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WormBase Tree Display for Variation: WBVar00091488

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Name Class

WBVar00091488EvidencePerson_evidenceWBPerson12335
NamePublic_nameok169
Other_nameF42G8.4a.1:c.-1+40_252+116delinsAGAGAGAAG
F42G8.4a.2:c.-1+40_252+116delinsAGAGAGAAG
HGVSgCHROMOSOME_IV:g.8139342_8140613delinsAGAGAGAAG
Sequence_detailsSMapS_parentSequenceF42G8
Flanking_sequencestttgtttttggtaaacttcataatagtggaagaaatcgaccttaatactctaaaaaggat
Mapping_targetF42G8
Type_of_mutationInsertionagagagaag
Deletion
PCR_productOK169_external
OK169_internal
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
StrainWBStrain00003942
LaboratoryRB
BS
PersonWBPerson46
WBPerson12335
KO_consortium_allele
StatusLive
AffectsGeneWBGene00004057
TranscriptF42G8.4a.3VEP_consequencesplice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant
VEP_impactHIGH
Intron_number2/8
Exon_number1-2/9
F42G8.4a.2VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant
VEP_impactHIGH
HGVScF42G8.4a.2:c.-1+40_252+116delinsAGAGAGAAG
Intron_number1-2/9
Exon_number2/10
F42G8.4a.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant
VEP_impactHIGH
HGVScF42G8.4a.1:c.-1+40_252+116delinsAGAGAGAAG
Intron_number1-2/8
Exon_number2/9
Interactor (13)
GeneticsMapping_dataIn_multi_point4595
DescriptionPhenotypeWBPhenotype:0000119Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
RemarkThis mutation suppressed the reduction of endogenous MEC-18 caused by colchicine.Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
Affected_byMoleculeWBMol:00003637Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
Phenotype_assayGenotypeuIs44(Pmec-18::praja::gfp)Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
WBPhenotype:0000386Paper_evidenceWBPaper00033433
Curator_confirmedWBPerson2987
RemarkCopper-induced germ cell apoptosis was slightly reduced in pmk-3(ok169) mutants (Figure 5B).Paper_evidenceWBPaper00033433
Curator_confirmedWBPerson2987
Affected_byMoleculeWBMol:00002862Paper_evidenceWBPaper00033433
Curator_confirmedWBPerson2987
Phenotype_assayTreatmentWorms were exposed to 10 micromolar of copper for 12 hoursPaper_evidenceWBPaper00033433
Curator_confirmedWBPerson2987
WBPhenotype:0000487Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
RemarkThis mutation suppressed the colchicine-dependent reduction in expression of the Praja::GFP reporter. This mutation suppressed the reduction of endogenous MEC-18 caused by colchicine. However, like wild-type animals, colchicine eliminated all microtubules in the soma, whereas other characteristic TRN physical attributes, such as the extracellular mantle, were maintained.Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
Affected_byMoleculeWBMol:00003637Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
Phenotype_assayGenotypeuIs44(Pmec-18::praja::gfp)Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
WBPhenotype:0000615Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
Remark"Cilium length is reduced in adult gpa-3QL(syIs25) animals [26]. We tested whether cilium length is restored in the suppressor strains. First, we measured cilium length in the ASI neurons of uev-3, dlk-1 and pmk-3 single mutants using a pgpa-4::gfp construct, resulting in expression of GFP specifically in this pair of neurons. uev-3(ju639) animals had slightly shorter cilia than wild type, while the other single mutants showed wild type lengths (Fig 3A). Cilium length in ASI neurons of the suppressor mutants was significantly longer than in gpa-3QL(syIs25) (Fig 3A)... To confirm that the effects on cilium length are specific, we expressed uev-3 or pmk-3 specifically in the ASI neurons of uev-3(ju639); gpa-3QL(syIs25) or pmk-3(ok169); gpa-3QL(syIs25) mutants, respectively. In both cases, this lead to a decrease in ASI cilium length (Fig 3A)."Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0005666PATO:0000460Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
Phenotype_assayGenotypePgpa-4::gfp; gpa-3QL(syIs25)Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
WBPhenotype:0000679Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
