WormMine: Gene WBGene00000942

• WormBase Gene ID: WBGene00000942
• Gene Name: deb-1
• Sequence Name: ZC477.9
• Brief Description: The deb-1 gene encodes a vinculin ortholog highly conserved amongst metazoans including Drosophila, chick, and humans (OMIM:193065); DEB-1 is a muscle attachment protein found in dense bodies, and is required for attaching actin thin filaments to the basal sarcolemma; DEB-1 requires PAT-4/integrin-linked kinase for full assembly into nascent attachments.
• Organism: Caenorhabditis elegans
• Automated Description: A structural constituent of cytoskeleton. Involved in positive regulation of ovulation. Located in several cellular components, including cytoskeleton; dense body; and striated muscle dense body. Expressed in gonad. Human ortholog(s) of this gene implicated in dilated cardiomyopathy 1W and hypertrophic cardiomyopathy 15. Is an ortholog of human VCL (vinculin).
• Biotype: SO:0001217
• Genetic Position: IV :3.28945 ±0.000234
• Length (nt): 9052

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000942

Genomics

8 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:ZC477.9a.1	ZC477.9a.1	3506	IV: 7085215-7094266
Transcript:ZC477.9c.1	ZC477.9c.1	3472	IV: 7085216-7094266
Transcript:ZC477.9b.1	ZC477.9b.1	1590	IV: 7085218-7087907
Transcript:ZC477.9d.1	ZC477.9d.1	3630	IV: 7085331-7094266
Transcript:ZC477.9g.1	ZC477.9g.1	666	IV: 7085688-7086779
Transcript:ZC477.9h.1	ZC477.9h.1	699	IV: 7085688-7086779
Transcript:ZC477.9f.1	ZC477.9f.1	1077	IV: 7085688-7087897
Transcript:ZC477.9e.1	ZC477.9e.1	3240	IV: 7085688-7094266

Other

8 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:ZC477.9a	ZC477.9a	3033	IV: 7085688-7085857
CDS:ZC477.9b	ZC477.9b	1110	IV: 7085688-7085857
CDS:ZC477.9g	ZC477.9g	666	IV: 7085688-7085857
CDS:ZC477.9h	ZC477.9h	699	IV: 7085688-7085857
CDS:ZC477.9c	ZC477.9c	3000	IV: 7085688-7085857
CDS:ZC477.9d	ZC477.9d	3273	IV: 7085688-7085857
CDS:ZC477.9e	ZC477.9e	3240	IV: 7085688-7085857
CDS:ZC477.9f	ZC477.9f	1077	IV: 7085688-7085857

28 RNAi Result

• WBRNAi00058962
• WBRNAi00099871
• WBRNAi00100517
• WBRNAi00027597
• WBRNAi00109637
• WBRNAi00109249
• WBRNAi00100891
• WBRNAi00099265
• WBRNAi00099669
• WBRNAi00099467
• WBRNAi00080643
• WBRNAi00100143
• WBRNAi00113651
• WBRNAi00109346
• WBRNAi00100330
• WBRNAi00113650
• WBRNAi00100704
• WBRNAi00101078
• WBRNAi00091679
• WBRNAi00091694
• WBRNAi00091709
• WBRNAi00091724
• WBRNAi00091739
• WBRNAi00091754
• WBRNAi00091775
• WBRNAi00109540
• WBRNAi00113652
• WBRNAi00109443

81 Allele

• gk964500
• gk963722
• gk963417
• gk963416
• st385
• st554
• st555
• WBVar02123471
• WBVar02123395
• gk625312
• gk509044
• gk957203
• WBVar01794777
• WBVar01786414
• gk204793
• gk204794
• gk204791
• gk204792
• gk204789
• gk204790
• gk204788
• gk204801
• gk204802
• gk204799
• ok5692
• gk204800
• gk204797
• gk204798
• WBVar00190395
• gk204795

