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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
Remarkcdf-2(tm788) mutant animals displayed reduced zinc content at dietary zinc concentrations of 30 M and higher compared to wild-type animalsPaper_evidenceWBPaper00033166
Curator_confirmedWBPerson712
In contrast to wild-type, bilobed gut granules were not stained asymmetrically with FluoZin-3 in cdf-2(tm788) mutant animals (Figure S7B). These results indicate that CDF-2 activity is necessary for the asymmetric accumulation of zinc.Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
cdf-2(tm788) mutant animals precultured with 50 μM supplemental zinc and then transferred to medium supplemented with 100 μM TPEN (zinc chelator,N,N,N0,N0-tetrakis (2-pyridylmethyl) ethylenediamine) did not display a significant increase in growth rate compared to cdf-2(tm788) mutant animals not precultured with supplemental zinc and then transferred to medium supplemented with 100 μM TPEN (Figures 7C), unlike wild type animals. These results indicate that CDF-2 is necessary for zinc storage, which promotes the resistance to zinc deficiency.Paper_evidenceWBPaper00040622
Curator_confirmedWBPerson2987
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
Remark28668/28669-AAAGCAATATAAATTTTAAAAGCAATACCTCTCCGATTGCTATCATGTGAATCTGTTGAGTCAGCTTC-29472/29473 (804 bp deletion +69 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_evidenceWBPaper00041807
MethodNBP_knockout_allele