WormMine: Gene WBGene00000417

• WormBase Gene ID: WBGene00000417
• Gene Name: ced-3
• Sequence Name: C48D1.2
• Brief Description: ced-3 encodes a caspase, a cysteine-aspartate protease; CED-3 activity is required for execution of apoptosis and functions in a conserved genetic pathway with CED-4, CED-9, and EGL-1 to regulate apoptosis during C. elegans development.
• Organism: Caenorhabditis elegans
• Automated Description: Enables cysteine-type endopeptidase activator activity involved in apoptotic process; cysteine-type endopeptidase activity involved in execution phase of apoptosis; and identical protein binding activity. Involved in several processes, including apoptotic process; muscle cell cellular homeostasis; and regulation of developmental process. Located in several cellular components, including mitochondrion; neuronal cell body; and perinuclear region of cytoplasm. Part of caspase complex. Expressed in several structures, including ABaraapapaa; ABaraapppaa; NSM; apoptotic cell; and germ line. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; carcinoma (multiple); gastrointestinal system cancer (multiple); and prostate disease (multiple). Is an ortholog of human CASP3 (caspase 3); CASP6 (caspase 6); and CASP7 (caspase 7).
• Biotype: SO:0001217
• Genetic Position: IV :8.46735 ±0.004319
• Length (nt): 5877

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000417

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C48D1.2a.1	C48D1.2a.1	2552	IV: 13198261-13204137
Transcript:C48D1.2b.1	C48D1.2b.1	864	IV: 13199230-13201889

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C48D1.2b	C48D1.2b	864	IV: 13199230-13199292
CDS:C48D1.2a	C48D1.2a	1512	IV: 13199230-13199292

25 RNAi Result

• WBRNAi00077190
• WBRNAi00097559
• WBRNAi00042732
• WBRNAi00007269
• WBRNAi00087666
• WBRNAi00065428
• WBRNAi00060982
• WBRNAi00060983
• WBRNAi00060984
• WBRNAi00087675
• WBRNAi00027590
• WBRNAi00097925
• WBRNAi00066191
• WBRNAi00062689
• WBRNAi00085818
• WBRNAi00077441
• WBRNAi00077443
• WBRNAi00077442
• WBRNAi00097658
• WBRNAi00097556
• WBRNAi00098457
• WBRNAi00098460
• WBRNAi00098461
• WBRNAi00097528
• WBRNAi00097914

156 Allele

• gk964278
• gk964078
• gk963546
• gk963547
• gk964500
• gk962765
• ok2734
• WBVar01804688
• n2452
• gk216012
• gk381032
• gk862769
• gk539592
• gk915820
• gk725623
• gk401736
• gk490551
• gk807616
• gk760695
• gk406837
• gk673944
• gk591076
• gk735956
• gk922436
• gk370574
• gk849497
• gk843505
• gk917108
• gk464834
• gk481052

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000417
• Start: 13198261
• End: 13204137
• Strand: -1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_13197983..13198260
• Length (nt): 278
• Chromosome Location: IV: 13197983-13198260
• Organism: Caenorhabditis elegans

159 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_downregulated
	Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_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
	Top 300 transcripts enriched in ABalppppppa, ABpraaapppa 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:ASE_parent
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_regulated
25C vs. 20C	Transcripts that showed significantly increased 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_upregulated
	Transcripts that showed significantly increased 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_upregulated
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Transcripts that showed significantly decreased 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_downregulated
	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
	Transcripts that showed significantly increased expression in hira-1(gk835598) comparing to in N2 animals at L4 larva stage.	Differential expression analysis was done with Rversion 2.15.3 using DESeq_1.10.1. Fold change > 2, p-value < 0.01.	WBPaper00059739:hira-1(gk835598)_upregulated_L4
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
	Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated
	Transcripts that showed significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated

13 Expression Patterns

• Primary Identifier: Expr4563
• Pattern: Examination of transgenic embryos at different developmental stages revealed that GFP was expressed in all or nearly all cells, except intestinal cells and their precursors, starting at around 100 to 150 minutes post-fertilization and continuing throughout the comma stage of embryogenesis. Reporter expression disappeared after the 3-fold embryonic stage, and only 2 to 3 cells expressed GFP faintly in larva and adults. These cells, one of which was probably the head mesodermal cell, were present in the head and did not reliably express GFP. Reporter expression was similar between males and hermaphrodites, except that, in males, intense staining was observed in the tails of L4 animals.

