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WormBase Tree Display for Variation: WBVar00251054

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Name Class

WBVar00251054NamePublic_nametm2114
Other_nameF56E3.3a.1:c.486-5_894del
F56E3.3b.1:c.486-5_894del
HGVSgCHROMOSOME_X:g.3177192_3177938del
Sequence_detailsSMapS_parentSequenceF56E3
Flanking_sequencesgagcagccaggttaaaacagagtctcgataaagacgtttgttttatgtttttgcttttga
Mapping_targetF56E3
Source_location7CHROMOSOME_X31771913177939Inferred_automaticallyNational_Bioresource_Project
Type_of_mutationDeletion
PCR_producttm2114_external
tm2114_internal
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
StrainWBStrain00047316
LaboratoryFX
AuthorMitani S
DB_infoDatabaseNational_Bioresource_Projectseq2114
NBP_allele
StatusLive
AffectsGeneWBGene00002217
TranscriptF56E3.3b.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScF56E3.3b.1:c.486-5_894del
cDNA_position?-933
CDS_position?-894
Protein_position?-298
Intron_number5-7/25
Exon_number6-8/26
F56E3.3a.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScF56E3.3a.1:c.486-5_894del
cDNA_position?-927
CDS_position?-894
Protein_position?-298
Intron_number5-7/24
Exon_number6-8/25
InteractorWBInteraction000518842
IsolationMutagenTMP/UV
GeneticsMapX
Mapping_dataIn_multi_point5603
DescriptionPhenotypeWBPhenotype:0001236Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson10038
RemarkQuoted from paper: "We first validated this glr-1 reporter under control of both Pglr-1 and the glr-1 3'UTR by testing if GFP fluorescence was altered in klp-4/KIF13 trafficking mutants. Briefly, we measured the maximum fluorescence intensity of GFP in the nucleus of the GLR-1-expressing interneuron PVC in wild type and klp-4 (tm2114) loss-of-function mutants (see Materials and Methods). We found that GFP fluorescence increased in klp-4 (tm2114) mutants (Fig 1A), consistent with our previous RT-qPCR results [30]. Because klp-4 mutants have reduced GLR-1 at synapses in the VNC, this data implies that decreased synaptic GLR-1 may trigger a compensatory feedback pathway resulting in increased glr-1 transcript."Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson10038
Phenotype_assayStrainWBStrain00047316Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson10038
Control_strainWBStrain00047309Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson10038
GenotypepzEx329[Pglr-1::NLS-GFP::LacZ::glr-1 3'UTR]Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson10038
WBPhenotype:0001278Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson48820
RemarkQuoted from paper: "Briefly, we measured the maximum fluorescence intensity of GFP in the nucleus of the GLR-1-expressing interneuron PVC in wild type and klp-4 (tm2114) loss-of-function mutants (see Materials and Methods). We found that GFP fluorescence increased in klp-4(tm2114) mutants (Fig 1A), consistent with our previous RT-qPCR results [30]. Because klp-4 mutants have reduced GLR-1 at synapses in the VNC, this data implies that decreased synaptic GLR-1 may trigger a compensatory feedback pathway resulting in increased glr-1 transcript."Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson48820
Variation_effectLoss_of_function_undetermined_extentPaper_evidenceWBPaper00049891
Curator_confirmedWBPerson48820
EQ_annotationsAnatomy_termWBbt:0005840PATO:0000460Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson48820
Phenotype_assayStrainWBStrain00047316Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson48820
Control_strainWBStrain00047309Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson48820
GenotypepzEx329[Pglr-1::NLS-GFP::LacZ::glr-1 3'UTR]Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson48820
Phenotype_not_observedWBPhenotype:0000062Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkClassified as homozygous viable by the National Bioresource Project of Japan.Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidenceFX
WBPhenotype:0000306Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson10038
RemarkThe klp-4(tm2114) did not significantly change the expression of the nmr-1 promoter reporter (S1 Fig. A /Figure S1A)Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson10038
Phenotype_assayControl_strainWBStrain00047811Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson10038
GenotypepzEx342[Pnmr-1::NLS-GFP::LacZ::unc-54 3'UTR]Paper_evidenceWBPaper00049891
Curator_confirmedWBPerson10038
WBPhenotype:0000436Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkComments to the National Bioresource Project of Japan: Dr. C. Bargmann: normal GFP::UNC-2 localization.Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidenceCX
WBPhenotype:0000643Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkComments to the National Bioresource Project of Japan: Dr. C. Bargmann: locomotion OKPerson_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidenceCX
WBPhenotype:0001225Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkComment to the National Bioresource Project of Japan: Dr. H. Sawa: 0% Psa.Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidenceHS
WBPhenotype:0002535Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkComment from Dr. P. Sengupta to the National Bioresource Project of Japan: normal dye filling. Dr. O. Blacque: dye-filling normalPerson_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidencePY
OEB
ReferenceWBPaper00049891
Remark5626/5627-6373/6374 (747 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_evidenceWBPaper00041807
MethodNBP_knockout_allele