WormMine: Gene WBGene00006824

• WormBase Gene ID: WBGene00006824
• Gene Name: unc-95
• Sequence Name: Y105E8A.6
• Brief Description: unc-95 encodes a LIM domain-containing protein related to Drosophila and vertebrate paxillins; UNC-95 is required for locomotion and organization of thick and thin filaments in body wall muscle; by homology, UNC-95 may function as an anchor protein that links signaling and cytoskeletal proteins at focal adhesions; in vitro, UNC-95 interacts with RNF-5, a RING finger protein that may function as an E3 ligase to regulate UNC-95 levels via ubiquitin-mediated degradation; UNC-95 is expressed in body-wall and vulval muscles, and co-localizes with RNF-5 to muscle dense bodies (focal adhesion-like attachment sites).
• Organism: Caenorhabditis elegans
• Automated Description: Enables protein domain specific binding activity. Located in M band; nucleus; and striated muscle dense body.
• Biotype: SO:0001217
• Genetic Position: I :24.674 ±0.00615
• Length (nt): 3378

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006824

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y105E8A.6.1	Y105E8A.6.1	1148	I: 14381360-14384737

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y105E8A.6	Y105E8A.6	1053	I: 14381455-14381858

13 RNAi Result

• WBRNAi00089765
• WBRNAi00066056
• WBRNAi00055233
• WBRNAi00026554
• WBRNAi00064162
• WBRNAi00004485
• WBRNAi00026552
• WBRNAi00026553
• WBRNAi00036498
• WBRNAi00081086
• WBRNAi00090029
• WBRNAi00090188
• WBRNAi00090347

65 Allele

• gk963849
• gk964175
• gk962681
• h16266
• gk963947
• gk129143
• gk603317
• su33
• su106
• gk129144
• gk129146
• gk129145
• gk129147
• gk129140
• gk129139
• gk129142
• gk129141
• gk129138
• gk129137
• WBVar01714959
• WBVar01714961
• WBVar01714960
• WBVar01502459
• gk895953
• gk893098
• gk425449
• gk806039
• gk849279
• gk601071
• gk670723

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006824
• Start: 14381360
• End: 14384737
• Strand: -1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrI_14379426..14381359
• Length (nt): 1934
• Chromosome Location: I: 14379426-14381359
• Organism: Caenorhabditis elegans

159 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 expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	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_upregulated
	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 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 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)
	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	Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304.	N.A.	WBPaper00064229:B.thuringiensis-Cry5Ba_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 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
	mRNAs that showed differential expression in activated AAK-2(uthIs202[aak-2 (intron 1)::aak-2(aa1-aa321)::Tomato::unc-54 3'UTR + rol-6(su1006)]), activiated CRTC-1 (uthEx222[crtc-1p::crtc-1 cDNA (S76S, S179A)::tdTomato::unc-54 3'UTR + rol-6(su1006)]), or AAK-2;CRTC-1 comparing to in N2.	Genes were tested for differential expression between each mutant strain and wild-type using edgeRs glm method. Briefly, negative binomial models were fitted and dispersion estimates obtained. These were then used to calculate average levels of change between conditions and determine differential expression, using the generalized linear model likelihood ratio test. For each comparison, genes with less than 5 CPM were filtered and those with at least 50% change and False Discovery Rate (FDR) of 1% or less were considered differentially expressed.	WBPaper00046499:AMPK_regulated
Dietary restriction	Transcripts that showed significantly decreased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition.	Bioconductor package edgeR, p < 0.05.	WBPaper00056443:DietaryRestriction_downregulated
	Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in control animals.	NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%.	WBPaper00064727:daf-2(e1370)_upregulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_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
	Expression Pattern Group C, enriched for genes involved in metabolic processes.	The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05.	WBPaper00036286:Pattern_C
	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
Gamma irradiation 100 mGY per hour for 72 hours since L1 larva.	Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage.	DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3.	WBPaper00058958:100mGy-irradiation-72h_upregulated

9 Expression Patterns

• Primary Identifier: Expr8314
• Remark: Picture: Figure 5. Preabsorption of the antibody to the immunogens eliminated muscle staining.
• Subcellular Localization: Immunostaining with the antibody showed staining of body wall muscle in a striated pattern that is characteristic of myofibrils. Precise localization in body wall muscle was determined by costaining with marker antibodies for dense bodies (anti-actinin) and M-lines (anti-UNC-89). By this method, UNC-95 was localized at dense bodies and M-lines.

• Primary Identifier: Expr2036057
• 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: Expr8542
• Remark: Picture: Fig. 4F.
• Subcellular Localization: Expressed in muscle arms, but at much reduced levels compared with their levels in the cell body of the muscle.

• Primary Identifier: Expr1032888
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2991
• Pattern: Strong GFP expression in body wall muscles, vulval muscles, and the anal muscles.

• Primary Identifier: Expr2992
• Remark: Transgenic lines (n = 4) were made in the wild-type N2 background, harboring a shorter GFP fusion protein including only the first 144 amino acids of UNC-95, which corresponds to the predicted su33 allele, Ex[unc-95(su33)::GFP; rol-6]. Low GFP expression was detected in the dense bodies and M-lines of body wall muscles; however, there was no expression in the muscle-muscle cell boundaries. Weak expression was also detected in muscle nuclei. In addition, the expression was not equal along the body wall muscle cells and appeared in a mosaic pattern. In several cells (observed in all lines), the protein accumulated to very high levels that were not observed in the wild-type UNC-95 construct. In those cells, the organization of the M-lines and dense bodies was disrupted, and these structures appeared as intense stripes or aggregates. On the other hand, additional surrounding cells had no GFP expression at all.
• Subcellular Localization: Strong GFP expression was observed at the embryonic stage 350 min after the first cell division. The staining is dispersed in the muscle cell cytoplasm as was also shown for vinculin and integrin at this stage of muscle development, when muscle cell precursors are positioned in lateral rows adjacent to the seam cells. The staining gradually becomes more localized at the membrane until the muscles are fully positioned into quadrants and the expression is shown in two separate parallel stripes. Later on the expression becomes localized to the discrete spots of the newly formed muscle dense bodies, but through all stages GFP is also present in the cytoplasm. Nuclear localization of UNC-95 could be clearly observed from the threefold stage. In adult animals, UNC-95 is expressed in body wall muscles in the dense bodies, M-lines, and muscle-muscle cell boundaries. Strong expression is also detectable in muscle cell cytoplasm and nucleus. In the vulval muscles the protein is strongly localized at sites of muscle attachment to the hypodermis. Expression was also detected in the anal depressor muscle. A bright ring at the tip of the buccal cavity seems to be the attachment between the arcade cells to the hypodermal anterior hyp1 cell, the pharyngeal epithelium, and the associated cuticles. Thus, in different expressing cells UNC-95 is mainly localized to the cellular attachment sites between the cell membrane and the ECM.

• Primary Identifier: Expr1158771
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1012404
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2017921
• 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).

16 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006824
• Start: 14381360
• End: 14384737
• Strand: -1

16 Ontology Annotations

1 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes that showed more than 2 fold increase of expression in unc-95(su33) comparing with N2.	Genes with differences corresponding to P-value < 0.01 in either the high- or the low-photomultiplier scans (Students t-test) in all replicates were considered to be significantly regulated.	WBPaper00031097:unc-95(su33)_upregulated

1 Sequence

• Length: 3378

1 Sequence Ontology Term