WormMine: Gene WBGene00219420

• WormBase Gene ID: WBGene00219420
• Gene Name: T19C4.24
• Sequence Name: T19C4.24
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in ABplpppaapa and ABprpppaapa based on single-cell RNA-seq studies. Is affected by several genes including etr-1; xrep-4; and dpy-26 based on RNA-seq studies. Is affected by six chemicals including metformin; Sirolimus; and rifampin based on RNA-seq studies.
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 102

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00219420

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T19C4.24.1	T19C4.24.1	102	V: 11146907-11147008

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T19C4.24	T19C4.24	102	V: 11146907-11147008

0 RNAi Result

5 Allele

• gk963271
• gk963301
• gk964451
• gk964452
• gk246879

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00219420
• Start: 11146907
• End: 11147008
• Strand: -1

2 Data Sets

• WormBaseAcedbConverter
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_11144795..11146906
• Length (nt): 2112
• Chromosome Location: V: 11144795-11146906
• Organism: Caenorhabditis elegans

23 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts of coding genes that showed significantly decreased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_depleted_coding-RNA
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_upregulated
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	Transcripts that showed significantly decreased expression in N2 day 5 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq.	DESeq fold change > 2, FDR < 0.05.	WBPaper00067499:Day5_vs_Day1_downregulated_Illumina
	Transcripts that showed significantly decreased expression in N2 day 7 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq.	DESeq fold change > 2, FDR < 0.05.	WBPaper00067499:Day7_vs_Day1_downregulated_Illumina
	Transcripts that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
	Transcripts that showed significantly increased expression in lin-29(n333) comparing to in N2 at day 1 adult stage.	DESeq2, FDR < 0.01, fold change > 2.	WBPaper00066970:lin-29(n333)_upregulated
	Transcripts that showed significantly decreased expression in let-767(RNAi) L4 animals comparing to animals fed with empty vector.	log2 fold change > 1.5 or < -1.5, p-value < 0.05	WBPaper00066679:let-767(RNAi)_downregulated
Bacteria: B.subtilis	Transcripts that showed significantly increased expression when animals were fed by probiotic bacteria strain B.subtilis PXN21 comparing to animals fed with OP50 from L1 till day 1 adult.	edgeR 3.16.5, FDR < 0.05, fold change > 2.	WBPaper00059117:B.subtilis_upregulated
	Transcripts that showed significantly increased expression in diploid N2 animals after exposure to 5 uM doxorubicin for 72 hours at 15C from L1 to L4 larve stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:Doxorubicin_upregulated_diploid
	Transcripts that showed significantly increased expression in skn-1gf(lax188) comparing to in N2 animals at L4 stage fed with OP50 and exposed to PA14 for 4 hours.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00067255:skn-1(lax188)_upregulated_PA
	Transcripts that showed significantly increased expression in sdc-3(ubs20);dpy-26(ubs4) comparing to in control animals.	DESeq2 v.1.34, fold change > 2, FDR < 0.05.	WBPaper00067078:sdc-3(ubs20);dpy-26(ubs4)_upregulated
	Transcripts that showed significantly increased expression in N2 animals exposed to 30 uM CdCl2 for five days starting from L4.	edgeR, fold change > 2, p < 0.05.	WBPaper00066204:CdCl2_upregulated_mRNA
	Transcripts that showed significantly decreased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_downregulated_neural
	Transcripts that showed significantly increased expression in unc-70(cas983) comparing to in N2 at L1 larva stage.	DESeq2, fold change >= 2, FDR <= 0.05	WBPaper00057041:unc-70(cas983)_upregulated
	Transcripts that showed significantly decreased expression in nfki-1(cer1) animals at L4 larva stage, comparing to in N2 animals.	Differentially expressed genes between wild type and knockouts were explored using DESeq2 R package (v.1.20.0) considering a threshold of adjusted p value < 0.01.	WBPaper00060445:nfki-1(cer1)_downregulated_L4
Bacteria: P.aeruginosa strain PA14	Transcripts that showed significantly increased expression after infection by P. aeruginosa PA14.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:P.aeruginosa_PA14_upregulated
	Top 300 transcripts enriched in ABplpppaapa, ABprpppaapa according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:Neuroblast_PVC_LUA
	Transcripts that showed significantly decreased expression in adr-1(tm668) comparing to in N2.	DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5.	WBPaper00055226:adr-1(tm668)_downregulated
Acidic Environment: PH 4.33 vs. PH 6.33.	Transcripts that showed significantly decreased expression after 3 hours of exposure to acidic environment (PH 4.33), comparing to control animals exposed to PH 6.33 environment.	DESeq2 (1.16.1). The Benjamini and Hochberg's approach was used to adjust the resulting P-values to control the false discovery rate. Corrected value of P < 0.05 and fold change > 2 were set as the threshold for significantly differential expression.	WBPaper00060434:pH4.33_vs_pH6.33_downrgulated

2 Expression Patterns

• Primary Identifier: Expr2024470
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr2006252
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00219420
• Start: 11146907
• End: 11147008
• Strand: -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 102

1 Sequence Ontology Term