WormBase Tree Display for Variation: WBVar01429551

WBVar01429551 Name: Public_name: tm2078
    Other_name: F11F1.7.1:c.20_328-55del
    HGVSg: CHROMOSOME_III:g.13404780_13405510del
  Sequence_details: SMap: S_parent: Sequence: F11F1
    Flanking_sequences: tttcaaaacatatgtcgagatttttgattt cttatagatcagaaagccaaacttttttgc
    Mapping_target: F11F1
    Source_location: 7 CHROMOSOME_III 13404779 13405511 Inferred_automatically: National_Bioresource_Project
    Type_of_mutation: Deletion
    PCR_product: tm2078_external
      tm2078_internal
    SeqStatus: Sequenced
  Variation_type: Allele
  Origin: Species: Caenorhabditis elegans
    Laboratory: FX
    Author: Mitani S
    DB_info: Database: National_Bioresource_Project seq 2078
    NBP_allele
    Status: Live
  Affects: Gene: WBGene00008719
    Transcript: F11F1.7.1 VEP_consequence: splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
        VEP_impact: HIGH
        HGVSc: F11F1.7.1:c.20_328-55del
        cDNA_position: 63-?
        CDS_position: 20-?
        Protein_position: 7-?
        Intron_number: 2-3/4
        Exon_number: 2-3/5
  Isolation: Mutagen: TMP/UV
  Genetics: Map: III
  Description: Phenotype: WBPhenotype:0000590 Paper_evidence: WBPaper00041205
        Curator_confirmed: WBPerson3997
      WBPhenotype:0001911 Paper_evidence: WBPaper00046306
        Curator_confirmed: WBPerson9270
        Remark: Table S2 Paper_evidence: WBPaper00046306
            Curator_confirmed: WBPerson9270
      WBPhenotype:0002365 Paper_evidence: WBPaper00046306
        Curator_confirmed: WBPerson9270
        Remark: Table S1 Paper_evidence: WBPaper00046306
            Curator_confirmed: WBPerson9270
    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
      WBPhenotype:0000243 Paper_evidence: WBPaper00050421
        Curator_confirmed: WBPerson2987
        Remark: No persistent corpses in the pharynx of L1 (Supplemental Table 1) Paper_evidence: WBPaper00050421
            Curator_confirmed: WBPerson2987
        Variation_effect: Predicted_null_via_sequence: Paper_evidence: WBPaper00050421
            Curator_confirmed: WBPerson2987
        EQ_annotations: Anatomy_term: WBbt:0003681 PATO:0000460 Paper_evidence: WBPaper00050421
                Curator_confirmed: WBPerson2987
          Life_stage: WBls:0000024 PATO:0000460 Paper_evidence: WBPaper00050421
                Curator_confirmed: WBPerson2987
      WBPhenotype:0002486 Paper_evidence: WBPaper00050421
        Curator_confirmed: WBPerson2987
        Remark: "Mutations in genes within the ced-1/6/7 pathway (ced-1, ced-7, nrf-5, ttr-52), the ced-2/5/12 pathway (ced-2, ced-5), or both pathways (ced-1;ced-2 and ced-7;ced-5) did not cause PGC lobes to persist in L1 larvae (Supplementary Table 1), indicating that ced-10 functions in PGC lobe scission in a different context than it does in cell corpse engulfment." (PGC = 'primordial germ cell') Paper_evidence: WBPaper00050421
            Curator_confirmed: WBPerson2987
        Variation_effect: Predicted_null_via_sequence: Paper_evidence: WBPaper00050421
            Curator_confirmed: WBPerson2987
        EQ_annotations: Anatomy_term: WBbt:0004576 PATO:0000460 Paper_evidence: WBPaper00050421
                Curator_confirmed: WBPerson2987
            WBbt:0004575 PATO:0000460 Paper_evidence: WBPaper00050421
                Curator_confirmed: WBPerson2987
          Life_stage: WBls:0000024 PATO:0000460 Paper_evidence: WBPaper00050421
                Curator_confirmed: WBPerson2987
        Phenotype_assay: Treatment: All strains include the xnIs360 or xnSi1 transgenes to visualize PGC membranes. Paper_evidence: WBPaper00050421
              Curator_confirmed: WBPerson2987
  Reference: WBPaper00041205
    WBPaper00046306
    WBPaper00050421
  Remark: 8240/8241-8971/8972 (731 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