WormBase Tree Display for Variation: WBVar00600877

WBVar00600877 Name: Public_name: tm5503
    Other_name: H27M09.1.1:c.168+3_537del
    HGVSg: CHROMOSOME_I:g.6851551_6852169del
  Sequence_details: SMap: S_parent: Sequence: H27M09
    Flanking_sequences: gactgcattacagagaaaacgagaaaaagt gaaggtgatcatattccaccgccaatcggc
    Mapping_target: H27M09
    Source_location: 7 CHROMOSOME_I 6851550 6852170 Inferred_automatically: National_Bioresource_Project
    Type_of_mutation: Deletion
    PCR_product: tm5503_external
      tm5503_internal
    SeqStatus: Sequenced
  Variation_type: Allele
  Origin: Species: Caenorhabditis elegans
    Strain: WBStrain00005694
    Laboratory: FX
    Author: Mitani S
    DB_info: Database: National_Bioresource_Project seq 5503
    NBP_allele
    Status: Live
  Affects: Gene: WBGene00019245
    Transcript: H27M09.1.1 VEP_consequence: splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
        VEP_impact: HIGH
        HGVSc: H27M09.1.1:c.168+3_537del
        cDNA_position: ?-546
        CDS_position: ?-537
        Protein_position: ?-179
        Intron_number: 2-4/13
        Exon_number: 3-5/14
    Interactor (13)
  Isolation: Mutagen: TMP/UV
  Genetics: Map: I
  Description: Phenotype: WBPhenotype:0000050 Paper_evidence: WBPaper00041364
        Curator_confirmed: WBPerson712
        Remark: Upon mating, sacy-1(tm5503) females produce embryos that arrest without properly undergoing morphogenesis and fail to hatch. Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
        Variation_effect: Probable_null_via_phenotype: Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
      WBPhenotype:0000062 Paper_evidence: WBPaper00041364
        Person_evidence: WBPerson7743
        Curator_confirmed: WBPerson712
        Remark: Classified as lethal OR sterile by the National Bioresource Project of Japan. Person_evidence: WBPerson7743
            Curator_confirmed: WBPerson712
            Laboratory_evidence: FX
          an analysis of the strong loss-of-function sacy-1(tm5503) allele (Figure 4A) shows it to be an essential gene with a zygotic sterile phenotype Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
        Variation_effect: Probable_null_via_phenotype: Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
      WBPhenotype:0000688 Paper_evidence: WBPaper00041364
        Person_evidence: WBPerson7743
        Curator_confirmed: WBPerson712
        Remark: Classified as lethal OR sterile by the National Bioresource Project of Japan. Person_evidence: WBPerson7743
            Curator_confirmed: WBPerson712
            Laboratory_evidence: FX
          Homozygous hermaphrodites produced from heterozygous parents develop to adulthood but are sterile. Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
        Rescued_by_transgene: WBTransgene00015492
        Variation_effect: Probable_null_via_phenotype: Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
      WBPhenotype:0000692 Paper_evidence: WBPaper00041364
        Curator_confirmed: WBPerson712
        Remark: sacy-1(tm5503) adult males were never observed to sire cross-progeny. Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
        Variation_effect: Probable_null_via_phenotype: Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
      WBPhenotype:0001675 Paper_evidence: WBPaper00041364
        Curator_confirmed: WBPerson712
        Remark: sacy-1(tm5503) adult hermaphrodites do not produce fertilized embryos (Table 4); instead they contain oocytes and sperm that become vacuolated and appear to degenerate. We also observed a similar sperm degeneration phenotype in sacy-1(tm5503) adult males (Figure 7A), which were never observed to sire cross-progeny. Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
        Variation_effect: Probable_null_via_phenotype: Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
      WBPhenotype:0002260 Paper_evidence: WBPaper00041364
        Curator_confirmed: WBPerson712
        Remark: sacy-1(tm5503) adult hermaphrodites do not produce fertilized embryos (Table 4); instead they contain oocytes and sperm that become vacuolated and appear to degenerate. We observed that acridine orange stains early degenerating gametes in the proximal gonad of sacy-1(tm5503) single mutant hermaphrodites. We did not observe mating to wild-type males to overtly increase the penetrance or severity of oocyte degeneration. Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
        Variation_effect: Probable_null_via_phenotype: Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
    Phenotype_not_observed: WBPhenotype:0000399 Paper_evidence: WBPaper00041364
        Curator_confirmed: WBPerson712
        Remark: The somatic gonad appeared to develop normally in sacy-1(tm5503) hermaphrodites. Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
        Variation_effect: Probable_null_via_phenotype: Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
      WBPhenotype:0002188 Paper_evidence: WBPaper00041364
        Curator_confirmed: WBPerson712
        Remark: The somatic gonad appeared to develop normally in sacy-1(tm5503) males. Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
        Variation_effect: Probable_null_via_phenotype: Paper_evidence: WBPaper00041364
            Curator_confirmed: WBPerson712
  Reference: WBPaper00041364
  Remark: 9477/9478-10096/10097 (619 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_evidence: WBPaper00041807
  Method: NBP_knockout_allele