WormMine: Gene WBGene00003930

• WormBase Gene ID: WBGene00003930
• Gene Name: pat-3
• Sequence Name: ZK1058.2
• Brief Description: pat-3 encodes the C. elegans beta-integrin subunit; pat-3 is an essential gene that is required for muscle cell attachment to the overlying hypodermis and for normal muscle filament assembly and function; in addition, pat-3 is required for normal axon guidance and for ovulation; antibody staining reveals that PAT-3 is expressed in body wall muscle as well as in the anal depressor, sphincter, intestinal, vulval, and uterine muscles and the somatic gonad; PAT-3 localizes to dense bodies, M-lines, and intercellular borders.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable integrin binding activity. Involved in several processes, including muscle cell cellular homeostasis; positive regulation of cellular component organization; and regulation of locomotion. Located in several cellular components, including contractile muscle fiber; focal adhesion; and lateral plasma membrane. Part of integrin complex. Expressed in several structures, including GABAergic neurons; egg-laying apparatus; enteric muscle; gonad; and vulval precursor cell. Used to study cancer. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); blood platelet disease (multiple); and lung carcinoma (multiple). Is an ortholog of human ITGB1 (integrin subunit beta 1).
• Biotype: SO:0001217
• Genetic Position: III :-4.22486±
• Length (nt): 5219

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003930

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:ZK1058.2.1	ZK1058.2.1	2848	III: 3908931-3914149

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:ZK1058.2	ZK1058.2	2430	III: 3909329-3909400

62 RNAi Result

• WBRNAi00009448
• WBRNAi00063787
• WBRNAi00024328
• WBRNAi00066954
• WBRNAi00067007
• WBRNAi00067118
• WBRNAi00067120
• WBRNAi00067145
• WBRNAi00067217
• WBRNAi00067219
• WBRNAi00067392
• WBRNAi00067498
• WBRNAi00067613
• WBRNAi00067844
• WBRNAi00067952
• WBRNAi00068095
• WBRNAi00059083
• WBRNAi00109190
• WBRNAi00097795
• WBRNAi00077797
• WBRNAi00091713
• WBRNAi00092227
• WBRNAi00085487
• WBRNAi00078235
• WBRNAi00065778
• WBRNAi00078234
• WBRNAi00109288
• WBRNAi00078237
• WBRNAi00078236
• WBRNAi00091728

92 Allele

• gk962532
• gk963881
• gk963882
• rh54
• rh96
• rh151
• WBVar00248664
• st423
• st552
• st564
• WBVar01541701
• WBVar01541700
• WBVar01656382
• WBVar01656381
• WBVar01656380
• WBVar01962645
• WBVar01893132
• WBVar01962644
• WBVar01999505
• WBVar01962643
• WBVar01999506
• WBVar01771081
• WBVar02117639
• WBVar01785364
• WBVar02034109
• mu337
• gk171768
• gk171767
• gk171770
• gk171769

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003930
• Start: 3908931
• End: 3914149
• 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_chrIII_3907688..3908930
• Length (nt): 1243
• Chromosome Location: III: 3907688-3908930
• Organism: Caenorhabditis elegans

131 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 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 decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
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
	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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours.	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:Cisplatin_downregulated_WT
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:hypodermis_L3-L4-larva_expressed
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
	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 significantly increased expression after N2 animals were exposed to BL21 bacteria carrying pET28a-cry5B, comparing to animals exposed to BL21 control bacteria.	Differentially expressed genes were identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05.	WBPaper00065732:Cry5Ba_upregulated_N2
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)
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	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
heat-shock hlh-1	Genes enriched in HLH-1 heat shock dataset.	A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets.	WBPaper00031003:hlh_1_enriched
	Embryonic class (E): genes that significantly increase in abundance at some point during embryogenesis.	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_E
	WT-Pico Pan-neural Depleted Genes, with genes found multiple times in a single dataset removed (without dups).	To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%.	WBPaper00031532:Larva_Pan_Neuronal_Depleted
	Genes that showed significantly altered expression between N2 and npr-1(ur89) strains exposed to either the nematocidal B. thuringiensis B-18247, the pathogenic P. aeruginosa PA14, or the control E. coli OP50 for 12 or 24 hours.	Estimation of transcript abundance and significantly differentially expressed genes were identified by Cuffdiff using the quartile normalization method. Transcripts with a significant change between different conditions (adjusted p-value < 0.01 by the false discovery rate, FDR) were treated as signature for each comparison.	WBPaper00049498:npr-1(ur89)_regulated_3
	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:bodywall-muscle_L2-larva_expressed

21 Expression Patterns

• Primary Identifier: Expr4554
• Pattern: Expression of major cytoskeletal proteins were detected in the myoepithelial sheath, and, interestingly, some of them were also expressed in other parts of the somatic gonad.

