WormBase Tree Display for Variation: WBVar00091488
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WBVar00091488 | Evidence | Person_evidence | WBPerson12335 | ||||||
---|---|---|---|---|---|---|---|---|---|
Name | Public_name | ok169 | |||||||
Other_name | F42G8.4a.1:c.-1+40_252+116delinsAGAGAGAAG | ||||||||
F42G8.4a.2:c.-1+40_252+116delinsAGAGAGAAG | |||||||||
HGVSg | CHROMOSOME_IV:g.8139342_8140613delinsAGAGAGAAG | ||||||||
Sequence_details | SMap | S_parent | Sequence | F42G8 | |||||
Flanking_sequences | tttgtttttggtaaacttcataatagtgga | agaaatcgaccttaatactctaaaaaggat | |||||||
Mapping_target | F42G8 | ||||||||
Type_of_mutation | Insertion | agagagaag | |||||||
Deletion | |||||||||
PCR_product | OK169_external | ||||||||
OK169_internal | |||||||||
SeqStatus | Sequenced | ||||||||
Variation_type | Allele | ||||||||
Origin | Species | Caenorhabditis elegans | |||||||
Strain | WBStrain00003942 | ||||||||
Laboratory | RB | ||||||||
BS | |||||||||
Person | WBPerson46 | ||||||||
WBPerson12335 | |||||||||
KO_consortium_allele | |||||||||
Status | Live | ||||||||
Affects | Gene | WBGene00004057 | |||||||
Transcript | F42G8.4a.3 | VEP_consequence | splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant | ||||||
VEP_impact | HIGH | ||||||||
Intron_number | 2/8 | ||||||||
Exon_number | 1-2/9 | ||||||||
F42G8.4a.2 | VEP_consequence | splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant | |||||||
VEP_impact | HIGH | ||||||||
HGVSc | F42G8.4a.2:c.-1+40_252+116delinsAGAGAGAAG | ||||||||
Intron_number | 1-2/9 | ||||||||
Exon_number | 2/10 | ||||||||
F42G8.4a.1 | VEP_consequence | splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant | |||||||
VEP_impact | HIGH | ||||||||
HGVSc | F42G8.4a.1:c.-1+40_252+116delinsAGAGAGAAG | ||||||||
Intron_number | 1-2/8 | ||||||||
Exon_number | 2/9 | ||||||||
Interactor (13) | |||||||||
Genetics | Mapping_data | In_multi_point | 4595 | ||||||
Description | Phenotype | WBPhenotype:0000119 | Paper_evidence | WBPaper00038206 | |||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | This mutation suppressed the reduction of endogenous MEC-18 caused by colchicine. | Paper_evidence | WBPaper00038206 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Affected_by | Molecule | WBMol:00003637 | Paper_evidence | WBPaper00038206 | |||||
Curator_confirmed | WBPerson712 | ||||||||
Phenotype_assay | Genotype | uIs44(Pmec-18::praja::gfp) | Paper_evidence | WBPaper00038206 | |||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0000386 | Paper_evidence | WBPaper00033433 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | Copper-induced germ cell apoptosis was slightly reduced in pmk-3(ok169) mutants (Figure 5B). | Paper_evidence | WBPaper00033433 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
Affected_by | Molecule | WBMol:00002862 | Paper_evidence | WBPaper00033433 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Treatment | Worms were exposed to 10 micromolar of copper for 12 hours | Paper_evidence | WBPaper00033433 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0000487 | Paper_evidence | WBPaper00038206 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | This 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_evidence | WBPaper00038206 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Affected_by | Molecule | WBMol:00003637 | Paper_evidence | WBPaper00038206 | |||||
Curator_confirmed | WBPerson712 | ||||||||
Phenotype_assay | Genotype | uIs44(Pmec-18::praja::gfp) | Paper_evidence | WBPaper00038206 | |||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0000615 | Paper_evidence | WBPaper00048972 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
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_evidence | WBPaper00048972 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
EQ_annotations | Anatomy_term | WBbt:0005666 | PATO:0000460 | Paper_evidence | WBPaper00048972 | ||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | Pgpa-4::gfp; gpa-3QL(syIs25) | Paper_evidence | WBPaper00048972 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0000679 | Paper_evidence | WBPaper00048972 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
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_evidence | WBPaper00048972 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
"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_evidence | WBPaper00048972 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | GFP::RAB-5 | Paper_evidence | WBPaper00048972 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
GFP::RAB-5; gpa-3QL(syIs25) | Paper_evidence | WBPaper00048972 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
GFP::RAB-5; sql-1(tm2409) | Paper_evidence | WBPaper00048972 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0000750 | Paper_evidence | WBPaper00049830 | |||||||
Curator_confirmed | WBPerson23367 | ||||||||
Remark | Figure S10, pmk-3(ok169) rescues vhp-1 RNAi larval arrest in nuo-6(qm200) | Paper_evidence | WBPaper00049830 | ||||||
Curator_confirmed | WBPerson23367 | ||||||||
Phenotype_assay | Genotype | vhp-1(RNAi); nuo-6(qm200) | Paper_evidence | WBPaper00049830 | |||||
Curator_confirmed | WBPerson23367 | ||||||||
WBPhenotype:0001171 | Paper_evidence | WBPaper00049830 | |||||||
Curator_confirmed | WBPerson23367 | ||||||||
Remark | Figure 8A, pmk-3(ok169) shows little to no life extension on atp-3 RNAi | Paper_evidence | WBPaper00049830 | ||||||
Curator_confirmed | WBPerson23367 | ||||||||
