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WormBase Tree Display for Variation: WBVar00249311

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Name Class

WBVar00249311NamePublic_nametm259
Other_nameZK1193.5c.2:c.373-110_699+7del
ZK1193.5a.1:c.997-110_1323+7del
ZK1193.5d.3:c.373-110_690+7del
ZK1193.5c.1:c.373-110_699+7del
ZK1193.5e.1:c.997-110_1314+7del
ZK1193.5d.4:c.373-110_690+7del
ZK1193.5d.1:c.373-110_690+7del
ZK1193.5d.2:c.373-110_690+7del
ZK1193.5d.5:c.373-110_690+7del
HGVSgCHROMOSOME_X:g.427814_428797del
Sequence_detailsSMapS_parentSequenceZK1193
Flanking_sequencestcgataactagtaatcagtattaatatagaattcagattttcggccgtagtgttaggtct
Mapping_targetZK1193
Source_location7CHROMOSOME_X427813428798Inferred_automaticallyNational_Bioresource_Project
Type_of_mutationDeletion
PCR_producttm259_external
tm259_internal
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
LaboratoryFX
AuthorMitani S
DB_infoDatabaseNational_Bioresource_Projectseq259
NBP_allele
StatusLive
AffectsGeneWBGene00022861
TranscriptZK1193.5c.2VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScZK1193.5c.2:c.373-110_699+7del
Intron_number5-7/8
Exon_number6-7/9
ZK1193.5e.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScZK1193.5e.1:c.997-110_1314+7del
Intron_number6-8/8
Exon_number7-8/9
ZK1193.5c.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScZK1193.5c.1:c.373-110_699+7del
Intron_number6-8/9
Exon_number7-8/10
ZK1193.5d.4VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScZK1193.5d.4:c.373-110_690+7del
Intron_number5-7/8
Exon_number6-7/9
ZK1193.5d.3VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScZK1193.5d.3:c.373-110_690+7del
Intron_number6-8/9
Exon_number7-8/10
ZK1193.5d.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScZK1193.5d.1:c.373-110_690+7del
Intron_number7-9/10
Exon_number8-9/11
ZK1193.5d.2VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScZK1193.5d.2:c.373-110_690+7del
Intron_number7-9/10
Exon_number8-9/11
ZK1193.5a.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScZK1193.5a.1:c.997-110_1323+7del
Intron_number7-9/10
Exon_number8-9/11
ZK1193.5d.5VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScZK1193.5d.5:c.373-110_690+7del
Intron_number4-6/7
Exon_number5-6/8
InteractorWBInteraction000520533
WBInteraction000536221
IsolationMutagenTMP/UV
GeneticsMapX
DescriptionPhenotypeWBPhenotype:0000062Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkClassified as lethal or sterile by the National Bioresource Project of Japan. Comment to the NBP from Dr. W.B. Derry: non-Mendelian inheritance. Deletion is unstable extrachromosomal?Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidenceFX
WD
WBPhenotype:0000688Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkClassified as lethal or sterile by the National Bioresource Project of Japan. Comment to the NBP from Dr. W.B. Derry: non-Mendelian inheritance. Deletion is unstable extrachromosomal?Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidenceFX
WD
WBPhenotype:0000867Paper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
Remark"Homozygous dve-1(tm259) X mutant animals develop normally until 330 min postfertilization , after which they arrest and degenerate (Figure 2B)."Paper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
EQ_annotationsLife_stageWBls:0000003PATO:0000460Paper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
WBPhenotype:0001278Paper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
Remark"Though morphologically normal at this early stage of development, homozygous dve-1(tm259) X mutant embryos born to spg-7(RNAi) mothers have attenuated hsp-60pr::gfp expression , whereas wild-type embryos from spg-7(RNAi) mothers express higher levels of hsp-60pr::gfp (Figure 2C) . These findings indicate that activation of the UPRmt in early embryos depends on endogenous dve-1."Paper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
Phenotype_assayGenotypespg-7(RNAi); hsp-60pr::gfpPaper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
WBPhenotype:0002268Paper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
Remark"To further examine dve-1's effect on mitochondria , we compared the staining pattern of MitoTracker , a mitochon- drial vital dye , in wild-type embryos and early dve-1(tm259) X mutant embryos , following an established protocol ( Jagasia et al. , 2005 ) . In wild-type embryos , MitoTracker staining was most conspicuous in a reticular network surrounding the large DVE-1-positive nuclei of the intestinal precursor cells , whereas staining in the mutant embryos was consistently diminished by 50% ( Figure 2D ) . As MitoTracker is a vital dye taken up actively by the organelle , these observations are consistent with reduced mitochondrial mass , defective membrane potential, or both."Paper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
" To expand on these observations , we sought a marker for mitochondrial mass . A ligand blot assay with a peroxidase-tagged avidin probe identifies a single major species of 75 kDa in worm lysates that is enriched in the mitochondrial fraction and probably corresponds to the biotinylated mitochondrial enzyme propionyl-CoA carboxylase ( Figure S2 ; Benedetti et al. , 2006 ) . Histochemical analysis of fixed embryos with FITC-conjugated avidin re- veals a signal that largely overlaps MitoTracker in dve-1 / + embryos ( Figure S2 ) and is reduced 55% in dve-1 ( tm259 ) X mutant embryos ( Figure 2E ) . These observations are consistent with reduced mitochondrial mass , possibly com- pounded by a functional defect in the mitochondria of the mutant embryos."Paper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
EQ_annotationsLife_stageWBls:0000003PATO:0000460Paper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
GO_termGO:0005739PATO:0000460Paper_evidenceWBPaper00031084
Curator_confirmedWBPerson2987
Phenotype_not_observedWBPhenotype:0000729Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkComment to the NBP from Dr. C. Yang: normal cell death phenotype.Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidenceFU
WBPhenotype:0002535Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkComment to the NBP from Dr. P. Sengputa: normal dye filling.Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidencePY
ReferenceWBPaper00031084
Remark21397/21398-22381/22382 (984 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