Remark"Next, we measured GFP::RAB-5 levels in pmk-3(ok169), uev-3(ju639) and uev-3(gj204) animals and in double mutants of these with gpa-3QL(syIs25). In pmk-3(ok169) animals, in which presumably GDI-1 is less active, resulting in inactive, membrane bound RAB-5, we would expect accumulation of GFP::RAB-5. Indeed, in these animals GFP::RAB-5 accumulated significantly at the base of the cilium, in the distal part of the dendrite and in the cell body (Fig 6A and 6D and 6E). Similar increases in GFP::RAB-5 fluorescence intensity were observed in the AWB neurons (S6 Fig). Also pmk-3(ok169); gpa-3QL(syIs25) double mutant animals displayed accumulation of GFP::RAB-5 at the ends of the dendrites and in the cell bodies similar to the pmk-3(ok169) single mutant (Fig 6A and 6D and 6E)."Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
"To analyze whether sql-1 and pmk-3 function in the same genetic pathway in the regulation of GFP::RAB-5 levels we visualized GFP::RAB-5 levels in sql-1(tm2409); pmk-3(ok169) double mutant and in sql-1(tm2409); pmk-3(ok169); gpa-3QL(syIs25) triple mutant animals. Interestingly, sql-1(tm2409); pmk-3(ok169) double mutant animals showed very low GFP::RAB-5 levels, both at the end of the dendrite and in the cell body (Fig 9C and 9D), suggesting that the effects of mutation of sql-1 and pmk-3 are mediated by different mechanisms, e.g by changes in supply of membrane and protein on the one hand and changes in removal on the other. sql-1(tm2409); pmk-3(ok169); gpa-3QL(syIs25) triple mutant animals showed similar GFP::RAB-5 levels as wild type animals, consistent with the hypothesis that suppression of the short cilium phenotype of gpa-3QL animals by both sql-1(tm2409) and pmk-3(ok169) involves effects on RAB-5 mediated endocytosis."Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
Phenotype_assayGenotypeGFP::RAB-5Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
GFP::RAB-5; gpa-3QL(syIs25)Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
GFP::RAB-5; sql-1(tm2409)Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
WBPhenotype:0000750Paper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
RemarkFigure S10, pmk-3(ok169) rescues vhp-1 RNAi larval arrest in nuo-6(qm200)Paper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
Phenotype_assayGenotypevhp-1(RNAi); nuo-6(qm200)Paper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
WBPhenotype:0001171Paper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
RemarkFigure 8A, pmk-3(ok169) shows little to no life extension on atp-3 RNAiPaper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
Figure 8B, pmk-3(ok169) shows reduced life extension on cco-1 RNAiPaper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
Figure 8C & 9, pmk-3(ok169) shows reduced life extension on isp-1 RNAiPaper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
Figure 8D, pmk-3(ok169) shows reduced life extension on nuo-2 RNAiPaper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
Phenotype_assayGenotypeatp-3(RNAi)Paper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
cco-1(RNAi)Paper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
isp-1(RNAi)Paper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
nuo-2(RNAi)Paper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
WBPhenotype:0001203Paper_evidenceWBPaper00046636
Curator_confirmedWBPerson557
RemarkAnimals are all partially resistant to nicotine.Paper_evidenceWBPaper00046636
Curator_confirmedWBPerson557
Phenotype_assayTreatmentAnimals exposed to a solution of 0.1 percent nicotine.Paper_evidenceWBPaper00046636
Curator_confirmedWBPerson557
Phenotype_not_observedWBPhenotype:0000039Paper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
RemarkFigure 8, pmk-3(ok169) lifespan is no different than N2 under normal conditionsPaper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
Phenotype_assayControl_strainWBStrain00000001Paper_evidenceWBPaper00049830
Curator_confirmedWBPerson23367
WBPhenotype:0000315Paper_evidenceWBPaper00035070
Curator_confirmedWBPerson712
RemarkAnimals are touch sensitive.Paper_evidenceWBPaper00035070
Curator_confirmedWBPerson712
WBPhenotype:0000615Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