• Primary Identifier: Expr1031863
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1162513
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr11792
• Subcellular Localization: PAT-2::mCherry and PAT-3::GFP were co-localized to the dense bodies and M-lines in muscle cells.

• Primary Identifier: Expr8766
• Remark: Picture: Fig S2A.
• Pattern: Overexpression of the full-length integrin subunit PAT-3::GFP transgene resulted in intracellular accumulation in the AC, as well as neighboring somatic gonad and vulval cells. PAT-3::GFP was consistently expressed at higher levels in the AC relative to neighboring cells.

• Primary Identifier: Expr1545
• Pattern: It was also detected in single sarcomere muscles. It is located in the anal depressor muscle at the ventral attachment of the muscle, apposing the anus. Staining was detected along the middle strut that straddles the anus. beta-pat-3 was also detected on the ventral surface of the sphincter muscle and the basal surface of the intestinal muscles. In the vulva muscles, beta-pat-3 was located ventrally, in apposition to the opening of the vulva, and laterally, along the uterus. It was also detected in the uterine muscles localized to the lateral ridge. No staining was detected in pharyngeal muscle.
• Subcellular Localization: beta-pat-3 is localized to the dense bodies, the M-lines, and the borders between cells.

• Primary Identifier: Expr14788
• Pattern: The pat-3 gene is expressed in D-type motor neurons.

• Primary Identifier: Expr9933
• Pattern: PAT-3-GFP localizes in DTCs.

• Primary Identifier: Expr9307
• Pattern: PAT-3::GFP was expressed throughout the uterine and vulval tissues at the mid-to-late L3 stage and became enriched at the boundary of the basement membrane gap by the mid-L4 stage. Mosaic expression studies indicated that the boundary-localized INA-1/PAT-3::GFP was derived from the vulval cells, most strongly within the vulD cells.

• Primary Identifier: Expr13257
• Pattern: Wild-type PAT-3::GFP was expressed on the lateral membranes of the vulval cells and along the basal laminae that separate the vulval cells from the uterus. Since PAT-3::GFP was also expressed in the adjacent uterine cells, both tissues are likely to contribute to the strong signal along the basal laminae. PAT-3::GFP localization on the lateral membranes of the vulval cells was most prominent at the onset of vulval invagination in mid to late L3 larvae.

• Primary Identifier: Expr15709
• Pattern: The translational LIN-12::GFP reporter was expressed on the apical membrane of the VPCs, while the LIN-18::GFP and PAT-3::GFP translational reporters localized predominantly to the basolateral compartment.

• Primary Identifier: Expr11859
• Pattern: PAT-3::GFP localized uniformly to the VPCs throughout vulval development.

• Primary Identifier: Expr11787
• Pattern: At initiation of migration, DTCs express PAT-3.

• Primary Identifier: Expr1018497
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2777
• Subcellular Localization: Although both SUP-9 and PAT-3::GFP were localized to dense bodies, their distribution patterns were only partially superimposable. Unlike PAT-3::GFP, SUP-9 was present in the spaces between adjacent dense bodies, weakly diffused throughout the muscle membrane, and primarily excluded from the M-lines.

• Primary Identifier: Expr11965
• Subcellular Localization: In wild-type embryos, PAT-3/integrin is located in an ordered array of recognizable dense bodies and M lines.

• Primary Identifier: Chronogram1610
• Remark: Original chronogram file: chronogram.491.xml
• Reporter Gene: [ZK1058.2:gfp] transcriptional fusion.

• Primary Identifier: Chronogram1836
• Remark: Original chronogram file: chronogram.746.xml
• Reporter Gene: [ZK1058.2:gfp] transcriptional fusion.

• Primary Identifier: Expr14843
• Subcellular Localization: Endogenously tagged INA-1:: mNG, PAT-2::2XmNG, and PAT-3::mNG were expressed in the gonad and pharyngeal cells and localized to the cell-BM interface.

• Primary Identifier: Expr2032985
• 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: Expr2014751
• 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).

43 GO Annotation

38 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003930
• Start: 3908931
• End: 3914149
• Strand: -1

43 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 5219

1 Sequence Ontology Term

• Name: gene

8 Strains

• WBStrain00033527
• WBStrain00040278
• WBStrain00047295
• WBStrain00047296
• WBStrain00047217
• WBStrain00047373
• WBStrain00047390
• WBStrain00002787

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_3914150..3916966
• Length (nt): 2817
• Chromosome Location: III: 3914150-3916966
• Organism: Caenorhabditis elegans