WormMine: Gene WBGene00000788

• WormBase Gene ID: WBGene00000788
• Gene Name: cpz-1
• Sequence Name: F32B5.8
• Brief Description: cpz-1 encodes a homolog of cathepsin z-like cysteine protease cyclicallyexpressed in hypodermal cells throughout development (along with adultgonad and pharynx) and required for normal molting; CPZ-1 protein ispresent in cuticle regions shortly before their degradation duringecydsis, and this expression pattern is conserved in Onchocerca volvulus;cpz-1(ok497) and cpz-1(RNAi) worms have defective molting, along withmisshapen heads and tails, defective gonads, and embryonic lethality.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable cysteine-type endopeptidase activity. Involved in several processes, including ecdysis, collagen and cuticulin-based cuticle; gonad morphogenesis; and post-embryonic development. Located in collagen and cuticulin-based cuticle extracellular matrix; extracellular space; and yolk granule. Expressed in several structures, including anterior hypodermis; cuticle; intestine; pharynx; and vulva. Is an ortholog of human CTSZ (cathepsin Z).
• Biotype: SO:0001217
• Genetic Position: I :-7.97279 ±0.169868
• Length (nt): 2790

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000788

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F32B5.8a.1	F32B5.8a.1	993	I: 2686640-2689429
Transcript:F32B5.8b.1	F32B5.8b.1	513	I: 2686698-2687780

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F32B5.8a	F32B5.8a	921	I: 2686698-2687119
CDS:F32B5.8b	F32B5.8b	513	I: 2686698-2687119

12 RNAi Result

• WBRNAi00063117
• WBRNAi00063118
• WBRNAi00046109
• WBRNAi00116051
• WBRNAi00076368
• WBRNAi00116790
• WBRNAi00003564
• WBRNAi00075877
• WBRNAi00115197
• WBRNAi00089065
• WBRNAi00063119
• WBRNAi00063120

65 Allele

• gk963902
• gk964159
• gk962616
• gk964303
• gk724658
• ok497
• gk680155
• gk773168
• gk725225
• gk582147
• gk369033
• gk673201
• gk838539
• WBVar02028317
• gk344894
• WBVar00535133
• gk627300
• gk540532
• gk931909
• gk308669
• gk672813
• WBVar01246806
• gk422364
• gk916841
• gk797933
• gk731988
• WBVar00535139
• WBVar00535138
• WBVar00235798
• WBVar00535136

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000788
• Start: 2686640
• End: 2689429
• 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_chrI_2684998..2686639
• Length (nt): 1642
• Chromosome Location: I: 2684998-2686639
• Organism: Caenorhabditis elegans

234 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
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
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
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
	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
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 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_N2
	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 that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	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 that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day11_vs_Day1_downregulated
	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 that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_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)
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 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 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	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 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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
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
	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
Dietary restriction	Transcripts that showed significantly decreased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition.	Bioconductor package edgeR, p < 0.05.	WBPaper00056443:DietaryRestriction_downregulated

9 Expression Patterns

• Primary Identifier: Expr1030489
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2400
• Remark: Reporter gene fusion type not specified.
• Pattern: The expression of Ce-cpz-1::gfp in transgenic C. elegans was restricted to the cuticular region along the length of the worm throughout development, and in the pharynx of only L3, L4 and adults.

• Primary Identifier: Expr2893
• Pattern: Beta-Galactosidase expression was observed in many cells, including gut, hypodermal, and other cells within the developing embryos. However, because of the intense staining in some parts of the developing embryos, the identification of the many stained cells was not possible. In post-embryonic stages, beta-galactosidase staining was present in the hypodermal cells of all larval stages mature gravid hermaphrodites (710 days after L4 adult hermaphrodite). Beta-Galactosidase staining was also detected in intestinal cells. The cpz-1:lacZ expression in all stages was specifically detected in the large hypodermal syncytium covering most of the worm (hyp7), and in the hypodermal cells of the head (hyp4 and hyp6) and occasionally in hypodermal cells in the tail. Beta-Galactosidase staining was also present in few pharyngeal cells of the adult worms but not in the pharyngeal cells of larval stages. Expression of cpz-1:gfp translational construct was detected in all developmental stages except embryos. The cpz-1:gfp expression was restricted to the hypodermis, with additional expression in the pharynx and the gonad only in the L4 and adult worms stages. The specific expression in the pharynx of adult stages was similar to that observed in cpz-1:lacZ transgenic worms. There was no embryonic expression of the gfp construct.

• Primary Identifier: Expr7868
• Remark: Picture: Figure 2A, 2B.
• Pattern: The cpi-2a transcript was present throughout development; however, its expression varied between stages. Notably, the cpi-2a transcript increased ~2.5-3.5 h before each molt: the L1/L2 molt (11.5 h after hatching), the L2/L3 molt (18.5 h), the L3/L4 molt (26 h), and the L4/adult molt (36 h). Subsequent to each molt, the transcript levels decreased. Transcription levels of Ce-cpl-1 were also elevated before each molt and at the same times as those of Ce-cpi-2a. The decrease in the transcription levels after the L2/L3, L3/L4, and L4/adult was also similar, except that after the L1/L2 molt, the cpi-2a transcript went up, but the cpl-1 remained low. The elevated cpi-2a transcription profile before each molt also coincided with the C. elegans Ce-cpz-1 transcript levels but only before the L2/L3, L3/L4, and L4/adult molt, and the timing before the molt was 2 h.

• Primary Identifier: Expr2010522
• 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: Expr1014352
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1149993
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2028762
• 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: Expr2892
• Remark: Type: quantitative real-time PCR. ama-1 was used as an internal control transcript to allow the relative quantification of cpz-1 expression in each stage.
• Pattern: Although the cpz-1 transcript is present throughout development, it is least expressed in embryos and during L1 to L2 growth. The level of the cpz-1 transcript increased significantly prior to the L2/L3 molt at 16 h and decreased after the L2/L3 molt (~20 h), and then periodically increased before the L3/L4 molt (~24 h) and the L4/adult molt (~34 h). In addition, a significant increase in its level occurred during the period when the early part of embryogenesis takes place (~40 h after L1). During adulthood there is a 23-h period when the fertilized eggs go through the process of embryogenesis.

18 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000788
• Start: 2686640
• End: 2689429
• Strand: -1

18 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2790

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00031453

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_2689430..2692108
• Length (nt): 2679
• Chromosome Location: I: 2689430-2692108
• Organism: Caenorhabditis elegans