WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00000822 Gene Name  csq-1
Sequence Name  ? F40E10.3 Brief Description  csq-1 encodes a calsequestrin that is required to normal survival in media containing either excess or deficient Ca[2+], and that also binds UNC-68's intraluminal domain; CSQ-1 binds Ca[2+] in vitro, and is thought to buffer Ca[2+] stores in sarcoplasmic reticulum; CSQ-1 is expressed in bodywall muscle cells from mid-embryogenesis to adulthood, as well as in vulval muscles, and in the isthmus and terminal bulb regions of the pharynx; within bodywall muscle cells, CSQ-1 is distributed in a meshlike pattern, which ultrastructurally corresponds with apical sarcoplasmic reticulum, and which is very much like that of the UNC-68 ryanodine receptor; a 17-residue C-terminal domain of CSQ-1 binds the intraluminal loops of UNC-68 in vitro, and deletion of this domain disrupts CSQ-1 subcellular localization in vivo, as do K111A mutations; an N-terminal domain (residues 32-43) is required for CSQ-1's normal subcellular distribution, with a deletion mutant showing aggregate rather than meshlike distribution; in unc-68(e540) or unc-68(r1161) mutants, CSQ-1 is instead distributed randomly within muscle cells, indicating that the subcellular localization of CSQ-1 requires UNC-68; csq-1(RNAi) animals and csq-1(jh109) mutants show no grossly obvious phenotypes, do not enhance unc-68(e540) phenotypes, and display normal muscle cell development and locomotion; however, csq-1(jh109) mutants have abnormally low viability in media containing either excess or deficient Ca[2+]; sca-1 mRNA levels are reduced in csq-1(jh109) mutants; CSQ-1 is orthologous to human CASQ1 (OMIM:114250) and CASQ2 (OMIM:114251, mutated in catecholamine-induced polymorphic ventricular tachycardia).
Organism  Caenorhabditis elegans Automated Description  Enables calcium ion binding activity. Involved in calcium ion homeostasis. Located in several cellular components, including apical plasma membrane; nucleus; and sarcolemma. Expressed in body wall musculature; isthmus; terminal bulb; and vulval muscle. Human ortholog(s) of this gene implicated in catecholaminergic polymorphic ventricular tachycardia 2 and type 2 diabetes mellitus. Is an ortholog of human CASQ1 (calsequestrin 1) and CASQ2 (calsequestrin 2).
Biotype  SO:0001217 Genetic Position  X :19.8517 ±0.039613
Length (nt)  ? 3446
Quick Links:
 

1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00000822

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F40E10.3.1 F40E10.3.1 1409   X: 14684877-14688322
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:F40E10.3 F40E10.3 1254   X: 14684878-14685012

6 RNAi Result

WormBase ID
WBRNAi00046839
WBRNAi00092206
WBRNAi00092208
WBRNAi00014644
WBRNAi00032018
WBRNAi00092207

80 Allele

Public Name
gk964260
gk964029
gk962707
gk964028
gk963810
gk963581
WBVar01928534
WBVar01928535
WBVar01928536
WBVar01928537
tm11466
gk301609
gk301611
gk301610
gk301613
gk301612
gk301614
WBVar01545013
WBVar01788183
WBVar01788184
WBVar02083484
WBVar01553028
gk564901
gk583360
gk621210
gk325042
gk876502
gk358872
WBVar00218650
WBVar02113417

1 Chromosome

WormBase ID Organism Length (nt)
X Caenorhabditis elegans 17718942  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00000822 14684877 14688322 1

4 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  
C. elegans genomic annotations (GFF3 Gene)  
Panther orthologue and paralogue predictions  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrX_14688323..14688599   277 X: 14688323-14688599 Caenorhabditis elegans

