WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

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
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Quick Links:
SummaryGenomicsOther
 
Lists
This Gene is in 2 lists:
C. elegans transcription factor genes (1075)
metrics_list_union (10192)

1 Organism

Name Taxon Id
Caenorhabditis elegans 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

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

65 Allele

Public Name
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 Organism Length (nt)
I Caenorhabditis elegans 15072434  

1 Chromosome Location


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

3 Data Sets

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

1 Downstream Intergenic Region

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

188 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
  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
  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 in eif-2alpha(RNAi) animals at N2 background. DESeq2, fold change > 2 and p-value < 0.01. WBPaper00067953:eif-2alpha(RNAi)_upregulated_N2
  Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at zip-2(tm4248) background. DESeq2, fold change > 2 and p-value < 0.01. WBPaper00067953:eif-2alpha(RNAi)_upregulated_zip-2(tm4248)
  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 GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:GABAergic-neuron_expressed
  Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. N.A. WBPaper00064071:NHR-49_interacting
  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 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 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 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
  Transcripts that showed significantly increased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults. DESeq2, FDR < 0.05, fold change > 2. WBPaper00066978:Day1Adult_vs_Day8Adult_upregulated_neuron
Bacteria: Pseudomonas donghuensis HYS Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to OP50. DESeq2, fold change > 2, FDR < 0.05. WBPaper00068216:FUR_vs_OP50_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
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 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 detected in germline isolated from day-1 adult hermaphrodite animals. All three experiments have CPM >= 1. WBPaper00067147:germline_expressed
  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
  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
starvation 12 hours Transcripts that showed significantly increased expression in dissected intestines of N2 L1 larva that were starved for 12 hours, comparing to fed animals. EdgeR, FDR < 0.05, fold change >= 2. WBPaper00067259:starvation_upregulated_intestine
  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

9 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
Picture: Figure 5. Preabsorption of the antibody to the immunogens eliminated muscle staining.   Expr8314   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.
    Expr2036057 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).  
Picture: Fig. 4F.   Expr8542   Expressed in muscle arms, but at much reduced levels compared with their levels in the cell body of the muscle.
    Expr1032888 Tiling arrays expression graphs  
    Expr2991 Strong GFP expression in body wall muscles, vulval muscles, and the anal muscles.  
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.   Expr2992   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.
    Expr1158771 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr1012404 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
    Expr2017921 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).  

20 GO Annotation

Annotation Extension Qualifier
  enables
  located_in
  located_in
  located_in
  located_in
  located_in
  enables
  enables
  enables
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in

0 Homologues

1 Locations


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

20 Ontology Annotations

Annotation Extension Qualifier
  enables
  located_in
  located_in
  located_in
  located_in
  located_in
  enables
  enables
  enables
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in

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

Identifier Name Description
gene  

2 Strains

WormBase ID
WBStrain00035931
WBStrain00008387

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrI_14384738..14390332   5595 I: 14384738-14390332 Caenorhabditis elegans