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WormBase Tree Display for Variation: WBVar00249436

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Name Class

WBVar00249436NamePublic_nametm388
Other_nameB0414.2.1:c.307+18_381+200del
B0414.2.2:c.307+18_381+200del
B0414.2.3:c.307+18_381+200del
HGVSgCHROMOSOME_I:g.5785318_5786375del
Sequence_detailsSMapS_parentSequenceB0414
Flanking_sequencescggtccggcagaggtgagtactgtagccaatgtgctatttttgaggcaaaatagattttt
Mapping_targetB0414
Source_location7CHROMOSOME_I57853175786376Inferred_automaticallyNational_Bioresource_Project
Type_of_mutationDeletion
PCR_producttm388_external
tm388_internal
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
LaboratoryFX
AuthorMitani S
DB_infoDatabaseNational_Bioresource_Projectseq388
NBP_allele
StatusLive
AffectsGeneWBGene00004393
TranscriptB0414.2.3VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScB0414.2.3:c.307+18_381+200del
Intron_number7-8/12
Exon_number8/13
B0414.2.2VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScB0414.2.2:c.307+18_381+200del
Intron_number7-8/12
Exon_number8/13
B0414.2.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant
VEP_impactHIGH
HGVScB0414.2.1:c.307+18_381+200del
Intron_number4-5/9
Exon_number5/10
InteractorWBInteraction000502237
WBInteraction000502238
WBInteraction000524653
WBInteraction000538733
WBInteraction000538734
WBInteraction000538735
IsolationMutagenTMP/UV
GeneticsMapI
DescriptionPhenotypeWBPhenotype:0000070Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Remark"rnt-1(tm388) has a deletion spanning from intron 3 to intron 4, resulting in a frame shift and a premature stop codon in the Runt domain (Fig. 1). Molecular data indicate rnt-1(tm388) is a null mutation. The tm388 transcript lacks the C-terminal half of the RNT-1 coding sequences, including residues critical for DNA recognition in the Runt domain. rnt-1(tm388) homozygous animals were viable and showed no gross morphological defects in hermaphrodites. However, the rnt-1(tm388) males showed striking phenotypes in which many copulatory rays in the tail were lost and the overall structure of the male tail was often destroyed (Fig. 2). rnt-1(tm388) males failed to mate with hermaphrodites (Table 1)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Variation_effectPredicted_null_via_sequencePaper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0005741PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBPhenotype:0000324Person_evidenceWBPerson7743
Curator_confirmedWBPerson48
RemarkComment from Dr. J. Lee: short body length.Person_evidenceWBPerson7743
Curator_confirmedWBPerson48
Laboratory_evidenceFX
WBPhenotype:0000828Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Remark"The defect of rnt-1 mutants in asymmetrical division was also ascertained by a direct cell lineage analysis. In eight out of the eleven T lineages examined in the rnt-1(tm388) animals, the T cell divided symmetrically, giving rise solely to hypodermal cells from both T.a and T.p (Figs. 4B, C). All these data demonstrated that mutations in rnt-1 result in the loss of asymmetry in the T cells and T.p sublineage."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
PenetranceIncomplete72Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0004946PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBbt:0004944PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBPhenotype:0000961Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Remark"In wild-type, the level of GFP::POP-1 was higher in T.a (T.a > T.p) in 100% of the wild-type T cell lineages examined (Figs. 5A, E). In rnt-1, most of the T cell lineages (91%) exhibited a higher level of GFP::POP-1 in T.a (T.a > T.p), and the rest of the lineages (9%) showed the same level of expression in T.a and T.p (T.a = T.p) (Figs. 5B, E)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
"In the present study, we also confirmed that the level of TLP-1::GFP was higher in T.p (T.a < T.p) in 76% of wild-type animals. In rnt-1(tm388), however, the expression level of TLP-1::GFP is significantly reduced and the proportion showing a normal, asymmetrical expression of TLP-1::GFP (T.a < T.p) was decreased to 20% (Figs. 5D, E)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
PenetranceLow9Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0004946PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBbt:0004944PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Phenotype_assayGenotypeGFP::POP-1Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
TLP-1::GFPPaper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBPhenotype:0001225Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Remark"We first examined the Psa phenotype in the T cells of hermaphrodites of all the rnt-1 alleles. A large proportion (51%-77%) of the mutants exhibited the Psa phenotype (Table 2)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
PenetranceIncomplete77Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0005425PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Life_stageWBls:0000027PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Phenotype_assayTreatment"Psa phenotype (see Materials and methods) was scored during the L2 stage."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBPhenotype:0001414Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Remark"rnt-1(tm388) has a deletion spanning from intron 3 to intron 4, resulting in a frame shift and a premature stop codon in the Runt domain (Fig. 1). Molecular data indicate rnt-1(tm388) is a null mutation. The tm388 transcript lacks the C-terminal half of the RNT-1 coding sequences, including residues critical for DNA recognition in the Runt domain. rnt-1(tm388) homozygous animals were viable and showed no gross morphological defects in hermaphrodites. However, the rnt-1(tm388) males showed striking phenotypes in which many copulatory rays in the tail were lost and the overall structure of the male tail was often destroyed (Fig. 2). rnt-1(tm388) males failed to mate with hermaphrodites (Table 1)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Variation_effectPredicted_null_via_sequencePaper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Phenotype_assayGenotypehim-8(e1489)Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBPhenotype:0001509Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Remark"rnt-1(tm388) has a deletion spanning from intron 3 to intron 4, resulting in a frame shift and a premature stop codon in the Runt domain (Fig. 1). Molecular data indicate rnt-1(tm388) is a null mutation. The tm388 transcript lacks