214 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
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
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours. Transcripts that showed significantly decreased expression in N2 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_N2
  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
mitochondrial sulfide delivery molecule (mtH2S) AP39 Transcripts that showed significantly increased expression in N2 animals treated with mitochondrial sulfide delivery molecule (mtH2S) AP39 starting from 1-day-post L4 until 11 days post L4. DESeq2, fold change > 2, FDR < 0.05 WBPaper00065835:mtH2S-AP39-D0-treatment_upregulated_Day11
  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
  Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:pharynx_expressed
  Transcripts that showed significantly decreased expression in prx-5(RNAi) animals. Fold change > 2, p-value < 0.05. WBPaper00060911:prx-5(RNAi)_downregulated_mRNA
  Genes with expression level regulated by genotype (N2 vs CB4856) and age 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_age_regulated_aging
  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 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)
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 12h), according to RNAseq. Cuffdiff, ajusted p-value < 0.01. WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
  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
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 changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. Sleuth WBPaper00051558:aging_regulated

12 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr1030511 Tiling arrays expression graphs  
Picture: Figure 5B.   Expr7870 Western blot analysis showed that CSQ-1 was detectable at all stages of the development. During larval stages, CSQ-1 levels appeared to increase compared to the embryonic stages and these higher levels were maintained through the adult stages.  
Picture: Figure 9.   Expr7872 Transgenic animals carrying the csq-1::gfp fusion constructs showed expressions of GFP in body-wall muscles beginning from the 2-fold stage embryo through to adult stages. In addition, GFP signals were observed in vulval muscles and in the isthmus and terminal bulb regions of the pharynx.  
Picture: Fig. 6A. Fig. 7A-C, Fig. 8A,B. The staining pattern of CSQ-1 looked very similar, if not identical, to that of UNC-68 antibody staining, which also showed a mesh-like pattern, in addition to punctate staining, in body-wall muscle cells.   Expr7871   A mesh-like staining was observed in the body-wall muscle cells. Co-staining with MH24: The mesh-like signals of CSQ-1 (red) overlapped with the punctate vinculin signals (green/yellow). Although the double-labeling of body-wall muscles with anti-CSQ-1 and anti-vinculin show that both the proteins are localized around the same areas, the strong mesh-like staining of CSQ-1 spanning the muscle bands indicates that CSQ-1 is expressed over a wider range in the myofilament lattice. Immunogold electron microscopy: In body-wall muscle cells of wild-type animals, CSQ-1 signals were observed in the cytoplasmic regions of muscle cells, at sarcoplasmic membranes surrounding myofibril bundles, and also at spaces between sarcomeric bundles, where the dense body structures could be observed . Clustered signals were observed at the apical SR membranes juxtaposed to the basement membranes. These regions of flattened SR-like vesicles have already been reported to be the sites for the localization of RYR (UNC-68), suggesting that CSQ-1 may be localized at the SR membranes in the regions where RYR are located.
    Expr1150709 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
In control hybridization experiments with a sense-strand probe no signal was detected.   Expr1104 In situ hybridization experiments with anti-sense probe showed that the csq-1 gene began to be expressed in 2-fold-stage embryos along their mid-body lines where body-wall muscle precursor cells are located. No signal was detected in embryos earlier than the 2-fold stage, suggesting that the csq-1 gene is not expressed maternally. All the embryos in stages later than 2-fold showed csq-1 expression in their body-wall muscle precursor cells. Larvae and adult animals showed robust signals in body-wall muscle cells.  
    Expr1105 A mesh like staining was observed in the body-wall muscle cells.  
    Expr1279 Different levels of GFP were observed in the body-wall muscle depending on the fusion constructs.  
    Expr2010560 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).  
    Expr1103 Northern blot analysis revealed a single transcript of 1.5 kb detectable at all developmental stages. During the embryonic stages a very weak signal was detected, which increased significantly during larval and adult stages.  
    Expr1028346 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
    Expr2028800 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).  

13 GO Annotation

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

7 Homologues

Type
least diverged orthologue
least diverged orthologue
least diverged orthologue
orthologue
orthologue
orthologue
orthologue

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00000822 14684877 14688322 1

13 Ontology Annotations

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

0 Regulates Expr Cluster

1 Sequence

Length
3446

1 Sequence Ontology Term