WormMine: Gene WBGene00015418

• WormBase Gene ID: WBGene00015418
• Gene Name: pac-1
• Sequence Name: C04D8.1
• Brief Description: pac-1 encodes a RhoGAP (Rho guanosine triphosphatase (GTPase) activating protein); in the embryo, PAC-1 is essential for establishment of radial (inner-outer) asymmetry and specifically, for differential localization of PAR-6, PAR-3, and PKC-3 to outer somatic cell surfaces devoid of cell-cell contacts; in regulating PAR protein localization, PAC-1 appears to act by spatially regulating activity of the CDC-42 Rho GTPase which can bind PAR-6 and is required, genetically, for PAR-6 localization to the outer cell surface; a PAC-1::GFP fusion protein expressed in the early embryo and in cultured embryos localizes to points of cell-cell contact.
• Organism: Caenorhabditis elegans
• Automated Description: Enables GTPase activator activity. Involved in protein localization; regulation of gastrulation; and small GTPase-mediated signal transduction. Located in cell junction. Expressed in anus; epithelial cell; hypodermis; pharynx; and pm7. Is an ortholog of human ARHGAP23 (Rho GTPase activating protein 23).
• Biotype: SO:0001217
• Genetic Position: III :-0.25513 ±0.000591
• Length (nt): 23909

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00015418

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C04D8.1f.1	C04D8.1f.1	5436	III: 8495008-8518916
Transcript:C04D8.1b.1	C04D8.1b.1	5383	III: 8495018-8518881
Transcript:C04D8.1a.1	C04D8.1a.1	5292	III: 8495110-8518879
Transcript:C04D8.1g.1	C04D8.1g.1	4350	III: 8500126-8518878
Transcript:C04D8.1d.1	C04D8.1d.1	3890	III: 8507635-8518878
Transcript:C04D8.1e.1	C04D8.1e.1	2301	III: 8514103-8518405

Other

6 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C04D8.1b	C04D8.1b	4815	III: 8495110-8495262
CDS:C04D8.1f	C04D8.1f	4692	III: 8495110-8495262
CDS:C04D8.1g	C04D8.1g	3732	III: 8500271-8500358
CDS:C04D8.1d	C04D8.1d	3417	III: 8507635-8507734
CDS:C04D8.1a	C04D8.1a	4818	III: 8495110-8495262
CDS:C04D8.1e	C04D8.1e	2301	III: 8514103-8514110

7 RNAi Result

• WBRNAi00039589
• WBRNAi00058797
• WBRNAi00111060
• WBRNAi00010104
• WBRNAi00021621
• WBRNAi00005216
• WBRNAi00005915

340 Allele

• gk799236
• gk724328
• gk686699
• gk621353
• gk539405
• gk437041
• gk374466
• gk577681
• gk479920
• gk509632
• gk695427
• gk577682
• gk636192
• gk399300
• gk446722
• gk590989
• gk860541
• gk823811
• gk755446
• gk408099
• gk452148
• gk849403
• gk832808
• gk780036
• gk921348
• gk460414
• gk363157
• gk656743
• gk548136
• gk931557

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00015418
• Start: 8495008
• End: 8518916
• Strand: 1

4 Data Sets

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

0 Downstream Intergenic Region

134 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased 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_upregulated_neural
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	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 food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
Bacteria: E.faecalis strain OG1RF	Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:E.faecalis_OG1RF_upregulated
	Transcripts that showed altered expression in cat-1(RNAi) animals comparing to control animals injected with empty vector.	p-value <= 0.05	WBPaper00066902:cat-1(RNAi)_regulated
	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 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 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
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
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
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
starvation 12 hours	Transcripts that showed significantly increased expression in dissected intestines of N2 L1 larva that were starved for 12 hours, comparing to fed animals.	EdgeR, FDR < 0.05, fold change >= 2.	WBPaper00067259:starvation_upregulated_intestine
	Transcripts that showed significantly increased 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)_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 significantly increased expression in daf-2(e1370) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:daf-2(e1370)_upregulated
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_SM
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	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
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
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
	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

10 Expression Patterns

• Primary Identifier: Expr13517
• Pattern: A functional mCherry-PAC-1 fusion protein expressed from a recombineered fosmid was detected in epithelial cells and concentrated at adherens junctions (AJs). mCherry-PAC-1 colocalized nearly completely with HMR-1, but was significantly more apical than DLG-1, which is found basal to AJs, indicating that PAC-1 is present at adherens junctions. mCherry-PAC-1 also overlapped with the more broadly localized GFP-CDC-42 at AJs.

• Primary Identifier: Expr68
• Remark: Legacy Data: Author "Lynch AS" "Bauer PK" "Hope IA"Date 1996-06.
• Pattern: The M2 interneurons and m7 muscles in the terminal bulb of the pharynx express ZC21.4 in adulthood only. A neuronal cell abutting the mass of the nerve ring also stains, but expression here is weaker (marked * in the image).

• Primary Identifier: Expr2035
• Remark: Other strains-- UL1009, UL1015, UL1012
• Pattern: Very strong diffuse expression is seen throughout the pharynx of larval and adult stages. In young larvae expression is also seen in cells along the body of the worm (probably hypodermal seam cells), and in a few cells of the anal region.

• Primary Identifier: Expr8161
• Remark: Picture: Figure 3C.
• Subcellular Localization: GFP-PAC-1 rescued PAR-6 localization in pac-1 embryos and localized to inner but not outer surfaces of EES cells.

• Primary Identifier: Expr1036597
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1016440
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2032910
• 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: Expr12368
• Subcellular Localization: Full-length GFP::PAC-1 localized to cell contacts.

• Primary Identifier: Expr2014677
• 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: Expr1143693
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

21 GO Annotation

22 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00015418
• Start: 8495008
• End: 8518916
• Strand: 1

21 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 23909

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00032310
• WBStrain00007531
• WBStrain00007530

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_8494321..8495007
• Length (nt): 687
• Chromosome Location: III: 8494321-8495007
• Organism: Caenorhabditis elegans