WormMine: Gene WBGene00003918

• WormBase Gene ID: WBGene00003918
• Gene Name: par-3
• Sequence Name: F54E7.3
• Brief Description: par-3 encodes a PDZ domain-containing protein orthologous to mammalian atypical PKC isotype-specific interacting protein (ASIP) and Drosophila Bazooka; PAR-3 is required maternally for polarization of the zygote along the anterior-posterior (A-P) axis; PAR-3, PAR-6, and PKC-3 form a complex that localizes to the anterior cytoplasmic cortex of the one- and two-cell embryo; this localization is regulated spatially by PAR-2, which segregates to the posterior cortex.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable phosphatidylinositol binding activity. Involved in several processes, including establishment of mitotic spindle orientation; gonad development; and polarity specification of anterior/posterior axis. Located in several cellular components, including P granule; basal part of cell; and cell cortex. Is extrinsic component of cytoplasmic side of plasma membrane. Expressed in several structures, including AB; Psub1; excretory cell; hermaphrodite gonad; and vulval cell. Is an ortholog of human PARD3B (par-3 family cell polarity regulator beta).
• Biotype: SO:0001217
• Genetic Position: III :-1.46058 ±0.000572
• Length (nt): 12563

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003918

Genomics

16 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F54E7.3j.1	F54E7.3j.1	4690	III: 5664233-5676732
Transcript:F54E7.3i.1	F54E7.3i.1	5019	III: 5664233-5676732
Transcript:F54E7.3h.1	F54E7.3h.1	5010	III: 5664233-5676732
Transcript:F54E7.3a.1	F54E7.3a.1	4900	III: 5664233-5676795
Transcript:F54E7.3b.1	F54E7.3b.1	4909	III: 5664233-5676795
Transcript:F54E7.3b.2	F54E7.3b.2	4894	III: 5664235-5676730
Transcript:F54E7.3b.3	F54E7.3b.3	4844	III: 5664356-5676795
Transcript:F54E7.3k.1	F54E7.3k.1	3993	III: 5664372-5675902
Transcript:F54E7.3g.1	F54E7.3g.1	3903	III: 5668541-5675902
Transcript:F54E7.3m.1	F54E7.3m.1	3756	III: 5668541-5675902
Transcript:F54E7.3c.2	F54E7.3c.2	4522	III: 5668541-5676606
Transcript:F54E7.3l.1	F54E7.3l.1	4317	III: 5668541-5676677
Transcript:F54E7.3e.1	F54E7.3e.1	4692	III: 5668541-5676732
Transcript:F54E7.3f.1	F54E7.3f.1	4519	III: 5668541-5676732
Transcript:F54E7.3c.1	F54E7.3c.1	4706	III: 5668541-5676738
Transcript:F54E7.3d.1	F54E7.3d.1	4707	III: 5668541-5676738

Other

13 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F54E7.3j	F54E7.3j	3984	III: 5664372-5664539
CDS:F54E7.3g	F54E7.3g	3903	III: 5668541-5668732
CDS:F54E7.3m	F54E7.3m	3756	III: 5668541-5668732
CDS:F54E7.3l	F54E7.3l	3747	III: 5668541-5668732
CDS:F54E7.3e	F54E7.3e	4356	III: 5668541-5668732
CDS:F54E7.3c	F54E7.3c	4023	III: 5668541-5668861
CDS:F54E7.3d	F54E7.3d	4365	III: 5668541-5668732
CDS:F54E7.3a	F54E7.3a	4131	III: 5664372-5664539
CDS:F54E7.3b	F54E7.3b	4140	III: 5664372-5664539
CDS:F54E7.3f	F54E7.3f	3894	III: 5668541-5668732
CDS:F54E7.3h	F54E7.3h	4593	III: 5664372-5664539
CDS:F54E7.3i	F54E7.3i	4602	III: 5664372-5664539
CDS:F54E7.3k	F54E7.3k	3993	III: 5664372-5664539

65 RNAi Result

• WBRNAi00068264
• WBRNAi00091309
• WBRNAi00083243
• WBRNAi00083245
• WBRNAi00083244
• WBRNAi00067520
• WBRNAi00067554
• WBRNAi00008858
• WBRNAi00048350
• WBRNAi00048356
• WBRNAi00063233
• WBRNAi00083963
• WBRNAi00087530
• WBRNAi00063495
• WBRNAi00077103
• WBRNAi00111796
• WBRNAi00086673
• WBRNAi00086672
• WBRNAi00086675
• WBRNAi00086674
• WBRNAi00086677
• WBRNAi00086676
• WBRNAi00087579
• WBRNAi00087580
• WBRNAi00077258
• WBRNAi00077267
• WBRNAi00063232
• WBRNAi00063234
• WBRNAi00086696
• WBRNAi00063235

