WormMine: Gene WBGene00000301

• WormBase Gene ID: WBGene00000301
• Gene Name: cav-1
• Sequence Name: T13F2.8
• Brief Description: cav-1 encodes one of two C. elegans caveolin orthologs; cav-1 is required for viability and Ras/MAP-kinase-dependent progression through the meiotic cell cycle; CAV-1 is expressed in the adult germ line and during embryonic development; CAV-1::GFP localizes to cortical granules that function to secrete chondroitin and mucin-like proteoglycans to the extracellular space following fertilization.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable molecular adaptor activity. Involved in Ras protein signal transduction; meiotic cell cycle; and regulation of egg-laying behavior. Located in cytoplasm and cytoplasmic side of plasma membrane. Expressed in several structures, including germ cell; gonad arm; nervous system; pharynx; and tail. Human ortholog(s) of this gene implicated in several diseases, including distal myopathy Tateyama type; glaucoma (multiple); lipodystrophy (multiple); and systemic scleroderma (multiple). Is an ortholog of human CAV1 (caveolin 1).
• Biotype: SO:0001217
• Genetic Position: IV :4.40589 ±0.001071
• Length (nt): 1050

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000301

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T13F2.8a.1	T13F2.8a.1	925	IV: 9772510-9773559
Transcript:T13F2.8b.1	T13F2.8b.1	381	IV: 9772984-9773364

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T13F2.8b	T13F2.8b	381	IV: 9772984-9773364
CDS:T13F2.8a	T13F2.8a	708	IV: 9772532-9772807

20 RNAi Result

• WBRNAi00068261
• WBRNAi00067832
• WBRNAi00053276
• WBRNAi00077479
• WBRNAi00066698
• WBRNAi00109166
• WBRNAi00116121
• WBRNAi00077476
• WBRNAi00018681
• WBRNAi00109555
• WBRNAi00035544
• WBRNAi00077477
• WBRNAi00062372
• WBRNAi00077478
• WBRNAi00109264
• WBRNAi00065628
• WBRNAi00066654
• WBRNAi00109458
• WBRNAi00094898
• WBRNAi00109361

27 Allele

• gk964278
• gk964078
• gk964500
• gk962765
• gk963883
• gk963884
• gk964226
• gk964227
• gk466706
• gk732378
• WBVar01772263
• gk392399
• gk737265
• gk594466
• gk724426
• gk682231
• gk681679
• gk917087
• WBVar00191569
• WBVar00191567
• WBVar00191568
• tm2702
• ok2089
• tm13126
• WBVar01856247
• WBVar01856246
• gk209573

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000301
• Start: 9772510
• End: 9773559
• 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_chrIV_9773560..9774604
• Length (nt): 1045
• Chromosome Location: IV: 9773560-9774604
• Organism: Caenorhabditis elegans

369 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 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 significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage.	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_larva_enriched
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
	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 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 NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Genes up regulated in alg-1(gk214) comparing to in N2.	Differential expression was assessed using an empirical Bayes statistics using the eBayes function.	WBPaper00040823:alg-1(gk214)_upregulated
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_developing
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
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
	Transcripts that showed significantly decreased expression in lipl-4 overexpression transgenic lines comparing to wild type control animals.	DESeq2 fold change > 2, FDR < 0.05.	WBPaper00064156:lipl-4(overexpress)_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 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
	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
	Top 300 transcripts enriched in ABalppppppa, ABpraaapppa according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:ASE_parent
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_regulated
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated

16 Expression Patterns

• Primary Identifier: Expr4880
• Remark: Picture: Fig. 1C.
• Subcellular Localization: In control oocytes prior to fertilization, GFP:CAV-1 is concentrated in intracellular vesicles and large ring-like cytoplasmic structures as well as localizing weakly to the plasma membrane. Immediately after oocytes pass through the spermatheca and are fertilized, the amount of GFP:CAV-1 on the cell surface rapidly increases, followed by its internalization and degradation. Since, adult C. elegans hermaphrodites ovulate approximately every 20 minutes, examination of the string of newly fertilized embryos present in an adult worm provides a convenient means of monitoring the timecourse of the changes in the GFP:CAV-1 distribution. Newly fertilized embryos exhibited bright GFP:CAV-1 fluorescence, initially at the cell surface and subsequently on internal membranes, but embryos beyond the 2-cell stage, approximately 90 minutes post fertilization, lacked visible fluorescence.

• Primary Identifier: Expr4814
• Remark: Picture: Figure 1, A, C, and G.
• Subcellular Localization: CAV-1-GFP labeled ring-like structures (CAV-1 bodies) and puncta. In mitotic and early meiotic cells of the distal germline CAV-1-GFP is mainly localized to the plasma membrane. As oocytes form in the bend region CAV-1-GFP additionally accumulates in small vesicles, and in larger oocytes appears in large ring-like structures deeper in the cytoplasm.

