WormMine: Gene WBGene00004287

• WormBase Gene ID: WBGene00004287
• Gene Name: rac-2
• Sequence Name: K03D3.10
• Brief Description: rac-2 encodes a small Rho family GTPase that, along with CED-10 and MIG-2, is one of three C. elegans Rac-related proteins; genetic studies indicate that rac-2 functions redundantly with mig-2 and ced-10 to regulate CAN and PDE axon pathfinding and CAN cell migration; in addition, rac-2 functions slightly redundant with mig-2 during distal tip cell movement and slightly redundant with ced-10 during cell-corpse phagocytosis; as unc-73 mutations enhance rac-2 defects in axon pathfinding and CAN cell migration, UNC-73/Trio is a likely candidate to act upstream of RAC-2 and positively regulate its GTPase activity in vivo; further, as UNC-115 activity is required to mediate the morphogenetic effects of constitutively active RAC-2(G12V), UNC-115, an actin-binding protein, is likely to be a downstream effector of RAC-2; GFP::RAC-2 reporters expressed in neurons and neuroblasts reveal localization at cell margins and the nerve ring, the latter suggesting that GFP::RAC-2 associates with the axonal plasma membrane.
• Organism: Caenorhabditis elegans
• Automated Description: Enables GTP binding activity and GTPase activity. Involved in actin filament organization and generation of neurons. Located in axon and plasma membrane. Expressed in nerve ring and neurons. Human ortholog(s) of this gene implicated in several diseases, including autosomal dominant intellectual developmental disorder 48; colon adenoma; and gastrointestinal system cancer (multiple). Is an ortholog of human RAC1 (Rac family small GTPase 1).
• Biotype: SO:0001217
• Genetic Position: IV :14.9995 ±0.003782
• Length (nt): 1605

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004287

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K03D3.10.1	K03D3.10.1	588	IV: 16308225-16309829

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K03D3.10	K03D3.10	588	IV: 16308225-16308329

56 RNAi Result

• WBRNAi00082792
• WBRNAi00107897
• WBRNAi00082783
• WBRNAi00024330
• WBRNAi00024331
• WBRNAi00082791
• WBRNAi00082790
• WBRNAi00049811
• WBRNAi00086851
• WBRNAi00086853
• WBRNAi00086852
• WBRNAi00086855
• WBRNAi00086854
• WBRNAi00086859
• WBRNAi00086858
• WBRNAi00086850
• WBRNAi00086857
• WBRNAi00086856
• WBRNAi00078693
• WBRNAi00078694
• WBRNAi00016530
• WBRNAi00016536
• WBRNAi00016538
• WBRNAi00082785
• WBRNAi00082793
• WBRNAi00082794
• WBRNAi00082784
• WBRNAi00082786
• WBRNAi00024329
• WBRNAi00075655

55 Allele

• gk964078
• gk964500
• gk962765
• gk963378
• gk963590
• gk963377
• gk963795
• gk963704
• gk962529
• gk963948
• gk963888
• WBVar02123836
• WBVar02121229
• WBVar02123109
• tm10006
• WBVar02123691
• WBVar02124716
• WBVar02124220
• WBVar02122633
• WBVar02121890
• WBVar02123524
• WBVar02124488
• WBVar00091102
• ok326
• WBVar01828197
• WBVar01658915
• WBVar01658916
• WBVar01658917
• WBVar01658918
• WBVar01658912

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004287
• Start: 16308225
• End: 16309829
• 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_16309830..16311078
• Length (nt): 1249
• Chromosome Location: IV: 16309830-16311078
• Organism: Caenorhabditis elegans