the C-terminal half of the RNT-1 coding sequences, including residues critical for DNA recognition in the Runt domain. rnt-1(tm388) homozygous animals were viable and showed no gross morphological defects in hermaphrodites. However, the rnt-1(tm388) males showed striking phenotypes in which many copulatory rays in the tail were lost and the overall structure of the male tail was often destroyed (Fig. 2). rnt-1(tm388) males failed to mate with hermaphrodites (Table 1)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Variation_effectPredicted_null_via_sequencePaper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0006941PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBPhenotype:0001585Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Remark"The defect of rnt-1 mutants in asymmetrical division was also ascertained by a direct cell lineage analysis. In eight out of the eleven T lineages examined in the rnt-1(tm388) animals, the T cell divided symmetrically, giving rise solely to hypodermal cells from both T.a and T.p (Figs. 4B, C). All these data demonstrated that mutations in rnt-1 result in the loss of asymmetry in the T cells and T.p sublineage." (Table 3)Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
"In wild-type, the level of GFP::POP-1 was higher in T.a (T.a > T.p) in 100% of the wild-type T cell lineages examined (Figs. 5A, E). In rnt-1, most of the T cell lineages (91%) exhibited a higher level of GFP::POP-1 in T.a (T.a > T.p), and the rest of the lineages (9%) showed the same level of expression in T.a and T.p (T.a = T.p) (Figs. 5B, E)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
"In the present study, we also confirmed that the level of TLP-1::GFP was higher in T.p (T.a < T.p) in 76% of wild-type animals. In rnt-1(tm388), however, the expression level of TLP-1::GFP is significantly reduced and the proportion showing a normal, asymmetrical expression of TLP-1::GFP (T.a < T.p) was decreased to 20% (Figs. 5D, E)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
PenetranceIncomplete72Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Low9Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0004946PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBbt:0004944PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Phenotype_assayGenotypeGFP::POP-1Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
TLP-1::GFPPaper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBPhenotype:0002211Paper_evidenceWBPaper00035069
WBPaper00026860
Curator_confirmedWBPerson557
WBPerson2987
Remark"We next performed phasmid dye-filling analysis on hermaphrodites from all the alleles. Again, a large proportion (46%-73%) of the mutants displayed the Dyf phenotype (Table 2)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
PenetranceIncompletePaper_evidenceWBPaper00035069
Curator_confirmedWBPerson557
61Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0005425PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Phenotype_assayTemperature20Paper_evidenceWBPaper00035069
Curator_confirmedWBPerson557
WBPhenotype:0002535Person_evidenceWBPerson7743
Curator_confirmedWBPerson48
RemarkComment from Dr. M. Herman: phasmid Dyf.Person_evidenceWBPerson7743
Curator_confirmedWBPerson48
Laboratory_evidenceFX
Phenotype_not_observedWBPhenotype:0000062Paper_evidenceWBPaper00026860
Person_evidenceWBPerson7743
Curator_confirmedWBPerson48
WBPerson2987
RemarkClassified as homozygous viable by the National Bioresource Project of Japan.Person_evidenceWBPerson7743
Curator_confirmedWBPerson48
Laboratory_evidenceFX
"rnt-1(tm388) has a deletion spanning from intron 3 to intron 4, resulting in a frame shift and a premature stop codon in the Runt domain (Fig. 1). Molecular data indicate rnt-1(tm388) is a null mutation. The tm388 transcript lacks the C-terminal half of the RNT-1 coding sequences, including residues critical for DNA recognition in the Runt domain. rnt-1(tm388) homozygous animals were viable and showed no gross morphological defects in hermaphrodites. However, the rnt-1(tm388) males showed striking phenotypes in which many copulatory rays in the tail were lost and the overall structure of the male tail was often destroyed (Fig. 2). rnt-1(tm388) males failed to mate with hermaphrodites (Table 1)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Variation_effectPredicted_null_via_sequencePaper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBPhenotype:0000155Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
RemarkTable 3Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0004946PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBbt:0004944PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBPhenotype:0000529Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Remark"In rnt-1 mutants, although the T cells fail to divide asymmetrically, their seam-lineage descendants appear to keep features of the seam cells; (1) they express the seam cell specific marker scm0GFP (data not shown); (2) they fuse with the anterior seam cells to form the seam syncytium at the L4 stage like in wild-type; (3) they retain an eye-shaped morphology typical to the seam cells until seam syncytium formation as seen in Fig. 5. These data indicated that RNT-1 is required for some of the T cell functions, i.e. the asymmetrical (stem-like) cell division, but not for the seam cell differentiation."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
EQ_annotationsAnatomy_termWBbt:0005753PATO:0000460Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
WBPhenotype:0001025Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Remark"rnt-1(tm388) has a deletion spanning from intron 3 to intron 4, resulting in a frame shift and a premature stop codon in the Runt domain (Fig. 1). Molecular data indicate rnt-1(tm388) is a null mutation. The tm388 transcript lacks the C-terminal half of the RNT-1 coding sequences, including residues critical for DNA recognition in the Runt domain. rnt-1(tm388) homozygous animals were viable and showed no gross morphological defects in hermaphrodites. However, the rnt-1(tm388) males showed striking phenotypes in which many copulatory rays in the tail were lost and the overall structure of the male tail was often destroyed (Fig. 2). rnt-1(tm388) males failed to mate with hermaphrodites (Table 1)."Paper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
Variation_effectPredicted_null_via_sequencePaper_evidenceWBPaper00026860
Curator_confirmedWBPerson2987
ReferenceWBPaper00035069
WBPaper00026860
Remark13728/13729-14786/14787 (1058 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