• Primary Identifier: Expr2009847
• 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: Expr1019728
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1030233
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13239
• Remark: A fluorescent caspase 3 indicator substrate, Z-DEVD-ProRed.
• Subcellular Localization: A fluorescent caspase 3 indicator substrate, Z-DEVD-ProRed™, from t = 24 h adult animals expressing GFPlocalized to the mitochondria and nuclei of muscle.

• Primary Identifier: Expr9220
• Subcellular Localization: CED-3 was observed around pachytene germ cell nuclei in both hermaphrodites and males.

• Primary Identifier: Expr13375
• Pattern: The CED-3::GFP translational reporter was expressed mostly in embryos and the adult germline. In embryos, we often found an enrichment of GFP signal within the apoptotic corpses compared with the surrounding cells. In the germline, CED-3::GFP was expressed primarily in the oocyte region, with very weak to no expression in the mitotic and early meiotic zones.
• Subcellular Localization: In oocytes, CED-3::GFP showed a significant enrichment in the nuclei, whereas, in the rest of the germline, we observed an accumulation of GFP signal in the perinuclear region.

• Primary Identifier: Expr12630
• Pattern: CED-3::GFP (representing both proCED-3::GFP and active CED-3::GFP) was observed in the NSM neuroblast (NSMnb) before its division into the NSMsc and NSM. During NSMnb division, CED-3::GFP was equally segregated into the NSMsc and NSM so that the concentrations of CED-3::GFP in the two daughter cells after the completion of cytokinesis were almost identical (t = 0 min). However, starting 10 min post cytokinesis, CED-3::GFP concentration gradually increased in the NSMsc. This increase reached a maximum 21min post cytokinesis, by which time the NSMsc had adopted the morphology typical of a cell corpse (t = 21 min). Conversely, starting 10min post cytokinesis, CED-3::GFP concentration gradually decreased in the NSM. As a result, at 21 min post cytokinesis, the concentration of CED-3::GFP in the NSMsc was more than twofold higher than that in the NSM.

• Primary Identifier: Expr2028087
• 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: Expr13316
• Pattern: ced-3 transcripts were visible in only a subset of cells, usually including B.al/rapaav, and only rarely in the B.al/rapaav homolog.

• Primary Identifier: Expr1522
• Pattern: The 2.8 kb ced-3 transcript was most abundant during embryogenesis, and was also detected at later stages.

• Primary Identifier: Expr11815
• Subcellular Localization: Both CED-3 and CED-4 proteins localize in the pachytene region of wild-type worms.

• Primary Identifier: Expr1146722
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

99 GO Annotation

33 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000417
• Start: 13198261
• End: 13204137
• Strand: -1

99 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes differentially expressed in ced-3(n717) and ced-1(e1735) but not in pgrn-1(tm985) as compared to N2E.	Differential expression analysis was performed using the EdgeR Bioconductor package (19910308), and differentially expressed genes were selected based on False Discovery Rate (FDR Benjamini Hochberg adjusted p-values) estimated at <=5%.	WBPaper00044246:ced-3_ced-1_upregulated
	Genes differentially expressed in ced-3(n717) and ced-1(e1735) but not in pgrn-1(tm985) as compared to N2E.	Differential expression analysis was performed using the EdgeR Bioconductor package (19910308), and differentially expressed genes were selected based on False Discovery Rate (FDR Benjamini Hochberg adjusted p-values) estimated at <=5%.	WBPaper00044246:ced-3_ced-1_downregulated

1 Sequence

• Length: 5877

1 Sequence Ontology Term