Remark"Cilium length is reduced in adult gpa-3QL(syIs25) animals [26]. We tested whether cilium length is restored in the suppressor strains. First, we measured cilium length in the ASI neurons of uev-3, dlk-1 and pmk-3 single mutants using a pgpa-4::gfp construct, resulting in expression of GFP specifically in this pair of neurons. uev-3(ju639) animals had slightly shorter cilia than wild type, while the other single mutants showed wild type lengths (Fig 3A)."Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0005666PATO:0000460Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
Phenotype_assayGenotypePgpa-4::gfpPaper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
WBPhenotype:0000633Paper_evidenceWBPaper00045955
Curator_confirmedWBPerson557
RemarkAnimals did not have PLM branch defects.Paper_evidenceWBPaper00045955
Curator_confirmedWBPerson557
WBPhenotype:0000679Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
Remark"Since UEV-3 directly binds PMK-3 we tested whether the localization of PMK-3::GFP was dependent on UEV-3, or vice versa, by expressing pgpa-4::pmk-3::gfp in the uev-3(ju639) mutant and pgpa-4::uev-3::gfp in the pmk-3(ok169) mutant. No change in localization was detected compared to wild type animals, indicating that the localization of UEV-3::GFP or PMK-3::GFP does not depend on PMK-3 or UEV-3, respectively (Fig 4A)."Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
"To confirm that the effects of gpa-3QL(syIs25) and pmk-3(ok169) on GFP::RAB-5 reflect changes in endocytosis, we visualized DPY-23, the mu2 subunit of adaptor protein complex 2, that mediates endocytosis of membrane proteins. We combined the prab-3::dpy-23::gfp construct that expresses the DPY-23::GFP fusion in all neurons [43] with pgpa-4::mCherry, to visualize the ASI neurons. Quantification of the DPY-23::GFP fluorescence intensities at the base of the cilia of the ASI neurons revealed significantly lower DPY-23::GFP levels in gpa-3QL (syIs25) animals, and wild type levels in pmk-3(ok169) animals (Fig 8)."Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
Phenotype_assayGenotypePgpa-4::uev-3::gfpPaper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
DPY-23::GFPPaper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
WBPhenotype:0000905Paper_evidenceWBPaper00035070
Curator_confirmedWBPerson712
RemarkAnimals exhibited normal cell-body morphology.Paper_evidenceWBPaper00035070
Curator_confirmedWBPerson712
EQ_annotationsAnatomy_termWBbt:0005237PATO:0000460Paper_evidenceWBPaper00035070
Curator_confirmedWBPerson712
WBPhenotype:0001173Paper_evidenceWBPaper00040855
Curator_confirmedWBPerson557
RemarkAdult males show appropriate cell death of the linker cell.Paper_evidenceWBPaper00040855
Curator_confirmedWBPerson557
WBPhenotype:0001588Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
Remarkpmk-3 mutants on average appeared to have slightly more microtubules when grown on control plates (no colchicine), but this increase was not statistically significant. Further, like wild-type animals, colchicine eliminated all microtubules in the soma, whereas other characteristic TRN physical attributes, such as the extracellular mantle, were maintained.Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
Affected_byMoleculeWBMol:00003637Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
Phenotype_assayGenotypeuIs43, uIs44(Pmec-18::praja::gfp)Paper_evidenceWBPaper00038206
Curator_confirmedWBPerson712
WBPhenotype:0001933Paper_evidenceWBPaper00035070
Curator_confirmedWBPerson712
WBPhenotype:0002212Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
RemarkFigure 1A,BPaper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0005391PATO:0000460Paper_evidenceWBPaper00048972
Curator_confirmedWBPerson2987
ReferenceWBPaper00038206
WBPaper00040855
WBPaper00033433
WBPaper00035070
WBPaper00045955
WBPaper00048972
WBPaper00049830
WBPaper00065298
WBPaper00066032
WBPaper00046636
RemarkLast updated on 29 Nov 2002
Allele sequenced by Christopher HooverCurator_confirmedWBPerson2970
Sequenced by the C. elegans Gene Knockout ConsortiumPaper_evidenceWBPaper00041807
MethodKO_consortium_allele