WormMine: Gene WBGene00235374

• WormBase Gene ID: WBGene00235374
• Gene Name: R11E3.19
• Sequence Name: R11E3.19
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in AINL; AINR; and DVA based on single-cell RNA-seq studies. Is affected by several genes including csr-1; npr-8; and jmjd-1.2 based on RNA-seq and microarray studies. Is affected by seven chemicals including Psoralens; allantoin; and Sirolimus based on RNA-seq and microarray studies.
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 894

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00235374

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:R11E3.19.1	R11E3.19.1	471	IV: 4775208-4776101

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:R11E3.19	R11E3.19	432	IV: 4775242-4775287

0 RNAi Result

13 Allele

• gk964500
• gk963722
• gk963150
• gk963908
• gk200811
• tm10416
• gk346147
• gk550154
• gk598493
• gk790810
• gk899043
• gk544505
• gk838216

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00235374
• Start: 4775208
• End: 4776101
• Strand: -1

2 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_4775134..4775207
• Length (nt): 74
• Chromosome Location: IV: 4775134-4775207
• Organism: Caenorhabditis elegans

37 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C.	Transcripts that showed significantly decreased expression in N2 animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C.	DESeq2, fold change > 2.	WBPaper00061081:E.faecalis_downregulated_N2
Bacteria infection: Bacillus thuringiensis	Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304.	N.A.	WBPaper00064229:B.thuringiensis-Cry5Ba_upregulated
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	Transcripts that showed signifcantly increased expression in pabp-2(RNAi) animals comparing to in N2 animals injected with empty vector at L1 larva stage and collected at L4 larva stage.	FDR < 0.05, fold change > 2	WBPaper00067368:pabp-2(RNAi)_upregulated_N2
	Transcripts that showed significantly decreased 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)_downregulated
	Transcripts that showed significantly decreased expression in pals-22(jy3) comparing to in N2 animals.	limma-voom, fold change > 2, FDR < 0.05	WBPaper00064532:pals-22(jy3)_downregulated
	Transcripts that showed significantly decreased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_downregulated
	Genes from N2 animals with significantly increased expression after 72 hours of treatment on growth media with 10uM rapamycin in 2% DMSO.	Analysis of gene expression data was carried out with the Affymetrix Transcriptome Analysis Console. Data preprocessing (using RMA normalization) and QC metrics were performed using Affymetrix Expression Console TM and manually inspected afterwards. Expression analysis was carried out for each two pairwise conditions. FDR statistical correction for multiple testing resulted in a slightly lower number of DEGs in most cases. P-value < 0.05 and fold change > 2.0 were used to determine differentially expressed genes.	WBPaper00048989:N2_rapamycin_upregulated
	Transcripts that showed significantly decreased expression in csr-1a(tor159) comparing to in N2 at 25C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_downregulated_25C
	Gene transcripts in this set are up-regulated at 5% FDR between L4 lethargus and L4 AND between L4 lethargus and 4-hour old adults.	Analysis of variance (ANOVA) methods were used to determine differential gene expression using the R/maanova package.	WBPaper00045960:L4-lethargus_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 tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_upregulated
	Transcripts that showed significantly increased expression in jmjd-5(zr1234) comparing to in N2 animals.	DESeq2, adjusted p value < 0.01 and absolute log2FC > = 1.	WBPaper00062156:jmjd-5(zr1234)_upregulated
25C vs. 20C	Transcripts that showed significantly decreased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_downregulated
	Transcripts that showed significantly increased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:eat-2(ad1116)_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin, 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Psora-Allantoin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin, 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Rifampicin-Psora_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Psora_upregulated
	Transcripts that showed significantly decreased expression in csr-1a(tor159) comparing to in N2 at 20C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_downregulated_20C
	Transcripts that showed significantly increased expression in lipl-4 overexpression transgenic lines comparing to wild type control animals.	DESeq2 fold change > 2, FDR < 0.05.	WBPaper00064156:lipl-4(overexpress)_upregulated
	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
	Gene transcripts in this set are in the L4-lethargus_upregulated gene set AND are also up-regulated at 30% FDR between 2-hour old embryos and 3-hour old L1 animals.	Analysis of variance (ANOVA) methods were used to determine differential gene expression using the R/maanova package.	WBPaper00045960:L1-L4-lethargus_upregulated
	Transcripts that showed significantly increased expression in jmjd-1.2(zr1010) comparing to in N2 animals.	DESeq2, adjusted p value < 0.01 and absolute log2FC > = 1.	WBPaper00062156:jmjd-1.2(zr1010)_upregulated
	Transcripts that showed significantly decreased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_downregulated
	Transcripts that showed significantly increased expression in malt-1(db1194);npr-1(ad609) animals, in npr-1(ad609) ilc-17.1(tm5218) animals, and in npr-1(ad609) nfki-1(db1198) animals, comparing to the wild type control npr-1(ad609).	Cufflinks (v2.2.1). q < 0.05.	WBPaper00059609:malt-1_ilc-17.1_nfki-1_upregulated
Diet: supplemented with milk fat-containing protein powder from L1 to day 2 adult stage.	Transcripts that showed significantly increased expression in N2 animals fed with OP50 supplemented with milk fat-containing protein powder from L1 to day 2 adult stage.	Differential expression analysis between two conditions (three biological replicates per condition) was performed using DESeq2. Genes with p-value < 0.05 and Fold Change > 2 found by DESeq2 were assigned as differentially expressed.	WBPaper00067530:Milk-protein_upregulated
	Top 300 transcripts enriched in AINL, AINR 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:AIN
	Transcripts that showed significantly decreased expression in mdt-15(tm2182) comparing to in N2 at L4 larva stage.	p-value < 0.05, fold change > 2.	WBPaper00065288:mdt-15(tm2182)_downregulated
	Top 300 transcripts enriched in DVA 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:DVA

2 Expression Patterns

• Primary Identifier: Expr2023804
• 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: Expr2005586
• 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: WBGene00235374
• Start: 4775208
• End: 4776101
• Strand: -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 894

1 Sequence Ontology Term