Figure 8B, pmk-3(ok169) shows reduced life extension on cco-1 RNAi | Paper_evidence | WBPaper00049830 | |||||||
Curator_confirmed | WBPerson23367 | ||||||||
Figure 8C & 9, pmk-3(ok169) shows reduced life extension on isp-1 RNAi | Paper_evidence | WBPaper00049830 | |||||||
Curator_confirmed | WBPerson23367 | ||||||||
Figure 8D, pmk-3(ok169) shows reduced life extension on nuo-2 RNAi | Paper_evidence | WBPaper00049830 | |||||||
Curator_confirmed | WBPerson23367 | ||||||||
Phenotype_assay | Genotype | atp-3(RNAi) | Paper_evidence | WBPaper00049830 | |||||
Curator_confirmed | WBPerson23367 | ||||||||
cco-1(RNAi) | Paper_evidence | WBPaper00049830 | |||||||
Curator_confirmed | WBPerson23367 | ||||||||
isp-1(RNAi) | Paper_evidence | WBPaper00049830 | |||||||
Curator_confirmed | WBPerson23367 | ||||||||
nuo-2(RNAi) | Paper_evidence | WBPaper00049830 | |||||||
Curator_confirmed | WBPerson23367 | ||||||||
WBPhenotype:0001203 | Paper_evidence | WBPaper00046636 | |||||||
Curator_confirmed | WBPerson557 | ||||||||
Remark | Animals are all partially resistant to nicotine. | Paper_evidence | WBPaper00046636 | ||||||
Curator_confirmed | WBPerson557 | ||||||||
Phenotype_assay | Treatment | Animals exposed to a solution of 0.1 percent nicotine. | Paper_evidence | WBPaper00046636 | |||||
Curator_confirmed | WBPerson557 | ||||||||
Phenotype_not_observed | WBPhenotype:0000039 | Paper_evidence | WBPaper00049830 | ||||||
Curator_confirmed | WBPerson23367 | ||||||||
Remark | Figure 8, pmk-3(ok169) lifespan is no different than N2 under normal conditions | Paper_evidence | WBPaper00049830 | ||||||
Curator_confirmed | WBPerson23367 | ||||||||
Phenotype_assay | Control_strain | WBStrain00000001 | Paper_evidence | WBPaper00049830 | |||||
Curator_confirmed | WBPerson23367 | ||||||||
WBPhenotype:0000315 | Paper_evidence | WBPaper00035070 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Animals are touch sensitive. | Paper_evidence | WBPaper00035070 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0000615 | Paper_evidence | WBPaper00048972 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
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_evidence | WBPaper00048972 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
EQ_annotations | Anatomy_term | WBbt:0005666 | PATO:0000460 | Paper_evidence | WBPaper00048972 | ||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | Pgpa-4::gfp | Paper_evidence | WBPaper00048972 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0000633 | Paper_evidence | WBPaper00045955 | |||||||
Curator_confirmed | WBPerson557 | ||||||||
Remark | Animals did not have PLM branch defects. | Paper_evidence | WBPaper00045955 | ||||||
Curator_confirmed | WBPerson557 | ||||||||
WBPhenotype:0000679 | Paper_evidence | WBPaper00048972 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
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_evidence | WBPaper00048972 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
"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_evidence | WBPaper00048972 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Phenotype_assay | Genotype | Pgpa-4::uev-3::gfp | Paper_evidence | WBPaper00048972 | |||||
Curator_confirmed | WBPerson2987 | ||||||||
DPY-23::GFP | Paper_evidence | WBPaper00048972 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
WBPhenotype:0000905 | Paper_evidence | WBPaper00035070 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Animals exhibited normal cell-body morphology. | Paper_evidence | WBPaper00035070 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
EQ_annotations | Anatomy_term | WBbt:0005237 | PATO:0000460 | Paper_evidence | WBPaper00035070 | ||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0001173 | Paper_evidence | WBPaper00040855 | |||||||
Curator_confirmed | WBPerson557 | ||||||||
Remark | Adult males show appropriate cell death of the linker cell. | Paper_evidence | WBPaper00040855 | ||||||
Curator_confirmed | WBPerson557 | ||||||||
WBPhenotype:0001588 | Paper_evidence | WBPaper00038206 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | pmk-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_evidence | WBPaper00038206 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Affected_by | Molecule | WBMol:00003637 | Paper_evidence | WBPaper00038206 | |||||
Curator_confirmed | WBPerson712 | ||||||||
Phenotype_assay | Genotype | uIs43, uIs44(Pmec-18::praja::gfp) | Paper_evidence | WBPaper00038206 | |||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0001933 | Paper_evidence | WBPaper00035070 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0002212 | Paper_evidence | WBPaper00048972 | |||||||
Curator_confirmed | WBPerson2987 | ||||||||
Remark | Figure 1A,B | Paper_evidence | WBPaper00048972 | ||||||
Curator_confirmed | WBPerson2987 | ||||||||
EQ_annotations | Anatomy_term | WBbt:0005391 | PATO:0000460 | Paper_evidence | WBPaper00048972 | ||||
Curator_confirmed | WBPerson2987 | ||||||||
Reference | WBPaper00038206 | ||||||||
WBPaper00040855 | |||||||||
WBPaper00033433 | |||||||||
WBPaper00035070 | |||||||||
WBPaper00045955 | |||||||||
WBPaper00048972 | |||||||||
WBPaper00049830 | |||||||||
WBPaper00065298 | |||||||||
WBPaper00066032 | |||||||||
WBPaper00046636 | |||||||||
Remark | Last updated on 29 Nov 2002 | ||||||||
Allele sequenced by Christopher Hoover | Curator_confirmed | WBPerson2970 | |||||||
Sequenced by the C. elegans Gene Knockout Consortium | Paper_evidence | WBPaper00041807 | |||||||
Method | KO_consortium_allele |