194 Allele

• gk964518
• gk175161
• gk175162
• gk175163
• gk175164
• gk175165
• gk175166
• gk175167
• gk175168
• gk175169
• gk175170
• gk175171
• gk175172
• gk175173
• gk175174
• gk175175
• gk175176
• gk175177
• gk175178
• gk175179
• gk175180
• gk175181
• gk964338
• gk964339
• cxTi9074
• WBVar02067566
• WBVar00245080
• t1558
• t1591
• t1688

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003918
• Start: 5664233
• End: 5676795
• 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

166 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 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 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
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:all-neurons_L1-larva_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
	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 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
	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
	Transcripts expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
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
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
	Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_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
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
	Transcripts that showed significantly increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_downregulated
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	Transcripts that showed significantly decreased 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_downregulated
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
	Transcripts that showed significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	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
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_downregulated
	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

10 Expression Patterns

• Primary Identifier: Expr1031851
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1019819
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr11916
• Pattern: Fluorescently tagged PAR-3 was present along the length of the canal lumen.

• Primary Identifier: Expr2934
• Remark: The appearance of AJM-1 at apical junctions roughly correlated with the disappearance of PAR-3.
• Pattern: PAR-3 was detected in the vulval cells, as well as in most or all somatic gonad precursor cells, including ancestors of uterus, sheath, and spermatheca starting during the third larval stage (L3; about 25-29 hours at 25 centigrades). PAR-3 began to accumulate in developing uterine, sheath and spermathecal cells during the late-L3 stage. By the mid-L4 stage most somatic gonad precursors expressed PAR-3, with the exception of cells at the boundary of the uterus and the spermatheca, which were presumed to be precursors of the spemathecal valve.
• Subcellular Localization: At late-L3 stage, PAR-3 appeared to accumulate below the cell membranes that face neighboring cells. As development proceeded, asymmetric distribution of PAR-3 became evident.

• Primary Identifier: Expr1821
• Remark: Previous data: analysis of the PAR proteins has focused primarily on their anterior-posterior localization at the 1-cell stage and their roles in subsequent anterior-posterior polarity. After cell division begins, however, this anterior-posterior asymmetry is reiterated only in the lineage of cells that form the germline. In contrast, some somatic (non-germline) cells show an apical-basal polarity in PAR localization.
• Pattern: The apical-basal polarity of the PAR proteins persists through early gastrulation, cells in the interior of the embryo accumulate PAR-3 on their blastocoel-facing surfaces; these and later changes in PAR distribution were not analyzed further.
• Subcellular Localization: By the middle of the 4-cell stage, the anterior PAR protein PAR-3 is present over the entire cortex of each somatic blastomere. However by the end of the 4-cell stage and at later stages PAR-3 is concentrated in a broad `cap' centered on the apical surface.

• Primary Identifier: Expr1558
• Remark: No detailed description on cellular expression pattern at later stages.
• Subcellular Localization: No staining was seen in gonads or unfertilized oocytes. The PAR-3 protein was first detected at the cell periphery in fertilized eggs during the meiotic divisions. In 10 out of 13 positively stained embryos, the protein was undetectable in the posterior third of the embryo. stained very strongly on the lateral periphery, and stained weakly at the periphery at the extreme anterior pole. The other embryos showed uniform peripheral staining. After meiosis II is completed and as the pronuclei start to decondense, PAR-3 is restricted to the anterior periphery at all cases, extending to about 65% of the total length of the embryo. As pronuclear migration processes, PAR-3 become more concentrated at the anterior pole, extending to about 54% of the embryonic length. During prophase, metaphase, and early anaphase of the first mitosis, the signal is strongest and extends to 48% embryo length. In addition to peripheral staining, at all stages, unlocalized PAR-3 appears to be present in the cytoplasm.

• Primary Identifier: Expr1152146
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2014728
• 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: Expr3436
• Remark: No GO_term assigned.
• Subcellular Localization: A tight spatial correlation between NMY-2 and a second anterior PAR protein, PAR-3, was observed in fixed embryos between meiosis II and pseudocleavage; the NMY-2 cap extended slightly posterior to the PAR-3 cap consistent with the de novo formation of NMY-2::GFP foci at the posterior.

• Primary Identifier: Expr2032962
• 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).

48 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003918
• Start: 5664233
• End: 5676795
• Strand: 1

48 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 12563

1 Sequence Ontology Term