WormMine: Gene WBGene00000424

• WormBase Gene ID: WBGene00000424
• Gene Name: ced-10
• Sequence Name: C09G12.8
• Brief Description: ced-10 encodes a GTPase orthologous to human RAC1 (OMIM:602048) that is required for phagocytosis during programmed cell death and for migration of the distal tip cells of the somatic gonad; CED-10 functions in the engulfing cell during apoptosis, and is activated by a complex of CED-2(CrkII) and CED-5(DOCK180) to promote formation of the polarized cell extensions associated with cell corpse engulfment.
• Organism: Caenorhabditis elegans
• Automated Description: Enables GTP binding activity and GTPase activity. Involved in several processes, including axon development; establishment or maintenance of cell polarity; and regulation of cellular component organization. Located in cytoplasmic side of plasma membrane; cytoplasmic vesicle; and neuronal cell body. Expressed in several structures, including CAN; GABAergic neurons; distal tip cell; intestine; and somatic nervous system. Used to study epilepsy. Human ortholog(s) of this gene implicated in several diseases, including autosomal dominant intellectual developmental disorder 48; combined immunodeficiency (multiple); and gastrointestinal system cancer (multiple). Is an ortholog of human RAC1 (Rac family small GTPase 1).
• Biotype: SO:0001217
• Genetic Position: IV :-3.32061 ±0.028381
• Length (nt): 3200

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000424

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C09G12.8b.1	C09G12.8b.1	1661	IV: 3506328-3509527
Transcript:C09G12.8a.1	C09G12.8a.1	424	IV: 3507379-3509527

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C09G12.8b	C09G12.8b	576	IV: 3507379-3507571
CDS:C09G12.8a	C09G12.8a	390	IV: 3507379-3507571

46 RNAi Result

• WBRNAi00107897
• WBRNAi00091307
• WBRNAi00107684
• WBRNAi00078690
• WBRNAi00078691
• WBRNAi00040224
• WBRNAi00091305
• WBRNAi00073507
• WBRNAi00073508
• WBRNAi00072240
• WBRNAi00078693
• WBRNAi00078694
• WBRNAi00010543
• WBRNAi00094827
• WBRNAi00109614
• WBRNAi00108424
• WBRNAi00027610
• WBRNAi00075652
• WBRNAi00109226
• WBRNAi00073506
• WBRNAi00073509
• WBRNAi00073511
• WBRNAi00073510
• WBRNAi00072241
• WBRNAi00072242
• WBRNAi00075650
• WBRNAi00075654
• WBRNAi00065786
• WBRNAi00109323
• WBRNAi00113813

65 Allele

• gk963722
• gk964245
• gk964439
• gk356412
• gk964246
• gk513728
• WBVar02073328
• WBVar01922831
• WBVar01514851
• t1875
• tm597
• WBVar02020385
• WBVar00187459
• WBVar00187458
• WBVar00187457
• WBVar00187456
• WBVar00187455
• WBVar00187454
• WBVar00187453
• WBVar00187452
• gk495420
• gk752054
• gk359057
• gk881922
• gk527751
• gk729560
• gk530686
• gk740165
• WBVar01727003
• WBVar01727004

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000424
• Start: 3506328
• End: 3509527
• 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_3506116..3506327
• Length (nt): 212
• Chromosome Location: IV: 3506116-3506327
• Organism: Caenorhabditis elegans

88 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_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 expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_regulated_developing
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:A-class-motor-neurons_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:coelomocytes_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:excretory-cell_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:GABAergic-motor-neurons_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:glr-1(+)-neurons_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:intestine_L2-larva_expressed
	Proteins interacting with HA-PPM-1.D.	N.A.	WBPaper00062498:PPM-1.D_interacting
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
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 of coding genes that showed significantly increased 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_enriched_coding-RNA
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2 at early embryo stage.	DESeq2, FDR < 0.05	WBPaper00058691:sin-3(tm1276)_upregulated
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
Oxidative stress.	Genes upregulated by oxidative stress.	Assessed by SAM (Significance Analysis of Microarray) [false discovery rate (FDR) = 11%]	WBPaper00034757:up_by_oxidative_stress
	Transcripts that showed significantly increased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:jmjd-3.1(+)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:bodywall-muscle_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (Young adult all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:CEP-sheath-cells_Day1-adult_expressed
	Transcripts enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector.	Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples.	WBPaper00051039:germline_enriched