32 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
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
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 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	Coexpression clique No. 203, sre-33-ZK1025.1_8337, on the genome-wide coexpression clique map for the nematode GPL200 platform.	All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.	WBPaper00061527:sre-33-ZK1025.1_8337
Fungi infection: Myzocytiopsis humicola	Transcripts that showed significantly altered expression 12 hours after animals were infected by M. humicola.	Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1).	WBPaper00060871:M.humicola-infection_12h_regulated
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	Transcripts that showed significantly decreased 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)_downregulated
Fungi infection: Haptoglossa zoospora.	Transcripts that showed significantly altered expression after L4 N2 animals were exposed to omycete Haptoglossa zoospora for 6 hours.	Kalisto abundance files were converted and analysed using Sleuth in a R pipeline. Standard Sleuth protocols were used to calculate differential expression. P value < 0.01 and FDR < 0.01.	WBPaper00062354:H.zoospora_6h_regulated
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
	Genes with significantly increased expression in eat-2(ad465) treated with 2% DMSO for 72 hours, comparing to in N2 treated with 2% DMSO for 72 hours.	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:eat-2(ad465)_upregulated_in-DMSO
	Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01.	N.A.	WBPaper00026929:Resveratrol_regulated_daf-16
	Genes with expression level regulated by genotype (N2 vs CB4856) at Old adults stage (214 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0136.	WBPaper00040858:eQTL_regulated_old
	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
	Transcripts that showed significantly decreased 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)_downregulated_neuron
Exposed to fungi M.humicola extract.	Transcripts that showed significantly altered expression 4 hours after animals were exposed to M. humicola extract.	Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1).	WBPaper00060871:M.humicola-extract_4h_regulated
Fungi: Myzocytiopsis humicola extract	Transcripts that showed significantly decreased expression in N2 L4 larva animals after 4 hours of exposure to oomycete Myzocytiopsis humicola extract.	Differentially expressed genes as determined by Kallisto and Sleuth (pval < 0.01, qval < 0.1, fold change > 2).	WBPaper00065995:M.humicola-extract_downregulated_N2
Fungi infection: Myzocytiopsis humicola	Transcripts that showed significantly altered expression 24 hours after animals were infected by M. humicola.	Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1).	WBPaper00060871:M.humicola-infection_24h_regulated
Fungi infection: Myzocytiopsis humicola	Transcripts that showed significantly altered expression 48 hours after animals were infected by M. humicola.	Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1).	WBPaper00060871:M.humicola-infection_48h_regulated
	Genes from eat-2(ad465) animals with significantly decreased 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:eat-2(ad465)_rapamycin_downregulated
	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
	Genes with variation in expression level across genotypes (AB2, CB4856, RC301, CB4857, N2, HC445).	two-way ANOVA	WBPaper00041174:genotypic
	Genes from N2 animals with significantly decreased 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_downregulated
	Transcripts that showed significantly decreased expression in spn-4(tm291) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	RPKM fold change > 2.	WBPaper00058598:spn-4(tm291)_downregulated
	Transcripts that showed significantly increased expression in drh-3(rrr2) comparing to in N2.	edgeR, log2 fold change > 2 or < -2.	WBPaper00053888:drh-3(rrr2)_upregulated
	Genes with significant variation in expression level only across genotypes(AB2, CB4856, RC301, CB4857, N2, HC445), but not environments (control, 25C, High-pH-Salt, Liquid, infection).	two-way ANOVA	WBPaper00041174:genotypic_prime
Bacteria infection: N.ferruginous	Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ferruginous microsporidia spores for 72 hours at 21C starting from L1 larva stage.	FDR < 0.01	WBPaper00065086:JU1400_N.ferruginous_regulated
Bacteria infection: N.ironsii	Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ironsii microsporidia spores for 72 hours at 21C starting from L1 larva stage.	FDR < 0.01	WBPaper00065086:JU1400_N.ironsii_regulated

5 Expression Patterns

• Primary Identifier: Expr2278
• Remark: Wild-type rac-2 and rac-2(G12V)-coding regions displayed indistinguishable localization, and gfp::rac-2(G12V) caused dominant effects on PDE development. Expression of GFP from a transgene that contained a frameshift between the gfp- and rac-2-coding regions failed to accumulate at the cell margins and in the nerve ring and instead was uniformly distributed in the cytoplasm, indicating that RAC-2 sequences mediate accumulation of GFP::RAC-2 at the plasma membrane, presumably via C-terminal CAAX motif.
• Subcellular Localization: Animals harboring the unc-115::gfp::rac-2 transgene showed expression of GFP::RAC-2 that accumulate at the cell margins of neuroblasts and neurons as well as in the nerve ring. Nerve ring accumulation suggests that GFP::RAC-2 localized to the plasma membranes of axons.

• Primary Identifier: Expr1153530
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1011573
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2015236
• 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: Expr2033470
• 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).

34 GO Annotation

25 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004287
• Start: 16308225
• End: 16309829
• Strand: 1

34 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1605

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00035892
• WBStrain00035523

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_16306840..16308224
• Length (nt): 1385
• Chromosome Location: IV: 16306840-16308224
• Organism: Caenorhabditis elegans