Questions, Feedback & Help
Send us an email and we'll get back to you ASAP. Or you can read our Frequently Asked Questions.

WormBase Tree Display for Variation: WBVar00250785

expand all nodes | collapse all nodes | view schema

Name Class

WBVar00250785NamePublic_nametm1821
HGVSgCHROMOSOME_III:g.6451657_6452587del
Sequence_detailsSMapS_parentSequenceT26A5
Flanking_sequencestttccatggagattcttttgtcgcatcgatggaaaagccatcttggatgtacctgaaaaa
Mapping_targetT26A5
Source_location7CHROMOSOME_III64516566452588Inferred_automaticallyNational_Bioresource_Project
Type_of_mutationDeletion
PCR_producttm1821_external
tm1821_internal
SeqStatusSequenced
Variation_typeAllele
OriginSpeciesCaenorhabditis elegans
LaboratoryFX
AuthorMitani S
DB_infoDatabaseNational_Bioresource_Projectseq1821
NBP_allele
StatusLive
AffectsGeneWBGene00004781
TranscriptT26A5.7b.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant
VEP_impactHIGH
cDNA_position?-543
CDS_position?-102
Protein_position?-34
Intron_number1-2/5
Exon_number1-4/6
T26A5.7a.1VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant
VEP_impactHIGH
cDNA_position?-529
CDS_position?-513
Protein_position?-171
Intron_number2-3/5
Exon_number1-4/6
T26A5.7b.2VEP_consequencesplice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant
VEP_impactHIGH
cDNA_position?-359
CDS_position?-102
Protein_position?-34
Intron_number1/4
Exon_number1-3/5
IsolationMutagenTMP/UV
GeneticsMapIII
DescriptionPhenotypeWBPhenotype:0000062Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkClassified as lethal OR sterile by the National Bioresource Project of Japan. Comment to the NBP from Dr.R. H. Horvitz: not synMuv with class A or B mutations and not a synMuv suppressor.Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidenceFX
MT
WBPhenotype:0000688Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
RemarkClassified as lethal OR sterile by the National Bioresource Project of Japan. Comment to the NBP from Dr. R.H. Horvitz: recessive sterile.Person_evidenceWBPerson7743
Curator_confirmedWBPerson712
Laboratory_evidenceFX
MT
RecessivePerson_evidenceWBPerson7743
Curator_confirmedWBPerson712
WBPhenotype:0000718Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
Remark"H4K20me1 reduction due to set-1 or dpy-21 null mutation led to a significant increase in X chromosome expression compared to autosomes in L3 larvae (Fig 5C). We observed a small but significant increase in X expression compared to autosomes in the set-4(n4600) mutant L3 (Fig 5C) and mixed stage embryos (Fig 5D). Expression of previously defined dosage compensated genes [11,23,42] were increased in dpy-21(e428), set-1(tm1821), but not as much in set-4 (n4600) mutant (Fig 5E). To test if a subset of X chromosomal genes were responsible for the effect seen in the set-4(n4600) mutant (Fig 5C), we plotted the distribution of expression ratios on the X and autosomes (Fig 5F). This indicated a slight shift between X and autosomes, suggesting that set-4(n4600) has a subtle effect across all genes, rather than a large effect on a subset of X chromosomal genes."Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
"To understand the role of dpy-21 in the DCC, we compared gene expression changes in dpy-27 RNAi, dpy-21(e428), set-1(tm1821) and set-4(n4600) mutant L3 larvae by clustering differential expression ratios on the X chromosome and autosomes (Fig 6A). We note that while the effect of dpy-27 RNAi and dpy-21(e428) were generally similar on the X, genes in several clusters were affected differently between dpy-27 RNAi and dpy-21 (e428). We performed gene ontology (GO) analyses comparing enriched functions in each cluster compared to the whole genome (Fig 6B). Interestingly, the effect of dpy-27 RNAi and dpy-21(e428) on clusters enriched for cuticle genes were opposite, yet both mutations result in a dumpy phenotype."Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
WBPhenotype:0001348Paper_evidenceWBPaper00046016
Curator_confirmedWBPerson557
RemarkDecreased X chromosome compaction leading to enlarged X chromosomes.Paper_evidenceWBPaper00046016
Curator_confirmedWBPerson557
WBPhenotype:0001361Paper_evidenceWBPaper00046016
Curator_confirmedWBPerson557
RemarkDecreased X chromosome compaction leading to enlarged X chromosomes.Paper_evidenceWBPaper00046016
Curator_confirmedWBPerson557
WBPhenotype:0001504Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
Remark"We analyzed genome-wide expression changes that occur in dpy-21(e428), set-1(tm1821) and set-4(n4600) null mutants [18,19]. Set-1 null mutant is maternal effect sterile, and RNAi knockdown of set-1 leads to germline deficient adults, thus we could not isolate embryos. Therefore, we collected set-1(tm1821) homozygous and heterozygous L3 larvae (see Material and Methods). Western blot analysis in whole-larval extracts showed expected changes in H4K20me1 (Fig 5B) [18,19]. H4K20me1 reduced in dpy-21(e428), increased in set-4(n4600), and was eliminated in set-1(tm1821)."Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
WBPhenotype:0002078Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
Remark"We analyzed genome-wide expression changes that occur in dpy-21(e428), set-1(tm1821) and set-4(n4600) null mutants [18,19]. Set-1 null mutant is maternal effect sterile, and RNAi knockdown of set-1 leads to germline deficient adults, thus we could not isolate embryos. Therefore, we collected set-1(tm1821) homozygous and heterozygous L3 larvae (see Material and Methods). Western blot analysis in whole-larval extracts showed expected changes in H4K20me1 (Fig 5B) [18,19]. H4K20me1 reduced in dpy-21(e428), increased in set-4(n4600), and was eliminated in set-1(tm1821)."Paper_evidenceWBPaper00048953
Curator_confirmedWBPerson2987
ReferenceWBPaper00048953
WBPaper00046016
Remark3813/3814-4744/4745 (931 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