11 Expression Patterns

• Primary Identifier: Expr4493
• Pattern: The embryos near the vulva assumed stronger fluorescence of the CED-10::GFP::CED-10 marker than their younger, more distant siblings. The signal was not detectable until the 50-cell stage of the gastrulating embryo, when the marker started to accumulate beneath the cell boundaries. The signal gradually strengthened until the 3-fold stage, and remained unchanged thereafter until adulthood. The marker was expressed ubiquitously in all cells except the germ line Z2 and Z3 cells.
• Subcellular Localization: At the subcellular level, the signal was absent in the nucleus, easily identified as a circular void within the cell. The distribution of the marker in cytosol sometimes assumed a vesicular structure. The intracellular vesicles in the scanned images overlapped with most, if not all, the granules observed by differential interference contrast microscopy. The marker accumulated at the boundaries between neighboring cells, appearing much more sparsely at cell surfaces facing the egg shell where no neighboring cell was present, and little accumulation was seen at the boundary facing the germ line cells Z2 and Z3. Large round vesicular structures exhibiting the strongest signals correspond to the cells undergoing apoptosis, indicating the cell boundaries between cells undergoing programmed cell death and the cells engulfing the dying cells.

• Primary Identifier: Expr2009841
• 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: Expr1030240
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1734
• Remark: Lines expressing GFP::CED-10 were generated by injection of ced-10::gfp::ced-10 with an unc-76-rescuing construct, P76-16B, both at 75 ng/l, into unc-76(e911) animals.
• Pattern: Cell type identifications were confirmed by the examination of a nuclear-localized GFP expressed from the ced-10 promoter. GFP::CED-10 was expressed broadly, perhaps in all cells, including neurons (CANs, VDs and DDs), engulfing cell types (including the hypodermis, intestine and pharynx) and the distal tip cells. Expression was first seen in early embryogenesis and continued throughout adulthood in all cell types.
• Subcellular Localization: Strong fluorescence was observed within the axons of the nerve ring. The GFP::CED-10 fusion protein accumulated at the plasma membrane.

• Primary Identifier: Expr10205
• Pattern: GFP- CED-10 localized strongly to the apical domain of intestinal epithelial cells (likely to the microvilli).
• Subcellular Localization: GFP-CED-10 localized to intracellular puncta in the cytoplasm. The authors identified the intracellular puncta labeled by CED-10 as endosomes by performing a series of colocalization studies with a previously established set of intestine-specific compartment markers. CED-10 appeared specifically enriched on endosomes along the early and recycling pathway. Direct overlap of intestinal GFP-CED-10-labeled puncta and a subset of early endosomes marked by RFP-RAB-5 was observed. GFP-CED-10 showed the strongest colocalization with recycling endosome marker RFP-RAB-10, and displayed less overlap with later acting recycling endosome protein RFP-RME-1. Little overlap was observed between GFP-CED-10 and markers for late endosomes (GFP-RAB-7), the Golgi (MANS-GFP), or multi-vesicular bodies (GFP-HGRS-1/Hrs) indicating specificity in endosome-type associated with CED-10.

• Primary Identifier: Expr2322
• Remark: No signal was detected using the antibody when it was blocked with its GST fusion protein. Ubiquitous. CeRac1 = ced-10 --wjc according to WS97
• Pattern: Ubiquitously expressed throughout embryogenesis. However, at the stage when hypodermal cell fusion was occurring CeRac1 was found to localize with CePAK at the cell boundaries.
• Subcellular Localization: cell boundaries

• Primary Identifier: Expr2028081
• 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: Expr3974
• Subcellular Localization: functional GFP fusions to CED-10/Rac were dispersed across the entire HSN cell membrane.

• Primary Identifier: Expr1144297
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr588
• Remark: The locus is mentioned as CErac1 cDNA in the article instead of rac-1, correlation is made by curator. The author did not include Genbank accession number of this cDNA in the article. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: This gene transcribes into 1.7 and 0.9 kb mRNA bands, 1.7 kb band being more abundant. 0.9 kb mRNA is detected only in embryo and L1 stages (after 3 days exposure). 1.7 kb mRNA is detected at all developmental stages but the level of expression is highest in embryos and decreased dramatically during development being minimal (10% of embryonic level) in adults. There was a 12% increase at the L3 stage compared with L2.

• Primary Identifier: Expr1028622
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

83 GO Annotation

25 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000424
• Start: 3506328
• End: 3509527
• Strand: -1

83 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3200

1 Sequence Ontology Term