WormBase Tree Display for Variation: WBVar00249340

WBVar00249340 Name: Public_name: tm291
    Other_name: ZC404.8.1:c.75_*186delinsGGGGG
    HGVSg: CHROMOSOME_V:g.6783467_6784781delinsCCCCC
  Sequence_details: SMap: S_parent: Sequence: ZC404
    Flanking_sequences: cattcctacaaaataacaccgggggggtcg ggattcgcactgttaaacggtaatctgaaa
    Mapping_target: ZC404
    Source_location: 7 CHROMOSOME_V 6782466 6783782 Inferred_automatically: National_Bioresource_Project
    Type_of_mutation: Insertion: ccccc
      Deletion: atatagaagctacagggaagaaaaactagcaacgaatcatttgacaaggacaacgagtgtcgctgtacaagaagattccgtaaaaaatttgttaaagctttttggttaagtgaaagtttaggggtgttcgataaaatgcaaaacacgcagttagtagaaataaaatgggcgtatcagttgaactgattactggcttgacgattcttttggtggagaaacagactttccgtggaacgatgtggaaccttcgtagagagcagcgagaagataatcagggctgttatgtggggaccaatgaatctcttcgtctaaaatttgatttttaaatgaaaatcgacaatctagaatctaaactatttacctgaaactgtctcgctctctgatgatctcaatccagaagatgtcacagatggtgctctctttcctttgttagcactattatttcctgatccaaaatggtttgaagtgtcgagaagagcagtaatctggtcacgaagatgatgtgggaatatagagttcaactccacatcagacagctcgtgattcgaagaatcagaacacttattgctgcatggtgagttttgtctgtgcatgcacatcagaatacttgtttccgtcgtaggctcgccgtttttgcagaagtattcaccagctgaagaaagcttgagctcgctgtgcttggtgcatcgaggtggtttggtctgcacaagactacgcgtgttgaaaattccattgctacggtatggtgccatcatgaatccagcttcgggaaaacatgttgtgttctccttttccttgaacaactgatgcattggctcagctctccataaattatgaggggctcgaagatcgacacacagctttggtggtggcaaaacttcattttgtggattgttgataagctttctgcgggttggtgtcgctcttctcacttctataattcttccttgaacatgtgattcgtgaagcgcagcacgagctttctcacaggattcgatggaatcgagtgtgacaaacccgaaccctttggatccacgatcatttgtgacgatttccacactcaggactcttccatatctgaaattaatattcttattcagaacttgttgtaaattgaaaactcacgcgaagaacattgccgccaaatcttgttcacgaaacgagaagggaatattgctgacatatatcctaaaagttttttgatgaattcattaaaacggcacgacaaatttacctgttatctgtgaaagaagccggctcacgagttttcggtttgaccgatattggcattgtgaaaattggatctttgttggaa
    PCR_product: tm291_external
      tm291_internal
    SeqStatus: Sequenced
  Variation_type: Allele
  Origin: Species: Caenorhabditis elegans
    Strain: WBStrain00005726
      WBStrain00005728
      WBStrain00007559
    Laboratory: FX
    Author: Mitani S
    DB_info: Database: National_Bioresource_Project seq 291
    NBP_allele
    Status: Live
  Affects: Gene: WBGene00004984
    Transcript: ZC404.8.1 VEP_consequence: splice_acceptor_variant,splice_donor_variant,stop_lost,3_prime_UTR_variant,intron_variant
        VEP_impact: HIGH
        HGVSc: ZC404.8.1:c.75_*186delinsGGGGG
        cDNA_position: 76-1243
        CDS_position: 75-?
        Protein_position: 25-?
        Intron_number: 3-5/6
        Exon_number: 3-7/7
    Interactor: WBInteraction000501863
  Isolation: Mutagen: TMP/UV
  Genetics: Map: V
  Description: Phenotype: WBPhenotype:0000062 Person_evidence: WBPerson7743
        Curator_confirmed: WBPerson712
        Remark: Classified as lethal OR sterile by the National Bioresource Project of Japan. Dr. Y. Kohara: Development 130; 2495-2503 (2003). Person_evidence: WBPerson7743
            Curator_confirmed: WBPerson712
            Laboratory_evidence: FX
      WBPhenotype:0000688 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
  Reference: WBPaper00018364
    WBPaper00017790
  Remark: 12753/12754-6G?-14068/14069 (1315 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
    Original flanks cgagaaaatattttcgaaaattgagcccgt ttgatttttaaatgaaaatcgacaatctag seem to have been calculated 1000bp out of place.
    The original publication describing tm291 indicates that this deletion starts in exon 2 of the spn-4 gene and removes the rest of the spn-4 coding region (Ogura et al. 2003, a.k.a. WBPaper00005822, see Figure 3C in that publication). We recently sequenced tm291 and confirmed that the published location of the deletion is correct. The precise sequence of tm291 with respect to the spn-4 gene is shown below. In addition to a 1315 bp deletion, there is a small insertion at the deletion site (the inserted nucleotides are underlined). ATGCAAAACACACAGATATTTACTAACTTCGCTCACAGAGCACATGATGGgtatgtttatcatttttaaatgttggtattaagtatttctttttcagATTACCGTTTAACAGTGCGAATCC[ccccc]cgacccccccggtgttattttgtaggaatgcgtttcagcatcttccctattttgccatctctcacatacactcaacattagcaatcggaaaacagatcttctatattgaaaatatactaccagtccgtttaacctacctcgcttgctaacattattgaatgtgcccacgtattgtattttctgagcatctttctgttttttttgtattttatagacgctgtgttcgccagttatttttgcattcctgtattgctcgaagtcaaatgaagtgcttcgccat Paper_evidence: WBPaper00005822
      Person_evidence: WBPerson616
      Curator_confirmed: WBPerson1983
  Method: NBP_knockout_allele