• Primary Identifier: Expr4762
• Pattern: CAV-1::GFP was expressed in most, if not all, cells in embryos. It was predominantly localised to, or close to, the membrane in these cells although some small intracellular bodies were also visible. This widespread expression continued into the early larval stages, but with maturation, CAV-1::GFP became restricted to most, but not all, neurons. Staining was seen in the ventral nerve cord (VNC), and was also frequently observed in the commissures. Of particular interest was the punctate nature of labelling which is most obvious in the VNC, this staining suggests possible localisation to synapses.

• Primary Identifier: Expr4763
• Subcellular Localization: No substantial co-localisation was detected with pre-synaptic markers. Thus cav-1 is unlikely to be presynaptic within the VNC. Confocal images of worms carrying both cav-1::YFP and unc-63::CFP revealed that CAV-1::YFP and UNC-63::CFP co-localise in some parts of the nervous system and in structures that are either part of, or close to, the VNC. The latter localisation suggests that CAV-1 and UNC-63 co-localise in muscle arms. This pattern may include localisation to the post-synaptic regions of NMJs and extrasynaptic positioning. Within the nervous system as a whole, obvious area without co-localisation also exist, these are particularly evident in neurons that express only unc-63 and not cav-1 or vice versa, confirming that cav-1 is not expressed in all neurons.

• Primary Identifier: Expr2009736
• 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: Expr1030192
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13814
• Pattern: Strong cav-1 promoter activity was observed in developing embryos as well as in all larval stages. During larval development, the signal was most prominent in and around the pharynx (including the nerve ring), along the worm's ventral cord, and in the tail. In adult worms cav-1 is foremost expressed in neurons. Higher magnification showed prominent cav-1 expression in the nerve ring, implying the existence of caveolae in neurons of this cluster.

• Primary Identifier: Expr15073
• Pattern: Imaging endogenous CAV-1::GFP revealed similar patterns as previously reported in the germ line (Sato et al. 2006). However, unlike the pie-1 driven exogenous line, endogenous CAV-1::GFP was not clearly detected in the distal gonad until the bend region of the gonad arm, where it localized to the plasma membrane, and vesicle-shaped structures. Oocytes had slightly higher expression showing enrichment at plasma membrane localization but faint cytoplasmic signal, and no obvious enrichment to vesicles. After ovulation, CAV-1::GFP remained on the plasma membrane during meiosis I and was no longer detected by meiosis II. In 5/5 anaphase I embryos, CAV-1::GFP was not significantly localized to cortical granules at a time when separase could be observed on vesicles. Overall, endogenous CAV-1::GFP signal is less intense in the germline than exogenous pie-1-driven lines. However, endogenous CAV-1::GFP signal became increasingly intense at the plasma membrane sometime after the 16-cell embryo stage. The membrane signal remains intense through later stages of embryonic development. Finally, adult somatic expression appeared to follow previously observed patterns (Parker et al. 2007).

• Primary Identifier: Expr1284
• Pattern: CAV-1 is expressed at low levels in adults, where it is found in germ cells. The protein is strongly expressed in most, if not all, cells throughout embryonic development. In late embryos and L1 larvae, cav-1 expression becomes restricted to the nervous system and diminishes during larval development.

• Primary Identifier: Expr2027976
• 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: Expr1027971
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2723
• Pattern: The message for Cavce-1 was more abundant in eggs than mixed stages.

• Primary Identifier: Expr14418
• Subcellular Localization: In wild-type worms, caveolin (GFP::CAV-1) localises at the PCMC.

• Primary Identifier: Expr1156861
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr15074
• Subcellular Localization: However, unlike the pie-1 driven exogenous line, endogenous CAV-1::GFP was not clearly detected in the distal gonad until the bend region of the gonad arm, where it localized to the plasma membrane, and vesicle-shaped structures.

• Primary Identifier: Expr15075
• Subcellular Localization: After ovulation, CAV-1::GFP remained on the plasma membrane during meiosis I and was no longer detected by meiosis II. Oocytes had slightly higher expression showing enrichment at plasma membrane localization but faint cytoplasmic signal, and no obvious enrichment to vesicles.

21 GO Annotation

14 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000301
• Start: 9772510
• End: 9773559
• Strand: 1

21 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly decreased expression in cav-1(RNAi) comparing to control RNAi animals.	DESeq2 from R 3.2.1, adjusted p-value < 0.1	WBPaper00054796:cav-1(RNAi)_downregulated
	Transcripts that showed significantly increased expression in cav-1(RNAi) comparing to control RNAi animals.	DESeq2 from R 3.2.1, adjusted p-value < 0.1	WBPaper00054796:cav-1(RNAi)_upregulated

1 Sequence

• Length: 1050

1 Sequence Ontology Term