not_observedWBPhenotype:0000062Person_evidenceWBPerson7743
Curator_confirmedWBPerson557
RemarkClassified as homozygous viable by the National Bioresource Project of Japan. Comment to the NBP from Dr. J. Ewbank: Curr. Biol. 18, 481 (2008).Person_evidenceWBPerson7743
Curator_confirmedWBPerson557
Laboratory_evidenceFX
IG
WBPhenotype:0001725Paper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
RemarkOsmotic stress triggered upregulation of nlp-29 was not affected, based on the fluorescent ratio of control to experiment animals.Paper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
Phenotype_assayTreatmentOsmotic stress was done in liquid by incubating young adult worms in 300 mM NaCl for 6 h, with analysis occuring 24 hours later.Paper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
GenotypefrIs7Paper_evidenceWBPaper00032031
Curator_confirmedWBPerson712
WBPhenotype:0001839Paper_evidenceWBPaper00033094
Curator_confirmedWBPerson2021
RemarkMutants were not resistant to PMAPaper_evidenceWBPaper00033094
Curator_confirmedWBPerson2021
Phenotype_assayGenotypefrIs7 [pnlp-29::GFP]Paper_evidenceWBPaper00033094
Curator_confirmedWBPerson2021
ReferenceWBPaper00037959
WBPaper00039901
WBPaper00033094
WBPaper00032031
WBPaper00031666
WBPaper00056945
WBPaper00065298
WBPaper00065833
WBPaper00066032
Remark2308/2309-2577/2578 (269 bp deletion)
This knockout was generated by the National Bioresource Project, Tokyo, Japan, which is part of the International C. elegans Gene Knockout Consortium, which should be acknowledged in any publications resulting from its use.Paper_evidenceWBPaper00041807
MethodNBP_knockout_allele