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WormBase Tree Display for Variation: WBVar00249816

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Name Class

WBVar00249816NamePublic_nametm788
HGVSgCHROMOSOME_X:g.12466567_12467370delinsAAAGCAATATAAATTTTAAAAGCAATACCTCTCCGATTGCTATCATGTGAATCTGTTGAGTCAGCTTC
Sequence_detailsSMapS_parentSequenceT18D3
Flanking_sequencesatcatgtgaatctgttgagtcagcttcatctaaattcatatgcatatggctcactctgac
Mapping_targetT18D3
Source_location7CHROMOSOME_X1246656612467371Inferred_automaticallyNational_Bioresource_Project
Type_of_mutationInsertionAAAGCAATATAAATTTTAAAAGCAATACCTCTCCGATTGCTATCATGTGAATCTGTTGAGTCAGCTTC
Deletion
PCR_producttm788_external
tm788_internal
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
LaboratoryFX
AuthorMitani S
DB_infoDatabaseNational_Bioresource_Projectseq788
NBP_allele
StatusLive
AffectsGeneWBGene00011821
TranscriptT18D3.3a.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant
VEP_impactHIGH
cDNA_position?-245
CDS_position?-105
Protein_position?-35
Intron_number2/9
Exon_number1-3/10
InteractorWBInteraction000524618
IsolationMutagenTMP/UV
GeneticsMapX
DescriptionPhenotypeWBPhenotype:0000136Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
RemarkAn analysis of ttm-1 transcripts using qRT-PCR showed a small increase in ttm-1 transcript levels in cdf-2 mutant animals compared to wild-type animals (data not shown).Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
WBPhenotype:0000137Paper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
RemarkThe abundance of the cdf-2 transcript was dramatically reduced by approximately 1,000-fold in the cdf-2(tm788) mutant compared to wild typePaper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
Variation_effectProbable_null_via_phenotypePaper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
Phenotype_assayTreatmentQuantitative, real-time PCR analysisPaper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
WBPhenotype:0001747Paper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
Remarkcdf-2(tm788) mutant animals displayed reduced population growth compared to wild-type animals in 30 M to 480 M dietary zincPaper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
Variation_effectProbable_null_via_phenotypePaper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
Affected_byMoleculeWBMol:00003477Paper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
Phenotype_assayTreatmentEggs were transferred to CeMM with 18-19 different concentrations of zinc, ranging from no added zinc to 2 mM zincPaper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
WBPhenotype:0001749Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
Remarkcdf-2(tm788) mutant animals displayed significantly lower growth rates than wild-type animals at all concentrations of supplemental zinc (Figure 6B).Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
Affected_byMoleculeWBMol:00005064Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
Phenotype_assayTreatmentHermaphrodites were synchronized at the L1 stage and cultured on noble agar minimal medium (NAMM) dishes for 3 days with supplemental zinc. The length of individual animals was measured using microscopy and ImageJ software.Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
WBPhenotype:0001849Paper_evidenceWBPaper00033166
WBPaper00040622
Curator_confirmedWBPerson712
WBPerson2987
Remark (3)
Variation_effectProbable_null_via_phenotypePaper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
Affected_byMoleculeWBMol:00005064Paper_evidenceWBPaper00033166
WBPaper00040622
Curator_confirmedWBPerson712
WBPerson2987
Phenotype_assayTreatmentDetermination of zinc content of C. elegans using inductively coupled plasma-mass spectrometry (ICP-MS)Paper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
cdf-2(tm788) L1 stage hermaphrodites were precultured for 12 hours on noble agar minimal medium (NAMM) dishes containing 0 or 50 micromolar supplemental zinc, cultured for 3 days on NGM dishes with 100 micromolar TPEN (zinc chelator,N,N,N0,N0-tetrakis (2-pyridylmethyl) ethylenediamine), and analyzed individually for length.Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
WBPhenotype:0002245Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
Remarkcdf-2(tm788) mutant animals displayed significantly lower FluoZin-3 fluorescence at both 0 mM and 100 mM supplemental zinc compared to wild-type animals (Figures 3C and 3D), indicative of reduced endogenous zinc levels. cdf-2(tm788) mutants also exhibited reduced zinc content as determined by inductively coupled plasma-mass spectrometry (ICP-MS) (Figure 2B).Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
Phenotype_not_observed (11)
ReferenceWBPaper00040622
WBPaper00033166
Remark (2)
MethodNBP_knockout_allele