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WormBase Tree Display for Variation: WBVar00252541

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Name Class

WBVar00252541NamePublic_nametm3976
Other_nameCE40450:p.Tyr76PhefsTer3
D1007.16.1:c.226_482del
HGVSgCHROMOSOME_I:g.4603526_4603782del
Sequence_detailsSMapS_parentSequenceD1007
Flanking_sequencesgtaccaagcgaaggagacaatatgactgtattcgagtagtgattctgatggatcatctga
Mapping_targetD1007
Source_location7CHROMOSOME_I46035254603783Inferred_automaticallyNational_Bioresource_Project
Type_of_mutationDeletion
PCR_producttm3976_external
tm3976_internal
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
LaboratoryFX
AuthorMitani S
DB_infoDatabaseNational_Bioresource_Projectseq3976
NBP_allele
StatusLive
AffectsGeneWBGene00017011
TranscriptD1007.16.1VEP_consequenceframeshift_variant
VEP_impactHIGH
HGVScD1007.16.1:c.226_482del
HGVSpCE40450:p.Tyr76PhefsTer3
cDNA_position232-488
CDS_position226-482
Protein_position76-161
Exon_number3/4
Codon_changeTATAAAGGATCGAAAAAAGAAGCAAAACCGAAAGAATGTCTTCTGTTCTTCGACAAAAAGACCAACACAGTTCGCTTGGAGAAAATTACGAGCAATATTAATGTAAAAAAGACGAGAGATCTAGATCAAGGAACAGAACTCGCATTGAAACGTGGAATCGAAAGATTGAGAACTTCTTCTAATAATCAGCGATCTGGACCATCTTCACCGGAGGAGAAAGCGAAAATTCAGAAACAAATGCAGAGAGATACATCAGAt/t
Amino_acid_changeYKGSKKEAKPKECLLFFDKKTNTVRLEKITSNINVKKTRDLDQGTELALKRGIERLRTSSNNQRSGPSSPEEKAKIQKQMQRDTSD/X
InteractorWBInteraction000505000
WBInteraction000505002
WBInteraction000505003
WBInteraction000505004
WBInteraction000517211
WBInteraction000517212
WBInteraction000525339
IsolationMutagenTMP/UV
GeneticsMapI
DescriptionPhenotypeWBPhenotype:0000038Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
Remarkeaf-1(tm3976) has a similar phenotype as ell-1 RNAi in terms of vulval morphology adult ell-1 RNAi-treated worms often had a rupture of the intestines through the vulva.Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
WBPhenotype:0000062Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
Remarkeaf-1(tm3976) has a similar phenotype as ell-1 RNAi in terms of mortality; about half of the worms treated with ell-1 RNAi died by the 4th day of treatment.Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
WBPhenotype:0000134Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
RemarkMultiple collagen genes were down-regulated in both ell-1 RNAi treated and eaf-1(tm3976) worms. | Realtime PCR analysis confirmed the downregulation of dpy-3, dpy-13 and sqt-3 inboth ell-1 RNAi-treated and eaf-1(tm3976) worms.Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
WBPhenotype:0000583Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson14253
WBPhenotype:0000679Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
RemarkBoth ell-1 RNAi treatment and eaf-1(tm3976) dramatically decreased GFP expression in the cuticle.Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
WBPhenotype:0000699Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson14253
WBPhenotype:0001384Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
Remarkeaf-1(tm3976) has a similar phenotype as ell-1 RNAi in terms of fertility; ell-1 RNAi-treated worms laid half as many eggs as the control-RNAi treated wormsPaper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
Phenotype_not_observedWBPhenotype:0000037Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
RemarkEggs from eaf-1(tm3976) mutants had a normal, cobblestone shape.Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
WBPhenotype:0000062Person_evidenceWBPerson7743
Curator_confirmedWBPerson2021
RemarkClassified as homozygous viable by the National Bioresource Project of JapanPerson_evidenceWBPerson7743
Curator_confirmedWBPerson2021
WBPhenotype:0000645Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
WBPhenotype:0001691Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
RemarkNo obvious changes in germline structure were detected, using a H2B:GFP transgene expressed in the germline.Paper_evidenceWBPaper00040146
Curator_confirmedWBPerson712
ReferenceWBPaper00040146
Remark45967/45968-46224/46225 (257 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