WormBase Tree Display for Variation: WBVar00250696

WBVar00250696 Name: Public_name: tm1729
    Other_name: F54A5.3b.1:c.-250_-111+268delinsAT
      F54A5.3a.1:c.138-67_210+268delinsAT
      F54A5.3b.2:c.-266-67_-194+268delinsAT
    HGVSg: CHROMOSOME_I:g.972380_972787delinsAT
  Sequence_details: SMap: S_parent: Sequence: F54A5
    Flanking_sequences: tgcaccatgtaacctttctctaataacctg cttcatgcctgcctaccgcctgatttctaa
    Mapping_target: F54A5
    Source_location: 7 CHROMOSOME_I 972379 972788 Inferred_automatically: National_Bioresource_Project
    Type_of_mutation: Insertion: AT
      Deletion
    PCR_product: tm1729_external
      tm1729_internal
    SeqStatus: Sequenced
  Variation_type: Allele
  Origin: Species: Caenorhabditis elegans
    Laboratory: FX
    Author: Mitani S
    DB_info: Database: National_Bioresource_Project seq 1729
    NBP_allele
    Status: Live
  Affects: Gene: WBGene00018788
    Transcript: F54A5.3a.1 VEP_consequence: splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
        VEP_impact: HIGH
        HGVSc: F54A5.3a.1:c.138-67_210+268delinsAT
        Intron_number: 3-4/7
        Exon_number: 4/8
      F54A5.3b.3 VEP_consequence: splice_donor_variant,5_prime_UTR_variant,intron_variant
        VEP_impact: HIGH
        Intron_number: 1/5
        Exon_number: 1/6
      F54A5.3b.2 VEP_consequence: splice_acceptor_variant,splice_donor_variant,5_prime_UTR_variant,intron_variant
        VEP_impact: HIGH
        HGVSc: F54A5.3b.2:c.-266-67_-194+268delinsAT
        Intron_number: 2-3/7
        Exon_number: 3/8
      F54A5.3b.1 VEP_consequence: splice_donor_variant,5_prime_UTR_variant,intron_variant
        VEP_impact: HIGH
        HGVSc: F54A5.3b.1:c.-250_-111+268delinsAT
        cDNA_position: 3725-?
        Intron_number: 2/6
        Exon_number: 2/7
    Interactor: WBInteraction000503796
  Isolation: Mutagen: TMP/UV
  Genetics: Map: I
  Description: Phenotype: WBPhenotype:0000591 Paper_evidence: WBPaper00032209
        Curator_confirmed: WBPerson712
        Remark: Animals were hypersensitive to copper, and cadmium. Animals grew poorly on plates containing these metal ions and failed to reach the adult stage within 4 days. Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
        Variation_effect: Null: Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
      WBPhenotype:0000593 Person_evidence: WBPerson7743
        Curator_confirmed: WBPerson712
        Remark: Comments to the National Bioresource Project of Japan: Dr. K. Matsumoto: sensitive to copper. Person_evidence: WBPerson7743
            Curator_confirmed: WBPerson712
            Laboratory_evidence: FX
      WBPhenotype:0001349 Paper_evidence: WBPaper00032209
        Curator_confirmed: WBPerson712
        Remark: Phosphorylated PMK-1 levels were normal. Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
        Variation_effect: Null: Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
      WBPhenotype:0001351 Paper_evidence: WBPaper00032209
        Curator_confirmed: WBPerson712
        Remark: Phosphorylated KGB-1 levels were significantly decreased, whether treated with Cu2+ or not. Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
        Variation_effect: Null: Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
      WBPhenotype:0001724 Paper_evidence: WBPaper00032209
        Curator_confirmed: WBPerson712
        Variation_effect: Null: Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
        Phenotype_assay: Treatment: Animals were cultured from embryogenesis on normal plates containing 1 ug/ml tunicamycin. The percentage of worms reaching adulthood 4 days after egg laying was scored. Paper_evidence: WBPaper00032209
              Curator_confirmed: WBPerson712
    Phenotype_not_observed: WBPhenotype:0000062 Person_evidence: WBPerson7743
        Curator_confirmed: WBPerson712
        Remark: Classified as homozygous viable by the National Bioresource Project of Japan. Person_evidence: WBPerson7743
            Curator_confirmed: WBPerson712
            Laboratory_evidence: FX
      WBPhenotype:0000631 Paper_evidence: WBPaper00032209
        Curator_confirmed: WBPerson712
        Remark: Unlike sek-1(km4) animals, tm1729 mutants did not show any arsenite-sensitive phenotypes. Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
        Variation_effect: Null: Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
        Affected_by: Molecule: WBMol:00004596 Paper_evidence: WBPaper00032209
              Curator_confirmed: WBPerson712
        Phenotype_assay: Treatment: Well-fed young adults of each animal were transferred to normal plates containing 5 mM sodium arsenite. The percentage of animals surviving after incubation for 1 day were scored. Paper_evidence: WBPaper00032209
              Curator_confirmed: WBPerson712
      WBPhenotype:0000643 Paper_evidence: WBPaper00032209
        Curator_confirmed: WBPerson712
        Variation_effect: Null: Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
        Phenotype_assay: Treatment: Well-fed young adults were spotted in the center of normal plates and then killed by chloroform at 4 min after spotting. The percentage of worms located outside of the 2 cm circle was recorded. Paper_evidence: WBPaper00032209
              Curator_confirmed: WBPerson712
      WBPhenotype:0000664 Paper_evidence: WBPaper00032209
        Curator_confirmed: WBPerson712
        Variation_effect: Null: Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
      WBPhenotype:0000699 Paper_evidence: WBPaper00032209
        Curator_confirmed: WBPerson712
        Variation_effect: Null: Paper_evidence: WBPaper00032209
            Curator_confirmed: WBPerson712
  Reference: WBPaper00032209
  Remark: 20469/20470-AT-20877/20878 (408 bp deletion + 2 bp insertion)
    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