WormMine: Gene WBGene00044416

• WormBase Gene ID: WBGene00044416
• Gene Name: C08E3.15
• Sequence Name: C08E3.15
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in ALA based on single-cell RNA-seq studies. Is affected by several genes including rsr-2; hrpr-1; and lpd-3 based on microarray; tiling array; and RNA-seq 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): 189

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00044416

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C08E3.15.1	C08E3.15.1	189	II: 1627695-1627883

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C08E3.15	C08E3.15	189	II: 1627695-1627883

1 RNAi Result

• WBRNAi00019837

38 Allele

• WBVar02124326
• WBVar02123182
• WBVar02121537
• WBVar02123791
• gk964317
• gk963801
• WBVar02122524
• WBVar02120604
• WBVar02121124
• WBVar02124543
• WBVar02120776
• WBVar02121946
• gk963786
• WBVar02122430
• WBVar02122773
• WBVar02123007
• gk963339
• WBVar00091178
• WBVar02122094
• WBVar00091053
• WBVar01295760
• WBVar01295759
• WBVar01295758
• WBVar01295757
• gk879542
• WBVar01716895
• WBVar02119323
• WBVar01716897
• WBVar01716896
• WBVar01716899

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00044416
• Start: 1627695
• End: 1627883
• Strand: -1

2 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrII_1626884..1627694
• Length (nt): 811
• Chromosome Location: II: 1626884-1627694
• Organism: Caenorhabditis elegans

47 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	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 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:Psora-Allantoin_upregulated
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
Bacteria infection: Serratia marcescens	Genes with increased expression after 24 hours of infection by S.marcescens Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:S.marcescens_24hr_upregulated_TilingArray
Bacteria infection: N.ausubeli	Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ausubeli microsporidia spores for 72 hours at 21C starting from L1 larva stage.	FDR < 0.01	WBPaper00065086:JU1400_N.ausubeli_regulated
Temprature shift to 28C for 48 hours.	Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 48 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_48h_upregulated
	Transcripts that showed significantly increased expression in daf-2(e1370) neurons comparing to in N2 neurons at day 8adult stage.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00066978:daf-2(e1370)_upregulated_neuron
	Transcripts that showed significantly increased expression in daf-16(mu86);daf-2(e1370) neurons comparing to in daf-2(e1370) neurons at day 8adult stage.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00066978:daf-16(mu86)_upregulated_neuron
	Transcripts that showed significantly increased expression in smn-1(ok355) heterozygots using balancer hT2 comparing to in N2.	DESeq v1.14.0, log2FC > 1, q <= 0.05.	WBPaper00056809:smn-1(ok355)_upregulated
	Transcripts that showed significantly increased expression in pals-17(syb3980) comparing to in N2 animals at young adult stage.	Differential expression analyses were performed using limma-voom in Galaxy, adj p <= 0.05, logFC > 2	WBPaper00065984:pals-17(syb3980)_upregulated
Bacteria infection: Photorhabdus luminescens	Genes with increased expression after 24 hours of infection by P.lumniescens Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:P.lumniescens_24hr_upregulated_TilingArray
	Down-regulated genes (fold change > 1.5) in two CoQ-deficient clk-1 mutant strains (e2519, qm30) compared to wild types N2.	Fold-changes of intensities were calculated from the arithmetic mean of gene expression values between experimental and corresponding control group. Fold change >= 1.5 was used as cut-off.	WBPaper00045774:clk-1_downregulated
Bacteria infection: Photorhabdus luminescens	Genes with increased expression after 24 hours of infection by P.lumniescens Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:P.lumniescens_24hr_upregulated_RNAseq
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_RNAseq
	Transcripts that showed significantly increased expression in pals-22(jy3) comparing to in N2 animals.	limma-voom, fold change > 2, FDR < 0.05	WBPaper00064532:pals-22(jy3)_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 100uM Rapamycin and 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Rifampicin_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 increased expression after N2 animals were exposed to 20 uM bortezomib for 4 hours.	Differential expression analyses were performed using limma-voom in Galaxy. Fold change > 2, FDR < 0.05.	WBPaper00062345:bortezomib_4h_upregulated_N2
	Genes that showed significantly increased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control.	Fold change > 1.2 or < 0.8.	WBPaper00042477:rsr-2(RNAi)_upregulated_TilingArray
Bacteria infection: N.ausubeli	Transcripts that showed significantly altered expression in C. elegans wild isolate strain N2 infected by N.ausubeli microsporidia spores for 72 hours at 21C starting from L1 larva stage.	FDR < 0.01	WBPaper00065086:N2_N.ausubeli_regulated
	Transcripts that showed significantly increased expression in lpd-3(ok2138) comparing to in N2 animals.	DESeq2, fold change > 4, FDR < 0.05.	WBPaper00064661:lpd-3(ok2138)_upregulated
	Transcripts that showed differential expression in dauer daf-2(e1370) vs dauer daf-2(e1370);mir-34(gk437) animals at 25C.	N.A.	WBPaper00050488:daf-2(e1370)_vs_daf-2(e1370);mir-34(gk437)_regulated_dauer_25C
	Transcripts that showed significantly increased expression in skn-1(lax188) gain of function comparing to in N2 at day 2 adult stage.	fold change > 2	WBPaper00058711:skn-1(lax188)_upregulated
	Genes down regulated in nhr-114(RNAi) comparing to glp-1(q224ts).	Differentially expressed genes had a fold change cutoff of 2.0 and an unpaired t test p value cutoff of 0.05 for WT+Trp versus WT and 0.01 for nhr-114 versus glp-1.	WBPaper00042194:nhr-114(RNAi)_downregulated
	Genes that showed significantly increased expression in hrp-2(RNAi) animals comparing to in control animals.	DESeq2, adjusted p-value < 0.1, log2 Fold change >= 2 or <= -2.	WBPaper00050504:hrp-2(RNAi)_upregulated
	Transcripts that showed significantly increased expression in lin-15B(n744) comparing to in N2 animals at starved L1 larva stage.	A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.	WBPaper00062056:lin-15B(n744)_upregulated
	Genes that showed significant differential expressed between control and 1000 mg\/L Fluoranthene treatment.	t-test, p < 0.05.	WBPaper00036123:Fluoranthene_regulated

2 Expression Patterns

• Primary Identifier: Expr1022228
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1144159
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00044416
• Start: 1627695
• End: 1627883
• Strand: -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 189

1 Sequence Ontology Term