WormMine: Gene WBGene00003964

• WormBase Gene ID: WBGene00003964
• Gene Name: pdi-3
• Sequence Name: H06O01.1
• Brief Description: pdi-3 encodes a protein disulfide isomerase (PDI) required for normal cuticle collagen deposition and, subliminally, for maintenance of normal body shape; PDI-3 has both PDI and calcium-dependent transglutaminase activity in vitro, crosslinking proteins through a gamma-glutamyl epsilon-lysine dual residue; PDI-3 is homologous to the human PDI ERp60, as well as a homolog in the dog heartworm Dirofilaria immitis that is required for larval molting; the joint PDI/transglutaminase activity of PDI-3 is biochemically conserved in nematodes and mammals; pdi-3 is constitutively and broadly expressed, particularly in gut and hypodermis.
• Organism: Caenorhabditis elegans
• Automated Description: Enables protein disulfide isomerase activity and protein-glutamine gamma-glutamyltransferase activity. Involved in several processes, including collagen and cuticulin-based cuticle development; egg-laying behavior; and male anatomical structure morphogenesis. Predicted to be located in endoplasmic reticulum. Expressed in hypodermis; intestine; and seam cell. Human ortholog(s) of this gene implicated in autoimmune hepatitis and liver cirrhosis. Is an ortholog of human PDIA3 (protein disulfide isomerase family A member 3).
• Biotype: SO:0001217
• Genetic Position: I :1.65339 ±0.000736
• Length (nt): 4890

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003964

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:H06O01.1.2	H06O01.1.2	1699	I: 7015908-7020790
Transcript:H06O01.1.1	H06O01.1.1	1702	I: 7015912-7020797

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:H06O01.1	H06O01.1	1467	I: 7016137-7016302

22 RNAi Result

• WBRNAi00022876
• WBRNAi00022877
• WBRNAi00022878
• WBRNAi00022879
• WBRNAi00022880
• WBRNAi00022881
• WBRNAi00022882
• WBRNAi00049331
• WBRNAi00025792
• WBRNAi00025793
• WBRNAi00025794
• WBRNAi00076517
• WBRNAi00084214
• WBRNAi00084216
• WBRNAi00084215
• WBRNAi00033680
• WBRNAi00113970
• WBRNAi00116856
• WBRNAi00003873
• WBRNAi00077197
• WBRNAi00022875
• WBRNAi00108783

54 Allele

• gk962858
• gk962706
• gk963902
• WBVar01432023
• WBVar01432022
• WBVar01602969
• gk482789
• gk114119
• gk650151
• gk114120
• gk687480
• gk114121
• gk481346
• gk114122
• WBVar01911810
• WBVar01283416
• gk382775
• gk680772
• gk587211
• WBVar01911809
• gk438532
• gk848200
• gk114123
• gk114124
• gk873831
• gk354175
• gk114125
• gk564984
• gk114126
• ttTi7089

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003964
• Start: 7015908
• End: 7020797
• 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_7015224..7015907
• Length (nt): 684
• Chromosome Location: I: 7015224-7015907
• Organism: Caenorhabditis elegans

168 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
	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 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 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
	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 that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	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
	Transcripts expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
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
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
	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 depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	Transcripts depleted in purified oocyte P bodies comparing to in the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	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
	Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:sek-1(km4)_downregulated_cisplatin
	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

10 Expression Patterns

• Primary Identifier: Expr1031888
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2298
• Pattern: Prominent beta-galactosidase reporter expression was observed in many tissues, included the lateral seam cell hypodermis, and additionally strong staining was also observed in the gut cells.

• Primary Identifier: Expr2350
• Pattern: In L1 larvae, PDI-3 localized in many tissues with predominant staining found in the hypodermal and the gut tissues. It can be noted that the pharynx, gut lumen, and body cavity were not stained with either antibody tested. Wild type embryos and larvae were probed with a PDI-3-specific polyclonal antibody in combination with a DPY-7-specific monoclonal antibody. DPY-7 is a cuticle collagen that is expressed solely in the hypodermis and is localized in the cuticular ECM from the elongated embryo stage onwards. In the 2-fold embryo (~500 min after fertilization), PDI-3 staining was observed in most tissues including the gut and the hypodermis. Conversely, DPY-7 localized exclusively in the hypodermal cells.
• Subcellular Localization: Gut nuclei did not stain and appeared as dark patches among the PDI-3-labeled gut tissue. DPY-7 antibody was localized solely to the annular furrows of the hypodermally derived cuticle.

• Primary Identifier: Expr2351
• Pattern: The initial four transgenic lines generated from the construct comprising the promoter region and the first exon and first large intron of pdi-3 (pPDI-3PLacZ1) did not produce a discernable beta-galactosidase staining pattern in the four independent lines generated. The second promoter reporter construct (pPDI-3PLacZ2), which only contained a few amino acids of pdi-3 exon one, resulted in the isolation of three transgenic lines in which each produced distinct beta-galactosidase staining patterns. Prominent beta-galac-tosidase reporter expression was observed in many tissues included the lateral seam cell hypodermis, and additionally, strong staining was also observed in the gut cells.

• Primary Identifier: Expr1153069
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1024250
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2352
• Pattern: The analysis of the pdi-3 temporal expression pattern via RT-PCR on staged mRNA samples demonstrated that it was constitutively expressed throughout the post-embryonic life cycle of C. elegans. However, peaks of highest relative abundance were observed at final L4 larval stage and in the young adult stages.

• Primary Identifier: Expr2033041
• 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: Expr2014807
• 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: Expr2299
• Pattern: The analysis of the pdi-3 temporal expression pattern via RT-PCR on staged mRNA samples demonstrated that it was constitutively expressed throughout the post-embryonic life cycle of C. elegans. Peaks of highest relative abundance were however observed at final L4 larval stage and in the young adult stages.

20 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003964
• Start: 7015908
• End: 7020797
• Strand: -1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4890

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00047528
• WBStrain00055430

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_7020798..7021294
• Length (nt): 497
• Chromosome Location: I: 7020798-7021294
• Organism: Caenorhabditis elegans