WormBase Tree Display for Variation: WBVar00252541
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WBVar00252541 | Name | Public_name | tm3976 | |||||
---|---|---|---|---|---|---|---|---|
Other_name | CE40450:p.Tyr76PhefsTer3 | |||||||
D1007.16.1:c.226_482del | ||||||||
HGVSg | CHROMOSOME_I:g.4603526_4603782del | |||||||
Sequence_details | SMap | S_parent | Sequence | D1007 | ||||
Flanking_sequences | gtaccaagcgaaggagacaatatgactgta | ttcgagtagtgattctgatggatcatctga | ||||||
Mapping_target | D1007 | |||||||
Source_location | 7 | CHROMOSOME_I | 4603525 | 4603783 | Inferred_automatically | National_Bioresource_Project | ||
Type_of_mutation | Deletion | |||||||
PCR_product | tm3976_external | |||||||
tm3976_internal | ||||||||
SeqStatus | Sequenced | |||||||
Variation_type | Allele | |||||||
Origin | Species | Caenorhabditis elegans | ||||||
Laboratory | FX | |||||||
Author | Mitani S | |||||||
DB_info | Database | National_Bioresource_Project | seq | 3976 | ||||
NBP_allele | ||||||||
Status | Live | |||||||
Affects | Gene | WBGene00017011 | ||||||
Transcript | D1007.16.1 | VEP_consequence | frameshift_variant | |||||
VEP_impact | HIGH | |||||||
HGVSc | D1007.16.1:c.226_482del | |||||||
HGVSp | CE40450:p.Tyr76PhefsTer3 | |||||||
cDNA_position | 232-488 | |||||||
CDS_position | 226-482 | |||||||
Protein_position | 76-161 | |||||||
Exon_number | 3/4 | |||||||
Codon_change | TATAAAGGATCGAAAAAAGAAGCAAAACCGAAAGAATGTCTTCTGTTCTTCGACAAAAAGACCAACACAGTTCGCTTGGAGAAAATTACGAGCAATATTAATGTAAAAAAGACGAGAGATCTAGATCAAGGAACAGAACTCGCATTGAAACGTGGAATCGAAAGATTGAGAACTTCTTCTAATAATCAGCGATCTGGACCATCTTCACCGGAGGAGAAAGCGAAAATTCAGAAACAAATGCAGAGAGATACATCAGAt/t | |||||||
Amino_acid_change | YKGSKKEAKPKECLLFFDKKTNTVRLEKITSNINVKKTRDLDQGTELALKRGIERLRTSSNNQRSGPSSPEEKAKIQKQMQRDTSD/X | |||||||
Interactor | WBInteraction000505000 | |||||||
WBInteraction000505002 | ||||||||
WBInteraction000505003 | ||||||||
WBInteraction000505004 | ||||||||
WBInteraction000517211 | ||||||||
WBInteraction000517212 | ||||||||
WBInteraction000525339 | ||||||||
Isolation | Mutagen | TMP/UV | ||||||
Genetics | Map | I | ||||||
Description | Phenotype | WBPhenotype:0000038 | Paper_evidence | WBPaper00040146 | ||||
Curator_confirmed | WBPerson712 | |||||||
Remark | eaf-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_evidence | WBPaper00040146 | |||||
Curator_confirmed | WBPerson712 | |||||||
WBPhenotype:0000062 | Paper_evidence | WBPaper00040146 | ||||||
Curator_confirmed | WBPerson712 | |||||||
Remark | eaf-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_evidence | WBPaper00040146 | |||||
Curator_confirmed | WBPerson712 | |||||||
WBPhenotype:0000134 | Paper_evidence | WBPaper00040146 | ||||||
Curator_confirmed | WBPerson712 | |||||||
Remark | Multiple 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_evidence | WBPaper00040146 | |||||
Curator_confirmed | WBPerson712 | |||||||
WBPhenotype:0000583 | Paper_evidence | WBPaper00040146 | ||||||
Curator_confirmed | WBPerson14253 | |||||||
WBPhenotype:0000679 | Paper_evidence | WBPaper00040146 | ||||||
Curator_confirmed | WBPerson712 | |||||||
Remark | Both ell-1 RNAi treatment and eaf-1(tm3976) dramatically decreased GFP expression in the cuticle. | Paper_evidence | WBPaper00040146 | |||||
Curator_confirmed | WBPerson712 | |||||||
WBPhenotype:0000699 | Paper_evidence | WBPaper00040146 | ||||||
Curator_confirmed | WBPerson14253 | |||||||
WBPhenotype:0001384 | Paper_evidence | WBPaper00040146 | ||||||
Curator_confirmed | WBPerson712 | |||||||
Remark | eaf-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 worms | Paper_evidence | WBPaper00040146 | |||||
Curator_confirmed | WBPerson712 | |||||||
Phenotype_not_observed | WBPhenotype:0000037 | Paper_evidence | WBPaper00040146 | |||||
Curator_confirmed | WBPerson712 | |||||||
Remark | Eggs from eaf-1(tm3976) mutants had a normal, cobblestone shape. | Paper_evidence | WBPaper00040146 | |||||
Curator_confirmed | WBPerson712 | |||||||
WBPhenotype:0000062 | Person_evidence | WBPerson7743 | ||||||
Curator_confirmed | WBPerson2021 | |||||||
Remark | Classified as homozygous viable by the National Bioresource Project of Japan | Person_evidence | WBPerson7743 | |||||
Curator_confirmed | WBPerson2021 | |||||||
WBPhenotype:0000645 | Paper_evidence | WBPaper00040146 | ||||||
Curator_confirmed | WBPerson712 | |||||||
WBPhenotype:0001691 | Paper_evidence | WBPaper00040146 | ||||||
Curator_confirmed | WBPerson712 | |||||||
Remark | No obvious changes in germline structure were detected, using a H2B:GFP transgene expressed in the germline. | Paper_evidence | WBPaper00040146 | |||||
Curator_confirmed | WBPerson712 | |||||||
Reference | WBPaper00040146 | |||||||
Remark | 45967/45968-46224/46225 (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_evidence | WBPaper00041807 | ||||||
Method | NBP_knockout_allele |