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000942
• Start: 7085215
• End: 7094266
• 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_7084683..7085214
• Length (nt): 532
• Chromosome Location: IV: 7084683-7085214
• Organism: Caenorhabditis elegans

202 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 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
	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:bodywall-muscle_L1-larva_expressed
	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
	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
	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
	Genes with expression level regulated by genotype (N2 vs CB4856) at old adults stage (214 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_regulated_aging
	Genes with expression level regulated by genotype (N2 vs CB4856) 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_regulated_developing
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	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 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)
	Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
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
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_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 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

10 Expression Patterns

• Primary Identifier: Expr4553
• 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: Expr1030589
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1162397
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr15723
• Pattern: The pattern of DEB-1 localization correlated with the known pattern, i.e. targeting DEB-1 within the muscle dense bodies and muscle-like fibers in the somatic gonad cells, as reported by Ono et al. Additionally, we observed a reproducible signal within the gonadal distal part, namely in the cytoplasm and the nuclear area of meiotic cells. More interestingly, we identified strong and reproducible labeling in meiotic cells using a polyclonal antibody against DEB-1/b*f. After a detailed investigation of DEB-1/b*f isoform localization in the cytosol, we also investigated its nuclear localization. To the best of author ́s knowledge, this is the first observation of its kind. We used structured illumination microscopy (SIM; Nikon) with lateral resolution around 100 nm and identified DEB-1 inside the germ cell nucleus, partially colocalizing with DNA of the transition zone as well as pachytene nuclei. Transmission electron microscopy (TEM) analysis of DEB-1/b*f localization in germ-line nuclei confirmed localization to the early prophase I - in both leptotene/zygotene and pachytene stages. During leptotene/zygotene, DEB-1/b*f is localized in clusters in close vicinity of the inner nuclear membrane. Moreover, in the mid-pachytene regions of wild-type worms, DEB-1 localizes to the vicinity of the axial elements comprising the SC.

• Primary Identifier: Expr15722
• Pattern: The labeling pattern of DEB-1/a*e in the distal gonad was weak and diffused, with low intensity in meiotic cells. Identical to a previously reported MH24 pattern.

• Primary Identifier: Expr15724
• Pattern: The pattern of DEB-1 localization correlated with the known pattern, i.e. targeting DEB-1 within the muscle dense bodies and muscle-like fibers in the somatic gonad cells, as reported by Ono et al. Additionally, we observed a reproducible signal within the gonadal distal part, namely in the cytoplasm and the nuclear area of meiotic cells. More interestingly, we identified strong and reproducible labeling in meiotic cells using a polyclonal antibody against DEB-1/b*f. After a detailed investigation of DEB-1/b*f isoform localization in the cytosol, we also investigated its nuclear localization. To the best of author ́s knowledge, this is the first observation of its kind. We used structured illumination microscopy (SIM; Nikon) with lateral resolution around 100 nm and identified DEB-1 inside the germ cell nucleus, partially colocalizing with DNA of the transition zone as well as pachytene nuclei. Transmission electron microscopy (TEM) analysis of DEB-1/b*f localization in germ-line nuclei confirmed localization to the early prophase I - in both leptotene/zygotene and pachytene stages. During leptotene/zygotene, DEB-1/b*f is localized in clusters in close vicinity of the inner nuclear membrane. Moreover, in the mid-pachytene regions of wild-type worms, DEB-1 localizes to the vicinity of the axial elements comprising the SC.

• Primary Identifier: Expr2010839
• 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: Expr15725
• Subcellular Localization: We also found DEB-1/b*f clusters in condensed chromatin.

• Primary Identifier: Expr2029077
• 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: Expr1018217
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

31 GO Annotation

6 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000942
• Start: 7085215
• End: 7094266
• Strand: -1

31 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 9052

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00033529
• WBStrain00033522

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_7094267..7096102
• Length (nt): 1836
• Chromosome Location: IV: 7094267-7096102
• Organism: Caenorhabditis elegans